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 Issues in Molecular Biology' source. Sun, 15 Jan 2012 08:35:44 +0100 http://www.medworm.com/index.php?rid=5415490&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22086198%26dopt%3DAbstract Authors: Trevors JT Abstract It has been assumed that diffusion of molecules in the bacterial cytoplasm is the mechanism that moves molecules in the absence of cytoplasmic streaming. However, is there an undiscovered mechanism present that mobilizes cytoplasm and its molecular contents, and delivers tRNAs to specific ribosomes at specific bacterial cytoplasmic locations? Mobilization of specific tRNA (and also mRNA transcripts and ribosomes) and cell division proteins to specific intracellular locations may suggest that instructions and/or mechanism(s) are needed. The alternative is that molecular crowding in the cytoplasm is sufficient for gentle contact between mRNA, ribosomes and tRNA. Or is it plausible that the bacterial cytoplasm (and its contents) are mobilized with the outc... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5415490 Wed, 16 Nov 2011 05:00:00 +0100 5415490 http://www.medworm.com/index.php?rid=5093055&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21795760%26dopt%3DAbstract Authors: Shevelyov YY, Nurminsky DI There is accumulating evidence that the nuclear periphery is a transcriptionally repressive compartment. A surprisingly large fraction of the genome is either in transient or permanent contact with nuclear envelope, where the majority of genes are maintained in a silent state, waiting to be awakened during cell differentiation. The integrity of the nuclear lamina and the histone deacetylase activity appear to be essential for gene repression at the nuclear periphery. However, the molecular mechanisms of silencing, as well as the events that lead to the activation of lamina-tethered genes, require further elucidation. This review summarizes recent advances in understanding of the mechanisms that link nuclear architecture, local chromatin structure, an... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5093055 Wed, 27 Jul 2011 23:00:00 +0100 5093055 http://www.medworm.com/index.php?rid=5093056&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21791713%26dopt%3DAbstract Authors: Munro JB, Silva JC Malaria is caused by species in the apicomplexan genus Plasmodium, which infect hundreds of millions of people each year and kill close to one million. While malaria is the most notorious of the apicomplexan-caused diseases, other members of eukaryotic phylum Apicomplexa are responsible for additional, albeit less well-known, diseases in humans, economically important livestock, and a variety of other vertebrates. Diseases such as babesiosis (hemolytic anemia), theileriosis and East Coast Fever, cryptosporidiosis, and toxoplasmosis are caused by the apicomplexans Babesia, Theileria, Cryptosporidium and Toxoplasma, respectively. In addition to the loss of human life, these diseases are responsible for losses of billions of dollars annually. Hence, the researc... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5093056 Mon, 25 Jul 2011 23:00:00 +0100 5093056 http://www.medworm.com/index.php?rid=4853422&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21555788%26dopt%3DAbstract Authors: Rampias TN, Fragoulis EG, Sideris DC Cloning of alternatively polyadenylated transcripts is crucial for studying gene expression and function. Recent transcriptome analysis has mainly focused on large EST clone collections. However, EST sequencing techniques in many cases are incapable of isolating rare transcripts or address transcript variability. In most cases, 3' RACE is applied for the experimental identification of alternatively polyadenylated transcripts. However, its application may result in nonspecific amplification and false positive products due to the usage of a single gene specific primer. Additionally, internal poly(A) stretches primed by oligo(dT) primer in mRNAs with AU-rich 3'UTR may generate truncated cDNAs. To overcome these limitations, we have developed a... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4853422 Mon, 09 May 2011 23:00:00 +0100 4853422 http://www.medworm.com/index.php?rid=4746946&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21502666%26dopt%3DAbstract Authors: Rakonjac J, Bennett NJ, Spagnuolo J, Gagic D, Russel M Filamentous bacteriophage, long and thin filaments that are secreted from the host cells without killing them, have been an antithesis to the standard view of head-and-tail bacterial killing machines. Episomally replicating filamentous phage Ff of Escherichia coli provide the majority of information about the principles and mechanisms of filamentous phage infection, episomal replication and assembly. Chromosomally- integrated "temperate" filamentous phage have complex replication and integration, which are currently under active investigation. The latter are directly or indirectly implicated in diseases caused by bacterial pathogens Vibrio cholerae, Pseudomonas aeruginosa and Neisseria meningitidis. In the first half of th... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4746946 Sun, 17 Apr 2011 23:00:00 +0100 4746946 http://www.medworm.com/index.php?rid=4575352&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21368338%26dopt%3DAbstract Authors: Trevors JT, Masson L During his famous 1943 lecture series at Trinity College Dublin, the reknown physicist Erwin Schrodinger discussed the failure and challenges of interpreting life by classical physics alone and that a new approach, rooted in Quantum principles, must be involved. Quantum events are simply a level of organization below the molecular level. This includes the atomic and subatomic makeup of matter in microbial metabolism and structures, as well as the organic, genetic information code of DNA and RNA. Quantum events at this time do not elucidate, for example, how specific genetic instructions were first encoded in an organic genetic code in microbial cells capable of growth and division, and its subsequent evolution over 3.6 to 4 billion years. However, due to r... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4575352 Wed, 02 Mar 2011 00:00:00 +0100 4575352 http://www.medworm.com/index.php?rid=4463388&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21297219%26dopt%3DAbstract Authors: O'Sullivan JM The genomes of unicellular organisms form complex 3-dimensional structures. This spatial organization is hypothesized to have a significant role in genomic function. Spatial organization is not limited solely to the three-dimensional folding of the chromosome(s) in genomes but also includes genome positioning, and the folding and compartmentalization of any additional genetic material (e.g. episomes) present within complex genomes. In this comment, I will highlight similarities in the spatial organization of eukaryotic and prokaryotic unicellular genomes. PMID: 21297219 [PubMed - as supplied by publisher] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4463388 Fri, 04 Feb 2011 00:00:00 +0100 4463388 http://www.medworm.com/index.php?rid=4396064&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21220789%26dopt%3DAbstract Authors: Signat B, Roques C, Poulet P, Duffaut D The pathogenesis of periodontitis involves the interplay of microbiota present in the subgingival plaque and the host responses. Inflammation and destruction of periodontal tissues are considered to result from the response of a susceptible host to a microbial biofilm containing gram-negative pathogens. Antimicrobial peptides are important contributors to maintaining the balance between health and disease in this complex environment. These include several salivary antimicrobial peptides such as beta-defensins expressed in the epithelium and LL-37 expressed in both epithelium and neutrophils. Among gram-negative bacteria implicated in periodontal diseases, Fusobacterium nucleatum, is one of the most interesting. This review will focus on ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4396064 Mon, 10 Jan 2011 00:00:00 +0100 4396064 http://www.medworm.com/index.php?rid=3809389&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20671312%26dopt%3DAbstract Authors: Muller G The pathogenesis of common diseases, such as metabolic diseases, is caused by the complex and individual interplay of many susceptibility genes, which necessitates both personalized diagnosis and therapy. Small-molecule drugs which adequately address the multiple tissue-specific target proteins affected probably will not become available in near future. In contrast, therapeutic proteins, such as growth factors and antibodies, specifically replacing or inactivating the corresponding susceptibility gene products, are currently being identified with increasing efficacy. However, the failure to be administered by the oral route and to reach the cytoplasm of the diseased cells typically prevents their therapeutic use. Recent developments suggest that these limitations may ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3809389 Thu, 29 Jul 2010 23:00:00 +0100 3809389 http://www.medworm.com/index.php?rid=3590550&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20484776%26dopt%3DAbstract Authors: Grove A Bacterial histone-like HU proteins are critical to maintenance of the nucleoid structure. In addition, they participate in all DNA-dependent functions, including replication, repair, recombination and gene regulation. In these capacities, their function is typically architectural, inducing a specific DNA topology that promotes assembly of higher-order nucleo-protein structures. Although HU proteins are highly conserved, individual homologs have been shown to exhibit a wide range of different DNA binding specificities and affinities. The existence of such distinct specificities indicates functional evolution and predicts distinct in vivo roles. Emerging evidence suggests that HU proteins discriminate between DNA target sites based on intrinsic flexure, and that two prim... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3590550 Wed, 19 May 2010 23:00:00 +0100 3590550 http://www.medworm.com/index.php?rid=3579895&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20472940%26dopt%3DAbstract Authors: Ross C, Abel-Santos E Bacterial spores are specialized cells that are exceptionally resistant to environmental stress. Spores convert back to actively growing cells, a process called germination, upon nutrient detection. The most common, initial step in the germination process is the recognition of small molecule germinants by germination (Ger) receptors. Ger receptors are inner-membrane heterocomplexes formed by three distinct protein products, the A-, B-, and C-subunits. In this review, we discuss and contrast published reports on representative Ger receptors from different Bacilli and Clostridia. We also present evidence for unrecognized germination pathways independent of Ger receptors. We further emphasize the function of L-alanine as a universal germinant. We also commen... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3579895 Sun, 16 May 2010 23:00:00 +0100 3579895 http://www.medworm.com/index.php?rid=3009060&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19918091%26dopt%3DAbstract Authors: Desilet N, Campbell TN, Choy FY Since its discovery in 1979, p53 has become the focus of intensive cancer-based research in laboratories around the world. The p53 protein mediates critical cellular functions including the response to genotoxic stress, differentiation, senescence, and apoptosis, and has been shown to be mutated in a large proportion of human cancers. These observations led many to speculate that targeting the p53 pathway would result in the development of successful anti-cancer treatments. In spite of this, 30 years later, p53 has yet to fulfill this promise. However, new insights into small molecule combination therapies, microRNA regulation, structuring of clinical trials, and potential involvement in stem cell regulation may help p53 reach its potential. ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3009060 Mon, 16 Nov 2009 00:00:00 +0100 3009060 http://www.medworm.com/index.php?rid=2863395&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19801719%26dopt%3DAbstract In this study, we evaluated two novel products for room temperature DNA storage: Biomatrica's DNA SampleMatrix technology and GenVault's GenTegra DNA technology. We compared the integrity and quality of DNA stored using these products against DNA stored in a -20 C freezer by performing downstream testing with short range PCR, long range PCR, DNA sequencing, and SNP microarrays. In addition, we tested Biomatrica's RNAstable product for its ability to preserve RNA at room temperature for use in a quantitative reverse transcription PCR assay. PMID: 19801719 [PubMed - as supplied by publisher] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2863395 Thu, 01 Oct 2009 23:00:00 +0100 2863395 http://www.medworm.com/index.php?rid=2829206&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776427%26dopt%3DAbstract Authors: Gallup JM, Sow FB, Van Geelen A, Ackermann MR Real-time quantitative polymerase chain reaction is subject to inhibition by substances that co-purify with nucleic acids during isolation and preparation of samples. Such materials alter the activity of reverse transcriptase (RT) and thermostable DNA polymerase enzymes on which the assay depends. When removal of inhibitory substances by column or reagent-based methods fails or is incomplete, the remaining option of appropriately, precisely and differentially diluting samples and standards to non-inhibitory concentrations is often avoided due to the logistic problem it poses. To address this, we invented the PREXCEL-Q software program to automate the process of calculating the non-inhibitory dilutions for all samples and standards ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2829206 Mon, 21 Sep 2009 23:00:00 +0100 2829206 http://www.medworm.com/index.php?rid=2823852&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767649%26dopt%3DAbstract Authors: Tatzelt J A conformational transition of the cellular prion protein (PrP(C)) into an aberrantly folded isoform designated scrapie prion protein (PrP(Sc)) is the hallmark of a variety of neurodegenerative disorders collectively called prion diseases. They include Creutzfeldt-Jakob disease and Gerstmann-Staussler-Scheinker syndrome in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle and chronic wasting disease (CWD) in free-ranging deer. In contrast to the deadly properties of misfolded PrP, PrP(C) seems to possess a neuroprotective activity. More-over, animal models indicated that the stress-protective activity of PrP(C) and the neurotoxic effects of PrP(Sc) are somehow interconnected. PMID: 19767649 [PubMed - as supplied by publisher] (Source: Cur... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823852 Thu, 17 Sep 2009 23:00:00 +0100 2823852 http://www.medworm.com/index.php?rid=2823851&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767650%26dopt%3DAbstract Authors: Solomon IH, Schepker JA, Harris DA The chemical nature of prions and the mechanism by which they propagate are now reasonably well understood. In contrast, much less is known about the identity of the toxic prion protein (PrP) species that are responsible for neuronal death, and the cellular pathways that these forms activate. In addition, the normal, physiological function of cellular PrP (PrP(C)) has remained mysterious, hampering efforts to determine whether loss or alteration of this function contributes to the disease phenotype. Considerable evidence now suggests that aggregation, toxicity, and infectivity are distinct properties of PrP that do no necessarily coincide. In this review, we will discuss several mutant forms of PrP that produce spontaneous neurodegeneration i... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823851 Thu, 17 Sep 2009 23:00:00 +0100 2823851 http://www.medworm.com/index.php?rid=2823850&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767651%26dopt%3DAbstract Authors: Martins VR, Beraldo FH, Hajj GN, Lopes MH, Lee KS, Prado MM, Linden R PrP(C) is highly expressed in both the central and peripheral nervous systems from early stages of development and in adulthood. Its major conformational change and conversion into an abnormal form (PrP(Sc)) has been associated with the generation of prions, the infectious agent of transmissible spongiform encephalopathies (TSEs). The massive neurodegeneration presented by individuals suffering from these diseases has been associated with the gain of neurotoxic activity of PrP(Sc). On the other hand, major neurodegeneration is also observed in transgenic mice expressing PrP(C) molecules deleted of specific domains, which points to important functional domains within this molecule, and supports the hypothesis... