MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Current Opinion in Biotechnology' source. Sun, 21 Mar 2010 17:09:04 +0100 http://www.medworm.com/index.php?rid=3386146&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20299203%26dopt%3DAbstract This article discusses multiple-locus variable-number tandem-repeat analysis, single-nucleotide polymorphisms, nucleic acid sequencing, whole genome sequencing, variable absent or present loci, microarrays and MS as potential subtyping methods to enhance our ability to detect foodborne disease outbreaks. PMID: 20299203 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3386146 Tue, 16 Mar 2010 00:00:00 +0100 3386146 http://www.medworm.com/index.php?rid=3362723&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20219344%26dopt%3DAbstract Authors: Arad SM, Levy-Ontman O The area of sugars and glycosylation is not as well developed as other fields in cell biology owing to biotechnological constraints. However, the biotechnological potential of sugars, including polysaccharides, is the driving force pushing research efforts to meet the challenge. Algae produce cell-wall sulfated polysaccharides, with those of the red unicells, which dissolve into the medium, having unique characteristics-structure, composition, fluid dynamics, and extreme stability. These characteristics, combined with polysaccharide bioactivities, offer a vast range of potential applications. Research has thus been directed toward an in-depth understanding of the molecular structure, biosynthesis, and characteristics of the red microalgal sulfated polysa... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3362723 Mon, 08 Mar 2010 00:00:00 +0100 3362723 http://www.medworm.com/index.php?rid=3347288&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206495%26dopt%3DAbstract Authors: Tracy BP, Gaida SM, Papoutsakis ET Flow cytometry (FC) and FC-based cell sorting have been established as critical tools in modern cell and developmental biology. Yet, their applications in bacteria, especially in the multiparametric mode, remain limited. We argue that FC technologies have the potential to greatly accelerate the analysis and development of microbial complex phenotypes through applications of metabolic engineering, synthetic biology, and evolutionary engineering. We demonstrate the importance of FC for elucidating population heterogeneity because of developmental processes or epigenetic regulation. FC can be engaged for both synthetic and analytical applications of complex phenotypes within a single species, multispecies, and microbial-library populations. Exam... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3347288 Wed, 03 Mar 2010 00:00:00 +0100 3347288 http://www.medworm.com/index.php?rid=3340100&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20202811%26dopt%3DAbstract Authors: Ortega-Morales BO, Chan-Bacab MJ, De la Rosa-García SD, Camacho-Chab JC Microbial communities are ubiquitous in marine intertidal environments. These communities, which grow preferentially as biofilms on natural and artificial surfaces, carry out key processes contributing to the functioning of coastal environments and providing valuable services to human society, including carbon cycling, primary productivity, trophic linkage, and transfer and removal of pollutants. In addition, their surface-associated life style greatly influences the integrity and performance of marine infrastructure and archaeological heritage materials. The fluctuating conditions of the intertidal zone make it an extreme environment to which intertidal biofilm organisms must adapt at varying levels.... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3340100 Tue, 02 Mar 2010 00:00:00 +0100 3340100 http://www.medworm.com/index.php?rid=3340099&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20202812%26dopt%3DAbstract Authors: Treffer R, Deckert V Recent advances in sequencing technologies exhibit a tendency towards single-molecule sequencing, which eventually will lead to the commercial implementation of such platforms. For this purpose dye labelling is currently the foundation of most approaches and an overview is provided on the latest developments. For label-free sequencing the detection of conductivity changes using nanopores or nano-edges will be discussed as well as another promising method that is based on Raman spectroscopy. Here the most recent advance aims to utilize the high lateral resolution of tip-enhanced Raman scattering. For this sequencing procedure Raman spectra must be collected along the DNA or RNA strand, while the difference spectra will provide a direct sequence reading with... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3340099 Tue, 02 Mar 2010 00:00:00 +0100 3340099 http://www.medworm.com/index.php?rid=3328156&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20197235%26dopt%3DAbstract Authors: Kołodziejek I, van der Hoorn RA Protein activity is essential functional information, yet difficult to predict from transcript or protein data. Activity-based protein profiling (ABPP) displays active proteins in proteomes using small molecule probes that irreversibly label proteins in their active state. Here, we review proof-of-concept ABPP studies in plant science. These studies displayed activities of dozens of plant cysteine proteases, lipases, methylesterases and the proteasome. ABPP in plants revealed differential protein activities in development and immunity and uncovered striking selectivity of pathogen-derived inhibitors and unexpected targets of commercial inhibitors. The unique, high-content information of ABPP and the robustness and simplicity of the assays ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3328156 Sun, 28 Feb 2010 00:00:00 +0100 3328156 http://www.medworm.com/index.php?rid=3320122&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189794%26dopt%3DAbstract Authors: Pardo JM Drought and salinity are among the environmental factors that constrain agricultural productivity most dramatically. Classical breeding programs aiming to improve stress tolerance have been hampered by the multigenic nature of the trait and the seemingly scarce natural genetic variability in crop plants. Novel genetic determinants governing the function of stomata and improving the performance of plants under water shortage have been identified and show promise of application in crops. Moreover, receptors of the stress hormone abscisic acid have been characterized and their interplay with key regulatory components is being understood. A critical factor of salinity tolerance in plants is the ability to exclude Na(+) from the shoot, and the modification of specific Na(+... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3320122 Fri, 26 Feb 2010 00:00:00 +0100 3320122 http://www.medworm.com/index.php?rid=3320121&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189795%26dopt%3DAbstract Authors: Lee HS, Kwon KK, Kang SG, Cha SS, Kim SJ, Lee JH The enormous pool of biodiversity in marine ecosystems is an excellent natural reservoir for acquiring an inventory of enzymes with potential for biotechnological applications. Moreover, the opportunity for sustainable resource management has been greatly enhanced by recent advances in culturing methods for recalcitrant microbes. In this review, we will focus primarily on successful examples in culturing marine microbes and provide an overview of work examining the biotechnological potential of the marine reservoir, mainly through genomic strategies, such as activity-based functional screening of genomic and metagenomic libraries and homology-driven screening of enormous amounts of sequence data. PMID: 20189795 [PubMed - as ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3320121 Fri, 26 Feb 2010 00:00:00 +0100 3320121 http://www.medworm.com/index.php?rid=3320123&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20189376%26dopt%3DAbstract Authors: Schmid A, Neubauer P PMID: 20189376 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3320123 Thu, 25 Feb 2010 00:00:00 +0100 3320123 http://www.medworm.com/index.php?rid=3316328&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185292%26dopt%3DAbstract Authors: Dauner M Fluxes and metabolites are the functional manifestations of a living cell. Metabolic flux analysis evolved as a powerful means for systems biology to quantitatively analyze intracellular flux distributions. With the integration of data from tracer experiments, the formerly descriptive methodology has turned into a versatile tool to validate assumptions on genome-derived flux networks. Powerful modeling frameworks balancing 'isotopomers', 'cumomers', or 'elementary modeling units' have reduced computational effort and introduced rigorous statistical quality measures. The advent of metabolomics, stimulus response experiments, and highly sensitive mass spectrometry techniques for mass isotopomer analysis has extended the reach of metabolic flux analysis from steady-state... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3316328 Tue, 23 Feb 2010 00:00:00 +0100 3316328 http://www.medworm.com/index.php?rid=3316327&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185293%26dopt%3DAbstract Authors: Neubauer P, Junne S Analytical approaches for a comprehensive understanding of the metabolic networks in microbial cultures are mostly based on small-scale cultures which are in a steady state or undergo dynamic changes. For drawing conclusions to industrial-scale bioprocesses, however, it is important to understand that cells in large-scale bioreactors are exposed steadily to fast changes, because of an inhomogeneous environment. Analytical approaches that aim for large-scale bioprocess understanding need to apply specific laboratory simulators. Recent developments in cell cultivation techniques and computational tools provide improved possibilities to evaluate how a process will behave in the final scale. These simulators will pave the way for screening robust strains and pr... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3316327 Tue, 23 Feb 2010 00:00:00 +0100 3316327 http://www.medworm.com/index.php?rid=3312095&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20181472%26dopt%3DAbstract Authors: Gust AA, Brunner F, Nürnberger T Saving the world's food supply constitutes one of the major challenges of the future. As a complement to classical and molecular breeding technologies, novel strategies for biotechnological improvement of plant immunity aim at enhancing host recognition capacities for potential pathogens, at boosting the executive arsenal of plant immunity, and at interfering with virulence strategies employed by microbial pathogens. In addition, chemical and biological priming provides means for triggering plant defenses in a non-transgenic manner. Major advances in our understanding of the molecular basis of plant immunity and of microbial infection strategies have opened new ways for engineering durable disease resistance in crop plants that are highlig... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3312095 Mon, 22 Feb 2010 00:00:00 +0100 3312095 http://www.medworm.com/index.php?rid=3312094&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20181473%26dopt%3DAbstract Authors: Vega-Sánchez ME, Ronald PC Research and development efforts for biofuel production are targeted at converting plant biomass into renewable liquid fuels. Major obstacles for biofuel production include lack of biofuel crop domestication, low oil yields from crop plants as well as recalcitrance of lignocellulose to chemical and enzymatic breakdown. Researchers are expanding the genetic and genomic resources available for crop improvement, elucidating lipid metabolism to facilitate manipulation of fatty acid biosynthetic pathways and studying how plant cell walls are synthesized and assembled. This knowledge will be used to produce the next generation of biofuel crops by increasing fatty acid content and by optimizing the hydrolysis of plant cell walls to release fermentable ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3312094 Mon, 22 Feb 2010 00:00:00 +0100 3312094 http://www.medworm.com/index.php?rid=3303140&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20171870%26dopt%3DAbstract Authors: Ohta D, Kanaya S, Suzuki H Metabolomics, as an essential part of genomics studies, intends holistic understanding of metabolic networks through simultaneous analysis of a myriad of both known and unknown metabolites occurring in living organisms. The initial stage of metabolomics was designed for the reproducible analyses of known metabolites based on their comparison to available authentic compounds. Such metabolomics platforms were mostly based on mass spectrometry (MS) technologies enabled by a combination of different ionization methods together with a variety of separation steps including LC, GC, and CE. Among these, Fourier-transform ion cyclotron resonance MS (FT-ICR/MS) is distinguished from other MS technologies by its ultrahigh resolution power in mass to charge rati... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3303140 Thu, 18 Feb 2010 00:00:00 +0100 3303140 http://www.medworm.com/index.php?rid=3303139&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20171871%26dopt%3DAbstract Authors: Pitkänen E, Rousu J, Ukkonen E In the wake of numerous sequenced genomes becoming available, computational methods for the reconstruction of metabolic networks have received considerable attention. Here, we review recent methods and software tools useful along the reconstruction workflow, from sequence annotation and network assembly to model verification and testing against experimental data. Reconstruction methods can be divided into three categories, depending on the magnitude of network context which is taken into account in the process of assembling the metabolic model: First, each enzyme may be predicted independently by annotation transfer or machine learning methods. Second, the presence of a metabolic pathway may be detected from genome and experimental evidence,... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3303139 Thu, 18 Feb 2010 00:00:00 +0100 3303139 http://www.medworm.com/index.php?rid=3291406&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167469%26dopt%3DAbstract Authors: Schmid A, Kortmann H, Dittrich PS, Blank LM Single cells represent the minimal functional unit of life. A major goal of biology is to understand the mechanisms operating in this minimal unit. Nowadays, analysis of the single cell can be performed at unprecedented resolution using new lab-on-a-chip devices and advanced analytical methods. While cell handling and cultivation devices can be classified into finite volume reactors and flow systems, the analytical approaches differ in respect to invasive (i.e. chemical) and noninvasive (i.e. biological/living cell) analysis. Using these new and exciting technologies cell-to-cell differences, originating from regulatory circuits and distinct microenvironments, can now be explored. For example, it could be shown that the rates of tran... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3291406 Tue, 16 Feb 2010 00:00:00 +0100 3291406 http://www.medworm.com/index.php?rid=3291405&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167470%26dopt%3DAbstract Authors: Okumoto S The spatiotemporal patterns of ion and metabolite levels in living cells are important in understanding signal transduction and metabolite flux. Imaging approaches using genetically encoded sensors are ideal for detecting such molecule dynamics, which are hard to capture otherwise. Recent years have seen iterative improvements and evaluations of sensors, which in turn are starting to make applications in more challenging experimental settings possible. In this review, we will introduce recent progress made in the variety and properties of biosensors, and how biosensors are used for the measurement of metabolite and ion in live cells. The emerging field of applications, such as parallel imaging of two separate molecules, high-resolution transport studies and high-thro... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3291405 Tue, 16 Feb 2010 00:00:00 +0100 3291405 http://www.medworm.com/index.php?rid=3291407&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20163950%26dopt%3DAbstract Authors: Niklas J, Schneider K, Heinzle E Metabolic flux analysis (MFA) represents a powerful tool for systems biology research on eukaryotic cells. This review describes recent advances, the challenges as well as applications of metabolic flux analysis comprising fungi, mammalian cells and plants. While MFA is widely established and applied in microorganisms, it remains still a challenge to adapt these methods to eukaryotic cell systems having a higher complexity particularly concerning compartmentation or media composition. In fungi MFA was used in the past few years to analyze a variety of conditions and factors and their effects on cellular metabolism. In mammalian cells MFA was applied mainly in cell culture technology and in medical and toxicological research. (13)C metabolic stu... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3291407 Mon, 15 Feb 2010 00:00:00 +0100 3291407 http://www.medworm.com/index.php?rid=3284745&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153627%26dopt%3DAbstract Authors: Mackenzie LA Laboratory and field studies of the passive solid-phase adsorption toxin tracking (SPATT) method have been carried out around the world. A wide range of marine micro-algal toxins have been detected and the potential of the method to provide reliable, sensitive, time-integrated sampling to monitor the occurrence of toxic algal bloom events has been demonstrated. The method has several important advantages over current phytoplankton and shellfish monitoring methods. Trials of various adsorption substrates have been carried out and the best candidates have been selected for the lipophilic marine biotoxin groups; however, research continues to locate suitable substrates for the more polar water-soluble compounds such as domoic acid and the saxitoxins. The technique ha... