Molecular Biology
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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 14.
A strategy to discover inhibitors of Bacillus subtilis surfactin-type phosphopantetheinyl transferase
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Adam Yasgar, Timothy Foley, Ajit Jadhav, James Inglese, Michael Burkart, Anton Simeonov
(Paper from Mol. BioSyst.)
Adam Yasgar, Mol. BioSyst., 2010, DOI: 10.1039/b913291k
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The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Mol. BioSyst. latest articles - October 12, 2009 Category: Molecular Biology Authors: Adam YasgarTimothy Foley Ajit Jadhav James Inglese Michael Burkart Anton Simeonov Source Type: journals
Thermal melting studies of alkyne- and ferrocene-containing PNA bioconjugatesEmail this article to a colleague.
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Anna M. Sosniak, Gilles Gasser, Nils Metzler-Nolte
(Paper from Org. Biomol. Chem.)
Anna M. Sosniak, Org. Biomol. Chem., 2009, DOI: 10.1039/b913964h
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Source: RSC - Organic Biomolecular Chemistry - October 12, 2009 Category: Molecular Biology Authors: Anna M. SosniakGilles Gasser Nils Metzler-Nolte Source Type: journals
Synthesis and characterization of coumarin-based europium complexes and luminescence measurements in aqueous mediaEmail this article to a colleague.
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Clementine Feau, Emmanuel Klein, Carsten Dosche, Paul Kerth, Luc Lebeau
(Paper from Org. Biomol. Chem.)
Clementine Feau, Org. Biomol. Chem., 2009, DOI: 10.1039/b907579h
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Source: RSC - Organic Biomolecular Chemistry - October 12, 2009 Category: Molecular Biology Authors: Clementine FeauEmmanuel Klein Carsten Dosche Paul Kerth Luc Lebeau Source Type: journals
Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomesEmail this article to a colleague.
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Conclusions:
The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.
Source: BMC Evolutionary Biology - Latest articles - October 12, 2009 Category: Molecular Biology Authors: Eve GazavePascal LapebieGemma RichardsFrederic BrunetAlexander EreskovskyBernard DegnanCarole BorchielliniMichel VervoortEmmanuelle Renard Source Type: journals
How to identify essential genes from molecular networks?Email this article to a colleague.
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Conclusions:
The method reported here describes a reliable procedure to predict essential genes from molecular networks. Our results show that essential genes may be predicted only by combining centrality measures, revealing the complex nature of the function of essential genes.
Source: BMC Systems Biology - Latest articles - October 12, 2009 Category: Molecular Biology Authors: Gabriel del RioDirk KoschutzkiGerardo Coello Source Type: journals
Morphine modulation of pain processing in medial and lateral pain pathwaysEmail this article to a colleague.
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Conclusions:
These results suggest that morphine exerts analgesic effects through suppressing both sensory and affective dimensions of pain.
Source: Molecular Pain - October 12, 2009 Category: Molecular Biology Authors: Jin-Yan WangJin HuangJing-Yu ChangDonald WoodwardFei Luo Source Type: journals
Synthesis and application of a new cleavable linker for "click"-based affinity chromatographyEmail this article to a colleague.
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Felicetta Landi, Conny M. Johansson, Dominic J. Campopiano, Alison N. Hulme
(Communication from Org. Biomol. Chem.)
Felicetta Landi, Org. Biomol. Chem., 2010, DOI: 10.1039/b916693a
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Source: RSC - Organic Biomolecular Chemistry - October 12, 2009 Category: Molecular Biology Authors: Felicetta LandiConny M. Johansson Dominic J. Campopiano Alison N. Hulme Source Type: journals
Synthesis and stereochemical determination of batzelladine C methyl esterEmail this article to a colleague.
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Michael Butters, Christopher D. Davies, Mark C. Elliott, Joseph Hill-Cousins, Benson M. Kariuki, Li-ling Ooi, John L. Wood, Stuart V. Wordingham
(Paper from Org. Biomol. Chem.)
