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'Cold fusion' moves closer to mainstream acceptanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(American Chemical Society) "Cold fusion," a controversial energy source once relegated to the scientific equivalent of banishment to Siberia, is now moving closer toward acceptance by the mainstream scientific community. A special two-day symposium entitled "New Energy Technology" will include 46 oral presentations on this topic and more than a dozen posters -- among the largest presentations of their kind to date -- March 22-23 at the American Chemical Society's 239th National Meeting. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 21, 2010 Category: Biology Source Type: news

EditorialEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
OMICS: A Journal of Integrative Biology , Vol. 0, No. 0. (Source: OMICS: A Journal of Integrative Biology)
Source: OMICS: A Journal of Integrative Biology - March 20, 2010 Category: Biology Tags: article Source Type: journals

Inhibition of Tubulogenesis and of Carcinogen-mediated Signaling in Brain Endothelial Cells Highlight the Antiangiogenic Properties of a Mumbaistatin AnalogEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A better understanding of the metabolic adaptations of the vascular endothelial cells (EC) that mediate tumor vascularization would help the development of new drugs and therapies. Novel roles in cell survival and metabolic adaptation to hypoxia have been ascribed to the microsomal glucose-6-phosphate translocase (G6PT). While antitumorigenic properties of G6PT inhibitors such as chlorogenic acid (CHL) have been documented, those of the G6PT inhibitor and semi-synthetic analog AD4-015 of the polyketide mumbaistatin are not understood. In the present study, we evaluated the in vitro antiangiogenic impact of AD4-015 on human...
Source: Chemical Biology and Drug Design - March 20, 2010 Category: Biology Authors: Elizabeth Tahanian, Simon Lord-Dufour, Abhirup Das, Chaitan Khosla, René Roy, Borhane Annabi Source Type: journals

The timing of mating influences reproductive success in Drosophila melanogaster: implications for sexual conflictEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite its potential importance, the role of the timing of mating(s) as a source of variation in female lifetime reproductive success has been largely overlooked. Here, using a laboratory-adapted population of the model species Drosophila melanogaster, we explore how temporal variation in the patterns of single and multiple matings influences female fecundity. We find that the boost to fecundity known to occur after a virgin female's initial mating also extends to subsequent matings as nonvirgins, but only for a short duration. This fecundity boost at least partially offsets the direct costs of multiple matings to females...
Source: Journal of Evolutionary Biology - March 20, 2010 Category: Biology Authors: T. A. F. LONG, A. PISCHEDDA, R. V. NICHOLS, W. R. RICE Source Type: journals

Northern Blotting Techniques for Small RNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In eukaryotes, RNA silencing encompasses a range of biochemical processes mediated by ∼20–25 nt small RNAs (smRNAs). This chapter describes northern blot hybridization techniques optimized for detection of such smRNAs, whether extracted from plant or animal tissues. The basic protocol is described, and control blots illustrate the detection specificity and sensitivity of this method using DNA oligonucleotide probes. Known endogenous smRNAs are analyzed in samples prepared from several model plant species, including Arabidopsis thaliana, Nicotiana benthamiana, Oryza sativa, Zea mays, and Physcomitrella patens, as ...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Analysis of Small RNA Populations Using Hybridization to DNA Tiling ArraysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Small RNA (sRNA) populations extracted from Arabidopsis plants submitted or not to biotic stress, were reverse-transcribed into cDNAs, and these were subsequently hybridized after labelling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by Massive Parallel Sequence Signature (MPSS) in the case of untreated plants, b...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation ChangesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is a modification of the Amplified Fragment Length Polymorphism (AFLP) technique that has been used to study methylation of anonymous CCGG sequences in different fungi, plant and animal species. The main variation of this technique is based on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent cutter restriction enzyme. For each sample, AFLP analysis is performed using both EcoRI/HpaII and EcoRI/MspI digested sa...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length PolymorphismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA ca...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