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823850 Thu, 17 Sep 2009 23:00:00 +0100 2823850 http://www.medworm.com/index.php?rid=2823849&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767652%26dopt%3DAbstract Authors: Heiseke A, Aguib Y, Schatzl HM Prion diseases are infectious and fatal neurodegenerative disorders of man and animals which are characterized by spongiform degeneration in the central nervous system. Prion propagation involves the endocytic pathway and endosomal and lysosomal compartments are implicated in trafficking and re-cycling as well as final degradation of prions. Shifting the equilibrium between propagation and lysosomal clearance to the latter impairs cellular prion load. This and earlier findings of autophagic vacuoles in correlation to prion infections both in in vitro and in vivo studies prompted us and others to analyze the role of autophagy in prion infection. Autophagy is a fundamental cellular bulk degradation process for e.g. organelles or cytoplasmic protein... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823849 Thu, 17 Sep 2009 23:00:00 +0100 2823849 http://www.medworm.com/index.php?rid=2823848&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767653%26dopt%3DAbstract Authors: Singh N, Das D, Singh A, Mohan ML Metal induced free radicals are important mediators of neurotoxicity in several neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. Similar evidence is now emerging for prion diseases, a group of neurodegenerative disorders of humans and animals. The main pathogenic agent in all prion disorders is PrP-scrapie (PrP(Sc)), a beta-sheet rich isoform of a normal cell surface glycoprotein known as the prion protein (PrP(C)). Deposits of PrP(Sc) in the brain parenchyma are believed to induce neurotoxicity through poorly understood mechanisms. Recent reports suggest that imbalance of brain metal homeostasis is a significant cause of PrP(Sc)-associated neurotoxicity, though the underlying mechanisms ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823848 Thu, 17 Sep 2009 23:00:00 +0100 2823848 http://www.medworm.com/index.php?rid=2823846&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767654%26dopt%3DAbstract Authors: Miesbauer M, Rambold AS, Winklhofer KF, Tatzelt J Prion diseases are characterized by the conformational transition of the cellular prion protein (PrP(C)) into an aberrant protein conformer, designated scrapie-prion protein (PrP(Sc)). A causal link between protein misfolding and neurodegeneration has been established for a variety of neurodegenerative disease, such as Alzheimer's disease, Parkinson's disease and polyglutamine diseases, but there is an ongoing debate about the nature of the neurotoxic species and how non-native conformers can damage neuronal populations. PrP is normally imported into the endoplasmic reticulum (ER) and targeted to the outer leaflet of the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor. However, several conditions, such as ER str... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823846 Thu, 17 Sep 2009 23:00:00 +0100 2823846 http://www.medworm.com/index.php?rid=2823845&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767655%26dopt%3DAbstract Authors: Radford HE, Mallucci GR There are two central phenomena in prion disease: prion replication and prion neurotoxicity. Underlying them both is the conversion of a host-encoded ubiquitously expressed protein, prion protein (PrP(C)), into a partially-protease resistant isoform, PrP(Sc), which accumulates in the brain. PrP(Sc) is associated with both pathology and infectivity. In the absence of PrP(C), PrP(Sc) cannot be generated and PrP-null mice do not propagate infectivity or develop pathology on infection with scrapie. However, while PrP(C) expression is fundamental to both prion infectivity and neurodegeneration, the uncoupling of these processes is a growing concept in the field. This dissociation is evident in subclinical states of prion infection, where PrP(Sc) levels are h... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2823845 Thu, 17 Sep 2009 23:00:00 +0100 2823845 http://www.medworm.com/index.php?rid=2788440&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19741272%26dopt%3DAbstract Authors: Macwana SR, Punj S, Cooper J, Schwenk E, John GH Azo dyes are commonly used in many commercial industries. Some of the azo dyes can produce carcinogenic compounds after being metabolized by azoreductase. Several human intestinal microbiota possess azoreductase activity which plays an important role in the toxicity and mutagenicity of these azo dye compounds. The acpD gene product (AzoEf1) responsible for the azoreductase activity of Enterococcus faecium, an intestinal bacterium, was heterologously expressed, purified and characterized. The protein sequence shares 67% identity with the azoreductase from Enterococcus faecalis, AzoA. Although AzoEf1 possesses many commonalities with AzoA, there are differences in coenzyme preference, residues associated with FMN binding, substrat... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2788440 Wed, 09 Sep 2009 23:00:00 +0100 2788440 http://www.medworm.com/index.php?rid=2611431&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19605938%26dopt%3DAbstract Authors: Beeckman DS, Vanrompay DC Numerous bacterial proteins exert their function outside the prokaryotic cell. To this end, both Gram-negative and Gram-positive bacteria have evolved specialized mechanisms to transport their proteins to the bacterial supernatant or host cell cytoplasm, so called secretion systems. These different strategies will be briefly discussed, followed by an in depth description of the Type III secretion system, an efficient molecular syringe assisting Gram-negative bacteria in entrance, growth and survival in eukaryotic host cells. Topics addressed include classification and role of multiple Type III secretion systems, the mechanism of protein translocation into the host cell as well as substrate recognition and chaperoning. Chlamydiales have also been found... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2611431 Wed, 15 Jul 2009 23:00:00 +0100 2611431 http://www.medworm.com/index.php?rid=2548425&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19494420%26dopt%3DAbstract This article describes a one-step procedure based on Taq polymerase for the precise assembly of DNA fragments into circular constructs as long as 6 kb. The only prior step needed was the amplification of the gene to be cloned and the linear vector backbone, and the whole process up to assembly and circularization lasted only 2 days, compared with the conventional method's 2 weeks. Furthermore, the final DNA construct was used to transform Escherichia coli directly without any further treatment. By circumventing the need for DNA ligase, our "Quick Assemble" method offers an improvement over the combination of long PCR and overlap extension PCR, and is expected to facilitate various kinds of complex genetic engineering projects that require precise in-frame assembly of multiple fragments, su... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2548425 Tue, 02 Jun 2009 23:00:00 +0100 2548425 http://www.medworm.com/index.php?rid=2548426&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19478349%26dopt%3DAbstract Authors: De Palma G, Capilla A, Nadal I, Nova E, Pozo T, Varea V, Polanco I, Castillejo G, López A, Garrote JA, Calvo C, García-Novo MD, Cilleruelo ML, Ribes-Koninckx C, Palau F, Sanz Y Coeliac disease (CD) development involves genetic (HLA-DQ2/DQ8) and environmental factors. Herein, the influence of the HLA-DQ genotype on the gut colonization process of breast-fed children was determined. A cohort of 20 newborns, with at least one first-degree relative with CD, were classified according to their HLA-DQ genotype into high, intermediate and low genetic risk groups, showing 24-28%, 7-8% and less than 1% probability to develop CD, respectively. Faecal microbiota was analysed at 7 days, 1 and 4 months of children's age by fluorescence in situ hybridization. When considering all d... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2548426 Wed, 27 May 2009 23:00:00 +0100 2548426 http://www.medworm.com/index.php?rid=2548427&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19430030%26dopt%3DAbstract Authors: Shah ZH, Munir M, Kazi AM, Mujtaba T, Ahmed Z The complexity of the wheat genome has delayed the development and application of molecular markers to this species and wheat now lies behind barley, maize and rice in marker development. However, improvements in marker detection systems and in the techniques used to identify markers linked to useful traits has allowed considerable advances to be made in recent years. To evaluate the genetic diversity 53 genotypes of Richard's selection were studied at National Agriculture Reseach Center (NARC) Islamabad. The present study found that RAPD analysis is a valuable diagnostic tool. Different sets of RAPD primers were used to study the polymorphism at molecular level. Highest number of amplifications was shown by primer OpG-2 in Richard... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2548427 Sun, 10 May 2009 23:00:00 +0100 2548427 http://www.medworm.com/index.php?rid=2548428&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19366999%26dopt%3DAbstract Authors: Chen S, Li XQ, Zhao A, Wang L, Li X, Shi Q, Chen M, Guo J, Zhang J, Qi D, Liu G How plant gene expression responds to grazing defoliation is critical for plant re-growth, survival, and composition in the natural and dairy farming grassland environments. Rice, with genome sequence available, was used as a model plant to study grazing-induced pathway selections. When seedlings were 18 cm in height, the top 12 cm was removed by simulated grazing. The gene expression activities within 2 to 24 hours in the remaining aboveground tissues were profiled using the Affymetrix Rice GeneChips and RT-qPCR. The seedlings responded to grazing by immediately adjusting their global gene expression, e.g. enhancing anaerobic respiration, starch-to-sugar conversion, sucrose synthesis, and sugar tr... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2548428 Mon, 13 Apr 2009 23:00:00 +0100 2548428 http://www.medworm.com/index.php?rid=2326970&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19351974%26dopt%3DAbstract Authors: Callaway TR, Carr MA, Edrington TS, Anderson RC, Nisbet DJ Escherichia coli are commensal bacteria that can account for up to 1% of the bacterial population of the gut. Ruminant animals are reservoirs of the pathogenic bacteria E. coli strain O157:H7, and approximately 30% of feedlot cattle shed E. coli O157:H7. Feedlot and high-producing dairy cattle are fed high grain rations in order to increase feed efficiency. When cattle are fed high grain rations, some starch escapes ruminal microbial degradation and passes to the hindgut where it undergoes fermentation. Ten years ago researchers demonstrated that populations of total E. coli were higher in grain-fed than in forage-fed cattle, and when cattle were abruptly switched from a high grain diet to an all hay diet, total E. col... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2326970 Wed, 08 Apr 2009 04:00:00 +0100 2326970 http://www.medworm.com/index.php?rid=2164333&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193959%26dopt%3DAbstract This study investigated whether the HRM analysis can distinguish alleles among potato (Solanum tuberosum) transcript abundances. Transcript properties of genes encoding seven carbohydrate metabolism enzymes/proteins in various tissues and cold storage durations were studied. The HRM assay measured differential expression of alleles between different organs, between different storage treatments and stages of tubers from the same variety, and between different varieties with the same treatment. The RT-PCR amplicons were directly sequenced to assist the interpretation of HRM data. The cDNA HRM curves correlated well with the nucleotide polymorphisms of the cDNA sequences and the transcript abundance of alleles and therefore can serve as functional allele activity (FAA) markers. By combining t... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164333 Mon, 02 Feb 2009 05:00:00 +0100 2164333 http://www.medworm.com/index.php?rid=2164332&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193960%26dopt%3DAbstract Authors: Iqbal MJ, Ahsan R, Afzal AJ, Jamai A, Meksem K, El-Shemy HA, Lightfoot DA Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isol... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164332 Mon, 02 Feb 2009 05:00:00 +0100 2164332 http://www.medworm.com/index.php?rid=2164331&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193961%26dopt%3DAbstract Authors: El-Shemy HA, Khalafalla MM, Ishimoto M The green fluorescent protein (GFP) of jellyfish (Aequorea victoria) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Recently, epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. Therefore, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. Both constructs contain a gene conferring resistance to hygromycin (hpt) as a selective marker and a modified glycinin (11S globulin) gene (V3-1) as a target. However, sGFP(S65T) as a reporter gene was used only in pHVS as a reporter gene for study the relation b... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164331 Mon, 02 Feb 2009 05:00:00 +0100 2164331 http://www.medworm.com/index.php?rid=2164330&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193962%26dopt%3DAbstract Authors: Attia KA, Abdelkhalik AF, Ammar MH, Wei C, Yang J, Lightfoot DA, El-Sayed WM, El-Shemy HA OsARF1 is the first full-length member of auxin response factor (ARF) gene family to be cloned from monocot plant. Using quantitative RT-PCR this study found that, the transcript abundance of OsARF1 was significantly higher in embryonic tissues than in vegetative tissues. To investigate the effect of OsARF1 on the phenotype of rice, a cDNA fragment of OsARF1 was inserted in inverse orientation to the 35S promoter in vector pBin438 to produce an antisense (AS) construction. The AS-OsARF1 construct was transferred into rice (Oryza sativa L. japonica) calli via Agrobacterium tumefaciens-mediated transformation. Molecular analysis of transgenic plants showed that the functional expression of ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164330 Mon, 02 Feb 2009 05:00:00 +0100 2164330 http://www.medworm.com/index.php?rid=2164329&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193963%26dopt%3DAbstract Authors: Ganjewala D, Kumar S, Luthra R Isoprenoids, also known as terpenoids, are biosynthesized by the condensation of the two C5 unit isopentenyl diphosphate (IPP) and isomer dimethylallyl diphosphate (DMAPP). Generally, plants use two separate pathways plastidial Methyl-erythritol-4-phosphate (MEP) and cytosolic acetate-mevalonate (MVA) pathways for formation of IPP. The genes, enzymes and intermediates of the MEP pathway have been unravelled in plants over the past few years. Interestingly, MEP pathway enzymes are encoded by nuclear genes but they function in plastids to produce precursors for isoprenes, monoterpenes, carotenoids, abscisic acid, gibberellins, and the side chain of chlorophylls, tocopherols, phylloquinones, and plastoquinone. In Arabidopsis thaliana, a complete set... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164329 Mon, 02 Feb 2009 05:00:00 +0100 2164329 http://www.medworm.com/index.php?rid=2164328&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193964%26dopt%3DAbstract In conclusion, a regeneration system was established suitable for both gene transformation and the isolation of somaclonal mutants. The regeneration system will be used in order to improve the nutritional value of faba bean. PMID: 19193964 [PubMed - as supplied by publisher] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164328 Mon, 02 Feb 2009 05:00:00 +0100 2164328 http://www.medworm.com/index.php?rid=2164327&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193965%26dopt%3DAbstract Authors: Mahmoud EA, El-Din SM, Aboul-Soud MA, Aboul-Enein AM, Sobhy GA, El-Shemy HA To investigate the transcriptional regulation of gene expression, chimeric fusions, between the beta-glucuronidase reporter gene (GUS) and the isolated promoter regions of the pvPDF gene (pvPDF-PRO: GUS), were constructed and introduced into Nicotiana tabacum. Analysis of transgenic pvPDF-PRO:GUS tobacco plants indicated that GUS activity was observed with all the promoter constructs with the strongest being in leaf followed by stem and roots. These results clearly demonstrate that pvPDF-PRO is a strong inducible and near-constitutive promoter and emphasize the great application potential for plant genetic engineering studies. Interestingly, a search for putative cis-acting elements in the pvPDF promot... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164327 Mon, 02 Feb 2009 05:00:00 +0100 2164327 http://www.medworm.com/index.php?rid=2164326&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193966%26dopt%3DAbstract Authors: Shukla A, Natarajan A, Bhaumik S, El-Shemy HA, Lightfoot D The function of a protein is governed by its interaction with other proteins inside a cell. Therefore, it is important to identify the interacting partners of a particular protein to decipher its function. The protein interaction networks are generally determined by bioinformatic as well as experimental methodologies such as yeast two hybrid, mass spectrometry, immunoprecipitation, and fluorescence resonance energy transfer assays. Here, we have analyzed bioinformatically the interactions of Rpb1p (the largest subunit of RNA Polymerase II) with other proteins in yeast, using Cytoscape software and Biogrid/Biomart database. We find that Rpb1p interacts with a large number of proteins involved in mRNA synthesis, processi... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164326 Mon, 02 Feb 2009 05:00:00 +0100 2164326 http://www.medworm.com/index.php?rid=2164325&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193967%26dopt%3DAbstract The objective of this analysis was to identify linkats in genomic regions underlying seed yield and root SCN resistance QTL. Used were groups of cultivars selected from a single recombinant inbred (RIL) population derived from 'Essex' by 'Forrest' (ExF). The yield was measured at four locations. SCN resistance was determined in greenhouse assays. The mean seed yield was used to define 3 groups (each n = 30), high, medium and low. SCN resistance formed 2 groups (SCN resistant (n = 21) and SCN susceptible (n = 69)). Microsatellite markers (213) alleles were compared with seed yield and root SCN (Hetrodera glycines) resistance using mean analysis. The number, size and position of potential linkats were determined. Loci, genomic regions and linkats associated with seed yield were identified on... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164325 Mon, 02 Feb 2009 05:00:00 +0100 2164325 http://www.medworm.com/index.php?rid=2164324&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19193968%26dopt%3DAbstract The objectives of the current study here were to characterize the Zmnbslrr1 gene and to determine whether it and Zmgc1 respond to the inducer PBZ. The transcript abundance of Zmnbslrr1 expression was significantly reduced in corn seedlings of the Gibberella ear rot resistant genotype CO387 48 h after PBZ treatment. In contrast, the transcript abundance of the maize Zmgc1 gene increased more than 10-fold 8h after the treatment. Therefore, the two genes do not appear to be coordinately regulated by PBZ. PMID: 19193968 [PubMed - as supplied by publisher] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2164324 Mon, 02 Feb 2009 05:00:00 +0100 2164324 http://www.medworm.com/index.php?rid=1795264&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18791262%26dopt%3DAbstract Authors: Punj S, John GH Azoreductases reduce the azo bond (N=N) in azo dyes to produce colorless amine products. Crude cell extracts from Enterococcus faecalis have been shown to utilize both NADH and NADPH as electron donors for azo dye reduction. An azoreductase was purified from E. faecalis by hydrophobic, anion exchange and affinity chromatography. The azoreductase activity of the purified preparation was tested on a polyacrylamide gel after electrophoresis under native conditions and the protein that decolorized the azo dye, Methyl Red, with both NADH and NADPH was identified by mass spectrometry to be AzoA. Previously, the heterologously expressed and purified AzoA was shown to utilize NADH only for the reduction of Methyl Red. However, AzoA purified from the wild-type organism ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1795264 Fri, 12 Sep 2008 04:00:00 +0100 1795264 http://www.medworm.com/index.php?rid=1783589&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18780946%26dopt%3DAbstract Authors: Zanello G, Meurens F, Berri M, Salmon H Health benefits attributed to probiotics have been described for decades. They include the treatment and the prevention of gastrointestinal diseases, vaginal and urinary infections and allergies. Saccharomyces boulardii, a species of yeast widely distributed, has been described as a biotherapeutic agent since several clinical trials displayed its beneficial effects in the prevention and the treatment of intestinal infections and in the maintenance of inflammatory bowel disease. All these diseases are characterized by acute diarrhoea. Administration of the yeast in combination or not with an antibiotherapy has shown to decrease significantly the duration and the frequency of diarrhoea. Experimental studies elucidated partially the molecul... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1783589 Mon, 08 Sep 2008 04:00:00 +0100 1783589 http://www.medworm.com/index.php?rid=1566950&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525101%26dopt%3DAbstract Authors: Chambers JP, Arulanandam BP, Matta LL, Weis A, Valdes JJ PMID: 18525101 [PubMed - in process] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566950 Thu, 03 Jul 2008 13:43:38 +0100 1566950 http://www.medworm.com/index.php?rid=1566949&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525102%26dopt%3DAbstract Discussion of considerations in the early development of LBPs may aid in preparation of an Investigational New Drug Application (IND) that is designed to collect clinical data to support marketing approval of a LBP in the U.S. for a specific clinical use. Product information is an important component of an IND to support a proposed clinical study. PMID: 18525102 [PubMed - in process] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566949 Thu, 03 Jul 2008 13:43:38 +0100 1566949 http://www.medworm.com/index.php?rid=1566948&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525103%26dopt%3DAbstract This study investigated the long-term stability of the bacterial community in such rats. Following the association of two strains of germ-free rats (12 male animals each) with fecal bacteria from a human donor the development of the microbiota was monitored for 12 months by PCR-denaturing gradient gel electrophoresis. During this time the Dice similarity coefficient (Cs) for the fecal microbial community of the rats associated with a human microbiota in comparison to the donor sample ranged between 73% +/- 8 and 74% +/- 3 for the Wistar and the Fischer 344 rats, respectively. After 12 months the similarity coefficients were 78% +/- 9 and 76% +/- 7, respectively, while the similarity coefficients for rat sample replicates ranged from 77% +/- 7 to 88% +/- 5; the similarity coefficient of the... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566948 Thu, 03 Jul 2008 13:43:38 +0100 1566948 http://www.medworm.com/index.php?rid=1566947&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525104%26dopt%3DAbstract Authors: Liu L, Li Y, Tollefsbol TO Most human diseases are related in some way to the loss or gain in gene functions. Regulation of gene expression is a complex process. In addition to genetic mechanisms, epigenetic causes are gaining new perspectives in human diseases related to gene deregulation. Most eukaryotic genes are packed into chromatin structures, which lead to high condensations of the genes that require dynamic chromatin remodeling processes to facilitate their transcription. DNA methylation and histone modifications represent two of the major chromatin remodeling processes. They also serve to integrate environmental signals for the cells to modulate the functional output of their genome. Complex human diseases such as cancer and type 2 diabetes are believed to have a stro... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566947 Thu, 03 Jul 2008 13:43:38 +0100 1566947 http://www.medworm.com/index.php?rid=1566946&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525105%26dopt%3DAbstract Authors: Delcenserie V, Martel D, Lamoureux M, Amiot J, Boutin Y, Roy D The intestinal microbiota is the largest source of microbial stimulation that exerts both harmful and beneficial effects on human health. The interaction between probiotic and enterocytes is the initiating event in immunomodulation and merits particular attention. The effects of probiotic is strain dependent and for each new probiotic strain, profiles of cytokines secreted by lymphocytes, enterocytes or dendritic cells that come in contact with the strain should be systematically established. To evaluate the effects of probiotics on the immune system, models that mimic the mucosa, and thus the physiological reality, should be preferred whenever it is possible. Then, the in vitro observed effects should be backed up... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566946 Thu, 03 Jul 2008 13:43:38 +0100 1566946 http://www.medworm.com/index.php?rid=1566945&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525106%26dopt%3DAbstract Authors: Basu C Cryopreservation is a way to store elite quality plant germplasms. The exact mechanism of stress tolerance during cryopreservation is unknown. Unavavailability of a detailed protocol for understanding the molecular genetics of plant cryostress is a major obstacle in plant cryobiology research. This paper describes the methods of extraction of total RNA from cryogenically stored plant tissues accompanied by successful amplication of cDNAs by reverse transcriptase PCR. The whole process can be completed in two to three days. Through this protocol, several genes were identified which were differentially expressed during cryostress. This protocol will help researchers to pursue further research in the field of molecular genetics of plant cryostress. Interesting genes identi... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566945 Thu, 03 Jul 2008 13:43:38 +0100 1566945 http://www.medworm.com/index.php?rid=1566944&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18525107%26dopt%3DAbstract Authors: Campbell TN, Robbins SM Eph receptor tyrosine kinases (Ephs) and their membrane-anchored ligands (ephrins) form a vital cell communication system capable of bi-directional signaling. This Eph receptor/ephrin system has classically been demonstrated to play a role in development. However, emerging evidence has revealed differential expression of Ephs and ephrins in numerous cancers. Recent studies suggest that this system influences invasive behaviour, promoting a more aggressive and metastatic phenotype. Hence, this minireview summarizes the current understanding of the contribution of both Eph receptors and their ephrin ligands to invasiveness in cancer, as well as their use as potential therapeutic targets. PMID: 18525107 [PubMed - in process] (Source: Current Issues in ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566944 Thu, 03 Jul 2008 13:43:38 +0100 1566944 http://www.medworm.com/index.php?rid=1566942&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18577779%26dopt%3DAbstract Authors: López MM, Llop P, Olmos A, Marco-Noales E, Cambra M, Bertolini E Plant pathogenic bacteria, phytoplasmas, viruses and viroids are difficult to control, and preventive measures are essential to minimize the losses they cause each year in different crops. In this context, rapid and accurate methods for detection and diagnosis of these plant pathogens are required to apply treatments, undertake agronomic measures or proceed with eradication practices, particularly for quarantine pathogens. In recent years, there has been an exponential increase in the number of protocols based on nucleic-acid tools being those based on PCR or RT-PCR now routinely applied worldwide. Nucleic acid extraction is still necessary in many cases and in practice inhibition problems are decreasing the... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566942 Wed, 25 Jun 2008 04:00:00 +0100 1566942 http://www.medworm.com/index.php?rid=1566943&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18541926%26dopt%3DAbstract Authors: Langhans MT, Palladino MJ The utility of restriction endonucleases as a tool in molecular biology is in large part due to the high degree of specificity with which they cleave well-characterized DNA recognition sequences. The specificity of restriction endonucleases is not absolute, yet many commonly used assays of biological phenomena and contemporary molecular biology techniques rely on the premise that restriction enzymes will cleave only perfect cognate recognition sites. In vitro, mispaired heteroduplex DNAs are commonly formed, especially subsequent to polymerase chain reaction amplification. We investigated a panel of restriction endonucleases to determine their ability to cleave mispaired heteroduplex DNA substrates. Two straightforward, non-radioactive assays are used... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566943 Mon, 19 May 2008 04:00:00 +0100 1566943 http://www.medworm.com/index.php?rid=1566954&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17489436%26dopt%3DAbstract Authors: Lavie M, Goffard A, Dubuisson J The two HCV envelope glycoproteins E1 and E2 are released from HCV polyprotein by signal peptidase cleavages. These glycoproteins are type I transmembrane proteins with a highly glycosylated N-terminal ectodomain and a C-terminal hydrophobic anchor. After their synthesis, HCV glycoproteins E1 and E2 associate as a noncovalent heterodimer. The transmembrane domains of HCV envelope glycoproteins play a major role in E1E2 heterodimer assembly and subcellular localization. The envelope glycoprotein complex E1E2 has been proposed to be essential for HCV entry. However, for a long time, HCV entry studies have remained limited because of the lack of a robust cell culture system to amplify this virus. A few years ago, a model mimicking the entry process... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566954 Sun, 01 Jul 2007 04:00:00 +0100 1566954 http://www.medworm.com/index.php?rid=1566953&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17489437%26dopt%3DAbstract Authors: Ratcliff RM, Chang G, Kok T, Sloots TP The diagnosis of infectious diseases has been revolutionized by the development of molecular techniques, foremost with the applications of the polymerase chain reaction (PCR). The achievable high sensitivity and ease with which the method can be used to detect any known genetic sequence have led to its wide application in the life sciences. More recently, real-time PCR assays have provided additional major contributions, with the inclusion of an additional fluorescent probe detection system resulting in an increase in sensitivity over conventional PCR, the ability to confirm the amplification product and to quantitate the target concentration. Further, nucleotide sequence analysis of the amplification products has facilitated epidemiologi... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566953 Sun, 01 Jul 2007 04:00:00 +0100 1566953 http://www.medworm.com/index.php?rid=1566952&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17489438%26dopt%3DAbstract Authors: Rao JR, Nelson DW, McClean S New variants of pathogenic fungal viruses are emerging and they are enigmatic in revealing their molecular identity and of their origin. Double-stranded RNAs, some in non-encapsidated forms are increasingly becoming causal agents for sporadic diseases and are consistently associated with a complex profile of dsRNAs, presumably of (multiple) viral origin present in the host while the same are conspicuously absent in healthy (looking) counterparts. The emergence of an unusual Agaricus bisporus mushroom 'patch disease' first reported in 1996, later termed as 'mushroom virus X' (MVX), exhibited a wide range of symptoms (e.g. barren patches beside healthy looking mushrooms, arrested pins, premature opening, brown, off-colour and distortions in shape). A... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566952 Sun, 01 Jul 2007 04:00:00 +0100 1566952 http://www.medworm.com/index.php?rid=1566951&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17489439%26dopt%3DAbstract Authors: Solá S, Aranha MM, Steer CJ, Rodrigues CM Apoptosis represents a universal and exquisitely efficient cellular suicide pathway essential for a variety of normal biological processes ranging from embryonic development to ageing. In fact, tissue homeostasis is dependent on the perfect balance between positive and negative signals that determines the decision between life and death. Therefore, any imbalance can result in a wide range of pathologic disorders associated with unwanted apoptosis or cell growth. During the apoptotic process, the molecular players interact closely with each other in ways relevant to accelerate or interrupt the cellular death process. In addition, two major pathways of apoptosis activation have been recognized as the "intrinsic" mitochondrial pathwa... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566951 Sun, 01 Jul 2007 04:00:00 +0100 1566951 http://www.medworm.com/index.php?rid=1566958&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17263143%26dopt%3DAbstract Authors: Frick DN The C-terminal portion of hepatitis C virus (HCV) nonstructural protein 3 (NS3) forms a three domain polypeptide that possesses the ability to travel along RNA or single-stranded DNA (ssDNA) in a 3' to 5' direction. Fueled byATP hydrolysis, this movement allows the protein to displace complementary strands of DNA or RNA and proteins bound to the nucleic acid. HCV helicase shares two domains common to other motor proteins, one of which appears to rotate upon ATP binding. Several models have been proposed to explain how this conformational change leads to protein movement and RNA unwinding, but no model presently explains all existing experimental data. Compounds recently reported to inhibit HCV helicase, which include numerous small molecules, RNA aptamers and antibodi... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566958 Mon, 01 Jan 2007 05:00:00 +0100 1566958 http://www.medworm.com/index.php?rid=1566957&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17263144%26dopt%3DAbstract Authors: Millar BC, Xu J, Moore JE Infectious diseases are common diseases all over the world. A recent World Health Organization report indicated that infectious diseases are now the world's biggest killer of children and young adults. Infectious diseases in non-industrialized countries caused 45% in all and 63% of death in early childhood. In developed countries, the emergence of new, rare or already-forgotten infectious diseases, such as HIV/AIDS, Lyme disease and tuberculosis, has stimulated public interest and inspired commitments to surveillance and control. Recently, it is reported that infectious diseases are responsible for more than 17 million deaths worldwide each year, most of which are associated with bacterial infections. Hence, the control of infectious diseases control ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566957 Mon, 01 Jan 2007 05:00:00 +0100 1566957 http://www.medworm.com/index.php?rid=1566956&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17263145%26dopt%3DAbstract Authors: Rehm BH Biopolyester (PHAs = polyhydroxyalkanoates) composed of hydroxy fatty acids represent a rather complex class of storage polymers synthesized by various eubacteria and archaea and are deposited as water-insoluble cytoplasmic nano-sized inclusions. These spherical shell-core particles are composed of a polyester core surrounded by phospholipids and proteins. The key enzymes of polyester biosynthesis and polyester particle formation are the polyester synthases, which catalyze the enantio-selective polymerization of (R)-hydroxyacyl-CoA thioesters to polyesters. Various metabolic routes have been identified and established in bacteria to provide substrate for polyester synthases. The role of the polyester synthases in morphogenesis and presumably self-assembly of these natu... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566956 Mon, 01 Jan 2007 05:00:00 +0100 1566956 http://www.medworm.com/index.php?rid=1566955&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17263146%26dopt%3DAbstract Authors: Welbourn S, Pause A The hepatitis C virus NS2/3 protein is a highly hydrophobic protease responsible for the cleavage of the viral polypeptide between non-structural proteins NS2 and NS3. However, many aspects of the NS2/3 protease's role in the viral life cycle and mechanism of action remain unknown. Based on the recently elucidated crystal structure of NS2, NS2/3 has been proposed to function as a cysteine protease despite its lack of sequence homology to proteases of known function. In addition, although shown to be required for HCV genome replication and persistent infection in a chimpanzee, the role of NS2/3 cleavage in the viral life cycle has not yet been fully investigated. However, several recent studies are beginning to clarify possible roles of the cleaved NS2 prote... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566955 Mon, 01 Jan 2007 05:00:00 +0100 1566955 http://www.medworm.com/index.php?rid=1566963&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16875414%26dopt%3DAbstract Authors: Loomis WF The 34 Mb genome of Dictyostelium discoideum is carried on 6 chromosomes and has been fully sequenced by an international consortium. The sequence was assembled on the classical and physical maps that had been built up over the years and refined by HAPPY mapping. Annotation of the sequence predicted about 12,000 genes for proteins of at least 50 amino acids in length. The total number of amino acids encoded (the proteome) is more than double that in yeast and rivals that of metazoans. The genome sequence shows all the proteins available to Dictyostelium as well as definitively showing which domains have been lost since Dictyostelium diverged from the line leading to metazoans. Genomics opens the door to determining the expression patterns of all the genes during grow... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566963 Sat, 01 Jul 2006 04:00:00 +0100 1566963 http://www.medworm.com/index.php?rid=1566962&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16875415%26dopt%3DAbstract Authors: Xu J The last two decades have seen tremendous growth in the development and application of molecular methods in the analyses of fungal species and populations. In this paper, I provide an overview of the molecular techniques and the basic analytical tools used to address various fundamental population and evolutionary genetic questions in fungi. With increasing availability and decreasing cost, DNA sequencing is becoming a mainstream data acquisition method in fungal evolutionary genetic studies. However, other methods, especially those based on the polymerase chain reaction, remain powerful in addressing specific questions for certain groups of taxa. These developments are bringing fungal population and evolutionary genetics into mainstream ecology and evolutionary biology. ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566962 Sat, 01 Jul 2006 04:00:00 +0100 1566962 http://www.medworm.com/index.php?rid=1566961&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16875416%26dopt%3DAbstract Authors: Asato Y The concepts of cell theory and the notions of coordinate regulation of the cell cycle have been known for centuries but the conundrum of coordinate regulation of the cell cycle remains to be resolved. The unique characteristics of the cell division cycle of Synechococcus, a photosynthetic bacterium, suggest the existence of a complex network of light/dark responsive gene regulatory factors that coordinate its cell cycle events. Evaluation of the highly ordered cell cycle of Synechococcus led to the construction of workable models that coordinate the cell cycle events. A central issue in bacterial cell growth is the elucidation of the genetic regulatory mechanisms that coordinate the cell cycle events. Synechococcus, a unicellular cyanobacterium, displays a peculiar ce... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566961 Sat, 01 Jul 2006 04:00:00 +0100 1566961 http://www.medworm.com/index.php?rid=1566960&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16875417%26dopt%3DAbstract Authors: Xu J Each diploid organism has two alleles at every gene locus. In sexual organisms such as most plants, animals and fungi, the two alleles in an individual may be genetically very different from each other. DNA sequence data from individual alleles (called a haplotype) can provide powerful information to address a variety of biological questions and guide many practical applications. The advancement in molecular technology and computational tools in the last decade has made obtaining large-scale haplotypes feasible. This review summarizes the two basic approaches for obtaining haplotypes and discusses the associated techniques and methods. The first approach is to experimentally obtain diploid sequence information and then use computer algorithms to infer haplotypes. The seco... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566960 Sat, 01 Jul 2006 04:00:00 +0100 1566960 http://www.medworm.com/index.php?rid=1566959&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16878362%26dopt%3DAbstract Authors: Johnson R, Streicher EM, Louw GE, Warren RM, van Helden PD, Victor TC Anti-tuberculosis drugs are a two-edged sword. While they destroy pathogenic M. tuberculosis they also select for drug resistant bacteria against which those drugs are then ineffective. Global surveillance has shown that drug resistant Tuberculosis is widespread and is now a threat to tuberculosis control programs in many countries. Application of molecular methods during the last decade has greatly changed our understanding of drug resistance in tuberculosis. Application of molecular epidemiological methods was also central to the description of outbreaks of drug resistance in Tuberculosis. This review describes recommendations for Tuberculosis treatment according to the WHO guidelines, the drug resistance ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566959 Sat, 01 Jul 2006 04:00:00 +0100 1566959 http://www.medworm.com/index.php?rid=1566967&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16450882%26dopt%3DAbstract Authors: Atkinson S, Sockett RE, Cámara M, Williams P Bacterial cell-to-cell communication ('quorum sensing') is mediated by structurally diverse, small diffusible signal molecules which regulate gene expression as a function of cell population density. Many different Gram-negative animal, plant and fish pathogens employ N-acylhomoserine lactones (AHLs) as quorum sensing signal molecules which control diverse physiological processes including bioluminescence, swarming, antibiotic biosynthesis, plasmid conjugal transfer, biofilm development and virulence. AHL-dependent quorum sensing is highly conserved in both pathogenic and non-pathogenic members of the genus Yersinia. Yersinia pseudotuberculosis for example, produces at least eight different AHLs and possesses two homologues of ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566967 Sun, 01 Jan 2006 05:00:00 +0100 1566967 http://www.medworm.com/index.php?rid=1566966&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16450883%26dopt%3DAbstract Authors: Nizet V The critical role played by antimicrobial peptides (AMPs) in mammalian innate immunity is increasingly recognized. Bacteria differ in their intrinsic susceptibility to AMPs, and the relative resistance of some important human pathogens to these defense molecules is now appreciated as an important virulence phenotype. Experimental analysis has identified diverse mechanisms of bacterial AMP resistance including altered cell surface charge, active efflux, production of proteases or trapping proteins, and modification of host cellular processes. The contribution of these resistance mechanisms to pathogenesis is confirmed through direct comparison of wild-type bacteria and AMP-sensitive mutants using in vivo infection models. Knowledge of the molecular basis of bacterial AM... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566966 Sun, 01 Jan 2006 05:00:00 +0100 1566966 http://www.medworm.com/index.php?rid=1566965&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16450884%26dopt%3DAbstract Authors: Schemarova IV The review summarizes for the first time the current concepts of the role of tyrosine phosphorylation in regulation of signal transduction pathways in unicellular eukaryotes. Evolutionary concepts are developed about the origin of protein tyrosine kinases (PTK)-signaling. PMID: 16450884 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566965 Sun, 01 Jan 2006 05:00:00 +0100 1566965 http://www.medworm.com/index.php?rid=1566964&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16450885%26dopt%3DAbstract Authors: Wilkinson SP, Grove A The MarR (multiple antibiotic resistance regulator) family of prokaryotic transcriptional regulators includes proteins critical for control of virulence factor production, bacterial response to antibiotic and oxidative stresses and catabolism of environmental aromatic compounds. Recognition of the adaptive cellular responses mediated by MarR homologs, and the clinical isolation of antibiotic-resistant bacterial strains harboring MarR mutations, has garnered increasing medical and agricultural attention to this family. MarR proteins exist as homodimers in both free and DNA-bound states. Sequence specific DNA-binding to palindromic or pseudopalindromic sites is mediated by a conserved winged helix fold and, for numerous homologs, this association is attenua... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566964 Sun, 01 Jan 2006 05:00:00 +0100 1566964 http://www.medworm.com/index.php?rid=1566972&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16053246%26dopt%3DAbstract Authors: Dale BA, Fredericks LP The oral cavity is a unique environment in which antimicrobial peptides play a key role in maintaining health and may have future therapeutic applications. Present evidence suggests that alpha-defensins, beta-defensins, LL-37, histatin, and other antimicrobial peptides and proteins have distinct but overlapping roles in maintaining oral health and preventing bacterial, fungal, and viral adherence and infection. The expression of the inducible hBD-2 in normal oral epithelium, in contrast to other epithelia, and the apparent differential signaling in response to commensal and pathogenic organisms, provides new insights into innate immunity in this body site. Commensal bacteria are excellent inducers of hBD-2 in oral epithelial cells, suggesting that the co... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566972 Fri, 01 Jul 2005 04:00:00 +0100 1566972 http://www.medworm.com/index.php?rid=1566971&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16053247%26dopt%3DAbstract Authors: Darwin AJ An obvious goal in the study of bacteria that cause human disease is to identify the bacterial genes required for growth within the host. Historically, this has presented a significant technological challenge. However, with this goal in mind, the in vivo expression technology (IVET) and signature-tagged mutagenesis (STM) techniques were developed during the 1990s. These techniques have been used to identify virulence genes in the three human pathogenic Yersinia species, Y. enterocolitica, Y. pseudotuberculosis and Y. pestis, using variations of their mouse models of infection. In this review, each of these studies is described individually, including the pertinent details of how each was done, and a brief discussion of the genes identified. In addition, the results o... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566971 Fri, 01 Jul 2005 04:00:00 +0100 1566971 http://www.medworm.com/index.php?rid=1566970&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16053248%26dopt%3DAbstract Authors: Marceau M In response to the ever-present need to adapt to environmental stress, bacteria have evolved complex (and often overlapping) regulatory networks that respond to various changes in growth conditions, including entry into the host. The expression of most bacterial virulence factors is regulated; thus the question of how bacteria orchestrate this process has become a recurrent research theme for every bacterial pathogen, and the three pathogenic Yersinia are no exception. The earliest studies of regulation in these species were prompted by the characterization of plasmid-encoded virulence determinants, and those conducted since have continued to focus on the principal aspects of virulence in these pathogens. Most Yersinia virulence factors are thermally regulated, and a... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566970 Fri, 01 Jul 2005 04:00:00 +0100 1566970 http://www.medworm.com/index.php?rid=1566969&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16053249%26dopt%3DAbstract Authors: Zanetti M The cathelicidin peptides comprise one of several families of antimicrobial peptides that are found in neutrophils and epithelia as components of the early host defenses of mammals against infection. All cathelicidin family members are synthesized and stored in cells as two-domain proteins. These are split on demand to produce a cathelin protein and an antimicrobial peptide. Accumulating evidence indicates that both the cathelin portion and the C-terminal peptide exert biological activities connected with host protection. This review presents an overview of the structure and biology of cathelicidins and discusses recent progress in cathelicidin research with emphasis on the functional properties and role in host defense of the human cathelicidin hCAP18/LL-37. Althoug... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566969 Fri, 01 Jul 2005 04:00:00 +0100 1566969 http://www.medworm.com/index.php?rid=1566968&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16053250%26dopt%3DAbstract Authors: Hinnebusch BJ Transmission by fleabite is a recent evolutionary adaptation that distinguishes Yersinia pestis, the agent of plague, from Yersinia pseudotuberculosis and all other enteric bacteria. The very close genetic relationship between Y. pestis and Y. pseudotuberculosis indicates that just a few discrete genetic changes were sufficient to give rise to flea-borne transmission. Y. pestis exhibits a distinct infection phenotype in its flea vector, and a transmissible infection depends on genes that are specifically required in the flea, but not the mammal. Transmission factors identified to date suggest that the rapid evolutionary transition of Y. pestis to flea-borne transmission within the last 1,500 to 20,000 years involved at least three steps: acquisition of the two Y.... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566968 Fri, 01 Jul 2005 04:00:00 +0100 1566968 http://www.medworm.com/index.php?rid=1566980&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580776%26dopt%3DAbstract Authors: Campbell TN, Choy FY RNA interference (RNAi) is the sequence-specific gene silencing induced by double-stranded RNA. RNAi is mediated by 21-23 nucleotide small interfering RNAs (siRNAs) which are produced from long double-stranded RNAs by RNAse II-like enzyme Dicer. The resulting siRNAs are incorporated into a RNA-induced silencing complex (RISC) that targets and cleaves mRNA complementary to the siRNAs. Since its inception in 1998, RNAi has been demonstrated in organisms ranging from trypanosomes to nematodes to vertebrates. Potential uses already in progress include the examination of specific gene function in living systems, the development of anti-viral and anti-cancer therapies, and genome-wide screens. In this review, we discuss the landmark discoveries that established ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566980 Sat, 01 Jan 2005 05:00:00 +0100 1566980 http://www.medworm.com/index.php?rid=1566979&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580777%26dopt%3DAbstract Authors: Mazurkiewicz P, Driessen AJ, Konings WN The extensive progress of genome sequencing projects in recent years has demonstrated that multidrug resistance (MDR) transporters are widely spread among all domains of life. This indicates that they play crucial roles in the survival of organisms. Moreover, antibiotic and chemotherapeutic treatments have revealed that microorganisms and cancer cells may use MDR transporters to fight the cytotoxic action of drugs. Currently, several MDR extrusion systems are being investigated in detail. It is expected that understanding of the molecular basis of multidrug recognition and the transport mechanisms will allow a more rational design of new drugs which either will not be recognized and expelled by or will efficiently inhibit the activity of... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566979 Sat, 01 Jan 2005 05:00:00 +0100 1566979 http://www.medworm.com/index.php?rid=1566978&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580778%26dopt%3DAbstract Authors: Carlton J, Silva J, Hall N The field of comparative genomics of malaria parasites has recently come of age with the completion of the whole genome sequences of the human malaria parasite Plasmodium falciparum and a rodent malaria model, Plasmodium yoelii yoelii. With several other genome sequencing projects of different model and human malaria parasite species underway, comparing genomes from multiple species has necessitated the development of improved informatics tools and analyses. Results from initial comparative analyses reveal striking conservation of gene synteny between malaria species within conserved chromosome cores, in contrast to reduced homology within subtelomeric regions, in line with previous findings on a smaller scale. Genes that elicit a host immune respons... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566978 Sat, 01 Jan 2005 05:00:00 +0100 1566978 http://www.medworm.com/index.php?rid=1566977&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580779%26dopt%3DAbstract Authors: Carvalho TG, Ménard R Genome manipulation, the primary tool for assigning function to sequence, will be essential for understanding Plasmodium biology and malaria pathogenesis in molecular terms. The first success in transfecting Plasmodium was reported almost ten years ago. Gene-targeting studies have since flourished, as Plasmodium is haploid and integrates DNA only by homologous recombination. These studies have shed new light on the function of many proteins, including vaccine candidates and drug resistance factors. However, many essential proteins, including those involved in parasite invasion of erythrocytes, cannot be characterized in the absence of conditional mutagenesis. Proteins also cannot be identified on a functional basis as random DNA integration has not b... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566977 Sat, 01 Jan 2005 05:00:00 +0100 1566977 http://www.medworm.com/index.php?rid=1566976&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580780%26dopt%3DAbstract Authors: Waller RF, McFadden GI The apicoplast is a plastid organelle, homologous to chloroplasts of plants, that is found in apicomplexan parasites such as the causative agents of Malaria Plasmodium spp. It occurs throughout the Apicomplexa and is an ancient feature of this group acquired by the process of endosymbiosis. Like plant chloroplasts, apicoplasts are semi-autonomous with their own genome and expression machinery. In addition, apicoplasts import numerous proteins encoded by nuclear genes. These nuclear genes largely derive from the endosymbiont through a process of intracellular gene relocation. The exact role of a plastid in parasites is uncertain but early clues indicate synthesis of lipids, heme and isoprenoids as possibilities. The various metabolic processes of the apic... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566976 Sat, 01 Jan 2005 05:00:00 +0100 1566976 http://www.medworm.com/index.php?rid=1566975&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580781%26dopt%3DAbstract Authors: Smith JD, Craig AG In order to navigate its complex lifecycle, the malaria parasites must interactwith a range of host cells. Examples of this are the invasion of hepatocytes by sporozoites and erythrocyte invasion by merozoites. This requirement for cell recognition brings with it the need to display cognate ligands on the parasite surface, and therefore the capacity of the host to develop defences against the infection. Even at a stage where the intracellular nature of erythrocyte development would appear to offer an opportunity for the parasite to be immunologically "silent", parasite-derived proteins are found on the surface of the infected erythrocyte. This review will discuss the proteins found on or associated with the surface of the infected erythrocyte and the resulti... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566975 Sat, 01 Jan 2005 05:00:00 +0100 1566975 http://www.medworm.com/index.php?rid=1566974&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580782%26dopt%3DAbstract Authors: Lemos JA, Abranches J, Burne RA To persist in the oral cavity, bacteria must be able to tolerate rapid and substantial environmental fluctuations, particularly in pH and nutrient source and availability. Various species of Streptococcus, one of the most abundant genera in the mouth, are associated with oral health, as well as with dental caries. Cariogenic streptococci depend on a biofilm lifestyle for survival and persistence in the oral cavity and have developed sophisticated mechanisms to cope with environmental stresses. Here, we analyze the primary factors that allow these bacteria to emerge as significant members of tooth biofilms during adverse conditions. Our focus is on the molecular mechanisms of biofilm formation, stress tolerance and sugar metabolism by pathogenic ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566974 Sat, 01 Jan 2005 05:00:00 +0100 1566974 http://www.medworm.com/index.php?rid=1566973&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15580783%26dopt%3DAbstract Authors: Asato Y The regulation of ribosome synthesis has been investigated for nearly five decades. In earlier studies, the control of rRNA synthesis in bacteria was found to be dependent on nutrient composition of the growth media or cell growth rates, and these observations led to the growth rate-dependent regulation model. Also developed were stringent control, feedback ribosome synthesis, passive regulation, and antitermination models. Current evidence indicates that upstream (UP) element, molecular effectors, ppGpp and iNTP (initiating nucleoside triphosphate), and trans-acting proteins, Fis and H-NS, play important roles in the control of rRNA synthesis in response to changing nutritional environments. The mechanisms for the ribosome feedback regulation, and growth rate-dependen... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566973 Sat, 01 Jan 2005 05:00:00 +0100 1566973 http://www.medworm.com/index.php?rid=1566989&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119819%26dopt%3DAbstract Authors: Zalfa F, Bagni C Mental retardation is a frequent cause of intellectual and physical impairment. Several genes associated with mental retardation have been mapped to the X chromosome, among them, there is FMR1. The absence of or mutation in the Fragile Mental Retardation Protein, FMRP, is responsible for the Fragile X syndrome. FMRP is an RNA binding protein that shuttles between the nucleus and the cytoplasm. FMRP binds to several mRNAs including its own mRNA at a sequence region containing a G quartet structure. Some of the candidate downstream genes recently identified encode for synaptic proteins. Neuronal studies indicate that FMRP is located at synapses and loss of FMRP affects synaptic plasticity. At the synapses, FMRP acts as a translational repressor and in particular... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566989 Thu, 01 Jul 2004 04:00:00 +0100 1566989 http://www.medworm.com/index.php?rid=1566988&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119820%26dopt%3DAbstract Authors: Passioura T, Symonds G Oncogenes are ideal targets for therapies which down-regulate gene expression. However, effective modalities for altering gene expression in vivo have thus far proven to be elusive. Whilst there has been recent success with small molecule inhibitors of oncoprotein function, evolution of resistance to these agents has been observed in the clinical setting, indicating the need for combinations of therapies for cancer treatment. Strategies for in vivo gene down-regulation still hold promise for the treatment of cancer. The technologies relevant to such therapeutic strategies are discussed in terms of molecular action, delivery and choice of target gene. Consideration is given to the pre-clinical and clinical efficacy these agents have demonstrated to date. ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566988 Thu, 01 Jul 2004 04:00:00 +0100 1566988 http://www.medworm.com/index.php?rid=1566987&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119821%26dopt%3DAbstract Authors: Johnson CH Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a timing mechanism that is independent of the cell division cycle. This biological clock orchestrates global regulation of gene expression and controls the timing of cell division. Proteins that may be involved in input pathways have been identified. Mutational screening has identified three clock genes that are organized as a gene cluster. The structure of cyanobacterial clock proteins, their phosphorylation, and regulation is described. A new model for the core clockwork in cyanobacteria proposes that rhythmic changes in the status of the chromosome underlie the rhythms of gene expression. Mixed-strain experiments demonstrate that this timekeeper confers adaptive value when dif... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566987 Thu, 01 Jul 2004 04:00:00 +0100 1566987 http://www.medworm.com/index.php?rid=1566986&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119822%26dopt%3DAbstract Authors: Desvaux M, Parham NJ, Henderson IR Since its discovery in the late 1980's, the family of secreted proteins termed the autotransporters has been expanding continuously to become the largest group of secreted proteins in Gram-negative bacteria. The type V secretion pathway, which includes the autotransporters (type Va) together with the two-partner secretion system (type Vb) and the Oca family (type Vc), can be defined by secreted proteins that are (i) translocated across the outer membrane via a transmembrane pore formed by a beta-barrel and (ii) contain all the information required for translocation through the cell envelope. In the light of new discoveries and controversies in this research field, the secretion process of autotransporters, or the type Va secretion system, wil... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566986 Thu, 01 Jul 2004 04:00:00 +0100 1566986 http://www.medworm.com/index.php?rid=1566985&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119823%26dopt%3DAbstract Authors: Phadtare S In response to temperature downshift, a number of changes occur in cellular physiology such as, (i) decrease in membrane fluidity, (ii) stabilization of secondary structures of nucleic acids leading to reduced efficiency of mRNA translation and transcription, (iii) inefficient folding of some proteins, and (iv) hampered ribosome function. Cold-shock response and adaptation has been quite extensively studied in Escherichia coli and Bacillus subtilis. A number of cold shock proteins are induced to counteract these harmful effects of temperature downshift. General principles of cold-shock response along with recent findings on desaturase system, RNA chaperone and transcription antitermination function of CspA homologues, cold shock induction of chaperones and synthesis... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566985 Thu, 01 Jul 2004 04:00:00 +0100 1566985 http://www.medworm.com/index.php?rid=1566984&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119824%26dopt%3DAbstract Authors: Grogan DW Evolutionary and physiological considerations argue that study of hyperthermophilic archaea should reveal new molecular aspects of DNA stabilization and repair. So far, these unusual prokaryotes have yielded a number of genes and enzymatic activities consistent with known mechanisms of excision repair, photo-reversal, and trans-lesion synthesis. However, other DNA enzymes of hyperthermophilic archaea show novel biochemical properties which may be related to DNA stability or repair at extremely high temperature but which remain difficult to evaluate rigorously in vivo. Perhaps the most striking feature of the hyperthermophilic archaea is that all of them whose genomes have been sequenced lack key genes of both the nucleotide excision repair and DNA mismatch repair pat... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566984 Thu, 01 Jul 2004 04:00:00 +0100 1566984 http://www.medworm.com/index.php?rid=1566983&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119825%26dopt%3DAbstract Authors: Muttucumaru DG, Parish T Recombination is a ubiquitous genetic process which results in the exchange of DNA between two substrates. Homologous recombination occurs between DNA species with identical sequence whereas illegitimate recombination can occur between DNA with very little or no homology. Site-specific recombination is often used by temperate phages to stably integrate into bacterial chromosomes. Characterisation of the mechanisms of recombination in mycobacteria has mainly focussed on RecA-dependent homologous recombination and phage-directed site-specific recombination. In contrast the high frequency of illegitimate recombination in slow-growing mycobacteria has not been explained. The role of DNA repair in dormancy and infection have not yet been fully established, ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566983 Thu, 01 Jul 2004 04:00:00 +0100 1566983 http://www.medworm.com/index.php?rid=1566982&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119826%26dopt%3DAbstract Authors: Vignais PM, Colbeau A Hydrogenases (H2ases) are metalloproteins. The great majority of them contain iron-sulfur clusters and two metal atoms at their active center, either a Ni and an Fe atom, the [NiFe]-H2ases, or two Fe atoms, the [FeFe]-H2ases. Enzymes of these two classes catalyze the reversible oxidation of hydrogen gas (H2 <--> 2 H+ + 2 e-) and play a central role in microbial energy metabolism; in addition to their role in fermentation and H2 respiration, H2ases may interact with membrane-bound electron transport systems in order to maintain redox poise, particularly in some photosynthetic microorganisms such as cyanobacteria. Recent work has revealed that some H2ases, by acting as H2-sensors, participate in the regulation of gene expression and that H2-evolving H... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566982 Thu, 01 Jul 2004 04:00:00 +0100 1566982 http://www.medworm.com/index.php?rid=1566981&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D15119827%26dopt%3DAbstract Authors: Milner M, Bansode AG, Lawrence AL, Nevagi SA, Patwardhan V, Modak SP Molecular phylogenetic trees are constructed in three dimensions relative to the distribution of MW and pl classes and immunocrossreactivity against polyclonal antibodies to lens crystallins, as well as multiple sequence alignment between amino acid sequences, coding nucleotide sequences and the gene nucleotide sequences for beta-globin. Euclidian distances are estimated to position species in x, y, z space by multidimensional scaling and merged with bootstrap-tested branching pattern of Fitch & Margoliash plots to obtain 3-D phylogenetic tree. Compared to single attributes, phylogenetic trees based on multiple parameters allow significant repositioning of rodents, chiroptera and primates. PMID: 15119... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566981 Thu, 01 Jul 2004 04:00:00 +0100 1566981 http://www.medworm.com/index.php?rid=1566994&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D14632255%26dopt%3DAbstract Authors: König R, Zhou W The immune system provides a highly sophisticated surveillance mechanism to detect diverse antigens and to protect the host organism from invading pathogens and altered cells (e.g., virus-infected and tumor cells). Adaptive immune responses depend on the recognition of antigen by specific antigen receptors that are expressed on the surface of T and B lymphocytes. Helper T cells provide regulatory functions and direct the adaptive immune system to respond appropriately to a particular antigen (i.e., cytotoxic T cell responses against viral infections and tumor cells, humoral responses against extracellular bacteria and parasitic worms). Helper T cells express CD4 coreceptors, which recognize conserved domains on proteins expressed by the class II major hist... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566994 Thu, 01 Jan 2004 05:00:00 +0100 1566994 http://www.medworm.com/index.php?rid=1566993&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D14632256%26dopt%3DAbstract Authors: Capecchi B, Serruto D, Adu-Bobie J, Rappuoli R, Pizza M The conventional approach to vaccine development is based on dissection of the pathogen using biochemical, immunological and microbiological methods. Although successful in several cases, this approach has failed to provide a solution to prevent several major bacterial infections. The availability of complete genome sequences in combination with novel advanced technologies, such as bioinformatics, microarrays and proteomics, have revolutionized the approach to vaccine development and provided a new impulse to microbial research. The genomic revolution allows the design of vaccines starting from the prediction of all antigens in silico, independently of their abundance and without the need to grow the pathogen in vitro. Th... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566993 Thu, 01 Jan 2004 05:00:00 +0100 1566993 http://www.medworm.com/index.php?rid=1566992&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D14632257%26dopt%3DAbstract Authors: Dejgaard S, Nicolay J, Taheri M, Thomas DY, Bergeron JJ The endoplasmic reticulum (ER) is the major site for folding and sorting of newly synthesized secretory cargo proteins. One central regulator of this process is the quality control machinery, which retains and ultimately disposes of misfolded secretory proteins before they can exit the ER. The ER quality control process is highly effective and mutations in cargo molecules are linked to a variety of diseases. In mammalian cells, a large number of secretory proteins, whether membrane bound or soluble, are asparagine (N)-glycosylated. Recent attention has focused on a sugar transferase, UDP-Glucose: glycoprotein glucosyl transferase (UGGT), which is now recognized as a constituent of the ER quality control machinery. UGGT is... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566992 Thu, 01 Jan 2004 05:00:00 +0100 1566992 http://www.medworm.com/index.php?rid=1566991&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D14632258%26dopt%3DAbstract Authors: Ivics Z, Kaufman CD, Zayed H, Miskey C, Walisko O, Izsvák Z Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrate species are inactive due to the accumulation of mutations. A representative of a subfamily of fish elements estimated to be last active > 10 million years ago has been reconstructed, and named Sleeping Beauty(SB). This element opened up new avenues for studies on DNA transposition in vertebrates, and for the development of transposon tools for genetic manipulation in important model species and in humans. Multiple transposase binding sites within the terminal inverted repeats, a transpositional enhancer sequence, unequal affinity of the transposase to the binding sites and the activity of the cellular HMGB1 protein all con... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566991 Thu, 01 Jan 2004 05:00:00 +0100 1566991 http://www.medworm.com/index.php?rid=1566990&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D14632259%26dopt%3DAbstract Authors: Silva JC, Loreto EL, Clark JB Transposable elements are characterized by their ability to spread within a host genome. Many are also capable of crossing species boundaries to enter new genomes, a process known as horizontal transfer. Focusing mostly on animal transposable elements, we review the occurrence of horizontal transfer and examine the methods used to detect such transfers. We then discuss factors that affect the frequency of horizontal transfer, with emphasis on the mechanism and regulation of transposition. An intriguing feature of horizontal transfer is that its frequency differs among transposable element families. Evidence summarized in this review indicates that this pattern is due to fundamental differences between Class I and Class II elements. There appears t... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566990 Thu, 01 Jan 2004 05:00:00 +0100 1566990 http://www.medworm.com/index.php?rid=1566997&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12921226%26dopt%3DAbstract Authors: Carattoli A The selective pressure imposed by the use of antimicrobials in both human and veterinary medicine promotes the spread of multiple antimicrobial resistance. The dissemination of antimicrobial resistance in Salmonella enterica strains, causing severe enteritis in human, has been reported worldwide and is largely attributed to conjugative DNA exchange. In the present review, the relevance of plasmids to the dissemination of antimicrobial resistance in S. enterica is discussed. Recent examples of plasmid-mediated resistance to expanded-spectrum cephalosporins are reported to illustrate the severity of current situation in enteric pathogens. The exchanges between plasmid(s) and the bacterial chromosome and the integration of resistance genes into specialised genetic ele... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566997 Wed, 01 Oct 2003 04:00:00 +0100 1566997 http://www.medworm.com/index.php?rid=1566996&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12921227%26dopt%3DAbstract Authors: Galas DJ, McCormack SJ Genomic technologies are best defined as technologies used to manipulate and analyze genomic information. The evolution of this collective power began in earnest with the invention of DNA cloning in the 1970's and most of the technology derives from the last quarter of the 20th century. The historical impact of these technologies is clearly immense. With the genome sequence becoming available for many organisms, including humans, another new view of biology has recently emerged. This review examines the shape and texture of this recent evolution, with a particular emphasis on new technology: DNA cloning, macromolecular structure analysis (X-ray crystallography and NMR), DNA sequencing, DNA synthesis, amplification by the polymerase chain reaction, and tr... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566996 Wed, 01 Oct 2003 04:00:00 +0100 1566996 http://www.medworm.com/index.php?rid=1566995&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12921228%26dopt%3DAbstract Authors: Diaz JE, Howard BE, Neubauer MS, Olszewski A, Weiss GA Polypeptide libraries cast a broad net for defining enzyme and binding protein specificities. In addition to uncovering rules for molecular recognition, the binding preferences and functional group tolerances from such libraries can reveal mechanisms underlying biochemical and cellular processes. Ligands obtained from protein libraries can also provide pharmaceutical lead compounds and even reagents to further explore cell biology. Here, we review selected recent examples of protein libraries demonstrating these principles. In particular, we focus on combinatorial libraries composed of randomized peptides or variations of a single protein. The characteristics of various techniques for library constructions and screening ar... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566995 Wed, 01 Oct 2003 04:00:00 +0100 1566995 http://www.medworm.com/index.php?rid=1567000&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12866830%26dopt%3DAbstract Authors: Ersfeld K Protozoan parasites are causing some of the most devastating diseases world-wide. It has now been recognised that a major effort is needed to be able to control or eliminate these diseases. Genome projects for the most important protozoan parasites have been initiated in the hope that the read-out of these projects will help to understand the biology of the parasites and identify new targets for urgently needed drugs. Here, I will review the current status of protozoan parasite genome projects, present findings obtained as a result of the availability of genomic data and discuss the potential impact of genome information on disease control. PMID: 12866830 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567000 Tue, 01 Jul 2003 04:00:00 +0100 1567000 http://www.medworm.com/index.php?rid=1566999&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12866831%26dopt%3DAbstract Authors: Shashikant CS, Ruddle FH Gene transfer technologies in mammals are the focus of renewed interest owing to the recent emphasis on analyzing gene function in the postgenomic era. Three important developments in this area include transgenics, gene targeting and nuclear transfer or animal cloning. These technological innovations have enhanced our ability to analyze gene function at the level of the whole organism and have provided the means to modify gene expression. This review discusses the origins and current status of transgenic technologies. Various applications and technologies including chromosome engineering, stem cells, gene traps and modification of livestock are presented. The impact of mouse technologies and genomics on functional analyses is also discussed. PMID: ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566999 Tue, 01 Jul 2003 04:00:00 +0100 1566999 http://www.medworm.com/index.php?rid=1566998&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12866832%26dopt%3DAbstract Authors: Cassimeris L, Skibbens RV Chromosome segregration and cell division requires the regulated assembly of the mitotic spindle apparatus. This mitotic spindle is composed of condensed chromosomes attached to a dynamic array of microtubules. The microtubule array is nucleated by centrosomes and organized by associated structural and motor proteins. Mechanical linkages between sister chromatids and microtubules are critical for spindle assembly and chromosome segregation. Defects in either chromosome or centrosome segregation can lead to aneuploidy and are correlated with cancer progression. In this review, we discuss current models of how centrosomes and chromosomes organize the spindle for their equal distribution to each daughter cell. PMID: 12866832 [PubMed - indexed for MED... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1566998 Tue, 01 Jul 2003 04:00:00 +0100 1566998 http://www.medworm.com/index.php?rid=1567003&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12793526%26dopt%3DAbstract Authors: Leiva IM, Emmert-Buck MR, Gillespie JW The relationship between gene expression profiles and cellular phenotypes is an important aspect of functional genomics. Clinical tissue specimens will play a vital role in this effort. The usefulness of tissue for molecular profiling is significantly influenced by the manner of specimen handling. Crucial components of this process include the optimization of the methods of tissue fixation and embedding, not only to obtain excellent histological detail, but also to promote the elucidation of the gene and protein expression profiles. In this article, we describe handling of clinical specimens using whole-mount prostate as an example, the use of new high-throughput techniques that allow molecular profiling analysis and the use of a web-base... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567003 Tue, 01 Apr 2003 05:00:00 +0100 1567003 http://www.medworm.com/index.php?rid=1567002&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12793527%26dopt%3DAbstract Authors: Danchin A Genomics today involves the study of many genes at a time in order to gain an integrated picture of the cell or organism as a whole. This review considers the architecture and evolution of bacterial genomes. The many facets of large-scale functional investigation in a variety of bacteria and the search to find common rules in their dynamic and structural organization are discussed. Such rules could aid the understanding of common properties and essential differences corresponding to elusive functions, or of still unknown bacterial biotopes. PMID: 12793527 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567002 Tue, 01 Apr 2003 05:00:00 +0100 1567002 http://www.medworm.com/index.php?rid=1567001&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12793528%26dopt%3DAbstract Authors: Kwok PY, Chen X Single nucleotide polymorphism (SNP) detection technologies are used to scan for new polymorphisms and to determine the allele(s) of a known polymorphism in target sequences. SNP detection technologies have evolved from labor intensive, time consuming, and expensive processes to some of the most highly automated, efficient, and relatively inexpensive methods. Driven by the Human Genome Project, these technologies are now maturing and robust strategies are found in both SNP discovery and genotyping areas. The nearly completed human genome sequence provides the reference against which all other sequencing data can be compared. Global SNP discovery is therefore only limited by the amount of funding available for the activity. Local, target, SNP discovery relies mo... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567001 Tue, 01 Apr 2003 05:00:00 +0100 1567001 http://www.medworm.com/index.php?rid=1567006&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12638659%26dopt%3DAbstract Authors: Schneegurt MA, Dore SY, Kulpa CF Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils. These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols. Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard. Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/or enzymic digestion with lysozyme and proteases. After typical organic extraction and alcohol precipitation, further ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567006 Wed, 01 Jan 2003 05:00:00 +0100 1567006 http://www.medworm.com/index.php?rid=1567005&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12638660%26dopt%3DAbstract Authors: Davey HM, Winson MK Flow cytometry is a powerful technique for the study of single cells, and thus it is of particular utility in the study of heterogeneity in microbial populations. This review seeks to highlight the role of flow cytometric analyses in studies of microbial heterogeneity, drawing wherever possible on recently published research articles. Whilst microbial heterogeneity is well documented in both natural and laboratory environments, the underlying causes are less well understood. Possible sources for the heterogeneity that is observed in microbial systems are discussed, together with the flow cytometric tools that aid its study. The role of flow cytometry in molecular biology is discussed with reference to gene reporter systems, which enable heterogeneity of gen... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567005 Wed, 01 Jan 2003 05:00:00 +0100 1567005 http://www.medworm.com/index.php?rid=1567004&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12638661%26dopt%3DAbstract Authors: Downs DM The field of bacterial metabolism and physiology is arguably the oldest in microbiology. Much of our understanding of biological processes and molecular paradigms has its roots In early studies of prokaryotic physiology. After a period of declining interest in metabolic studies (prompted by the insurgence of molecular techniques), genomic technologies are revitalizing the study of bacterial metabolism and physiology. These new technologies bring a means to approach metabolic questions with a global perspective. When used in combination with classical and molecular techniques, emerging global technologies will make it feasible to understand the complex integration of metabolic processes that result in an efficient physiology. At the same time, without increased computa... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567004 Wed, 01 Jan 2003 05:00:00 +0100 1567004 http://www.medworm.com/index.php?rid=1567009&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12432962%26dopt%3DAbstract Authors: Pagliarulo V, Datar RH, Cote RJ As the determination of gene sequences and their function gains speed at the dawn of the third millennium, biomedical research efforts are oriented towards definition of the genetic and molecular expression patterns that may drive different disease. A major part of these efforts is addressed to the definition of inter-individual variations that are expected to become integral for treatment planning, in terms of efficacy and adverse effects of drugs. It is this thrust on genome-based 'rational therapeutics' that is hoped to progressively lead to the era of 'personalized medicine'. This approach uses the technological expertise from genomics and functional genomics to define, predict and monitor the nature of the response of an individual to drugs... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567009 Tue, 01 Oct 2002 04:00:00 +0100 1567009 http://www.medworm.com/index.php?rid=1567008&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12432963%26dopt%3DAbstract Authors: Novik KL, Nimmrich I, Genc B, Maier S, Piepenbrock C, Olek A, Beck S Epigenetics is one of the key areas of future research that can elucidate how genomes work. It combines genetics and the environment to address complex biological systems such as the plasticity of our genome. While all nucleated human cells carry the same genome, they express different genes at different times. Much of this is governed by epigenetic changes resulting in differential methylation of our genome--or different epigenomes. Individual studies over the past decades have already established the involvement of DNA methylation in imprinting, gene regulation, chromatin structure, genome stability and disease, especially cancer. Now, in the wake of the Human Genome Project (HGP), epigenetic phenomena can ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567008 Tue, 01 Oct 2002 04:00:00 +0100 1567008 http://www.medworm.com/index.php?rid=1567007&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12432964%26dopt%3DAbstract "A system biology" approach to bioinformatics and functional genomics in complex human diseases: arthritis. Curr Issues Mol Biol. 2002 Oct;4(4):129-46 Authors: Attur MG, Dave MN, Tsunoyama K, Akamatsu M, Kobori M, Miki J, Abramson SB, Katoh M, Amin AR Human and other annotated genome sequences have facilitated generation of vast amounts of correlative data, from human/animal genetics, normal and disease-affected tissues from complex diseases such as arthritis using gene/protein chips and SNP analysis. These data sets include genes/proteins whose functions are partially known at the cellular level or may be completely unknown (e.g. ESTs). Thus, genomic research has transformed molecular biology from "data poor" to "data rich" science, allowing further division into subpopulation... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567007 Tue, 01 Oct 2002 04:00:00 +0100 1567007 http://www.medworm.com/index.php?rid=1567012&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12074196%26dopt%3DAbstract Authors: Bowen NJ, Jordan IK Eukaryotic transposable elements are ubiquitous and widespread mobile genetic entities. These elements often make up a substantial fraction of the host genomes in which they reside. For example, approximately 1/2 of the human genome was recently shown to consist of transposable element sequences. There is a growing body of evidence that demonstrates that transposable elements have been major players in genome evolution. A sample of this evidence is reviewed here with an emphasis on the role that transposable elements may have played in driving the evolution of eukaryotic complexity. A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567012 Mon, 01 Jul 2002 04:00:00 +0100 1567012 http://www.medworm.com/index.php?rid=1567011&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12074197%26dopt%3DAbstract Authors: Ratcliffe OJ, Riechmann JL The availability of the Arabidopsis genome sequence allows for novel approaches in the analysis of many aspects of plant biology. Approximately 6% of Arabidopsis genes code for transcription factors, which can be grouped into different families according to similarities within the DNA binding domains. Transcription factors are critical regulatory components of the pathways that underpin many aspects of plant growth, development, and physiology. In particular, a substantial number of them are emerging as having crucial roles in controlling one of the most important, but complex, steps in the plant life cycle: the transition to flowering. Genome-wide studies offer the opportunity to gain a comprehensive understanding of this polygenic process, making i... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567011 Mon, 01 Jul 2002 04:00:00 +0100 1567011 http://www.medworm.com/index.php?rid=1567010&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D12074198%26dopt%3DAbstract Authors: Roth CM Identifying those genes that are expressed and at what levels is an essential part of almost any biological inquiry at the cellular level. Techniques such as Northern blot have been in existence for decades to perform this task, but advances in molecular biology and bioinstrumentation have led to the development of a variety of new techniques with a range of sensitivities, throughputs and quantitative capabilities. This review focuses on the latter issue. For several commonly used gene expression techniques, the extent and range of quantitative applicability are reviewed, and approaches for maximizing the accuracy and precision of these measurements are discussed. PMID: 12074198 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567010 Mon, 01 Jul 2002 04:00:00 +0100 1567010 http://www.medworm.com/index.php?rid=1567015&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11931568%26dopt%3DAbstract Authors: Zheng XF, Chan TF The knowledge of complete sequences of different organisms is dramatically changing the landscape of biological research and pharmaceutical development. We are experiencing a transition from a trial-and-error approach in traditional biological research and natural product drug discovery to a systematic operation in genomics and target-specific drug design and selection. Small, cell-permeable and target-specific chemical ligands are particularly useful in systematic genomic approaches to study biological questions. On the other hand, genomic sequence information, comparative and structural genomics, when combined with the cutting edge technologies in synthetic chemistry and ligand screening/identification, provide a powerful way to produce target-specific and/... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567015 Mon, 01 Apr 2002 05:00:00 +0100 1567015 http://www.medworm.com/index.php?rid=1567014&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11931569%26dopt%3DAbstract Authors: Hamadeh HK, Amin RP, Paules RS, Afshari CA Toxicogenomics is a rapidly developing discipline that promises to aid scientists in understanding the molecular and cellular effects of chemicals in biological systems. This field encompasses global assessment of biological effects using technologies such as DNA microarrays or high throughput NMR and protein expression analysis. This review provides an overview of advancing multiple approaches (genomic, proteomic, metabonomic) that may extend our understanding of toxicology and highlights the importance of coupling such approaches with classical toxicity studies. PMID: 11931569 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567014 Mon, 01 Apr 2002 05:00:00 +0100 1567014 http://www.medworm.com/index.php?rid=1567013&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11931570%26dopt%3DAbstract Authors: Bilban M, Buehler LK, Head S, Desoye G, Quaranta V DNA microarrays are a powerful tool to investigate differential gene expression for thousands of genes simultaneously. Although DNA microarrays have been widely used to understand the critical events underlying growth, development, homeostasis, behavior and the onset of disease, the management of the resulting data has received little attention. Presently, the fluorescent dyes Cy3 and Cy5 are most often used to prepare labeled cDNA for microarray hybridizations. Raw microarray data are image files that have to be transformed into gene expression formats--a process that requires data manipulation due to systematic variations which may be attributed to differences in the physical and chemical dye applications is to identify diff... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567013 Mon, 01 Apr 2002 05:00:00 +0100 1567013 http://www.medworm.com/index.php?rid=1567018&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11838942%26dopt%3DAbstract This article describes the molecular methods that have been used to characterize cyanobacteria and their use as tools to identify toxin-producing strains. Different species and strains were compared using restriction fragment length polymorphism (RFLP) of amplified fragments of the phycocyanin gene and the 16S-23S rRNA internal transcribed spacer. PMID: 11838942 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567018 Tue, 01 Jan 2002 05:00:00 +0100 1567018 http://www.medworm.com/index.php?rid=1567017&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11838943%26dopt%3DAbstract This article describes the use of quantitative PCR for measuring bacterial abundance in environmental samples. The two approaches discussed are: 1) The use of an internal PCR standard constructed to be the same size and have the same sequence as the primary amplification target, but differing from the primary target by 2-3 bases, corresponding to a unique restriction site. This allows the amount of target amplicon to be compared with the internal standard and circumvents the problem of differential amplification efficiencies when using dissimilar targets and standard amplicons. 2) The use of Taqman technology (Applied Biosystems, Foster City, California) with a dual labeled oligonucleotide probe which binds internal to the PCR primers. The detection of Bacteroides is used as an example for... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567017 Tue, 01 Jan 2002 05:00:00 +0100 1567017 http://www.medworm.com/index.php?rid=1567016&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11838944%26dopt%3DAbstract This article highlights recent advances in nucleic acid-based technologies, and looks towards future advances that may address the broad needs and conditions imposed by environmental molecular microbiology. PMID: 11838944 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567016 Tue, 01 Jan 2002 05:00:00 +0100 1567016 http://www.medworm.com/index.php?rid=1567021&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11719970%26dopt%3DAbstract This article reviews the structure-function features of the eukaryotic RNase III family and their roles in dsRNA metabolism with an emphasis on the yeast RNase III. Yeast RNase III is involved in the maturation of the majority of snRNAs, snoRNAs, and rRNA. In addition, perturbation of the expression level of yeast RNase III alters meiosis and causes sterility. These basic functions of the yeast RNase III appear to be widely conserved which makes it a good model to understand the importance of eukaryotic dsRNA metabolism. PMID: 11719970 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567021 Mon, 01 Oct 2001 04:00:00 +0100 1567021 http://www.medworm.com/index.php?rid=1567020&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11719971%26dopt%3DAbstract Authors: Liu ZG, Han J TNF is a proinflammatory cytokine that plays an important role in many physiological and pathological conditions through the regulation of immunological reactions. Many of TNF functions have been proven to be cell type-specific, and the specificity of TNF-induced cellular responses in a given cell is determined by the specific intracellular signaling pathways that are activated by TNF. Although current information is insufficient to sort out how the cell type specificity is controlled by the different intracellular signaling pathways, a number of signaling pathways that are commonly activated in many types of cells by TNF have been revealed. This review weighs the current knowledge of these TNF-induced signaling pathways. PMID: 11719971 [PubMed - indexed for ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567020 Mon, 01 Oct 2001 04:00:00 +0100 1567020 http://www.medworm.com/index.php?rid=1567019&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11719972%26dopt%3DAbstract Authors: Ermolaeva MD In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid conservation, protein hydropathy, transcriptional selection and even RNA stability. The review discusses these factors and their contribution to bias in synonymous codon usage in bacterial genomes. PMID: 11719972 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567019 Mon, 01 Oct 2001 04:00:00 +0100 1567019 http://www.medworm.com/index.php?rid=1567024&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11488411%26dopt%3DAbstract Authors: Gasteiger E, Jung E, Bairoch A With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567024 Sun, 01 Jul 2001 04:00:00 +0100 1567024 http://www.medworm.com/index.php?rid=1567023&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11488412%26dopt%3DAbstract Degradation of mutant proteins, underlying "loss of function" phenotypes, plays a major role in genetic disease. Curr Issues Mol Biol. 2001 Jul;3(3):57-65 Authors: Waters PJ Many Mendelian monogenic disorders are caused by loss of the function of a single protein. This can result from rapid degradation of the mutant protein by cellular proteases, which reduces the steady-state concentration of the protein within the cell. The susceptibility of a protein to such proteolytic breakdown depends upon its kinetics of monomer folding and oligomer assembly and upon the intrinsic (thermodynamic) stability of its functional native-state conformation. Other cellular proteins, notably molecular chaperones, promote correct protein folding and assembly and thus provide some protection agains... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567023 Sun, 01 Jul 2001 04:00:00 +0100 1567023 http://www.medworm.com/index.php?rid=1567022&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11488413%26dopt%3DAbstract Authors: Nunez R Measurement of cellular DNA content and the analysis of the cell cycle can be performed by flow cytometry. Protocols for DNA measurement have been developed including Bivariate cytokeratin/DNA analysis, Bivariate BrdU/DNA analysis, and multiparameter flow cytometry measurement of cellular DNA content. This review summarises the methods for measurement of cellular DNA and analysis of the cell cycle and discusses the commercial software available for these purposes. PMID: 11488413 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567022 Sun, 01 Jul 2001 04:00:00 +0100 1567022 http://www.medworm.com/index.php?rid=1567040&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11471972%26dopt%3DAbstract Authors: Huttner E, Tucker W, Vermeulen A, Ignart F, Sawyer B, Birch R Potyviruses are the most important viral pathogens of crops worldwide. Under a contract with Gene Shears Pty Limited, we are using ribozyme genes to protect melon plants against two potyviruses: WMV2 and ZYMV. Different polyribozyme genes were designed, built and introduced into melons plants. Transgenic melon plants containing a resistance gene were obtained and their progeny was challenged by the appropriate virus. Most of the genes tested conferred some degree of resistance to the viruses in glasshouse trials. Melon plants from one family containing one gene directed against WMV2 were also field-trialed on small plots under natural infection pressure and were found immune to WMV2. Field trial is in progress for p... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567040 Sun, 01 Apr 2001 05:00:00 +0100 1567040 http://www.medworm.com/index.php?rid=1567039&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11471973%26dopt%3DAbstract Authors: Kuramitsu HK Dental caries and periodontitis, although generally not life threatening, are nevertheless of significant importance. An understanding of the molecular nature of these diseases could aid the development of novel methods of prevention and control, and increase our knowledge of their etiology. The identification of virulence factors in oral bacteria could lead to the development of vaccines directed against these organisms, the design of inhibitors of biofilm formation, and the development of replacement therapy strategies. PMID: 11471973 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567039 Sun, 01 Apr 2001 05:00:00 +0100 1567039 http://www.medworm.com/index.php?rid=1567038&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11471974%26dopt%3DAbstract Authors: Nunez R PMID: 11471974 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567038 Sun, 01 Apr 2001 05:00:00 +0100 1567038 http://www.medworm.com/index.php?rid=1567037&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11471975%26dopt%3DAbstract Authors: Nunez R PMID: 11471975 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567037 Sun, 01 Apr 2001 05:00:00 +0100 1567037 http://www.medworm.com/index.php?rid=1567041&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11471757%26dopt%3DAbstract Authors: Leigh JA The methanogenic Archaea bring a broadened perspective to the field of nitrogen fixation. Biochemical and genetic studies show that nitrogen fixation in Archaea is evolutionarily related to nitrogen fixation in Bacteria and operates by the same fundamental mechanism. At least six nif genes present in Bacteria (nif H, D, K, E, N and X) are also found in the diazotrophic methanogens. Most nitrogenases in methanogens are probably of the molybdenum type. However, differences exist in gene organization and regulation. All six known nif genes of methanogens, plus two homologues of the bacterial nitrogen sensor-regulator glnB, occur in a single operon in Methanococcus maripaludis. nif gene transcription in methanogens is regulated by what appears to be a classical prokaryoti... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567041 Sun, 01 Oct 2000 04:00:00 +0100 1567041 http://www.medworm.com/index.php?rid=1567036&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475693%26dopt%3DAbstract Authors: Tait RC Molecular biology methods have tremendous value not only in the investigation of basic scientific questions, but also in application to a wide variety of problems affecting the overall human condition. Disease prevention and treatment, generation of new protein products, and manipulation of plants and animals for desired phenotypic traits are all applications that are routinely addressed by the application of molecular biology methods. Because of the wide applicability of these methods, they are rapidly becoming a pervasive--some would argue invasive--aspect of our technologically based society. The public concerns that address the application of these methods should be addressed by informed public discussion and debate. While scientists can be extremely critical of th... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567036 Fri, 01 Jan 1999 05:00:00 +0100 1567036 http://www.medworm.com/index.php?rid=1567035&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475694%26dopt%3DAbstract Authors: Ørum H The use of affinity tagged PNA capture probes offers an efficient means for the purification of nucleic acids by hybridization. Two different approaches are described. A sequence specific method and a generic method. The sequence specific method requires sequence information on the target and synthesis of a dedicated PNA. It can be used to selectively purify the nucleic acid containing the target from non-related nucleic acids and other cellular components. The generic method uses a "universal" triplex forming PNA and requires no sequence information on the target. It can be used in the bulk purification of large nucleic acids. PMID: 11475694 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567035 Fri, 01 Jan 1999 05:00:00 +0100 1567035 http://www.medworm.com/index.php?rid=1567034&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475695%26dopt%3DAbstract Authors: Good L, Nielsen PE Antisense peptide nucleic acid (PNA) can be used to control cell growth, gene expression and growth phenotypes in the bacteria Escherichia coli. PNAs targeted to the RNA components of the ribosome can inhibit translation and cell growth, and PNAs targeted to mRNA can limit gene expression with gene and sequence specificity. In an E. coli cell extract, efficient inhibition is observed when using PNA concentrations in the nanomolar range, whereas micromolar concentrations are required for inhibition in growing cells. A mutant strain of E. coli that is more permeable to antibiotics also is more susceptible to antisense PNAs than the wild type. This chapter details methods for testing the antisense activities of PNA in E. coli. As an example of the specific anti... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567034 Fri, 01 Jan 1999 05:00:00 +0100 1567034 http://www.medworm.com/index.php?rid=1567033&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475696%26dopt%3DAbstract This article reviews the development of PNA biosensors, and discusses common PNA-biosensing protocols along with their prospects in DNA biosensor technology. PMID: 11475696 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567033 Fri, 01 Jan 1999 05:00:00 +0100 1567033 http://www.medworm.com/index.php?rid=1567032&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475697%26dopt%3DAbstract Authors: Rezaian MA Viroids are small autonomously replicating RNAs that share structural features with other subviral circular single-stranded RNAs of plants. Viroids and other circular single-stranded RNAs can be synthesised in vitro by a PCR-based procedure using a simple set of reactions. Two end-to-end primers are selected from a desired region of the viroid, one for the synthesis of the first strand cDNA and another for the production of the second strand DNA. The second primer contains an 18 nucleotide T7 promoter at its 5' end, and is selected such that the G nucleotide at the transcription start site represents a G in the viroid. Linked reverse transcription-PCR results in linear double-stranded DNA consisting of the viroid sequence and the T7 promoter. Run-off transcription o... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567032 Fri, 01 Jan 1999 05:00:00 +0100 1567032 http://www.medworm.com/index.php?rid=1567031&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475698%26dopt%3DAbstract Authors: Berlin YA Splicing by directed ligation (SDL) is a method of in-phase joining of PCR-generated DNA fragments that is based on a pre-designed combination of class IIS restriction endonuclease recognition and cleavage sites. Since these enzymes cleave outside of their recognition sites, the resulting sticky end can have any desired sequence, and the site itself can be removed and does not appear in the final spliced DNA product. SDL is based on the addition of class IIS recognition sites onto primers used to amplify DNA sequences. Cleavage of the PCR products results in elimination of the recognition site-containing flanking sequences and leaves the DNA fragments crowned with protruding ends. With careful design of the sticky ends, several segments can be ligated together in a p... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567031 Fri, 01 Jan 1999 05:00:00 +0100 1567031 http://www.medworm.com/index.php?rid=1567030&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475699%26dopt%3DAbstract Authors: Golemis EA, Serebriiskii I, Law SF In vivo transcription-based assays for protein-protein interactions such as the two-hybrid system are powerful methods for identifying novel proteins based on their physical association with known proteins of biological interest, or for characterizing the degree and nature of interactions between sets of proteins. Because of the complexity inherent in assays taking place within a living organism, a key issue for the effective use of two-hybrid approaches is the ability to determine whether apparent interactions are likely to be physiologically relevant. In this article, a number of the different two-hybrid systems currently available for use will be reviewed. Then, taking as a model one such system, the Interaction Trap, examples of different... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567030 Fri, 01 Jan 1999 05:00:00 +0100 1567030 http://www.medworm.com/index.php?rid=1567029&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475700%26dopt%3DAbstract We describe a simple PCR-based method for the isolation of genomic DNA that lies adjacent to a known DNA sequence. The method is based on the directional cloning of digested genomic DNA into the multiple cloning site of a pUC-based plasmid to generate a limited genomic library. The library is plated onto a number of selective LA plates which are incubated overnight, and recombinant plasmid DNA is then isolated from resistant colonies pooled from each plate. PCR amplification is performed on the pooled recombinant plasmid DNAs using primers specific for the pUC vector and the known genomic sequence. The combination of efficient directional cloning and bacterial transformation gives relative enrichment for the genomic sequence of interest and generates a simple DNA template, enabling easy am... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567029 Fri, 01 Jan 1999 05:00:00 +0100 1567029 http://www.medworm.com/index.php?rid=1567028&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475701%26dopt%3DAbstract Authors: Tannock GW Selective culture media and phenotypic tests enable lactobacilli to be differentiated from morphologically similar bacteria. The accurate identification of Lactobacillus species can be accomplished by reference to 16S rRNA gene sequences. Species-specific, PCR primers that target the 16S-23S rRNA spacer region are available for a limited number of Lactobacillus species. Molecular methods for the comprehensive identification of Bifidobacterium species are not yet available. Only DNA-DNA reassociation provides a reliable means of species identification for this genus at present. Bifidobacteria can be differentiated from morphologically similar bacteria by the use of genus-specific, PCR primers or oligonucleotide probes. PMID: 11475701 [PubMed - indexed for MEDLINE... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567028 Fri, 01 Jan 1999 05:00:00 +0100 1567028 http://www.medworm.com/index.php?rid=1567027&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475702%26dopt%3DAbstract Authors: Harris DA Studying PrPC and PrPSc in cell culture systems is advantageous because such systems contain all the organelles, membranes, and molecular cofactors that are likely to play an important role in the biology of the proteins. Using cultured cells expressing PrPC, we have discovered that this isoform constitutively cycles between the cell surface and an endocytic compartment, a process that is mediated by clathrin-coated pits and a putative PrPC receptor. We have also constructed stably transfected lines of CHO cells that express PrP molecules carrying mutations that are associated with familial prion diseases. The mutant PrP molecules in these cells are spontaneously converted to the PrPSc state, a phenomenon which has allowed us to analyze several key features of prion ... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567027 Fri, 01 Jan 1999 05:00:00 +0100 1567027 http://www.medworm.com/index.php?rid=1567026&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475703%26dopt%3DAbstract This article describes two novel applications of the long PCR technique, one which simplifies restriction mapping and another which enhances amplification specificity and yield. The same primers used to perform the long PCR amplification can be used as probes to perform restriction mapping of the DNA fragment amplified. Restriction digestion performed prior to long PCR amplification can be used to selectively suppress the amplification of members of families of closely related DNA sequences, thereby making it possible to selectively amplify one of a group of highly homologous sequences. These two complimentary techniques, both involving use of the long PCR paired with restriction digestion, have potential application in any laboratory in which PCR is performed. PMID: 11475703 [PubMed -... Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567026 Fri, 01 Jan 1999 05:00:00 +0100 1567026 http://www.medworm.com/index.php?rid=1567025&cid=s_37260_67_f&fid=37260&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D11475704%26dopt%3DAbstract Authors: Nielsen PE, Egholm M Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful biomolecular tools, antisense and antigene agents, molecular probes and biosensors. PMID: 11475704 [PubMed - indexed for MEDLINE] (Source: Current Issues in Molecular Biology) Current Issues in Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1567025 Fri, 01 Jan 1999 05:00:00 +0100 1567025