Michael Butters, Org. Biomol. Chem., 2009, DOI: 10.1039/b914744f
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Source: RSC - Organic Biomolecular Chemistry - October 12, 2009 Category: Molecular Biology Authors: Michael ButtersChristopher D. Davies Mark C. Elliott Joseph Hill-Cousins Benson M. Kariuki Li-ling Ooi John L. Wood Stuart V. Wordingham Source Type: journals
Four loci differentially expressed in muscle tissue depending on water-holding capacity are associated with meat quality in commercial pig herds.Email this article to a colleague.
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Four genes, VTN, KERA, LYZ, and a non-annotated EST (Affymetrix probe set ID: Ssc.25503.1.S1_at), whose candidacy for traits related to water-holding capacity of meat arises from their trait-dependent differential expression, were selected for candidate gene analysis. Based on in silico analysis SNPs were detected, confirmed by sequencing and used to genotype animals of 4 pig populations including 3 commercial herds of Pietrain (PI), Pietrain x (German Large White x German Landrace) (PIF1), German Landrace (DL) and 1 experimental F(2) population Duroc x Pietrain (DUPI). Comparative and genetic mapping established the l...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Srikanchai T, Murani E, Wimmers K, Ponsuksili S Tags: Mol Biol Rep Source Type: journals
Molecular cloning, expression and subcellular distribution of an alternative splice variant of the porcine Sirt2 gene.Email this article to a colleague.
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Sirt2, a NAD(+)-dependent histone deacetylase, plays a critical role in regulating lifespan, metabolism, mitosis and adipocyte differentiation. Here two bands of the porcine Sirt2 protein were found by western blotting, so we speculated existence of Sirt2 isoforms. Next, we cloned the porcine Sirt2 gene, and also found its alternative splice variant and named the novel splicing variant Sirt2(T). The complete cDNA sequence of Sirt2(T) is 1059 bp, encoding a deduced protein of 352 amino acids which is 39 amino acids shorter at the N-terminus than Sirt2. RT-PCR revealed that the Sirt2(T) mRNA is extensively expressed in p...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Liu B, Liu F, Bai L, Li Y, Yang G Tags: Mol Biol Rep Source Type: journals
Recombinant human elafin protects airway epithelium integrity during inflammation.Email this article to a colleague.
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Elafin, an antiprotease, is likely to protect pulmonary epithelial cells from inflammatory damages. We aimed to explore the molecule mechanisms of recombinant human elafin on protecting A549 cells integrity against inflammatory assault. We transfected A549 airway epithelial cells with eukaryotic expression vector pEGFP-N1-Elafin and negative control vector pEGFP-N1, respectively. Cells were co-incubated with polymorphonuclear neutrophils (PMN) and then were stimulated with lipopolysaccharide (LPS). Results revealed that, in pEGFP-N1-Elafin transfected cells, neutrophil elastase (NE) activity significantly decreased aft...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Li Q, Zhou XD, Xu XY, Yang J Tags: Mol Biol Rep Source Type: journals
Population genetic analysis of 6 Y-STR loci in Chinese northwestern Qinchuan yellow cattle breed.Email this article to a colleague.
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Six Y-STR loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404 and UMN0103) were analyzed using 576 healthy and unrelated males and 10 females of the Qinchuan cattle population in Chinese Shaanxi Province. Allele frequency, gene diversity, the polymorphic information content, and the number of effective gene were calculated. All loci were in accordance with the Hardy-Weinberg equilibrium (P > 0.05). The population data were compared with published data of other cattle breeds, suggesting that Qinchuan cattle were originated primarily from Bos Taurus. Results are valuable for individual identification, paternity testing,...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Xin Y, Zan L, Liu Y, Liu H, Tian W, Fan Y, Huang L Tags: Mol Biol Rep Source Type: journals
Fas inhibition attenuates lipopolysaccharide-induced apoptosis and cytokine release of rat type II alveolar epithelial cells.Email this article to a colleague.