In Situ Analysis of DNA Methylation in PlantsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Epigenetic changes in the plant genome are associated with differential genome methylation, histone modifications, and the binding of various chromatin-binding factors. Methylation of cytosine residues is one of the most versatile mechanisms of epigenetic regulation. The analysis of DNA methylation can be performed in different ways. However, most of these procedures involve the extraction of chromatin from cells with further isolation and analysis of DNA. Modest success has been achieved in DNA methylation analysis in plant tissues in situ. Here, we present an in situ method for DNA methylation analysis, which has high se...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Detection of Changes in Global Genome Methylation Using the Cytosine-Extension AssayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Methylation is a reversible covalent chemical modification of DNA intended to regulate gene expression, genome stability, and chromatin structure. Although there are various methods of methylation analysis, most of them are either laborious or expensive, or both. Here, we describe a quick, inexpensive method for analysis of global genome methylation using a cytosine extension assay. The assay can be used for analysis of the total level of CpG, CNpG, and asymmetrical methylation in a given cell culture or in a plant tissue sample. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) AssayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
DNA methylation is a major mechanism for the reversible control of gene expression, chromatin structure, and genome stability. Methylation analysis at a given locus allows one to evaluate levels of chromatin packaging, gene expression, and even homologous recombination. We have shown that the combined bisulfite restriction analysis (COBRA) assay makes it possible to analyze methylation levels at a defined locus. The major steps are: bisulfite conversion of nonmethylate cytosines to uracils, locus-specific PCR amplification of converted DNA, restriction digestion, and analysis of restriction patterns on the gel. Due to the ...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATEEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Amplifying and sequencing DNA after bisulfite treatment of genomic DNA reveals the methylation state of cytosine residues at the highest resolution possible. However, a thorough analysis is required for statistical evaluation of methylation at all sites in each genomic region. Several software tools were developed to assist in quantitative evaluation of bisulfite sequencing data from complex methylation patterns occurring in plants. This chapter describes the application of Cytosine Methylation Analysis Tool for Everyone (CyMATE). From aligned sequences, CyMATE quantifies and illustrates general and pattern-specific methyl...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Analysis of DNA Methylation in Plants by Bisulfite SequencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe the application of bisulfite sequencing for the analysis of DNA methylation at defined individual sequences of plant genomic DNA. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Plant TransgenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Epigenetic effects such as gene silencing and variable expression are unintended consequences of plant transformation, a problem that is present in the transformation of all plant species. There is not yet a reliable way to prevent epigenetic silencing; however, the probability of epigenetic effects may be reduced by choosing an appropriate method of transgene introduction into a plant cell. Most methods used in plant biotechnology, such as direct gene transfer and particle bombardment, result in the introduction of multiple DNA molecules and, as a consequence, multi-copy multi-locus insertion patterns. These multiple inse...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Reporter Gene-Based Recombination Lines for Studies of Genome StabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Homologous recombination is a double-strand break repair mechanism operating in somatic cells and involved in meiotic crossovers in plants. It is responsible for the maintenance of genome stability and thus plays a crucial role in adaptation to stress. Recombination between homologous loci is believed to be regulated in part by epigenetic machinery such as methylation. Therefore, the recombination frequency at a specific locus can reflect the chromatin status. (Source: Springer protocols feed by Plant Sciences)
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) AssayEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
DNA double strand breaks (DSBs) arise from spontaneous DNA damage due to metabolic activities or from direct and indirect damaging effects of stress. DSBs are also formed transiently during such processes as replication, transcription, and DNA repair. The level of DSBs positively correlates with the activities of homologous and nonhomologous DNA repair pathways, which in turn inversely correlate with methylation levels and chromatin structure. Thus, measurement of strand breaks can provide an informative picture of genome stability of a given cell. The use of random oligonucleotide-primed synthesis for the analysis of DSB ...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