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3284745 Thu, 11 Feb 2010 00:00:00 +0100 3284745 http://www.medworm.com/index.php?rid=3269943&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20149631%26dopt%3DAbstract Authors: van Gulik WM Targeted metabolomics, aimed at the study of metabolic reaction networks and their regulation in vivo, is a rapidly emerging field in systems biology. Obtaining proper quantitative snapshots of the microbial metabolome requires fast sampling, immediate quenching of enzymatic activity, separation of exometabolome and endometabolome, complete metabolite extraction from the cells, and reliable high-throughput analysis methods. This review addresses the current state of the art of rapid sampling and quenching for microbial metabolomics. Several robust and reliable rapid sampling devices have been developed. Various quenching and separation procedures have been proposed and applied, but with respect to the reliability of the different methods the literature is contradi... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3269943 Tue, 09 Feb 2010 00:00:00 +0100 3269943 http://www.medworm.com/index.php?rid=3269942&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20149632%26dopt%3DAbstract Authors: Critzer FJ, Doyle MP The recent recognition of fresh fruits and vegetables as major vehicles of foodborne illness has led to increased research on mechanisms by which enteric pathogens contaminate and persist on and in this non-host environment. Interactions between foodborne pathogens and plants as well among the naturally occurring microbial communities contribute to endophytic and epiphytic colonization. Scientific findings are just beginning to elucidate the mechanisms that contribute to colonization of produce. This review addresses current knowledge as well as future research needed to increase our understanding of the microbial ecology of enteric pathogens on fruits and vegetables. PMID: 20149632 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotec... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3269942 Mon, 08 Feb 2010 00:00:00 +0100 3269942 http://www.medworm.com/index.php?rid=3269941&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20149633%26dopt%3DAbstract Authors: Gálvez A, Abriouel H, Benomar N, Lucas R Application of natural antimicrobial substances (such as bacteriocins) combined with novel technologies provides new opportunities for the control of pathogenic bacteria, improving food safety and quality. Bacteriocin-activated films and/or in combination with food processing technologies (high-hydrostatic pressure, high-pressure homogenization, in-package pasteurization, food irradiation, pulsed electric fields, or pulsed light) may increase microbial inactivation and avoid food cross-contamination. Bacteriocin variants developed by genetic engineering and novel bacteriocins with broader inhibitory spectra offer new biotechnological opportunities. In-farm application of bacteriocins, bacterial protective cultures, or bacteriophage... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3269941 Mon, 08 Feb 2010 00:00:00 +0100 3269941 http://www.medworm.com/index.php?rid=3255269&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20138751%26dopt%3DAbstract Authors: Kim TY, Kim HU, Lee SY During the past decade, bottom-up and top-down approaches of network reconstruction have greatly facilitated integration and analysis of biological networks, including transcriptional, protein interaction, and metabolic networks. As increasing amounts of multidimensional high-throughput data become available, biological networks have also been upgraded, allowing more accurate understanding of whole cellular characteristics. The network size is constantly expanding as larger volume of information and omics data are further integrated into the biological networks previously built upon a single type of data. Such effort more recently led to the modeling of human metabolic network and prediction of its tissue-specific metabolism, reconstruction of consensus ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3255269 Fri, 05 Feb 2010 00:00:00 +0100 3255269 http://www.medworm.com/index.php?rid=3255268&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20138752%26dopt%3DAbstract Authors: Warriner K, Namvar A Through recent advances in our understanding of microbial:plant interactions it is becoming apparent that human pathogens, principally, Escherichia coli O157:H7 and Salmonella are adapted to survive in the plant environment. The aforementioned pathogens have surface epitopes that can bind to plant structures such as stomata to aid attachment. In addition, Salmonella is attracted and able to metabolize nutrients contained within the apoplastic fluid of plants. The question of internalization into the inner tissue of plants remains inconclusive largely because of the problems encountered in detecting low pathogen levels. Nevertheless, once internalized human pathogens can trigger and potentially evade plant defenses that are typically induced by phytopathoge... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3255268 Fri, 05 Feb 2010 00:00:00 +0100 3255268 http://www.medworm.com/index.php?rid=3255270&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20138500%26dopt%3DAbstract Authors: Müller S, Harms H, Bley T Heterogeneity of industrial production cultures is accepted to a certain degree; however, the underlying mechanisms are seldom perceived or included in the development of new bioprocess control strategies. Population heterogeneity and its basics, perceptible in the diverse proficiency of cells, begins with asymmetric birth and is found to recess during the life cycle. Since inefficient subpopulations have significant impact on the productivity of industrial cultures, cellular heterogeneity needs to be detected and quantified by using high speed detection tools like flow cytometry. Possible origins of population heterogeneity, sophisticated fluorescent techniques for detection of individual cell states, and cutting-edge Omics-technologies for exte... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3255270 Thu, 04 Feb 2010 00:00:00 +0100 3255270 http://www.medworm.com/index.php?rid=3229088&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20116994%26dopt%3DAbstract Authors: Shiloach J, Reshamwala S, Noronha SB, Negrete A The analysis of metabolic differences in bacterial strains is a useful tool for the development of strains with desired growth and production properties. Several methods are available for the evaluation and understanding of the differences: Biochemical methods to measure metabolites concentration and enzyme activity, mathematical methods to analyze metabolic fluxes through the various pathways, proteomic methods to identify expressed proteins, and genomic methods to detect and measure gene expression. A combination of the various methods is required to obtain a comprehensive understanding of metabolic activities. The genomic methods provide substantial amount information on global gene expression but do not always reflect the act... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3229088 Thu, 28 Jan 2010 00:00:00 +0100 3229088 http://www.medworm.com/index.php?rid=3000768&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19914057%26dopt%3DAbstract Authors: Taylor DA The definitive treatment for end-stage heart failure, organ transplant, is limited by the supply of donor organs. Successful allograft recipients suffer significant adverse effects from chronic antirejection medications. Positive clinical treatment of injured myocardium with stem/progenitor cells has led to hope that one day autologous stem-cell-derived whole or partial donor organs can be generated. Advances in the ability to isolate (or generate) stem or progenitor cells that can give rise to beating cardiocyte-like cells and vascular components, and the advent of human iPS cell technology when combined with recent advances in the generation of perfusable complex tissue scaffolds has moved the field closer to creation of a transplantable heart. As cardiac tissue en... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=3000768 Thu, 12 Nov 2009 00:00:00 +0100 3000768 http://www.medworm.com/index.php?rid=2978041&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19897353%26dopt%3DAbstract Authors: McInerney MJ, Sieber JR, Gunsalus RP Syntrophy is an essential intermediary step in the anaerobic conversion of organic matter to methane where metabolically distinct microorganisms are tightly linked by the need to maintain the exchanged metabolites at very low concentrations. Anaerobic syntrophy is thermodynamically constrained, and is probably a prime reason why it is difficult to culture microbes as these approaches disrupt consortia. Reconstruction of artificial syntrophic consortia has allowed uncultured syntrophic metabolizers and methanogens to be optimally grown and studied biochemically. The pathways for syntrophic acetate, propionate and longer chain fatty acid metabolism are mostly understood, but key steps involved in benzoate breakdown and cyclohexane carboxylate... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978041 Fri, 06 Nov 2009 00:00:00 +0100 2978041 http://www.medworm.com/index.php?rid=2978040&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19897354%26dopt%3DAbstract Authors: Chandran S, Naughton GK PMID: 19897354 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978040 Fri, 06 Nov 2009 00:00:00 +0100 2978040 http://www.medworm.com/index.php?rid=2978039&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19897355%26dopt%3DAbstract Authors: Watanabe K, Bennett G PMID: 19897355 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978039 Fri, 06 Nov 2009 00:00:00 +0100 2978039 http://www.medworm.com/index.php?rid=2978045&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896823%26dopt%3DAbstract Authors: Atala A Applications of regenerative medicine technology may offer novel therapies for patients with injuries, end-stage organ failure, or other clinical problems. Currently, patients suffering from diseased and injured organs can be treated with transplanted organs. However, there is a severe shortage of donor organs that is worsening yearly as the population ages and new cases of organ failure increase. Scientists in the field of regenerative medicine and tissue engineering are now applying the principles of cell transplantation, material science, and bioengineering to construct biological substitutes that will restore and maintain normal function in diseased and injured tissues. The stem cell field is also advancing rapidly, opening new avenues for this type of therapy. For... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978045 Thu, 05 Nov 2009 00:00:00 +0100 2978045 http://www.medworm.com/index.php?rid=2978044&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896824%26dopt%3DAbstract Authors: Strohl WR, Knight DM The establishment of recombinant DNA technologies in the past several decades has made it possible to develop a wide variety of therapeutic proteins to address a corresponding variety of unmet medical needs. Therapeutic proteins have had a major impact on health care, and are likely to grow in importance in the future. As the field of biotherapeutics evolves, there are many current and future challenges to be met. A highly competitive environment has emerged, in many cases with multiple products designed to modulate the same therapeutic target or pathway. The competition is resulting in more effective therapeutics as the need to differentiate among similar products becomes crucial. The costs and timelines for development of therapeutic proteins are increas... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978044 Thu, 05 Nov 2009 00:00:00 +0100 2978044 http://www.medworm.com/index.php?rid=2978043&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896825%26dopt%3DAbstract Authors: Muller PY, Milton M, Lloyd P, Sims J, Brennan FR Dose selection for first-in-human (FIH) clinical trials with monoclonal antibodies (mAbs) is based on specifically designed preclinical pharmacology and toxicology studies, mechanistic ex vivo/in vitro investigations with human and animal cells and pharmacokinetic/pharmacodynamic (PK/PD) modeling approaches and requires a thorough understanding of the biology of the target and the relative binding and pharmacological activity of the mAb in animals and humans. These investigations provide the essential information required for the selection of a safe starting dose and escalation for FIH trials based on toxicology and pharmacology data and the minimal anticipated biological effect level (MABEL) by integrating all available in vivo... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978043 Thu, 05 Nov 2009 00:00:00 +0100 2978043 http://www.medworm.com/index.php?rid=2978042&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896826%26dopt%3DAbstract Authors: Hunt DP, Jahoda C, Chandran S Skin-derived precursor cells (SKPs) are a novel population of neural crest-related precursor cells that can be isolated from embryonic and adult skin. SKPs are capable of generating neuronal, glial and mesodermal progeny. Fate mapping and microdissection experiments have demonstrated a neural crest origin of SKPs within defined niches in adult skin. The finding that SKP derivatives such as Schwann cells and neuronal cells have in vitro and in vivo function raises the possibility of SKPs being both an experimental and therapeutic resource for disease modelling and regenerative medicine. This review focuses on the increased understanding of the developmental and anatomical origins of SKPs and the biotechnological potential of these cells. PMID: ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978042 Thu, 05 Nov 2009 00:00:00 +0100 2978042 http://www.medworm.com/index.php?rid=2978046&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896358%26dopt%3DAbstract Authors: Strohl WR The engineering of therapeutic and clinical candidate monoclonal antibodies and Fc fusion proteins is becoming more sophisticated at generating molecules that are better suited to the pharmacological activity required of them. There are at least 14 marketed and clinical candidate antibodies and Fc fusion proteins in which the Fc has been modified, either via changes in amino acid sequence or in glycoforms. Recent research and development activities in Fc engineering to generate 'fit-for-purpose' antibodies and Fc fusion proteins are reviewed. PMID: 19896358 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2978046 Wed, 04 Nov 2009 00:00:00 +0100 2978046 http://www.medworm.com/index.php?rid=2972245&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19892543%26dopt%3DAbstract Authors: Stebbings R, Poole S, Thorpe R In 2006, a first-in-man phase-I clinical trial of an immunomodulatory mAb, TGN1412, ended in disaster when six healthy recipients suffered a life-threatening systemic inflammatory response, termed a 'Cytokine Storm'. A subsequent investigation concluded that these serious adverse events, not predicted by pre-clinical safety testing, were unforeseen biological effects in man. However, the adverse events had been exacerbated by administration of a near-maximum immuno-stimulatory dose to volunteers, because the calculation of a safe starting dose in man had been based upon results from pre-clinical safety testing in a non-responsive species. In hindsight, many lessons have been learnt from this experience and these have prompted a revision of the Eu... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2972245 Tue, 03 Nov 2009 00:00:00 +0100 2972245 http://www.medworm.com/index.php?rid=2972244&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19892544%26dopt%3DAbstract Authors: Sauerborn M, Schellekens H Recombinant human therapeutic proteins are increasingly being used to treat serious and life-threatening diseases like multiple sclerosis, diabetes mellitus, and cancer. An important side effect of these proteins is the development of antidrug antibodies, which can be neutralizing and thus interfere with the efficacy and safety of the drug. Some biophysical properties, for example, aggregation, also can initiate the immunogenic response to human therapeutics. Many other factors including patients' characteristics may influence this response. Besides induced antibodies, autoantibodies (i.e. naturally occurring antibodies [NAs]) against therapeutic relevant proteins in naïve patients are increasingly being identified. The role of autoreactive B ce... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2972244 Tue, 03 Nov 2009 00:00:00 +0100 2972244 http://www.medworm.com/index.php?rid=2972243&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19892545%26dopt%3DAbstract Authors: Li H, d'Anjou M Glycoproteins represent the major share of marketed and clinical development phase therapeutic proteins. A thorough understanding of the nature and function of the carbohydrate moiety and its impact on pharmacology properties is essential in discovering and developing safe and efficacious glycoprotein biopharmaceuticals. This review summarizes the processes of N-linked and O-linked glycosylation and both established and emerging platforms for expression of recombinant glycoproteins. Recent or illustrative examples of N-linked and/or O-linked glycosylation impacting drug pharmacology properties (including activity, pharmacokinetics, clearance, and immunogenicity) of marketed and developing therapeutic proteins are presented. PMID: 19892545 [PubMed - as suppl... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2972243 Tue, 03 Nov 2009 00:00:00 +0100 2972243 http://www.medworm.com/index.php?rid=2968174&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19889530%26dopt%3DAbstract Authors: Huang C Fc fusion proteins are molecules in which the immunoglobulin Fc is fused genetically to a protein of interest, such as an extracellular domain of a receptor, ligand, enzyme, or peptide. Fc fusion proteins have some antibody-like properties such as long serum half-life and easy expression and purification, making them an attractive platform for therapeutic drugs. Five Fc fusion based drugs are on the market presently, and many more are in different stages of clinical trials, demonstrating that Fc fusion proteins have become credible alternatives to monoclonal antibodies as therapeutics. This review summarizes the Fc fusion proteins that have been approved for use in the clinic and those that are currently in clinical trials, as well as the different approaches to design... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2968174 Mon, 02 Nov 2009 00:00:00 +0100 2968174 http://www.medworm.com/index.php?rid=2968173&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19889531%26dopt%3DAbstract Authors: Durocher Y, Butler M There are slightly over 165 recombinant pharmaceuticals currently approved for human use. Another 500 protein candidates are in preclinical and clinical development, about 70% of these being glycosylated proteins. The need for expression systems allowing the efficient manufacturing of high quality glycoproteins is thus becoming imperative. Recent developments with CHO cells, the predominant mammalian expression system, have focused on either increasing cell specific productivity or prolonging the life span of cells in culture that translates to high integrated viable cell densities. These two factors have allowed volumetric productivities in excess of 5g/L under conditions of controlled nutrient feeding. In addition to glycoengineering strategies, which ar... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2968173 Mon, 02 Nov 2009 00:00:00 +0100 2968173 http://www.medworm.com/index.php?rid=2960119&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19880307%26dopt%3DAbstract Authors: Tsai SL, Singh S, Chen W In nature, both prokaryotes and eukaryotes have evolved a wide spectrum of pathways such as oxidation/reduction, compartmentalization, exclusion, and immobilization [16] as the main natural defense mechanisms to arsenic. This review highlights our current understanding of the biochemistry and molecular biology involved in these natural arsenic metabolisms, and some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation. PMID: 19880307 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2960119 Fri, 30 Oct 2009 00:00:00 +0100 2960119 http://www.medworm.com/index.php?rid=2960118&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19880308%26dopt%3DAbstract Authors: Shire SJ An important challenge in the pharmaceutical development of a biologic is the optimization of safety and efficacy while ensuring the ability to manufacture the drug while maintaining quality and stability. The manufacturing process consists of several operational steps referred to as 'unit operations' where the biologic is subjected to different stresses and conditions that may compromise quality and stability. Moreover, recently the requirement for the development of subcutaneous formulations for high dose drugs, such as monoclonal antibodies, at high protein concentrations has created additional challenges for many of the unit operations. These challenges can be mitigated by modification of the manufacturing process and/or development of formulations to prevent degr... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2960118 Fri, 30 Oct 2009 00:00:00 +0100 2960118 http://www.medworm.com/index.php?rid=2960120&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19879127%26dopt%3DAbstract Authors: Deans TL, Elisseeff JH PMID: 19879127 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2960120 Wed, 28 Oct 2009 00:00:00 +0100 2960120 http://www.medworm.com/index.php?rid=2960122&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19875278%26dopt%3DAbstract Authors: Badri DV, Weir TL, van der Lelie D, Vivanco JM Every organism on earth relies on associations with its neighbors to sustain life. For example, plants form associations with neighboring plants, microflora, and microfauna, while humans maintain symbiotic associations with intestinal microbial flora, which is indispensable for nutrient assimilation and development of the innate immune system. Most of these associations are facilitated by chemical cues exchanged between the host and the symbionts. In the rhizosphere, which includes plant roots and the surrounding area of soil influenced by the roots, plants exude chemicals to effectively communicate with their neighboring soil organisms. Here we review the current literature pertaining to the chemical communication that exists bet... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2960122 Tue, 27 Oct 2009 00:00:00 +0100 2960122 http://www.medworm.com/index.php?rid=2960121&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19875279%26dopt%3DAbstract Authors: Gosset G The aromatic class of chemicals includes a large number of industrially important products. In bacteria and plants, the shikimate pathway and related biosynthetic pathways are a source of aromatic compounds having commercial value. Bacterial strains for the production of aromatic compounds from simple carbon sources as raw material have been generated by applying metabolic engineering and random/combinatorial strategies that modify central metabolism, aromatic biosynthetic pathways, transport, and regulatory functions. These strategies are complemented with heterologous gene expression and protein engineering. Engineered Escherichia coli and Pseudomonas putida strains are enabling the development of sustainable processes for the manufacture of 2-phenylethanol, p-hydro... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2960121 Tue, 27 Oct 2009 00:00:00 +0100 2960121 http://www.medworm.com/index.php?rid=2935504&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19857955%26dopt%3DAbstract Authors: Nichols J, Cooke A Type 1 diabetes (T1D) is an autoimmune disease where insulin producing pancreatic beta cells are progressively destroyed. In the absence of a cure, exogenous insulin is given to maintain glucose homeostasis. Tolerogenic strategies to halt destruction and facilitate recovery of beta cells are being explored. This disease is under polygenic control; the identification of specific candidate pathways to target for drug discovery or corrective therapy would enhance therapeutic options. Whilst islet transplantation combined with immune suppression has shown some efficacy, the availability of beta cells restricts its general use. Differentiation protocols directing cultured stem cells into pancreatic tissue are under development. The availability of embryonic stem ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2935504 Sat, 24 Oct 2009 00:00:00 +0100 2935504 http://www.medworm.com/index.php?rid=2924072&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850466%26dopt%3DAbstract Authors: Arita M After nearly a decade, metabolomics has begun to acquire some credence in the scientific community although its acceptance cannot be compared with that of its forerunners, genomics and proteomics. The legitimization of metabolomics as a valid scientific entity depends on the size of the research community it influences. By far the most effective medium for inoculation is the web infrastructure: public servers that accommodate experimental data, simple formats and guidelines for their interpretation, and connectivity between data and tools for analysis. When these elements satisfy the condition to initiate a social epidemic, metabolomics will be accepted as a fundamental data-driven science that can unite hitherto independently conducted research disciplines. PMID: ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2924072 Tue, 20 Oct 2009 00:00:00 +0100 2924072 http://www.medworm.com/index.php?rid=2924071&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850467%26dopt%3DAbstract Authors: Uchiyama T, Miyazaki K Metagenomics has emerged as an alternative approach to conventional microbial screening that allows exhaustive screening of microbial genomes in their natural environments. Despite the potential usefulness of this approach, functional analysis of the metagenome is often problematic because of insufficient and biased expression of the cloned genes in Escherichia coli. This review highlights recent studies on the screening of metagenomic libraries and discusses some possible solutions for overcoming the expression problem in function-based screening. PMID: 19850467 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2924071 Tue, 20 Oct 2009 00:00:00 +0100 2924071 http://www.medworm.com/index.php?rid=2912609&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19837579%26dopt%3DAbstract Authors: Kung JW, Forbes SJ The liver has considerable inherent regenerative capacity through hepatocyte division and hepatic progenitor cell proliferation. In chronic disease regeneration eventually fails and liver transplantation is the only curative treatment. Current work aims to restore liver mass and functionality either through transplantation of stem cell derived hepatocyte-like cells or by stimulating endogenous liver repair. Human embryonic stem cells (ESCs) and adult somatic cells can be differentiated into hepatocyte-like cells with potential use in drug testing, bio-artificial livers and transplantation. These cells still have some limitations in functionality, understanding further human liver development and improving tissue culture is required. The use of stem cells and... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2912609 Thu, 15 Oct 2009 23:00:00 +0100 2912609 http://www.medworm.com/index.php?rid=2912608&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19837580%26dopt%3DAbstract Authors: O'Malley J, Woltjen K, Kaji K Direct reprogramming of somatic cells to a pluripotent state, substantiated only three years prior, is one of the most rapidly developing areas of stem cell research. The generation of patient-derived pluripotent cells applicable to disease modelling, drug screening, toxicology tests and, ultimately, autologous cell-based therapies, has the potential to revolutionize medicine. Since 2006, when Takahashi and Yamanaka first reported the generation of induced pluripotent stem cells from murine fibroblasts via retroviral transduction of a defined set of transcription factors, various new methods have been developed to refine and improve reprogramming technology. This review focusses on these evolving strategies to generate genetically unmodified or re... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2912608 Thu, 15 Oct 2009 23:00:00 +0100 2912608 http://www.medworm.com/index.php?rid=2912610&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19836942%26dopt%3DAbstract Authors: Rossi SL, Keirstead HS Cell-based transplantation strategies are inherently combination therapies, as they may mediate spinal cord repair via trophic or phenotypic mechanisms. The growth factor expression profile and phenotype of transplanted cells are determined by the transplant population as well as by the site into which they are transplanted. Identifying the key pathways involved in transplant survival and differentiation, as well as neuroprotection and regeneration of endogenous tissue, will enable manipulation of both the transplanted cells and the microenvironment to improve transplant efficiency. High purity populations derived from stem cells will serve to better delineate lineage-specific mechanisms of repair, while providing both neurotrophic and phenotypic benefit... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2912610 Wed, 14 Oct 2009 23:00:00 +0100 2912610 http://www.medworm.com/index.php?rid=2902106&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833502%26dopt%3DAbstract Authors: Levis H, Daniels JT Destruction of the limbal epithelial stem cell (LESC) population in the cornea can lead to disorders that result in chronic inflammation, pain and impaired vision. Amniotic membrane (AM) is commonly used as a substrate for LESC transplantation for ocular surface repair but it is not an ideal substrate and so attempts have been made to find a more suitable alternative. The possible substitutes reviewed here include modified AM, cell carriers such as contact lenses or gauze as well as natural substrates fibrin and silk fibroin and many collagen-based scaffolds. Although there are a number of interesting systems in development, the search for an appropriate alternative continues. PMID: 19833502 [PubMed - as supplied by publisher] (Source: Current Opinion i... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2902106 Mon, 12 Oct 2009 23:00:00 +0100 2902106 http://www.medworm.com/index.php?rid=2902105&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833503%26dopt%3DAbstract Authors: Watanabe K, Manefield M, Lee M, Kouzuma A Electron-shuttling compounds (electron shuttles [ESs], or redox mediators) are essential components in intracellular electron transfer, while microbes also utilize self-produced and naturally present ESs for extracellular electron transfer. These compounds assist in microbial energy metabolism by facilitating electron transfer between microbes, from electron-donating substances to microbes, and/or from microbes to electron-accepting substances. Artificially supplemented ESs can create new routes of electron flow in the microbial energy metabolism, thereby opening up new possibilities for the application of microbes to biotechnology processes. Typical examples of such processes include halogenated-organics bioremediation, azo-dye decolo... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2902105 Mon, 12 Oct 2009 23:00:00 +0100 2902105 http://www.medworm.com/index.php?rid=2895385&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19822414%26dopt%3DAbstract Authors: Weiss R, Panke S PMID: 19822414 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2895385 Fri, 09 Oct 2009 23:00:00 +0100 2895385 http://www.medworm.com/index.php?rid=2887468&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19819686%26dopt%3DAbstract Authors: Papadeas ST, Maragakis NJ Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder characterized primarily by motor neuron loss in the motor cortex and spinal cord leading to progressive disability and death. Despite the relative selectivity of motor neuron loss, recent studies have implicated other cell types including astrocytes and microglia as contributors to this cell death. This understanding has resulted in stem-cell-replacement strategies of these cell types, which may result in neuroprotection. In addition to cell-replacement strategies, the development of induced pluripotent stem cell (iPSC) technologies has resulted in the establishment of motor neuron cell lines from patients with ALS. The use of iPSCs from ALS patients will allow for potential autologou... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2887468 Thu, 08 Oct 2009 23:00:00 +0100 2887468 http://www.medworm.com/index.php?rid=2847283&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19783134%26dopt%3DAbstract Authors: V Wood K, S Tawfik D PMID: 19783134 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2847283 Thu, 24 Sep 2009 23:00:00 +0100 2847283 http://www.medworm.com/index.php?rid=2847284&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782559%26dopt%3DAbstract Authors: Mansbridge J Recent advance in cellular tissue-engineered skin constructs have refined the applications already commercially available, in particular, by the use of genetically modified cells to enhance their properties on the treatment of wounds and to ease the application of epidermis using sprayed keratinocytes. This approach lends itself to use of chimeric epidermis, cultured allogeneic cells, to provide short-term coverage, together with minimally cultured autologous cells for long-term repair. Experimental models of skin include pathological conditions, phenomena such as aging and organogenesis, as in the hair follicle grown from isolated cells in vitro. The recent development of induced pluripotent stem cells raises the possibility of realizing the dream of skin and eve... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2847284 Wed, 23 Sep 2009 23:00:00 +0100 2847284 http://www.medworm.com/index.php?rid=2847282&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19783424%26dopt%3DAbstract Authors: Wagner J, Kean T, Young R, Dennis JE, Caplan AI Mesenchymal stem cell (MSC)-based therapeutics are showing significant benefit in multiple clinical trials conducted by both academic and commercial organizations, but obstacles remain for their large-scale commercial implementation. Recent studies have attempted to optimize MSC-based therapeutics by either enhancing their potency or increasing their delivery to target tissues. Overexpression of trophic factors or in vitro exposure to potency-enhancing factors are two approaches that are demonstrating success in preclinical animal models. Delivery enhancement strategies involving tissue-specific cytokine pathways or binding sites are also showing promise. Each of these strategies has its own set of distinct advantages and disadva... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2847282 Mon, 21 Sep 2009 23:00:00 +0100 2847282 http://www.medworm.com/index.php?rid=2810251&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19762224%26dopt%3DAbstract Authors: Tigges M, Fussenegger M Capitalizing on an era of functional genomic research, systems biology offers a systematic quantitative analysis of existing biological systems thereby providing the molecular inventory of biological parts that are currently being used for rational synthesis and engineering of complex biological systems with novel and potentially useful functions-an emerging discipline known as synthetic biology. During the past decade synthetic biology has rapidly developed from simple control devices fine-tuning the activity of single genes and proteins to multi-gene/protein-based transcription and signaling networks providing new insight into global control and molecular reaction dynamics, thereby enabling the design of novel drug-synthesis pathways as well as geneti... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2810251 Mon, 14 Sep 2009 23:00:00 +0100 2810251 http://www.medworm.com/index.php?rid=2810252&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19758796%26dopt%3DAbstract Authors: Marchisio MA, Stelling J Computer-aided design, pervasive in other engineering disciplines, is currently developing in synthetic biology. Concepts for standardization and hierarchies of parts, devices and systems provide a basis for efficient engineering in biology. Recently developed computational tools, for instance, enable rational (and graphical) composition of genetic circuits from standard parts, and subsequent simulation for testing the predicted functions in silico. The computational design of DNA and proteins with predetermined quantitative functions has made similar advances. The biggest challenge, however, is the integration of tools and methods into powerful and intuitively usable workflows-and the field is only starting to address it. PMID: 19758796 [PubMed - ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2810252 Sun, 13 Sep 2009 23:00:00 +0100 2810252 http://www.medworm.com/index.php?rid=2775257&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19733475%26dopt%3DAbstract Authors: Kolb P, Ferreira RS, Irwin JJ, Shoichet BK Computer-based docking screens are now widely used to discover new ligands for targets of known structure; in the last two years alone, the discovery of ligands for more than 20 proteins has been reported. Recently, investigators have also turned to predicting new substrates for enzymes of unknown function, taking docking in a wholly new direction. Increasingly, the hit rates, the true-positives, and the false-positives from the docking screens are being compared to those from empirical, high-throughput screens, revealing the strengths, weaknesses, and complementarities of both techniques. The recent efflorescence of GPCR structures has made these quintessential drug targets available to structure-based approaches. Consistent with the... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2775257 Wed, 02 Sep 2009 23:00:00 +0100 2775257 http://www.medworm.com/index.php?rid=2775258&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19733047%26dopt%3DAbstract Authors: Pai A, Tanouchi Y, Collins CH, You L Synthetic biology encompasses the design of new biological parts and systems as well as the modulation of existing biological networks to generate novel functions. In recent years, increasing emphasis has been placed on the engineering of population-level behaviors using cell-cell communication. From the engineering perspective, cell-cell communication serves as a versatile regulatory module that enables coordination among cells in and between populations and facilitates the generation of reliable dynamics. In addition to exploring biological 'design principles' via the construction of increasingly complex dynamics, communication-based synthetic systems can be used as well-defined model systems to study ecological and social interactions su... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2775258 Tue, 01 Sep 2009 23:00:00 +0100 2775258 http://www.medworm.com/index.php?rid=2766978&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19729295%26dopt%3DAbstract Authors: Chiarabelli C, Stano P, Luisi PL The term chemical synthetic biology defines that part of the field that, instead of assuming an engineering approach based on genome manipulation, is oriented towards the synthesis of chemical structures alternative to those present in nature. Several different literature projects will be illustrated, including the two of our group. One is concerned with the 'Never Born Proteins' (NBPs), namely polypeptide sequences that are not present in nature, the other is concerned with the notion of 'minimal cells', semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell. PMID: 19729295 [PubMed - as supplied by publisher] (Source: Current Opinion in B... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2766978 Mon, 31 Aug 2009 23:00:00 +0100 2766978 http://www.medworm.com/index.php?rid=2759299&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19720518%26dopt%3DAbstract Authors: Benenson Y Man-made molecular 'computers' that operate inside live cells will enable unprecedented level of control over cellular physiology. A promising approach to building these computers uses RNA molecules and RNA-based regulation. RNA naturally lends itself to create 'digital' molecular networks that embody standardized (normal) forms of logic functions. The network's inputs, that may or may not be inverted by single-input NOT logic gates, feed into multi-input AND gates whose outputs are in turn integrated in a multi-input OR gate. Below I review recent steps that have been taken toward implementing these networks with allosteric riboswitches and ribozymes in bacteria and yeast, and RNAi in mammalian cells. I also propose how to co-opt recently discovered additional RNA ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2759299 Fri, 28 Aug 2009 23:00:00 +0100 2759299 http://www.medworm.com/index.php?rid=2759298&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19720519%26dopt%3DAbstract Authors: Carothers JM, Goler JA, Keasling JD An immense array of naturally occurring biological systems have evolved that convert simple substrates into the products that cells need for growth and persistence. Through the careful application of metabolic engineering and synthetic biology, this biotransformation potential can be harnessed to produce chemicals that address unmet clinical and industrial needs. Developing the capacity to utilize biology to perform chemistry is a matter of increasing control over both the function of synthetic biological systems and the engineering of those systems. Recent efforts have improved general techniques and yielded successes in the use of synthetic biology for the production of drugs, bulk chemicals, and fuels in microbial platform hosts. Syntheti... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2759298 Fri, 28 Aug 2009 23:00:00 +0100 2759298 http://www.medworm.com/index.php?rid=2759297&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19720520%26dopt%3DAbstract Authors: Dougherty MJ, Arnold FH Constructing novel biological systems that function in a robust and predictable manner requires better methods for discovering new functional molecules and for optimizing their assembly in novel biological contexts. By enabling functional diversification and optimization in the absence of detailed mechanistic understanding, directed evolution is a powerful complement to 'rational' engineering approaches. Aided by clever selection schemes, directed evolution has generated new parts for genetic circuits, cell-cell communication systems, and non-natural metabolic pathways in bacteria. PMID: 19720520 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2759297 Fri, 28 Aug 2009 23:00:00 +0100 2759297 http://www.medworm.com/index.php?rid=2745820&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19713097%26dopt%3DAbstract Authors: Lappe M, Bagler G, Filippis I, Stehr H, Duarte JM, Sathyapriya R Novel high-throughput technologies for directed evolution enable experimental coverage of an impressive number of sequences. Nevertheless, the success of such experiments hinges on the initial sequence libraries. Here we consider the computational design of smart focused libraries and review insights from experimental strategies and theoretic advances in modelling their energy landscapes. In library design as in structure prediction, the applied energy function is the key. Current knowledge-based potentials have proven more successful than purely physics-based ones. Here we summarize novel approaches that extend the classical pairwise treatment of residue contacts towards adaptive knowledge-based multi-body poten... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2745820 Mon, 24 Aug 2009 23:00:00 +0100 2745820 http://www.medworm.com/index.php?rid=2742141&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19709874%26dopt%3DAbstract Authors: Mandell DJ, Kortemme T The field of computational protein design has produced striking successes, including the engineering of novel enzymes. Many of these achievements employed methodologies that sample amino acid side-chains on a fixed backbone, while methods that explicitly model backbone flexibility have so far largely focused on the design of new structures rather than functions. Recent methodological improvements in conformational sampling techniques, some borrowed from the field of robotics to model mechanically accessible conformations, now provide exciting opportunities to explore amino acid sequences and backbone structures simultaneously. Incorporating functional constraints into flexible backbone design should help to achieve challenging engineering goals that expl... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2742141 Sun, 23 Aug 2009 23:00:00 +0100 2742141 http://www.medworm.com/index.php?rid=2742140&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19709875%26dopt%3DAbstract Authors: Pogson M, Georgiou G, Iverson BL The engineering of novel and precise sequence specificity into proteases will provide an important route to the development of exciting new tools for analytical, biotechnological, and therapeutic applications. Significant progress has been made in reprogramming protease specificity, largely because of the development of high-throughput assay technologies allowing the isolation of protease variants from large libraries. For example, using directed evolution as well as other approaches, proteases have been reprogrammed to cleave substrates containing a variety of amino acids in the P1 and P1' positions including a post-translationally modified tyrosine, a specificity not yet identified in any naturally occurring protease. Together, these recent a... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2742140 Sun, 23 Aug 2009 23:00:00 +0100 2742140 http://www.medworm.com/index.php?rid=2742139&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19709876%26dopt%3DAbstract Authors: Enever C, Batuwangala T, Plummer C, Sepp A Most therapeutic antibodies in the clinic today are based on fully humanised immunoglobulins. They have proven to be outstandingly effective, especially for the treatment of cancer, autoimmune and inflammatory diseases where the target is a single, well-defined and accessible molecule. Many diseases however are complex, involving multiple mediators or signalling pathways that could be targeted simultaneously to maximise clinical benefit. There is also a wealth of validated intracellular and CNS-based targets which are currently inaccessible to monoclonal antibody therapy. A spectrum of next generation immunotherapeutics is in development to address these issues and a number of them have also entered clinical trials. PMID: 19709876... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2742139 Sun, 23 Aug 2009 23:00:00 +0100 2742139 http://www.medworm.com/index.php?rid=2735175&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19700301%26dopt%3DAbstract Authors: Buchholz F DNA has been a main focus of biomedical research ever since its discovery as the hereditary molecule. This discovery laid the foundation for scientists to begin both to elucidate and to manipulate its function. Since then many DNA processing enzymes have been discovered and many technologies have been developed to process and manipulate DNA with these enzymes. The sequencing of entire genomes has increased the demand for sophisticated DNA processing enzymes. This need is being addressed by engineering DNA processing enzymes using rational and evolutionary approaches to improve or design novel properties. It now appears feasible that engineered DNA processing enzymes will find utility in molecular medicine as tools for advanced genome engineering. PMID: 19700301 ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2735175 Thu, 20 Aug 2009 23:00:00 +0100 2735175 http://www.medworm.com/index.php?rid=2735174&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19700302%26dopt%3DAbstract Authors: Koide S Generation of novel protein functions is a major goal in biotechnology and also a rigorous test for our understanding of the relationship between protein structure and function. Early examples of protein engineering focused on design and directed evolution within the constraints of the original protein architecture, exemplified by the highly successful fields of antibody and enzyme engineering. Recent studies show that protein engineering strategies which step away from these natural architectures, that is by manipulating the organization of domains and modules thus mimicking nonhomologous recombination, are highly effective in producing complex and sophisticated functions in terms of both molecular recognition and regulation. PMID: 19700302 [PubMed - as supplied b... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2735174 Thu, 20 Aug 2009 23:00:00 +0100 2735174 http://www.medworm.com/index.php?rid=2735173&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19700303%26dopt%3DAbstract Authors: Danchin A Synthetic biology aims at reconstructing life. Besides understanding what life is, its ultimate goal is to design cell factories meant to satisfy pressing needs. The success of genome transplantation demonstrates that the cell is split into a machine and a program. The program codes for processes that reproduce the machine and replicate the program. Reproduction is tightly linked to evolution, because the program codes for information trapping. Degradation processes make room to cope with ageing and inaccurate syntheses. Yet they use energy to prevent degradation of functional entities, thus permitting accumulation of innovation. Synthetic biology faces a dilemma: it will either implement the corresponding genes, and cells will evolve in an unpredictable manner, or o... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2735173 Thu, 20 Aug 2009 23:00:00 +0100 2735173 http://www.medworm.com/index.php?rid=2682438&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19660930%26dopt%3DAbstract Authors: Wen F, Nair NU, Zhao H Lignocellulosic biofuels represent a sustainable, renewable, and the only foreseeable alternative energy source to transportation fossil fuels. However, the recalcitrant nature of lignocellulose poses technical hurdles to an economically viable biorefinery. Low enzymatic hydrolysis efficiency and low productivity, yield, and titer of biofuels are among the top cost contributors. Protein engineering has been used to improve the performance of lignocellulose-degrading enzymes, as well as proteins involved in biofuel synthesis pathways. Unlike its great success seen in other industrial applications, protein engineering has achieved only modest results in improving the lignocellulose-to-biofuels efficiency. This review will discuss the unique challenges that... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2682438 Mon, 03 Aug 2009 23:00:00 +0100 2682438 http://www.medworm.com/index.php?rid=2556791&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19560336%26dopt%3DAbstract Authors: Beer LL, Boyd ES, Peters JW, Posewitz MC There is currently substantial interest in utilizing eukaryotic algae for the renewable production of several bioenergy carriers, including starches for alcohols, lipids for diesel fuel surrogates, and H(2) for fuel cells. Relative to terrestrial biofuel feedstocks, algae can convert solar energy into fuels at higher photosynthetic efficiencies, and can thrive in salt water systems. Recently, there has been considerable progress in identifying relevant bioenergy genes and pathways in microalgae, and powerful genetic techniques have been developed to engineer some strains via the targeted disruption of endogenous genes and/or transgene expression. Collectively, the progress that has been realized in these areas is rapidly advancing our a... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2556791 Wed, 24 Jun 2009 23:00:00 +0100 2556791 http://www.medworm.com/index.php?rid=2556790&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19560337%26dopt%3DAbstract Authors: Jeffries T, Lindblad P PMID: 19560337 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2556790 Wed, 24 Jun 2009 23:00:00 +0100 2556790 http://www.medworm.com/index.php?rid=2556792&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19559595%26dopt%3DAbstract Authors: Landrain TE, Carrera J, Kirov B, Rodrigo G, Jaramillo A We review the current status of expression of heterologous systems for bioenergy and bioproduction in bacteria using a model-based approach. As an aim for synthetic biology, it requires mathematical models of genetic modules that could be characterized independently of their context. This fastens the design of metabolic circuits using a combinatorial design approach, where given pathways could be optimized for maximal bioproduction, while being nontoxic for the chassis. We show how recent characterization of genetic parts, such as promoters, RBS or sRNAs could be used to fine-tune the expression of individual genes to achieve that goal. We also present lists of enzymes that are used for bioproduction, enlarging such set o... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2556792 Tue, 23 Jun 2009 23:00:00 +0100 2556792 http://www.medworm.com/index.php?rid=2549109&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19553101%26dopt%3DAbstract Authors: Sheehan JJ Sustainable energy is the problem of the 21st century. If biofuels want to be part of the solution they must accept a degree of scrutiny unprecedented in the development of a new industry. That is because sustainability deals explicitly with the role of biofuels in ensuring the well-being of our planet, our economy, and our society both today and in the future. Life cycle assessment (LCA) has been the standard framework for assessing sustainability of biofuels. These assessments show that corn ethanol has a marginally lower fossil energy and greenhouse gas footprint compared to petroleum fuel. Sugarcane ethanol and some forms of biodiesel offer substantially lower footprints. New biofuels may offer low footprints. The science of LCA is being stretched to its limits ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549109 Sun, 21 Jun 2009 23:00:00 +0100 2549109 http://www.medworm.com/index.php?rid=2549110&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19545992%26dopt%3DAbstract Authors: Van Vleet J, Jeffries T Efficient fermentation of hemicellulosic sugars is critical for the bioconversion of lignocellulosics to ethanol. Efficient sugar uptake through the heterologous expression of yeast and fungal xylose/glucose transporters can improve fermentation if other metabolic steps are not rate limiting. Rectification of cofactor imbalances through heterologous expression of fungal xylose isomerase or modification of cofactor requirements in the yeast oxidoreductase pathway can reduce xylitol production while increasing ethanol yields, but these changes often occur at the expense of xylose utilization rates. Genetic engineering and evolutionary adaptation to increase glycolytic flux coupled with transcriptomic and proteomic studies have identified targets for furth... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549110 Fri, 19 Jun 2009 23:00:00 +0100 2549110 http://www.medworm.com/index.php?rid=2549111&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540103%26dopt%3DAbstract Authors: Angermayr SA, Hellingwerf KJ, Lindblad P, Teixeira de Mattos MJ The world's future energy demand calls for a sustainable alternative for the use of fossil fuels, to restrict further global warming. Harvesting solar energy via photosynthesis is one of Nature's remarkable achievements. Existing technologies exploit this process for energy 'production' via processing of, for example, part of plant biomass into ethanol, and of algal biomass into biodiesel. Fortifying photosynthetic organisms with the ability to produce biofuels directly would bypass the need to synthesize all the complex chemicals of 'biomass'. A promising way to achieve this is to redirect cyanobacterial intermediary metabolism by channeling (Calvin cycle) intermediates into fermentative metabolic pathways. This ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549111 Tue, 16 Jun 2009 23:00:00 +0100 2549111 http://www.medworm.com/index.php?rid=2549113&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19523812%26dopt%3DAbstract Authors: Wei H, Xu Q, Taylor LE, Baker JO, Tucker MP, Ding SY Natural processes of recycling carbon from plant cell walls are slow but very efficient, generally involving microbial communities and their secreted enzymes. Efficient combinations of microbial communities and enzymes act in a sequential and synergistic manner to degrade plant cell walls. Recent understanding of plant cell wall ultra-structure, as well as the carbon metabolism, ATP production, and ecology of participating microbial communities, and the biochemical properties of their cellulolytic enzymes have led to new perspectives on saccharification of biomass. Microbial communities are dynamic functions of the chemical and structural compositions of plant cell wall components. The primitive 'multicellularity' exhibited ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549113 Tue, 09 Jun 2009 23:00:00 +0100 2549113 http://www.medworm.com/index.php?rid=2549112&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19523813%26dopt%3DAbstract Authors: Himmel ME, Bayer EA PMID: 19523813 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549112 Tue, 09 Jun 2009 23:00:00 +0100 2549112 http://www.medworm.com/index.php?rid=2549114&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19520566%26dopt%3DAbstract Authors: Xu Q, Singh A, Himmel ME The U.S. DOE Energy Independence and Security Act (EISA) mandated attainment of a national production level of 36 billion gallons of biofuels (to be added to gasoline) by 2022, of which 21 billion gallons must be derived from renewable/sustainable feedstocks (e.g. lignocellulose). In order to attain these goals, the development of cost effective process technologies that can convert plant biomass to fermentable sugars must occur. An alternative route to production of bioethanol is the utilization of microorganisms that can both convert biomass to fermentable sugars and ferment the resultant sugars to ethanol in a process known as consolidated bioprocessing (CBP). Although various economic benefits and technology hurdles must be weighed in the course of... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2549114 Mon, 08 Jun 2009 23:00:00 +0100 2549114 http://www.medworm.com/index.php?rid=2472287&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19515552%26dopt%3DAbstract Authors: Morrison M, Pope PB, Denman SE, McSweeney CS Herbivores retain within their gastrointestinal tract a microbiome that specializes in the rapid hydrolysis and fermentation of lignocellulosic plant biomass. With the emergence of high-throughput DNA sequencing technologies and related 'omics' approaches, along with demands to better utilize lignocellulose materials as a feedstock for second-generation biofuels, these gut microbiomes are thought to be a potential source of novel biotechnologies relevant to meeting these needs. This review provides an insight into the new findings that have arisen from the (meta)genomic analysis of specialist cellulolytic bacteria and gut microbiomes of herbivorous insects, ruminants, native Australian marsupials, and other obligate herbivores. In a... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472287 Mon, 08 Jun 2009 04:00:00 +0100 2472287 http://www.medworm.com/index.php?rid=2472384&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19502046%26dopt%3DAbstract Authors: Wilson DB There is a major international effort to develop renewable alternatives to fossil fuels. One approach is to produce a liquid fuel by enzymatically hydrolyzing carbohydrate polymers in biomass to sugars and fermenting them to ethanol. Cellulose is the main polymer in biomass and cellulases can hydrolyze it to cellobiose, which can be converted to glucose by beta-glucosidase. Extensive research is being carried out to try to obtain cellulases with higher activity on pretreated biomass substrates by screening and sequencing new organisms, engineering cellulases with improved properties and by identifying proteins that can stimutate cellulases. Despite extensive research on cellulases there are major gaps in our understanding of how they hydrolyze crystalline cellulose, ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472384 Fri, 05 Jun 2009 04:00:00 +0100 2472384 http://www.medworm.com/index.php?rid=2472351&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19502047%26dopt%3DAbstract Authors: Martínez AT, Ruiz-Dueñas FJ, Martínez MJ, Del Río JC, Gutiérrez A Lignin removal is a central issue in paper pulp manufacture, and production of other renewable chemicals, materials, and biofuels in future lignocellulose biorefineries. Biotechnology can contribute to more efficient and environmentally sound deconstruction of plant cell wall by providing tailor-made biocatalysts based on the oxidative enzymes responsible for lignin attack in Nature. With this purpose, the already-known ligninolytic oxidoreductases are being improved using (rational and random-based) protein engineering, and still unknown enzymes will be identified by the application of the different 'omics' technologies. Enzymatic delignification will be soon at the pulp mill (combined ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472351 Fri, 05 Jun 2009 04:00:00 +0100 2472351 http://www.medworm.com/index.php?rid=2472312&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19502048%26dopt%3DAbstract Authors: Margeot A, Hahn-Hagerdal B, Edlund M, Slade R, Monot F The use of lignocellulosic biomass for the production of biofuels will be unavoidable if liquid fossil fuels are to be replaced by renewable and sustainable alternatives. Ethanol accounts for the majority of biofuel use worldwide, and the prospect of its biological production from abundant lignocellulosic feedstocks is attractive. The recalcitrance of these raw materials still renders proposed processes complex and costly, but there are grounds for optimism. The application of new, engineered enzyme systems for cellulose hydrolysis, the construction of inhibitor-tolerant pentose-fermenting industrial yeast strains, combined with optimized process integration promise significant improvements. The opportunity to test these a... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472312 Fri, 05 Jun 2009 04:00:00 +0100 2472312 http://www.medworm.com/index.php?rid=2472413&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19501503%26dopt%3DAbstract Authors: Lehr F, Posten C Production of biofuels from microalgae is a promising sustainable option for the future. Unfortunately, until now production of algae biomass is too expensive owing to costly plant designs or high demand of auxiliary energy. These problems are addressed in recent developments. Basic ideas that are followed in different novel pilot plants are efficient mixing, high light dilution via large external surfaces or internal light conducting structures and gas transport via membranes. Other attempts are directed towards cheaper constructions. These endeavours have brought microalgal biofuel production closer to economic viability as has been shown in some pilot plants. But until now, these plants operate only on a small area and a limited time frame, making economic ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472413 Thu, 04 Jun 2009 04:00:00 +0100 2472413 http://www.medworm.com/index.php?rid=2472481&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19481436%26dopt%3DAbstract Authors: Mansfield SD Photosynthetic carbon capture by terrestrial plants represents a major sink for atmospheric CO(2), ultimately terminating in the synthesis of a secondary plant cell wall-a complex matrix of polysaccharides intricately linked to lignin. The production and co-ordinated deposition of this lignocellulosic composite confers both protective and structural properties to the plant cell. The inherent properties of this complex cell wall also represent a major obstacle for its effective industrial utilization, as operationally effective mechanisms for the removal of lignin and the consequential release of carbohydrate constituents remain elusive. Perturbing plants by mis-regulating key genes/enzymes integral to major cell wall pathways can provide both rich insights into ce... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472481 Wed, 27 May 2009 04:00:00 +0100 2472481 http://www.medworm.com/index.php?rid=2472459&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19481437%26dopt%3DAbstract Authors: da Costa Sousa L, Chundawat SP, Balan V, Dale BE Pretreatment is considered to be a central unit process in a biorefinery to convert lignocellulosic biomass into fuels and chemicals, affecting all other operations in the process. A variety of technologies to pretreat lignocellulosic biomass are available today, which encompass a wide range of physical, chemical, and biological based processes. Among these, chemical based pretreatments are considered to be the most promising for future biorefineries. However, several key criteria regarding technical, economical, and environmental considerations should be critically analyzed when adapting these technologies for the nascent biorefinery industry. This review will discuss the most important pretreatment methods available today and ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472459 Wed, 27 May 2009 04:00:00 +0100 2472459 http://www.medworm.com/index.php?rid=2472422&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19481438%26dopt%3DAbstract Authors: Picataggio S Synthetic biology leverages advances in computational biology, molecular biology, protein engineering, and systems biology to design, synthesize, and assemble genetic elements for manipulating cell phenotypes. This emerging field is founded on a vast amount of gene sequence data available in public databases and our ability to rapidly and inexpensively synthesize DNA fragments of sufficient length to encode full-length genes, enzymes, metabolic pathways, and even entire genomes. Several thousand genetic elements encoding enzymes, reporters, repressors, activators, promoters, terminators, ribosome binding sites, signaling devices, and measurement systems are now available for engineering microbes. In addition to facilitating rational design, these new tools allow u... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472422 Wed, 27 May 2009 04:00:00 +0100 2472422 http://www.medworm.com/index.php?rid=2472502&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19473829%26dopt%3DAbstract Authors: Connor MR, Liao JC The production of alternative transportation fuels from renewable sources has gained increased attention due to energy and environmental concerns. Recently, progress has been made in the development of microbe-based processes for the production of biofuels beyond ethanol. These biofuels possess superior fuel properties relative to ethanol, such as increased energy density, low hygroscopicity, and low vapor pressure. These fuels are also advantageous as they may be transported using existing infrastructure. The isobutanol production process, in particular, has already reached near-industrial level. Although many of these processes are still being scaled-up for commercial production, their potential for practical application is promising. PMID: 19473829 [P... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472502 Mon, 25 May 2009 04:00:00 +0100 2472502 http://www.medworm.com/index.php?rid=2472746&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19327979%26dopt%3DAbstract Authors: Weyens N, van der Lelie D, Taghavi S, Vangronsveld J A promising field to exploit plant-endophyte partnerships is the remediation of contaminated soils and (ground) water. Many plant growth promoting endophytes can assist their host plant to overcome contaminant-induced stress responses, thus providing improved plant growth. During phytoremediation of organic contaminants, plants can further benefit from endophytes possessing appropriate degradation pathways and metabolic capabilities, leading to more efficient contaminant degradation and reduction of both phytotoxicity and evapotranspiration of volatile contaminants. For phytoremediation of toxic metals, endophytes possessing a metal-resistance/sequestration system can lower metal phytotoxicity and affect metal translocation ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472746 Wed, 01 Apr 2009 04:00:00 +0100 2472746 http://www.medworm.com/index.php?rid=2472727&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19328673%26dopt%3DAbstract Authors: Ruiz ON, Daniell H Most phytoremediation studies utilize merA or merB genes to modify plants via the nuclear or chloroplast genome, expressing organomercurial lyase and/or mercuric ion reductase in the cytoplasm, endoplasmic reticulum or within plastids. Several plant species including Arabidopsis, tobacco, poplar, rice, Eastern cottonwood, peanut, salt marsh grass and Chlorella have been transformed with these genes. Transgenic plants grew exceedingly well in soil contaminated with organic (approximately 400 microM PMA) or inorganic mercury (approximately 500 microM HgCl(2)), accumulating Hg in roots surpassing the concentration in soil (approximately 2000 microg/g). However, none of these plants were tested in the field to demonstrate real potential of this approach. Availab... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472727 Wed, 01 Apr 2009 04:00:00 +0100 2472727 http://www.medworm.com/index.php?rid=2472709&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19339169%26dopt%3DAbstract Authors: Matas AJ, Gapper NE, Chung MY, Giovannoni JJ, Rose JK Commercial regulation of ripening is currently achieved through early harvest, by controlling the postharvest storage atmosphere and genetic selection for slow or late ripening varieties. Although these approaches are often effective, they are not universally applicable and often result in acceptable, but poor quality, products. With increased understanding of the molecular biology underlying ripening and the advent of genetic engineering technologies, researchers have pursued new strategies to address problems in fruit shelf-life and quality. These have been guided by recent insights into mechanisms by which ethylene and a complex network of transcription factors regulate ripening, and by an increased appreciation of facto... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472709 Wed, 01 Apr 2009 04:00:00 +0100 2472709 http://www.medworm.com/index.php?rid=2472690&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19342218%26dopt%3DAbstract Authors: Irlinger F, Mounier J The cheese microbiota, whose community structure evolves through a succession of different microbial groups, plays a central role in cheese-making. The subtleties of cheese character, as well as cheese shelf-life and safety, are largely determined by the composition and evolution of this microbiota. Adjunct and surface-ripening cultures marketed today for smear cheeses are inadequate for adequately mimicking the real diversity encountered in cheese microbiota. The interactions between bacteria and fungi within these communities determine their structure and function. Yeasts play a key role in the establishment of ripening bacteria. The understanding of these interactions offers to enhance cheese flavour formation and to control and/or prevent the growth o... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472690 Wed, 01 Apr 2009 04:00:00 +0100 2472690 http://www.medworm.com/index.php?rid=2472669&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19342219%26dopt%3DAbstract Authors: James CA, Strand SE The efficacy of transgenic plants in the phytoremediation of small organic contaminants has been investigated. Two principal strategies have been pursued (1) the manipulation of phase I metabolic activity to enhance in planta degradation rates, or to impart novel metabolic activity, and (2) the enhanced secretion of reactive enzymes from roots leading to accelerated ex planta degradation of organic contaminants. A pair of dehalogenase genes from Xanthobacter autotrophicus was expressed in tobacco resulting in the dehalogenation of 1,2-dichloroethane, which was otherwise recalcitrant. A laccase gene from cotton was overexpressed in Arabidopsis thaliana resulting in increased secretory laccase activity and the enhanced resistance to trichlorophenol in soils. ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472669 Wed, 01 Apr 2009 04:00:00 +0100 2472669 http://www.medworm.com/index.php?rid=2472649&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19342220%26dopt%3DAbstract Authors: Teplitski M, Wright AC, Lorca G As the consumption of seafood and shellfish increases around the world, so is the incidence of associated outbreaks of illness. Various postharvest treatments are effective at killing seafood-associated bacteria, but most of these treatments also kill the mollusks. Because consumer preferences for raw live shellfish persist, biological approaches for promoting microbiological safety of live product are being considered. Applications of probiotic bacteria to reduce human pathogens in live shellfish could augment current practices for preharvest monitoring of water quality. Postharvest, biological controls will be important to remove shellfish-associated commensal Vibrio spp. that are pathogenic to humans. Further investigations will reveal whethe... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472649 Wed, 01 Apr 2009 04:00:00 +0100 2472649 http://www.medworm.com/index.php?rid=2472629&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19345572%26dopt%3DAbstract Authors: Wright AC, Teplitski M PMID: 19345572 [PubMed - in process] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472629 Wed, 01 Apr 2009 04:00:00 +0100 2472629 http://www.medworm.com/index.php?rid=2472606&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19346123%26dopt%3DAbstract Authors: Duong T, Konkel ME MLST, DNA microarrays, and genome sequencing has allowed for a greater understanding of the metabolic capacity and epidemiology of Campylobacter jejuni. While strain-specific genes may provide an isolate a selective advantage in environments and contribute to the organism's pathogenicity, recent work indicates that C. jejuni pathogenicity is dictated by variations in the nucleotide sequence of core genes. Challenges facing C. jejuni researchers include determining (a) the degree to which genomic diversity enables this bacterium to persist in particular environments; (b) if C. jejuni virulence and disease severity can be predicted on the basis of genotype; (c) the set of core and variable genes whose products contribute to virulence; and (d) the genes in whic... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472606 Wed, 01 Apr 2009 04:00:00 +0100 2472606 http://www.medworm.com/index.php?rid=2472585&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19349159%26dopt%3DAbstract Authors: Teplitski M, Barak JD, Schneider KR Recent outbreaks of gastroenteritis linked to the consumption of fresh produce raise questions about the mechanisms by which human pathogens colonize plants and persist within marketable produce. Neither Salmonella nor Escherichia coli appear to produce enzymes that degrade plant cell walls, therefore it is not yet certain how these bacteria enter plant tissues and spread within them. Similar to plant-associated bacteria, enterics use cellulose and aggregative fimbriae for their attachment to plant surfaces. Salmonella can be an effective plant endophyte, even though it is capable of triggering plant defenses. Plant-associated microbiota contributes to the fitness and translocation of these human pathogens within plant hosts, although intera... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472585 Wed, 01 Apr 2009 04:00:00 +0100 2472585 http://www.medworm.com/index.php?rid=2472563&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19356919%26dopt%3DAbstract Authors: Gallo M, Sayre R Genetic engineering is being applied to eliminate or substantially reduce plant-derived substances that can be harmful to human health in otherwise nutritious foods. Post-transcriptional gene silencing, most recently via RNA interference, has been used in efforts to remove allergens from rice, soybean, apple, tomato, and peanut. RNA silencing has the potential to simultaneously alter expression of all members of a multi-gene family in a tissue-specific manner with little collateral change in the plant. Similarly, RNA silencing, as well as the overexpression of a beneficial gene, have been used in transgenic cassava to reduce toxic cyanogens. These studies are illustrative of the future application of biotechnology toward production of foods that are of direct ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472563 Wed, 01 Apr 2009 04:00:00 +0100 2472563 http://www.medworm.com/index.php?rid=2472542&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19361978%26dopt%3DAbstract Authors: Dowling DN, Doty SL PMID: 19361978 [PubMed - in process] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472542 Wed, 01 Apr 2009 04:00:00 +0100 2472542 http://www.medworm.com/index.php?rid=2472521&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19372038%26dopt%3DAbstract Authors: Wright AC, Danyluk MD, Otwell WS Recent Salmonella outbreaks associated with consumption of fresh produce have increased public concern for the safety of raw food products, perhaps signaling a paradigm shift in approaches to food safety. Limitations to our capacity to ensure that raw foods are safe for the consumer include the availability of sufficiently rapid and reliable technology for prevention, intervention, and risk assessment. Other food products, such as shellfish, with greater historical precedent for real or perceived public health risk may offer perspective and insight into strategies for meeting these challenges. This review documents current practices for pathogen prevention and detection in raw oysters and presents technological advances and impediments that det... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2472521 Wed, 01 Apr 2009 04:00:00 +0100 2472521 http://www.medworm.com/index.php?rid=2295992&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19324541%26dopt%3DAbstract Authors: Andresen V, Alexander S, Heupel WM, Hirschberg M, Hoffman RM, Friedl P Multiphoton microscopy (MPM) is the method of choice for investigating cells and cellular functions in deep tissue sections and organs. Here we present the setup and applications of infrared-(IR-)MPM using excitation wavelengths above 1080nm. IR-MPM enables the use of red fluorophores and fluorescent proteins, doubles imaging depth, improves second harmonic generation of tissue structures, and strongly reduces phototoxicity and photobleaching, compared with conventional MPM. Furthermore, it still provides subcellular resolution at depths of several hundred micrometers and thus will enhance long-term live cell and deep tissue microscopy. PMID: 19324541 [PubMed - as supplied by publisher] (Source: Current... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2295992 Tue, 24 Mar 2009 04:00:00 +0100 2295992 http://www.medworm.com/index.php?rid=2295994&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19303764%26dopt%3DAbstract Authors: Zhu YG, Rosen BP Phytoremediation to clean up arsenic-contaminated environments has been widely hailed as environmentally friendly and cost effective, and genetic engineering is believed to improve the efficiency and versatility of phytoremediation. Successful genetic engineering requires the thorough understanding of the mechanisms involved in arsenic tolerance and accumulation by natural plant species. Key mechanisms include arsenate reduction, arsenic sequestration in vacuoles of root or shoot, arsenic loading to the xylem, and volatilization through the leaves. Key advances include the identification of arsenic (As) translocation from root to shoot in the As hyperaccumulator, Pteris vittata, and the characterization of related key genes from hyperaccumulator and nonaccumul... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2295994 Thu, 19 Mar 2009 04:00:00 +0100 2295994 http://www.medworm.com/index.php?rid=2283580&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19299118%26dopt%3DAbstract Authors: Binkowski B, Fan F, Wood K As a means for visualizing molecular physiology within living cells, new strategies are emerging for engineering luciferases into intracellular biosensors. These biosensors can be classified as bimolecular, relying on complementation of luciferase fragments, or intramolecular, relying on domain insertion within the luciferase structure. Multiple design strategies have recently surfaced for the development of intramolecular sensors, allowing dynamic detection of small molecules or post-translational modifications within cells. Building on successes achieved in cell culture, these sensors are now beginning to reveal molecular processes within living organisms. PMID: 19299118 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnol... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2283580 Tue, 17 Mar 2009 04:00:00 +0100 2283580 http://www.medworm.com/index.php?rid=2273618&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19285855%26dopt%3DAbstract Authors: Andrews-Polymenis HL, Santiviago CA, McClelland M Nontyphoidal Salmonellae are highly prevalent food-borne pathogens. High-throughput sequencing of Salmonella genomes is expanding our knowledge of the evolution of serovars and epidemic isolates. Genome sequences have also allowed the creation of complete microarrays. Microarrays have improved the throughput of in vivo expression technology (IVET) used to uncover promoters active during infection. In another method, signature tagged mutagenesis (STM), pools of mutants are subjected to selection. Changes in the population are monitored on a microarray, revealing genes under selection. Complete genome sequences permit the construction of pools of targeted in-frame deletions that have improved STM by minimizing the number of clone... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2273618 Thu, 12 Mar 2009 04:00:00 +0100 2273618 http://www.medworm.com/index.php?rid=2258684&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19278849%26dopt%3DAbstract Authors: Van Aken B Phytoremediation of organic pollutants, such as explosives, is often a slow and incomplete process, potentially leading to the accumulation of toxic metabolites that can be further introduced into the food chain. During the past decade, plants have been genetically modified to overcome the inherent limitations of plant detoxification capabilities, following a strategy similar to the development of transgenic crop. Bacterial genes encoding enzymes involved in the breakdown of explosives, such as nitroreductase and cytochrome P450, have been introduced in higher plants, resulting in significant enhancement of plant tolerance, uptake, and detoxification performances. Transgenic plants exhibiting biodegradation capabilities of microorganisms bring the promise of an effi... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258684 Mon, 09 Mar 2009 04:00:00 +0100 2258684 http://www.medworm.com/index.php?rid=2258683&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19278850%26dopt%3DAbstract Authors: Ben-Yakar A, Bourgeois F The use of ultrafast laser pulses in surgery has allowed for unprecedented precision with minimal collateral damage to surrounding tissues. For these reasons, ultrafast laser nanosurgery, as an injury model, has gained tremendous momentum in experimental biology ranging from in vitro manipulations of subcellular structures to in vivo studies in whole living organisms. For example, femtosecond laser nanosurgery on such model organism as the nematode Caenorhabditis elegans has opened new opportunities for in vivo nerve regeneration studies. Meanwhile, the development of novel microfluidic devices has brought the control in experimental environment to the level required for precise nanosurgery in various animal models. Merging microfluidics and laser nano... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258683 Mon, 09 Mar 2009 04:00:00 +0100 2258683 http://www.medworm.com/index.php?rid=2258685&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19272766%26dopt%3DAbstract Authors: Girkin JM, Poland S, Wright AJ Optical microscopy has been a cornerstone of life science investigations since its first practical application around 400 years ago with the goal being subcellular resolution, three-dimensional images, at depth, in living samples. Nonlinear microscopy brought this dream a step closer, but as one images more deeply the material through which you image can greatly distort the view. By using optical devices, originally developed for astronomy, whose optical properties can be changed in real time, active compensation for sample-induced aberrations is possible. Submicron resolution images are now routinely recorded from depths over 1mm into tissue. Such active optical elements can also be used to keep conventional microscopes, both confocal and widefi... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258685 Sat, 07 Mar 2009 05:00:00 +0100 2258685 http://www.medworm.com/index.php?rid=2258686&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19269806%26dopt%3DAbstract Authors: Pilon-Smits EA, Leduc DL Selenium (Se) is a micronutrient for many organisms but also toxic at higher concentrations. Both selenium deficiency and toxicity are serious problems worldwide. Owing to the similarity of selenium to sulfur, plants readily take up and assimilate selenate via sulfur transporters and enzymes and can even volatilize selenium. Selenium accumulating or volatilizing plants may be used for phytoremediation of selenium pollution and as fortified foods. Several transgenic approaches have been used successfully to further enhance plant selenium accumulation, tolerance, and volatilization: upregulation of genes involved in sulfur/selenium assimilation and volatilization, methylation of selenocysteine, and conversion of selenocysteine to elemental Se. Lab and fi... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258686 Fri, 06 Mar 2009 05:00:00 +0100 2258686 http://www.medworm.com/index.php?rid=2258688&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19269159%26dopt%3DAbstract Authors: Tsai PS, Blinder P, Migliori BJ, Neev J, Jin Y, Squier JA, Kleinfeld D Plasma-mediated ablation makes use of high energy laser pulses to ionize molecules within the first few femtoseconds of the pulse. This process leads to a submicrometer-sized bubble of plasma that can ablate tissue with negligible heat transfer and collateral damage to neighboring tissue. We review the physics of plasma-mediated ablation and its use as a tool to generate targeted insults at the subcellular level to neurons and blood vessels deep within nervous tissue. Illustrative examples from axon regeneration and microvascular research highlight the utility of this tool. We further discuss the use of ablation as an integral part of automated histology. PMID: 19269159 [PubMed - as supplied by publishe... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258688 Thu, 05 Mar 2009 05:00:00 +0100 2258688 http://www.medworm.com/index.php?rid=2258687&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19269160%26dopt%3DAbstract Authors: Kawahigashi H Herbicides are economically important, but the non-point pollution that they cause may disrupt the surrounding environment. Phytoremediation of herbicides has been well studied using conventional plants. Transgenic plants produced for metabolizing herbicides and long-persisting pollutants can be used for phytoremediation of foreign chemicals in contaminated soil and water. The genes involved in the metabolism of chemical compounds can be isolated from various organisms, including bacteria, fungi, plants, and animals, and these genes are then introduced into candidate plants. Transgenic plants expressing mammalian P450s and the other enzymes showed tolerance and phytoremediation activity toward target herbicides. Transgenic plants can also enhance the absorption a... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258687 Thu, 05 Mar 2009 05:00:00 +0100 2258687 http://www.medworm.com/index.php?rid=2258691&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19268566%26dopt%3DAbstract Authors: Wachsmann-Hogiu S, Weeks T, Huser T The gold standard for clinical diagnostics of tissues is immunofluorescence staining. Toxicity of many fluorescent dyes precludes their application in vivo. Raman spectroscopy, a chemically specific, label-free diagnostic technique, is rapidly gaining acceptance as a powerful alternative. It has the ability to probe the chemical composition of biological materials in a non-destructive and mostly non-perturbing manner. We review the most recent developments in Raman spectroscopy in the life sciences, detailing advances in technology that have improved the ability to screen for diseases. Its role in the monitoring of biological function and mapping the cellular chemical microenvironment will be discussed. Applications including endoscopy, surf... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258691 Wed, 04 Mar 2009 05:00:00 +0100 2258691 http://www.medworm.com/index.php?rid=2258690&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19268567%26dopt%3DAbstract Authors: Brown JQ, Vishwanath K, Palmer GM, Ramanujam N Methods of optical spectroscopy that provide quantitative, physically or physiologically meaningful measures of tissue properties are an attractive tool for the study, diagnosis, prognosis, and treatment of various cancers. Recent development of methodologies to convert measured reflectance and fluorescence spectra from tissue to cancer-relevant parameters such as vascular volume, oxygenation, extracellular matrix extent, metabolic redox states, and cellular proliferation have significantly advanced the field of tissue optical spectroscopy. The number of publications reporting quantitative tissue spectroscopy results in the UV-visible wavelength range has increased sharply in the past three years, and includes new and emerging stu... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258690 Wed, 04 Mar 2009 05:00:00 +0100 2258690 http://www.medworm.com/index.php?rid=2258689&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19268568%26dopt%3DAbstract Authors: Levitt JA, Matthews DR, Ameer-Beg SM, Suhling K Fluorescence lifetime imaging (FLIM) and fluorescence polarization imaging are complementary techniques that can be used to extract information about macromolecules from biological samples. Owing to the sensitivity of fluorescence to the physicochemical environment, and nanometer-scale interactions via Förster resonance energy transfer (FRET), FLIM has been implemented in many laboratories for numerous applications in the life sciences and beyond. This review seeks to provide a brief overview of some of the recent advances in the techniques and more pertinently their applications in cell and tissue imaging. The particular merits of polarization-resolved fluorescence measurements are highlighted, including the unique ability ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2258689 Wed, 04 Mar 2009 05:00:00 +0100 2258689 http://www.medworm.com/index.php?rid=2249311&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19264474%26dopt%3DAbstract Authors: Müller DJ, Krieg M, Alsteens D, Dufrêne YF Originally invented for imaging surfaces, atomic force microscopy (AFM) has evolved into a multifunctional molecular toolkit, enabling us to investigate the interactions of biological systems over scales ranging from single-molecules to whole cells. Specific highlights include the nanoscale imaging of the chemical properties of individual cells, the detection and functional analysis of cell surface receptors using single-molecule force spectroscopy and the quantitative measurement of cellular interactions using single-cell force spectroscopy. These advanced force spectroscopy modalities offer new opportunities for understanding the molecular bases of cell adhesion processes, which is a fundamental challenge in current life s... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2249311 Tue, 03 Mar 2009 05:00:00 +0100 2249311 http://www.medworm.com/index.php?rid=2249310&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19264475%26dopt%3DAbstract Authors: Bouma BE, Yun SH, Vakoc BJ, Suter MJ, Tearney GJ With the advent of Fourier-domain techniques, optical coherence tomography (OCT) has advanced from high-resolution 'point' imaging over small fields-of-view to comprehensive microscopic imaging over three-dimensional volumes that are comparable to the dimensions of luminal internal organs. This advance has required the development of new lasers, improved spectrometers, minimally invasive catheters and endoscopes, and novel optical and signal processing strategies. In recent cardiovascular, ophthalmic, and gastrointestinal clinical studies, the capabilities of Fourier-domain OCT have enabled a new paradigm for diagnostic screening of large tissue areas, which addresses the shortcomings of existing technologies and focal biopsy. ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2249310 Tue, 03 Mar 2009 05:00:00 +0100 2249310 http://www.medworm.com/index.php?rid=2233138&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19250817%26dopt%3DAbstract Authors: Sylvestre M, Macek T, Mackova M Recent investigations have shown that the three components of the biphenyl dioxygenase and the 2,3-dihydroxybiphenyl dioxygenase can be produced actively in transgenic plants. Both enzymes catalyze critical steps of the bacterial polychlorinated biphenyl (PCB) degrading pathway. On the basis of these observations, optimized plant-microbe bioremediation processes in which transgenic plants would initiate PCB metabolism and release the metabolites for further degradation by rhizobacteria has been proposed. Since this is still a relatively new approach for PCB remediation, its successful application will require efforts first, to engineer improved PCB-degrading enzymes; second, to co-ordinately express these enzymes' components in plants; and third... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2233138 Thu, 26 Feb 2009 05:00:00 +0100 2233138 http://www.medworm.com/index.php?rid=2233139&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19249200%26dopt%3DAbstract Authors: Charkowski AO Soft rot pathogens cause significant losses worldwide in fruit and vegetable production during the growing season and after harvest. These pathogens engage in molecular interactions with their plant hosts via acyl-homoserine lactone (AHL) quorum sensing, pectin metabolites, phenolic acids, and auxin. The AHL-based interactions can be disrupted enzymatically or with chemical inhibitors, which in some cases, leads to disease control. Since the wisdom of disrupting AHL-based quorum sensing for control of an agricultural problem is questionable when this may be a useful target for control of human pathogens, development of other control mechanisms more specific to plant pathogens would be beneficial. The recent identification of plant-specific compounds used in plant... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2233139 Wed, 25 Feb 2009 05:00:00 +0100 2233139 http://www.medworm.com/index.php?rid=2222677&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19243931%26dopt%3DAbstract Authors: Saulnier DM, Spinler JK, Gibson GR, Versalovic J The technologies of metagenomics and metabolomics are broadening our knowledge of the roles the human gut microbiota play in health and disease. For many years now, probiotics and prebiotics have been included in foods for their health benefits; however, we have only recently begun to understand their modes of action. This review highlights recent advances in deciphering the mechanisms of probiosis and prebiosis, and describes how this knowledge could be transferred to select for enhancing functional foods targeting different populations. A special focus will be given to the addition of prebiotics and probiotics in functional foods for infants and seniors. PMID: 19243931 [PubMed - as supplied by publisher] (Source: Current O... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2222677 Mon, 23 Feb 2009 05:00:00 +0100 2222677 http://www.medworm.com/index.php?rid=2210766&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19233638%26dopt%3DAbstract Authors: Dothager RS, Flentie K, Moss B, Pan MH, Kesarwala A, Piwnica-Worms D Many of the obligate steps of physiology and disease are dynamic in time and space, and thus, end-point assays do not always provide a full understanding of these processes. Comprehensive understanding of the functional complexity of protein interactions and cell trafficking requires mapping of cellular and molecular function within complex systems over biologically relevant time scales. New approaches to bioluminescence imaging of cell migration, signaling pathways, drug action, and interacting protein partners in vivo allow the study of biology and disease within the context of living animals. PMID: 19233638 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2210766 Sat, 21 Feb 2009 05:00:00 +0100 2210766 http://www.medworm.com/index.php?rid=2210765&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19233639%26dopt%3DAbstract Authors: Rasmussen JC, Tan IC, Marshall MV, Fife CE, Sevick-Muraca EM While the lymphatic system is increasingly associated with diseases of prevalence, study of these diseases is difficult owing to the paucity of imaging techniques with the sensitivity and temporal resolution to discriminate lymphatic function. Herein, we review the known, pertinent features of the human lymphatic system in health and disease and set the context for a number of emerging studies that use near-infrared fluorescence imaging to non-invasively assess tumor draining lymphatic basins in cancer patients, intraoperatively guide resection of first draining lymph nodes, and to interrogate the difference between normal and aberrant lymphatic structure and function. PMID: 19233639 [PubMed - as supplied by publ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2210765 Fri, 20 Feb 2009 05:00:00 +0100 2210765 http://www.medworm.com/index.php?rid=2200695&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19223167%26dopt%3DAbstract Authors: Carlson HJ, Campbell RE The phenomenon of Förster (or fluorescence) resonance energy transfer (FRET) between two fluorescent proteins of different hues provides a robust foundation for the design and construction of biosensors for the detection of intracellular events. Accordingly, FRET-based biosensors for a variety of biologically relevant ions, molecules, and specific enzymatic activities, have now been developed and used to investigate numerous questions in cell biology. An emerging trend in the use of FRET-based biosensors is to apply them in combination with a second biosensor in order to achieve simultaneous imaging of multiple biochemical parameters in a single living cell. Here we discuss the particular technological challenges facing the use of FRET-based biosen... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2200695 Fri, 13 Feb 2009 05:00:00 +0100 2200695 http://www.medworm.com/index.php?rid=2188100&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19216068%26dopt%3DAbstract Authors: Xia Z, Rao J Bioluminescence resonance energy transfer (BRET) operates with biochemical energy generated by bioluminescent proteins to excite fluorophores and offers additional advantages over fluorescence energy transfer (FRET) for in vivo imaging and biosensing. While fluorescent proteins are frequently used as BRET acceptors, both small molecule dyes and nanoparticles can also serve as acceptor fluorophores. Semiconductor fluorescent nanocrystals or quantum dots (QDs) are particularly well suited for use as BRET acceptors due to their high quantum yields, large Stokes shifts and long wavelength emission. This review examines the potential of QDs for BRET-based bioassays and imaging, and highlights examples of QD-BRET for biosensing and imaging applications. Future developme... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=2188100 Tue, 10 Feb 2009 05:00:00 +0100 2188100 http://www.medworm.com/index.php?rid=1996446&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19036576%26dopt%3DAbstract Authors: Dudley MN, Loutit J, Griffith DC Increasing antibiotic resistance and lack of R&D productivity of new classes of antimicrobial agents directed against Gram-negative bacteria necessitate new approaches to maximize the efficacy of existing classes of drugs. Direct administration of drugs to the lung via the inhalational route provides for high concentrations at the target site of action in patients with pulmonary infections. The efficacy of aerosol antibiotic administration has been best demonstrated with aerosolized tobramycin in the management of chronic infections because of Pseudomonas aeruginosa in cystic fibrosis (CF) patients. Unfortunately, inconvenient regimens leading to poor patient adherence to therapy, and the increasing frequency of multidrug-resistant strains ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1996446 Mon, 24 Nov 2008 05:00:00 +0100 1996446 http://www.medworm.com/index.php?rid=1964172&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000765%26dopt%3DAbstract Authors: Wood TK Bacteria have enormous catabolic potential for remediating wastes; however, the interactions between bacteria and pollutants are complex and suitable remediation does not always take place. Hence, molecular approaches are being applied to enhance bioremediation. Here, an overview is provided of the recent advances in bioremediation by utilizing rhizoremediation, protein engineering, metabolic engineering, whole-transcriptome profiling, and proteomics for the degradation of recalcitrant pollutants such as chlorinated aliphatics and polychlorinated biphenyls as well as for binding heavy metals. PMID: 19000765 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1964172 Fri, 07 Nov 2008 05:00:00 +0100 1964172 http://www.medworm.com/index.php?rid=1960908&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000760%26dopt%3DAbstract Authors: Lovley DR Broad application of microbial fuel cells will require substantial increases in current density. A better understanding of the microbiology of these systems may help. Recent studies have greatly expanded the range of microorganisms known to function either as electrode-reducing microorganisms at the anode or as electrode-oxidizing microorganisms at the cathode. Microorganisms that can completely oxidize organic compounds with an electrode serving as the sole electron acceptor are expected to be the primary contributors to power production. Several mechanisms for electron transfer to anodes have been proposed including: direct electron transfer via outer-surface c-type cytochromes, long-range electron transfer via microbial nanowires, electron flow through a conductiv... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1960908 Fri, 07 Nov 2008 05:00:00 +0100 1960908 http://www.medworm.com/index.php?rid=1960907&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000761%26dopt%3DAbstract Authors: de Lorenzo V Bioremediation involves the exposure of a whole mixture of chemical structures to an intricate multispecies metabolic network present in a polluted scenario. Physico-chemical conditions of the sites determine the dynamic interplay between the contaminants and the biological catalysts. The complexity involved in such events is growingly amenable to the conceptual frame and the tools of systems biology. The availability of genes, genomes, and metagenomes of biodegradative micro-organisms make it possible to model and even predict the fate of chemicals through the global metabolic network that results from connecting all known biochemical transactions. Recent computational resources increasingly help the design of superior biocatalysts for biodegradation and biotrans... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1960907 Fri, 07 Nov 2008 05:00:00 +0100 1960907 http://www.medworm.com/index.php?rid=1960906&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000762%26dopt%3DAbstract Authors: Bebbington C, Yarranton G Antibodies can be used for the prevention and treatment of bacterial infections in animal models of disease. Current antibody technology allows the generation of high affinity human/humanized antibodies that can be optimized for antibacterial activity and in vivo biodistribution and pharmacokinetics. Such antibodies have exquisite selectivity for their bacterial target antigen and promise efficacy and safety. Why are not there any monoclonal antibody products approved for the treatment or prevention of bacterial infections? Can antibodies succeed where antibiotics are failing? Some antibody therapies are currently being evaluated in clinical trials but several have failed despite positive data in animal disease models. This review will discuss the pro... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1960906 Fri, 07 Nov 2008 05:00:00 +0100 1960906 http://www.medworm.com/index.php?rid=1960905&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000763%26dopt%3DAbstract Authors: Hamill P, Brown K, Jenssen H, Hancock RE Resistance to anti-microbial agents and the limited development of novel agents are threatening to worsen the burden of infections that are already a leading cause of morbidity and mortality. This has increased interest in the development of novel strategies such as selective modulation of our natural immune defences. Innate immunity is a complex, evolutionarily conserved, multi-facetted response to defeating infection that is naturally stimulated by pathogenic organisms through pattern recognition receptors on host cells. It is amplifiable and broad spectrum but if overstimulated can lead to the potential for harmful inflammatory responses. A broad variety of therapies are already available or increasingly under development, to stimula... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1960905 Fri, 07 Nov 2008 05:00:00 +0100 1960905 http://www.medworm.com/index.php?rid=1960904&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19000764%26dopt%3DAbstract Authors: Payne D, Bush K PMID: 19000764 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1960904 Fri, 07 Nov 2008 05:00:00 +0100 1960904 http://www.medworm.com/index.php?rid=1952023&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18996193%26dopt%3DAbstract Authors: Scott RW, Degrado WF, Tew GN Antimicrobial peptides are small cationic amphiphiles that play an important role in the innate immune system. Given their broad specificity, they appear to be ideal therapeutic agents. As a result, over the last decade, there has been considerable interest in developing them as intravenously administered antibiotics. However, it has proven difficult to accomplish this goal with peptide-based structures. Although it has been possible to solve some relatively simple problems such as susceptibility to proteolysis, more severe problems have included the expense of the materials, toxicity, limited efficacy, and limited tissue distribution. As a result, we developed small synthetic oligomers designed to adopt amphiphilic conformations and exhibit potent... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1952023 Wed, 05 Nov 2008 05:00:00 +0100 1952023 http://www.medworm.com/index.php?rid=1952022&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18996194%26dopt%3DAbstract Authors: Lee SK, Chou H, Ham TS, Lee TS, Keasling JD The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and syn... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1952022 Wed, 05 Nov 2008 05:00:00 +0100 1952022 http://www.medworm.com/index.php?rid=1952025&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18992814%26dopt%3DAbstract Authors: Zhou H, Xie X, Tang Y Many biologically active natural products are produced by the host organisms using dedicated biosynthetic pathways. The programming rules of these pathways may be rationally manipulated through combinatorial biosynthesis to produce natural products that contain structural variations or enhanced pharmacological properties. Furthermore, these pathways contain enzymes that can be harvested as powerful biocatalysts for the synthesis of both new drugs and existing blockbuster therapeutics. This review will highlight recent advances in exploring natural product biosynthetic pathways for new compounds, novel enzymes and useful biocatalysts. PMID: 18992814 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1952025 Tue, 04 Nov 2008 05:00:00 +0100 1952025 http://www.medworm.com/index.php?rid=1952024&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18992815%26dopt%3DAbstract Authors: Chemler JA, Koffas MA Plant natural products (NPs) not only serve many functions in an organism's survivability but also demonstrate important pharmacological activities. Isolation of NPs from native sources is frequently limited by low abundance and environmental, seasonal, and regional variation while total chemical synthesis of what are often complex structures is typically commercially infeasible. Reconstruction of biosynthetic pathways in heterologous microorganisms offers significant promise for a scalable means to provide sufficient quantities of a desired NP while using inexpensive renewable resources. To this end, metabolic engineering provides the technological platform for enhancing NP production in these engineered heterologous hosts. Recent advancements in the pro... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1952024 Tue, 04 Nov 2008 05:00:00 +0100 1952024 http://www.medworm.com/index.php?rid=1939282&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18984052%26dopt%3DAbstract Authors: Cardenas E, Tiedje JM To discover and characterize microbial diversity, approaches based on new sequencing technologies, novel isolation techniques, microfluidics, and metagenomics among others are being used. These approaches have contributed to discovery of novel genes from environmental samples, to massive characterization of functional and phylogenetic genes and to isolation of members of formerly uncultured yet ubiquitous groups like Verrucomicrobia, Acidobacteria, OP10, and methanogenic Archaea. Cheaper sequencing is key in this process by making available applications that were previously restricted to big research centers, complementing previously available methodologies and potentially replacing some of them. The new tools are reshaping the way we study the environmen... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1939282 Sat, 01 Nov 2008 04:00:00 +0100 1939282 http://www.medworm.com/index.php?rid=1939283&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18983917%26dopt%3DAbstract Authors: Zell R, Krumbholz A, Wutzler P Global warming is believed to induce a gradual climate change. Hence, it was predicted that tropical insects might expand their habitats thereby transmitting pathogens to humans. Although this concept is a conclusive presumption, clear evidence is still lacking-at least for viral diseases. Epidemiological data indicate that seasonality of many diseases is further influenced by strong single weather events, interannual climate phenomena, and anthropogenic factors. So far, emergence of new diseases was unlinked to global warming. Re-emergence and dispersion of diseases was correlated with translocation of pathogen-infected vectors or hosts. Coupled ocean/atmosphere circulations and 'global change' that also includes shifting of demographic, social,... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1939283 Fri, 31 Oct 2008 04:00:00 +0100 1939283 http://www.medworm.com/index.php?rid=1934051&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18977299%26dopt%3DAbstract Authors: Gershoni JM Receptor-ligand interactions are fundamental to the regulation of cell physiology, enabling the communication between cells and their environment via signal transduction. Receptors are also exploited by toxins and infectious agents to mediate pathogenesis. Over the past 20 years, however, this bi-partite paradigm for cellular regulation, that is, receptors and their ligands, has been revised to include an unforeseen participant namely, soluble receptors or molecular decoys. Decoys function as nature's modifiers of potent responses such as inflammation, stimulation of cell proliferation and triggering apoptosis. Decoys not only provide the means to fine tune the regulation of these phenomena; they also serve as potential leads for the development of recombinant anti... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1934051 Wed, 29 Oct 2008 04:00:00 +0100 1934051 http://www.medworm.com/index.php?rid=1934050&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18977300%26dopt%3DAbstract Authors: Zhao H, Chen W PMID: 18977300 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1934050 Wed, 29 Oct 2008 04:00:00 +0100 1934050 http://www.medworm.com/index.php?rid=1934049&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18977301%26dopt%3DAbstract Authors: Hooshangi S, Bentley WE Cell-cell communication and coordinated population-based behavior among single cell organisms have gained considerable attention in the recent years. The ability to send, receive, and process information allows unicellular organisms to act as multicellular entities and increases their chances of survival in complex environments. Quorum sensing (QS), a density-dependent cell-signaling mechanism, is one way by which bacteria 'talk' to one another. QS is commonly associated with adverse health effects such as biofilm formation, bacteria pathogenicity, and virulence. But there exists great potential to harness QS circuitry and its properties for other applications, enabling even wider societal impact. Interesting avenues are envisioned for the detection of ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1934049 Wed, 29 Oct 2008 04:00:00 +0100 1934049 http://www.medworm.com/index.php?rid=1888311&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18926909%26dopt%3DAbstract Authors: Mattey M, Spencer J Recent animal and human trials of bacteriophage therapy have demonstrated its potential to alleviate bacterial diseases, both in internal and in external applications. The regulatory requirements are becoming clearer as more examples are presented. A core of GLP (Good Laboratory Practice) studies will be needed to validate safety and clinical trials to validate efficacy. GMP (Good Manufacturing Practice) production requirements and quality issues will mean that comparable costs to the production of conventional antibiotics should be anticipated. The definition of the 'active substance' will be central to the success of bacteriophage therapy to ensure that the variety and evolutionary potential of bacteriophages are exploited. PMID: 18926909 [PubMed - as... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1888311 Mon, 13 Oct 2008 04:00:00 +0100 1888311 http://www.medworm.com/index.php?rid=1815434&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18804166%26dopt%3DAbstract Authors: Chatterjee A, Kaznessis Y, Hu WS Many biological events are binary. The switch between mutually exclusive OFF to ON state in response to a stimulus is frequently mediated by a control circuit with a positive and/or a negative feedback. Such a system typically exhibits hysteresis with its switching ON and OFF stimulus levels dependent on the current state of the system. The system can be shown to be bistable both experimentally and mathematically. Work to synthesize such switches by combining natural or engineered components has begun to illustrate the potential of such control circuits in many areas of applications. PMID: 18804166 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology) Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1815434 Tue, 16 Sep 2008 04:00:00 +0100 1815434 http://www.medworm.com/index.php?rid=1754862&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18761088%26dopt%3DAbstract Authors: Atsumi S, Liao JC Global energy and environmental problems have stimulated increasing efforts toward synthesizing liquid biofuels as transportation energy. Compared to the traditional biofuel, ethanol, advanced biofuels should offer advantages such as higher energy density, lower hygroscopicity, lower vapor pressure, and compatibility with existing transportation infrastructure. However, these fuels are not synthesized economically using native organisms. Metabolic engineering offers an alternative approach in which synthetic pathways are engineered into user-friendly hosts for the production of these fuel molecules. These hosts could be readily manipulated to improve the production efficiency. This review summarizes recent progress in the engineering of Escherichia coli to pr... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754862 Wed, 27 Aug 2008 04:00:00 +0100 1754862 http://www.medworm.com/index.php?rid=1754870&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760353%26dopt%3DAbstract Authors: St Jean AT, Zhang M, Forbes NS Current cancer therapies have limited efficacy because they are highly toxic, ineffectively target tumors, and poorly penetrate tumor tissue. Engineered bacteria have the unique potential to overcome these limitations by actively targeting all tumor regions and delivering therapeutic payloads. Examples of transport mechanisms include specialized chemotaxis, preferred growth, and hypoxic germination. Deleting the ribose/galactose chemoreceptor has been shown to cause bacterial accumulation in therapeutically resistant tumor regions. Recent advances in engineered therapeutic delivery include temporal control of cytotoxin release, enzymatic activation of pro-drugs, and secretion of physiologically active biomolecules. Bacteria have been engineered t... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754870 Tue, 26 Aug 2008 04:00:00 +0100 1754870 http://www.medworm.com/index.php?rid=1754869&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760354%26dopt%3DAbstract Authors: Akinterinwa O, Khankal R, Cirino PC Sugar alcohols find applications in pharmaceuticals, oral and personal care products, and as intermediates in chemical synthesis. While industrial-scale production of these compounds has generally involved catalytic hydrogenation of sugars, microbial-based processes receive increasing attention. The past few years have seen a variety of interesting metabolic engineering efforts to improve the capabilities of bacteria and yeasts to overproduce xylitol, mannitol, and sorbitol. Examples include heterologous expression of yeast xylose reductase in Escherichia coli for the production of xylitol, coexpression of formate dehydrogenase, mannitol dehydrogenase, and a glucose facilitator protein in Corynebacterium glutamicum for mannitol production fr... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754869 Tue, 26 Aug 2008 04:00:00 +0100 1754869 http://www.medworm.com/index.php?rid=1754868&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760355%26dopt%3DAbstract Authors: Singh S, Kang SH, Mulchandani A, Chen W Given the immense risk posed by widespread environmental pollution by inorganic and organic chemicals, novel methods of decontamination and clean-up are required. Owing to the relatively high cost and the non-specificity of conventional techniques, bioremediation is a promising alternative technology for pollutant clean-up. Advances in bioremediation harness molecular, genetic, microbiology, and protein engineering tools and rely on identification of novel meta-sequestering peptides, rational and irrational pathway engineering, and enzyme design. Recent advances have been made for enhanced inorganic chemical remediation and organic chemical degradation using various pathway-engineering approaches and these are discussed in this review. ... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754868 Tue, 26 Aug 2008 04:00:00 +0100 1754868 http://www.medworm.com/index.php?rid=1754867&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760356%26dopt%3DAbstract Authors: Park JH, Lee SY Microorganisms capable of efficient production of amino acids have traditionally been developed by random mutation and selection method, which might cause unwanted physiological changes in cellular metabolism. Rational genome-wide metabolic engineering based on systems and synthetic biology tools, which is termed 'systems metabolic engineering', is rising as an alternative to overcome these problems. Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner. Here we review the current status of systems metabolic e... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754867 Tue, 26 Aug 2008 04:00:00 +0100 1754867 http://www.medworm.com/index.php?rid=1754866&cid=s_35489_70_f&fid=35489&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18760357%26dopt%3DAbstract Authors: McDevitt TC, Palecek SP In recent years, substantial progress has been made in identifying culture conditions and specific molecular factors that maintain human embryonic stem cells (hESCs) in a selfrenewing, pluripotent state. As science and medicine move closer to producing viable hESC-based therapeutics, effective methods of isolating and maintaining undifferentiated hESCs using clinically acceptable good manufacturing practices must be developed. In recent years, progress toward this goal has included the identification of molecular factors that induce or repress hESC selfrenewal and the development of defined media that support long-term hESC expansion. In addition, the recent discovery of novel means to derive pluripotent cells that avoid embryo destruction, including in... Current Opinion in Biotechnology journals http://www.medworm.com/rss/comments.php?id=1754866 Tue, 26 Aug 2008 04:00:00 +0100 1754866