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In conclusion, inhibition of Fas can diminish LPS-induced apoptosis and inflammatory cytokine production in type II AECs, and Fas specific siRNAs may have therapeutic potentials for intervention of ALI/ARDS.
PMID: 19823951 [PubMed - as supplied by publisher]
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Ma X, Xu D, Ai Y, Ming G, Zhao S Tags: Mol Biol Rep Source Type: journals
The common variant in the GSTM1 and GSTT1 genes is related to markers of oxidative stress and inflammation in patients with coronary artery disease: a case-only study.Email this article to a colleague.
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Recent studies suggest that the common variant in the GSTM1 and GSTT1 genes modifies the risk of coronary artery disease (CAD), however, it is unclear whether the risk of CAD modulated by variants in the GSTM1 and GSTT1 genes was associated with alterations of indices of oxidative stress and inflammation. Our study is an attempt to provide insight into the role of GST genetic variant and markers of oxidative stress and inflammation in CAD patients. A total of 719 Chinese CAD patients were successfully genotyped. Plasma total antioxidant status (TAOS), glutathione(GSH), C-reactive protein (CRP), fibrinogen (FIB) and whi...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Tang JJ, Wang MW, Jia EZ, Yan JJ, Wang QM, Zhu J, Yang ZJ, Lu X, Wang LS Tags: Mol Biol Rep Source Type: journals
Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences.Email this article to a colleague.
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The complete nucleotide sequence of mitochondrial genome of the Great bustard (Otis tarda) was determined by using polymerase chain reaction (PCR) method. The genome is 16,849 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. Sequences of the tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA-Cys and tRNA-Ser (AGY), which lose "DHU" arm. Sequence analysis showed that the O. tarda mitochondrial control region (mtCR) contained many elements in common with other avian mtCRs. A microsatellite repeat was found in the 3'-peripheral domain of the O. tarda mtCR...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Yang R, Wu X, Yan P, Su X, Yang B Tags: Mol Biol Rep Source Type: journals
Optimized procedure for expression and renaturation of recombinant human bone morphogenetic protein-2 at high protein concentrations.Email this article to a colleague.
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A prokaryotic expression system has been used to produce recombinant human bone morphogenetic protein-2 (rhBMP-2). However, low rhBMP-2 yields and protein loss during purification and renaturation are the hurdles in the clinical application. Previous studies have indicated that variables such as temperature, host cell, salt concentration, and culture time affect the final rhBMP-2 yield. The optimization of these conditions in an Escherichia coli culture yielded 28.258 mg of rhBMP-2 per liter of culture. To reduce rhBMP-2 loss during purification and renaturation, we performed purification before renaturation in the pro...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Zhang H, Wu J, Zhang Y, Fu N, Wang J, Zhao S Tags: Mol Biol Rep Source Type: journals
The interaction of lysozyme with caffeine, theophylline and theobromine in solution.Email this article to a colleague.
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The interactions of lysozyme with caffeine (Caf), theophylline (Tph) and theobromine (Tbr) were investigated using UV-Vis absorption, fluorescence, synchronous fluorescence, and three-dimensional fluorescence spectra techniques. The results revealed that Caf (Tph or Tbr) caused the fluorescence quenching of lysozyme by the formation of Caf (Tph or Tbr)-lysozyme complex. The binding constants (K (A)) and thermodynamic parameters (DeltaG degrees , DeltaH degrees , DeltaS degrees ) at two different temperatures, the binding locality, and the binding power were obtained. The results showed that the process of binding Caf (...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Zhang HM, Tang BP, Wang YQ Tags: Mol Biol Rep Source Type: journals
PriA participates in nascent DNA synthesis in Escherichia coli.Email this article to a colleague.