cDNA Libraries for Virus-Induced Gene SilencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Virus-induced gene silencing (VIGS) exploits endogenous plant antiviral defense mechanisms to posttranscriptionally silence the expression of targeted plant genes. VIGS is quick and relatively easy to perform and therefore serves as a powerful tool for high-throughput functional genomics in plants. Combined with the use of subtractive cDNA libraries for generating a collection of VIGS-ready cDNA inserts, VIGS can be utilized to screen a large number of genes to determine phenotypes resulting from the knockdown/knockout of gene function. Taking into account the optimal insert design for VIGS, we describe a methodology for p...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein–DNA Binding Analyses in ArabidopsisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Epigenetic gene regulation via histone modifications controls different processes ranging from embryonic development, vegetative development, floral induction, floral organ development, to pollen tube growth. The identification of an increasing number of epigenetically regulated processes was greatly advanced by genome-wide histone modification and chromatin-protein interaction surveys. However, genome-wide approaches are too global to access in detail a large number of histone modifications taking place at a single locus. Here we provide a robust Chromatin Immunoprecipitation (ChIP) protocol, allowing in vivo analyses of ...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Metaanalysis of ChIP-chip DataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome-wide analysis of histone modifications via ChIP-chip (chromatin immunoprecipitation followed by whole genome tiling array hybridization) may generate lists of up to several thousand potential target genes. In the case of the model organism Arabidopsis thaliana, several databases are available to alleviate further characterization and classification of genomic data sets. The term metaanalysis has been coined for this type of multidatabase comparison. In this chapter, we describe open source software and web tools that perform transcriptional and functional analysis of target genes. Sources of transcription data and c...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data AnalysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome-wide targets of chromatin-associated factors can be identified by a combination of chromatin-immunoprecipitation and oligonucleotide microarray hybridization. Genome-wide mircoarray data analysis represents a major challenge for the experimental biologist. This chapter introduces ChIPR, a package written in the R statistical programming language that facilitates the analysis of two-color microarrays from Roche-Nimblegen. The workflow of ChIPR is illustrated with sample data from Arabidopsis thaliana. However, ChIPR supports ChIP-chip data preprocessing, target identification, and cross-annotation of any species for ...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A: ChIP-chip Molecular MethodsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Chromatin immunoprecipitation in combination with DNA-microarray hybridization (ChIP-chip) allows the identification of chromatin regions that are associated with modified forms of histones on a genomic scale. The ChIP-chip workflow consists of the following steps: generation of biological material, in vivo formaldehyde-fixation of protein-DNA and protein-protein interactions, chromatin preparation and shearing, immunoprecipitation of chromatin with specific antibodies, fixation reversal and DNA purification, DNA amplification, microarray hybridization, and data analysis. In Part A of this chapter, we describe molecular me...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Cloning New Small RNA SequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Small RNAs are key molecules in RNA silencing pathways that exert sequence-specific regulation of gene expression and chromatin modifications in many eukaryotes. In plants, endogenous small RNAs, including microRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) play an important role in biological processes such as development and stress responses. In addition, viral genome-derived siRNAs are produced during viral infection, and they exhibit anti-viral defense by an RNA silencing pathway. These endogenous and exogenous small RNAs are mainly 21-24 nucleotides in length. Here, we describe a method to identify s...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

qRT-PCR of Small RNAsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Plant small RNAs are a class of 19- to 25-nucleotide (nt) RNA molecules that are essential for genome stability, development and differentiation, disease, cellular communication, signaling, and adaptive responses to biotic and abiotic stress. Small RNAs comprise two major RNA classes, short interfering RNAs (siRNAs) and microRNAs (miRNAs). Efficient and reliable detection and quantification of small RNA expression has become an essential step in understanding their roles in specific cells and tissues. Here we provide protocols for the detection of miRNAs by stem-loop RT-PCR. This method enables fast and reliable miRNA expr...
Source: Springer protocols feed by Plant Sciences - March 19, 2010 Category: Biology Source Type: info

Garbled messages and corrupted translationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 306 (2010). doi:10.1038/nchembio0410-306e Author: Tilman Schneider-Poetsch, Takeo Usui, Daisuke Kaida & Minoru Yoshida (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Tilman Schneider-PoetschTakeo UsuiDaisuke KaidaMinoru Yoshida Tags: Erratum Source Type: journals

Cover captionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 306 (2010). doi:10.1038/nchembio0410-306d (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Tags: Erratum Source Type: journals

An upfront investmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 306 (2010). doi:10.1038/nchembio0410-306c Author: Damian W Young (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Damian W Young Tags: Corrigendum Source Type: journals