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In this study, the participation of priA, B, C and rep genes in discontinuous DNA replication was examined by analyzing the size distribution of nascent DNA synthesized in wild-type, lig-7 and polA4113 genetic backgrounds. Inactivation of priA, but not priB, priC or rep, resulted in a significant increase of high molecular weight (HMW) DNA in the short pulse-labeled DNA in the wild-type lig ( + ) polA ( + ) strains. Inactivation of priA also produced a significant increase of HMW DNA in the nascent DNA synthesized in lig-7 and polA4113 strains. These results indicate that PriA is involved in the discontinuous synthesis of ...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Chen YY, Huang H, Wang TC Tags: Mol Biol Rep Source Type: journals
Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.).Email this article to a colleague.
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MicroRNAs (miRNAs) are a class of non-protein coding small RNAs that regulate expression of genes at post-transcriptional levels. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation and apoptosis. Based on the conservation of miRNAs sequence, using a computational homology search based on genomic survey sequence analysis, a total of 16 novel miRNAs were identified and characteristics such as family and evolutionary conservation have been described. By using these newly identified miRNAs, the mRNA database of silkworm was blasted and 21 potenti...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Huang Y, Zou Q, Tang SM, Wang LG, Shen XJ Tags: Mol Biol Rep Source Type: journals
A structurally novel salt-regulated promoter of duplicated carbonic anhydrase gene 1 from Dunaliella salina.Email this article to a colleague.
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In this study, the results of real time RT-PCR showed that the transcripts of DCA1 were induced by gradient concentration of sodium chloride. Subsequently, a structurally novel promoter containing highly repeated GT/AC sequences of the DCA1 gene was isolated, which was able to drive a stable expression of the foreign bar gene in transformed cells of D. salina, and the gradient concentrations of sodium chloride in media paralleled regulations in the levels of both proteins and mRNA of the bar gene driven by the DCA1 promoter. Furthermore, analysis of GUS activities revealed that the salt-inducible expression of the external...
Source: Molecular Biology Reports - October 12, 2009 Category: Molecular Biology Authors: Li J, Lu Y, Xue L, Xie H Tags: Mol Biol Rep Source Type: journals
Sesamin attenuates behavioral, biochemical and histological alterations induced by reversible middle cerebral artery occlusion in the rats.Email this article to a colleague.
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Restoration of blood flow to an ischemic brain region is associated with generation of reactive oxygen species (ROS) with consequent reperfusion injury. ROS cause lipid peroxidation, protein oxidation, and DNA damage, all of which are deleterious to cells. So diminishing the production of free radicals and scavenging them may be a successful therapeutic strategy for the protection of brain tissue in cerebral stroke. The present study investigated the neuroprotective effect of sesamin (Sn) to reduce brain injury after middle cerebral artery occlusion (MCAO). The middle cerebral artery (MCA) of adult male Wistar rat was ...
Source: Chemico-Biological Interactions - October 12, 2009 Category: Molecular Biology Authors: Khan MM, Ishrat T, Ahmad A, Hoda MN, Khan MB, Khuwaja G, Srivastava P, Raza SS, Islam F Tags: Chem Biol Interact Source Type: journals
Pistillata--Duplications as a Mode for Floral Diversification in (Basal) AsteridsEmail this article to a colleague.
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Basal asterid families, and to a lesser extent the asterids as a whole, are characterized by a high variation in petal and stamen morphology. Moreover, the stamen number, the adnation of stamens to petals, and the degree of sympetaly vary considerably among basal asterid taxa. The B group genes, members of the APETALA3 (AP3) and PISTILLATA (PI) gene lineages, have been shown to specify petal and stamen identities in several core eudicot species. Duplicate genes in these lineages have been shown in some cases to have diversified in their function; for instance in Petunia, a PI paralog is required for the fusion of stamens t...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Viaene, T., Vekemans, D., Irish, V. F., Geeraerts, A., Huysmans, S., Janssens, S., Smets, E., Geuten, K. Tags: Research Articles Source Type: journals
Age-Related Accumulation of Mutations Supports a Replication-Dependent Mechanism of Spontaneous Mutation at Tandem Repeat DNA Loci in MiceEmail this article to a colleague.
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Expanded simple tandem repeat (ESTR) loci belong to the class of highly unstable loci in the mouse genome. The mechanisms underlying the very high spontaneous instability at these loci still remain poorly understood. Using single-molecule polymerase chain reaction, here we have compared the pattern of mutation accumulation in tissues with different proliferation capacities in male mice of age 12, 26, 48, and 96 weeks. In the nonproliferating brain, we did not observe any measurable age-related accumulation of ESTR mutations. In contrast, a highly elevated frequency of ESTR mutation was detected in the sperm samples taken f...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hardwick, R. J., Tretyakov, M. V., Dubrova, Y. E. Tags: Research Articles Source Type: journals
Population Genomics of the Arabidopsis thaliana Flowering Time Gene NetworkEmail this article to a colleague.
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The time to flowering is a key component of the life-history strategy of the model plant Arabidopsis thaliana that varies quantitatively among genotypes. A significant problem for evolutionary and ecological genetics is to understand how natural selection may operate on this ecologically significant trait. Here, we conduct a population genomic study of resequencing data from 52 genes in the flowering time network. McDonald–Kreitman tests of neutrality suggested a strong excess of amino acid polymorphism when pooling across loci. This excess of replacement polymorphism across the flowering time network and a skewed de...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Flowers, J. M., Hanzawa, Y., Hall, M. C., Moore, R. C., Purugganan, M. D. Tags: Research Articles Source Type: journals
Evolution and Biochemistry of Family 4 Glycosidases: Implications for Assigning Enzyme Function in Sequence AnnotationsEmail this article to a colleague.
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This study emphasizes the importance of automatic annotation systems that by integrating phylogenetic analysis, functional motifs, and bioinformatics data, may lead to innovative experiments that further our understanding of biological systems.
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hall, B. G., Pikis, A., Thompson, J. Tags: Research Articles Source Type: journals
Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora liniEmail this article to a colleague.
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Genetic variation for pathogen infectivity is an important driver of disease incidence and prevalence in both natural and managed systems. Here, we use the interaction between the rust pathogen, Melampsora lini, and two host plants, Linum marginale and Linum usitatissimum, to examine how host–pathogen interactions influence the maintenance of polymorphism in genes underlying pathogen virulence. Extensive sequence variation at two effector loci (AvrP123, AvrP4) was found in M. lini isolates collected from across the native range of L. marginale in Australia, as well as in isolates collected from a second host, the cul...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Barrett, L. G., Thrall, P. H., Dodds, P. N., van der Merwe, M., Linde, C. C., Lawrence, G. J., Burdon, J. J. Tags: Research Articles Source Type: journals
The Evolutionary Rates of Eukaryotic RNA Polymerases and of Their Transcription Factors Are Affected by the Level of Concerted Evolution of the Genes They TranscribeEmail this article to a colleague.
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A defining characteristic of all eukaryotes is the presence of three RNA polymerases, each of which transcribes a particular subset of nuclear genes. RNA polymerase I transcribes rRNA genes; RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes; and RNA polymerase III transcribes 5S rRNA and tRNA genes. Here, we use the sequences of up to 25 Ascomycete species to show that the type of genes transcribed by each RNA polymerase affects their evolutionary rates and those of their transcription factors (TFs). The RNA polymerase subunits and TFs of genes whose promoters experience higher levels of concerted evolutio...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Carter, R., Drouin, G. Tags: Research Articles Source Type: journals
Evolution of Duplicated {beta}-Globin Genes and the Structural Basis of Hemoglobin Isoform Differentiation in MusEmail this article to a colleague.