Revealing the delta ladyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 306 (2010). doi:10.1038/nchembio0410-306b Author: Paul Workman & Rob L M van Montfort (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Paul WorkmanRob L M van Montfort Tags: Corrigendum Source Type: journals

The p110δ structure: mechanisms for selectivity and potency of new PI(3)K inhibitorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The p110δ structure: mechanisms for selectivity and potency of new PI(3)K inhibitors Nature Chemical Biology 6, 306 (2010). doi:10.1038/nchembio0410-306a Author: Alex Berndt, Simon Miller, Olusegun Williams, Daniel D Le, Benjamin T Houseman, Joseph I Pacold, Fabrice Gorrec, Wai-Ching Hon, Pingda Ren, Yi Liu, Christian Rommel, Pascale Gaillard, Thomas Rückle, Matthias K Schwarz, Kevan M Shokat, Jeffrey P Shaw & Roger L Williams (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Alex BerndtSimon MillerOlusegun WilliamsDaniel D LeBenjamin T HousemanJoseph I PacoldFabrice GorrecWai-Ching HonPingda RenYi LiuChristian RommelPascale GaillardThomas RückleMatthias K SchwarzKevan M ShokatJeffrey P ShawRoger L Williams Tags: Corrigendum Source Type: journals

Channels: Flies feel your painEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
outian Evolutionary conservation of TRPA1 underlies sensation of reactive noxious chemicals from flies to humans. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Lindsey J MacphersonArdem Patapoutian Tags: News and Views Source Type: journals

Biosynthesis: Unmasking morphineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bruner The final steps in the biosynthetic pathway to the morphine alkaloids have been revealed with the characterization of two key enzymes. In addition to the widely exploited parent compound, these new O-demethylases control metabolic flux to pharmaceutically useful opioid precursors. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Eric J DimiseSteven D Bruner Tags: News and Views Source Type: journals

Kinase inhibitors: Narrowing down the real targetsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 249 (2010). doi:10.1038/nchembio.336 Author: Henrik Daub Many kinase inhibitors for cancer therapy are rather nonselective, and their cellular mechanisms of action are incompletely understood. A nested chemical proteomics and chemical genetics strategy reveals which cellular targets of the clinical kinase inhibitor dasatinib functionally relate to its anti-oncogenic activity. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Henrik Daub Tags: News and Views Source Type: journals

The genetic code: An archaeal path to literacyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 248 (2010). doi:10.1038/nchembio.335 Author: Tamara L Hendrickson In most archaea, the enzyme TiaS post-transcriptionally modifies a cytidine in the anticodon of tRNAIle, converting it to agmatidine (agm2C or C+). This unique nucleoside allows translation at the AUA isoleucine codon and prevents misreading of the AUG methionine codon. (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Authors: Tamara L Hendrickson Tags: News and Views Source Type: journals

Our choices from the recent literatureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 246 (2010). doi:10.1038/nchembio.344 (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Tags: Research Highlights Source Type: journals

What's in a review?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nature Chemical Biology 6, 245 (2010). doi:10.1038/nchembio.346 Scientific referees accept a critical role in the peer review process. What do we expect of Nature Chemical Biology reviewers? (Source: Nature Chemical Biology)
Source: Nature Chemical Biology - March 19, 2010 Category: Biology Tags: Editorial Source Type: journals

Evidence indicates humans' early tree-dwelling ancestors were also bipedalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(University of Arizona) Experiments by University of Arizona anthropologist David Raichlen and his colleagues show that fossil footprints made 3.6 million years ago are the earliest direct evidence of early hominids using the kind of efficient, upright posture and gait now seen in modern humans. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

Sustainable energy: a challenge nearly as great as global warmingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Fundação de Amparo à Pesquisa do Estado de São Paulo) The Latin American Convention of the Global Sustainable Bioenergy Project which will be held in Sao Paulo, Brazil, on March 23-25. This is the third of a series of five conventions aiming to provide guidance on the feasibility of sustainable bioenergy production on a large scale as well as implementation paths and policies that foster this outcome. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