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The functional diversification of multigene families may be strongly influenced by mechanisms of concerted evolution such as interparalog gene conversion. The β-globin gene family of house mice (genus Mus) represents an especially promising system for evaluating the effects of gene conversion on the functional divergence of duplicated genes. Whereas the majority of mammalian species possess tandemly duplicated copies of the adult β-globin gene that are identical in sequence, natural populations of house mice are often polymorphic for distinct two-locus haplotypes that differ in levels of functional divergence bet...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Runck, A. M., Moriyama, H., Storz, J. F. Tags: Research Articles Source Type: journals
Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene ExpressionEmail this article to a colleague.
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We examined whether genes regulated by a single transcription factor (TF; single input module, SIM genes) or genes regulated by multiple TFs (multiple input module, MIM genes) are more susceptible to trans variation. Because a SIM gene is regulated by a single immediate upstream TF, the chance for a change to occur in its trans-acting factors would, on average, be smaller than that for a MIM gene. We chose 232 genes that exhibited expression divergence between BY and RM to test this hypothesis. We examined the expression patterns of these genes in a BY–RM coculture system and in a BY–RM diploid hybrid. We found...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Sung, H.-M., Wang, T.-Y., Wang, D., Huang, Y.-S., Wu, J.-P., Tsai, H.-K., Tzeng, J., Huang, C.-J., Lee, Y.-C., Yang, P., Hsu, J., Chang, T., Cho, C.-Y., Weng, L.-C., Lee, T.-C., Chang, T.-H., Li, W.-H., Shih, M.-C. Tags: Research Articles Source Type: journals
Dynamic Evolution of Immune System Regulators: The History of the Interferon Regulatory Factor FamilyEmail this article to a colleague.
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This manuscript presents the first extensive phylogenetics analysis of a key family of immune regulators, the interferon regulatory factor (IRF) family. The IRF family encodes transcription factors that play important roles in immune defense, stress responses, reproduction, development, and carcinogenesis. Several times during their evolution, the IRF genes have undergone expansion and diversification. These genes were also completely lost on two separate occasions in large groups of metazoans. The origin of the IRF family coincides with the appearance of multicellularity in animals. IRF genes are present in all principal ...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Nehyba, J., Hrdlickova, R., Bose, H. R. Tags: Research Articles Source Type: journals
Self-Recognition and Ca2+-Dependent Carbohydrate-Carbohydrate Cell Adhesion Provide Clues to the Cambrian ExplosionEmail this article to a colleague.
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The Cambrian explosion of life was a relatively short period approximately 540 Ma that marked a generalized acceleration in the evolution of most animal phyla, but the trigger of this key biological event remains elusive. Sponges are the oldest extant Precambrian metazoan phylum and thus a valid model to study factors that could have unleashed the rise of multicellular animals. One such factor is the advent of self-/non–self-recognition systems, which would be evolutionarily beneficial to organisms to prevent germ-cell parasitism or the introduction of deleterious mutations resulting from fusion with genetically diff...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Fernandez-Busquets, X., Kornig, A., Bucior, I., Burger, M. M., Anselmetti, D. Tags: Research Articles Source Type: journals
Positive Selection and Gene Conversion Drive the Evolution of a Brain-Expressed snoRNAs ClusterEmail this article to a colleague.
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HBII-52 small nucleolar RNAs (snoRNAs) are brain-expressed posttranscriptional modifiers of serotonin receptor 2C RNA. They are organized in a cluster of 47 highly homologous gene copies spanning 100 kb at chromosome 15q11.2. Nucleotide diversity at HBII-52 snoRNA gene cluster in African and European descent populations was analyzed via resequencing of 25 functional snoRNA gene copies. Ninety-four variants were detected, from which 74 are novel. Only 16 variants are shared between Africans and Europeans. We also report a novel Yoruba-specific copy-number variant representing a 5.2-kb polymorphic deletion and resulting in a...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Ogorelkova, M., Navarro, A., Vivarelli, F., Ramirez-Soriano, A., Estivill, X. Tags: Research Articles Source Type: journals
Alu-Mediated Acquisition of Unstable ATTCT Pentanucleotide Repeats in the Human ATXN10 GeneEmail this article to a colleague.
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Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into ATXN10 intron 9; Alu was then inserted in the middle of LINE-1; and endogenous retrovilcus K was lastly retrotransposed in the middle of Alu. The ATTCT repeat was located on the boundary between the 3'-end of the Alu element and the direct repeat arising from LINE-1. We determined nucleotide sequences of the or...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Kurosaki, T., Matsuura, T., Ohno, K., Ueda, S. Tags: Research Articles Source Type: journals
Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0Email this article to a colleague.
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Sequence simulation is an important tool in validating biological hypotheses as well as testing various bioinformatics and molecular evolutionary methods. Hypothesis testing relies on the representational ability of the sequence simulation method. Simple hypotheses are testable through simulation of random, homogeneously evolving sequence sets. However, testing complex hypotheses, for example, local similarities, requires simulation of sequence evolution under heterogeneous models. To this end, we previously introduced indel-Seq-Gen version 1.0 (iSGv1.0; indel, insertion/deletion). iSGv1.0 allowed heterogeneous protein evo...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Strope, C. L., Abel, K., Scott, S. D., Moriyama, E. N. Tags: Research Articles Source Type: journals
Quantitative Prediction of Molecular Clock and Ka/Ks at Short TimescalesEmail this article to a colleague.
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Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged recently. Using the Moran model, we calculate expected divergence as a function of time. Our findings suggest that the observed phenomenon of elevated rates at short timescales is consistent with standard population genetics theory. The apparent acceleration of the molecular clock at short timescales can be explained by segregating polymorphisms present at the time of the ancestral population, both neutral and slightly deleterious, and not newly arising slightly deleterious mutat...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Peterson, G. I., Masel, J. Tags: Research Articles Source Type: journals
Reconciling Ecological and Genomic Divergence among Lineages of Listeria under an "Extended Mosaic Genome Concept"Email this article to a colleague.
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There is growing evidence for a discontinuity between genomic and ecological divergence in several groups of bacteria. This evidence is difficult to reconcile with the traditional concept that ecologically divergent species maintain a cohesive gene pool isolated from other gene pools by barriers to homologous recombination (HR). There have been several innovative models of bacterial divergence that permit such discontinuity; we refer to these, collectively, as "mosaic genome concepts" (MGCs). These concepts remain a point of contention. Here, we undertake an investigation among ecologically divergent lineages of genus List...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Dunn, K. A., Bielawski, J. P., Ward, T. J., Urquhart, C., Gu, H. Tags: Research Articles Source Type: journals
Cross-Sectional Dating of Novel Haplotypes of HERV-K 113 and HERV-K 115 Indicate These Proviruses Originated in Africa before Homo sapiensEmail this article to a colleague.
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The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in A...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Jha, A. R., Pillai, S. K., York, V. A., Sharp, E. R., Storm, E. C., Wachter, D. J., Martin, J. N., Deeks, S. G., Rosenberg, M. G., Nixon, D. F., Garrison, K. E. Tags: Research Articles Source Type: journals
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Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Cover Source Type: journals
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Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
Functioning and Evolutionary Significance of Nutrient TransceptorsEmail this article to a colleague.
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The discovery of nutrient transceptors, transporter-like proteins with a receptor function, suggests that receptors for chemical signals may have been derived in evolution from nutrient transporters. Several examples are now available of nutrient transporters with an additional nutrient signaling function, nutrient receptors with a transporter-like sequence and structure but without transport capacity, and G protein–coupled receptors (GPCRs) that have nutrients as ligands. Recent results have revealed that transceptor signaling requires a specific ligand-induced conformational change, which indicates that transceptor...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Thevelein, J. M., Voordeckers, K. Tags: Review Source Type: journals
Peeling the Onion: Ribosomes Are Ancient Molecular FossilsEmail this article to a colleague.