Students discover new species of raptor dinosaurEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(University College London) A new species of dinosaur, a relative of the famous Velociraptor, has been discovered in Inner Mongolia by two Ph.D. students. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

GW Ph.D. candidate and UCL grad student discover new species of raptor dinosaurEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(George Washington University) A new species of raptor dinosaur being named Linheraptor exquisitus has been discovered by George Washington University doctoral candidate Jonah Choiniere and Michael D. Pittman, a graduate student at University College London. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

Silver proves its mettle for nanotech applicationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Arizona State University) Hao Yan and Yan Liu, professors at the Biodesign Institute's Center for Single Molecule Biophysics and their collaborators have introduced a new method to deterministically and precisely position silver nanoparticles onto self-assembling DNA scaffolds. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

ESA and Thales Alenia Space enter negotiations for MTGEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(European Space Agency) The tendering process that will result in the supply of Europe's next series of meteorological satellites, Meteosat Third Generation, has reached an advanced stage as ESA invites Thales Alenia Space to enter formal contract negotiations. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

Ben-Gurion University researcher receives rappaport prize for excellence in biomedical researchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(American Associates, Ben-Gurion University of the Negev) Professor Cohen received the prize for her research that led to an innovative and pioneering product using algae to prevent cardiac tissue damage following acute myocardial infarction. The hydrogel, is a resorbable liquid polymer that is administered through the coronary artery during standard catheterization and flows into the damaged heart muscle. BL-1040 forms a protective "scaffold" that enhances the mechanical strength of the heart. (Source: EurekAlert! - Biology)
Source: EurekAlert! - Biology - March 19, 2010 Category: Biology Source Type: news

OST-HTH: a novel predicted RNA-binding domainEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized domain (DUF88). We present evidence that it is an RNAse belonging to ...
Source: Biology Direct - March 19, 2010 Category: Biology Authors: Vivek AnantharamanDapeng ZhangL Aravind Source Type: journals

The Novel Ketoprofen Amides – Synthesis and Biological Evaluation as Antioxidants, Lipoxygenase Inhibitors and Cytostatic AgentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The novel amides of ketoprofen and its reduced derivatives (5a[ndash]f, 4a[ndash]n, 6a[ndash]g) with aromatic and cycloalkyl amines or hydroxylamines were prepared and screened for their reducing and cytostatic activity as well as for their ability to inhibit soybean lipoxygenase and lipid peroxidation. 1,1-Diphenyl-picrylhydrazyl test for reducing ability revealed that ketoprofen amides were more potent antioxidants than the amides of the reduced ketoprofen derivatives. The most active compound was benzhydryl ketoprofen amide 5f. Lipoxygenase inhibition of the tested compounds varied from strong to very weak. The most pot...
Source: Chemical Biology and Drug Design - March 19, 2010 Category: Biology Authors: Zrinka Rajić, Dimitra Hadjipavlou-Litina, Eleni Pontiki, Marijeta Kralj, Lidija [Scaron]uman, Branka Zorc Source Type: journals

Exploring QSARs for Inhibitory Activity of Non-peptide HIV-1 Protease Inhibitors by GA-PLS and GA-SVMEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The support vector machine (SVM) and partial least square (PLS) methods were used to develop quantitative structure activity relationship (QSAR) models to predict the inhibitory activity of non-peptide HIV-1 protease inhibitors. Genetic algorithm (GA) was employed to select variables that lead to the best-fitted models. A comparison between the obtained results using SVM with those of PLS revealed that the SVM model is much better than that of PLS. The root mean square errors of the training set and the test set for SVM model were calculated to be 0.2027, 0.2751, and the coefficients of determination (R2) are 0.9800, 0.935...
Source: Chemical Biology and Drug Design - March 19, 2010 Category: Biology Authors: Omar Deeb, Mohammad Goodarzi Source Type: journals

Comparative QSAR Studies on Toxicity of Phenol Derivatives Using Quantum Topological Molecular Similarity IndicesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Quantitative structure activity relationship (QSAR) analyses using a novel type of electronic descriptors called quantum topological molecular similarity (QTMS) indices were operated to describe and compare the mechanisms of toxicity of phenols toward five different strains (i.e., Tetrahymena pyriformis, L1210 Leukemia, Pseudomonas putida, Raja japonica and Cucumis sativus). The appropriate QSAR models for the toxicity data were obtained separately employing partial least squares (PLS) regression combined with genetic algorithms (GA), as a variable selection method. The resulting QSAR models were used to identify molecular...
Source: Chemical Biology and Drug Design - March 19, 2010 Category: Biology Authors: Bahram Hemmateenejad, Ahmad R. Mehdipour, Ramin Miri, Mojtaba Shamsipur Source Type: journals

Impact of plant flowering phenology on the cost/benefit balance in a nursery pollination mutualism, with honest males and cheating femalesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study documents the flowering phenology and its potential consequences on a nursery pollination mutualism between a dioecious plant, in which honest male plants, but not cheating females, allow the specific pollinator to reproduce within inflorescences. Very few pollinators were found to emerge during plant anthesis, leading to a low (if any) potential benefit through pollen dispersal. This opens the question why male plants do not also cheat their pollinators. Female plants flowered late in the season, when many males had just achieved their own anthesis, which increased the efficiency of pollen transfer. Finally, so...
Source: Journal of Evolutionary Biology - March 19, 2010 Category: Biology Authors: M. DUFAY Source Type: journals

Regulation of stress response is heritable and functionally linked to melanin-based colorationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sexual selection theory posits that ornaments can signal the genetic quality of an individual. Eumelanin-based coloration is such an ornament and can signal the ability to cope with a physiological stress response because the melanocortin system regulates eumelanogenesis as well as physiological stress responses. In the present article, we experimentally investigated whether the stronger stress sensitivity of light than dark eumelanic individuals stems from differential regulation of stress hormones. Our study shows that darker eumelanic barn owl nestlings have a lower corticosterone release after a stressful event, an ass...
Source: Journal of Evolutionary Biology - March 19, 2010 Category: Biology Authors: B. ALMASI, L. JENNI, S. JENNI-EIERMANN, A. ROULIN Source Type: journals

Clonal erosion and genetic drift in cyclical parthenogens – the interplay between neutral and selective processesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The occurrence of alternating phases of clonal and sexual reproduction may strongly impact the interplay between neutral and selective genetic variation in populations. Using a physiologically structured model of the life history of Daphnia, we investigated to what extent clonal erosion associated with selection during the clonal phase affects the genetic structure as observed by neutral markers. Incorporating conservative levels of quantitative genetic variation at 11 physiological and life history traits induces strong clonal erosion, reducing clonal diversity (CD) near the end of the simulations (1000 days) to a level b...
Source: Journal of Evolutionary Biology - March 19, 2010 Category: Biology Authors: J. VANOVERBEKE, L. DE MEESTER Source Type: journals

Parasites and deleterious mutations: interactions influencing the evolutionary maintenance of sexEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The restrictive assumptions associated with purely genetic and purely ecological mechanisms suggest that neither of the two forces, in isolation, can offer a general explanation for the evolutionary maintenance of sex. Consequently, attention has turned to pluralistic models (i.e. models that apply both ecological and genetic mechanisms). Existing research has shown that combining mutation accumulation and parasitism allows restrictive assumptions about genetic and parasite parameter values to be relaxed while still predicting the maintenance of sex. However, several empirical studies have shown that deleterious mutations ...
Source: Journal of Evolutionary Biology - March 19, 2010 Category: Biology Authors: A. W. PARK, J. JOKELA, Y. MICHALAKIS Source Type: journals

Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic BacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Author Summary Chemotaxis of bacteria plays an important role in their life, providing them with the ability to actively search for an optimal growth environment. The chemotaxis system is supposed to be highly optimized, because on the evolutionary time scale even a modest enhancement of its efficiency can give cells a large competitive advantage. For a long time it was believed that the only navigation mechanism of bacteria is increasing the run length toward the preferred direction. The tumble was assumed to be a purely random change of direction between runs. We analysed recently published experimental data that demons...
Source: PLoS Computational Biology - March 19, 2010 Category: Biology Authors: Nikita Vladimirov et al. Source Type: journals