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We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion, using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation combined with a shell-by-shell comparison captures significant information along the evolutionary time line reve...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hsiao, C., Mohan, S., Kalahar, B. K., Williams, L. D. Tags: Research Articles Source Type: journals
Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)Email this article to a colleague.
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We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1–15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Jackson, J. A., Baker, C. S., Vant, M., Steel, D. J., Medrano-Gonzalez, L., Palumbi, S. R. Tags: Research Articles Source Type: journals
Metabolic Adaptation after Whole Genome DuplicationEmail this article to a colleague.
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Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and metabolic adaptation after WGD. Using the metabolic network of Saccharomyces cerevisiae as an example, we primarily study the outcome of WGD on yeast as it currently is. However, similar results were obtained using a recontructed hypothetical metabolic network of the pre-WGD ancestor. We show that the retention ...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: van Hoek, M. J. A., Hogeweg, P. Tags: Research Articles Source Type: journals
Temporal Constraints on the Incorporation of Regulatory Mutants in Evolutionary PathwaysEmail this article to a colleague.
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Understanding the molecular details of the sequence of events in multistep evolutionary pathways can reveal the extent to which natural selection exploits regulatory mutations affecting expression, amino acid replacements affecting the active site, amino acid replacements affecting protein folding or stability, or variations affecting gene copy number. In experimentally exploring the adaptive landscape of the evolution of resistance to β-lactam antibiotics in enteric bacteria, we noted that a regulatory mutation that increases β-lactamase expression by about 2-fold has a very strong tendency to be fixed at or nea...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Brown, K. M., DePristo, M. A., Weinreich, D. M., Hartl, D. L. Tags: Research Articles Source Type: journals
MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian SelectionEmail this article to a colleague.
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The Chinese lantern, which is the inflated calyx syndrome (ICS) of Physalis, is formed by MPF2 in the presence of the plant hormones, cytokinin and gibberellin. MPF2 knockdown mutants of Physalis have small leaves, no ICS, and are male sterile, thus, revealing three MPF2-related functions. Of the close relatives of Physalis, Tubocapsicum has only a rudimentary calyx, whereas others, like the Withania species, have ICS. From all Withania samples tested, two classes of MPF2-like orthologs, MPF2-like-A and MPF2-like-B, were isolated, whereas only the latter class was obtained from tetraploid Tubocapsicum. Though distinct diff...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Khan, M. R., Hu, J.-Y., Riss, S., He, C., saedler, H. Tags: Research Articles Source Type: journals
Emerging investigators 2009Email this article to a colleague.
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(Profile from Mol. BioSyst.)
Mol. BioSyst., 2009, DOI: 10.1039/b919131n
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Source: RSC - Mol. BioSyst. latest articles - October 11, 2009 Category: Molecular Biology Authors: RSC Source Type: journals
The potential of microfluidic water-in-oil droplets in experimental biologyEmail this article to a colleague.
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Yolanda Schaerli, Florian Hollfelder
(Review from Mol. BioSyst.)
Yolanda Schaerli, Mol. BioSyst., 2009, DOI: 10.1039/b907578j
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Source: RSC - Mol. BioSyst. latest articles - October 11, 2009 Category: Molecular Biology Authors: Yolanda SchaerliFlorian Hollfelder Source Type: journals
Component match in rhodium catalyzed three-component reactions of ethyl diazoacetate, H2O and aryl imines: a highly diastereoselective one-step synthesis of [small beta]-aryl isoserine derivativesEmail this article to a colleague.
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Zhenqiu Guo, Taoda Shi, Jun Jiang, Liping Yang, Wenhao Hu
(Paper from Org. Biomol. Chem.)
Zhenqiu Guo, Org. Biomol. Chem., 2009, DOI: 10.1039/b915013g
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Source: RSC - Organic Biomolecular Chemistry - October 11, 2009 Category: Molecular Biology Authors: Zhenqiu GuoTaoda Shi Jun Jiang Liping Yang Wenhao Hu Source Type: journals
