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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 4.

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Fem1b, a proapoptotic protein, mediates proteasome inhibitor-induced apoptosis of human colon cancer cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, the proapoptotic protein Fem1b is downregulated by the proteasome in malignant colon cancer cells and mediates proteasome inhibitor-induced apoptosis of these cells. Therefore, Fem1b could represent a novel molecular target to overcome apoptosis resistance in therapy of colon cancer. © 2009 Wiley-Liss, Inc.
Source: Molecular Carcinogenesis - November 11, 2009 Category: Molecular Biology Authors: M. Cecilia Subauste, Owen J. Sansom, Nehal Porecha, Natacha Raich, Liqin Du, Joseph F. Maher Source Type: journals

Silibinin inhibits human nonsmall cell lung cancer cell growth through cell-cycle arrest by modulating expression and function of key cell-cycle regulatorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent studies show that silibinin possesses a strong antineoplastic potential against many cancers; however, its efficacy and underlying molecular mechanisms in nonsmall cell lung cancer (NSCLC) are not well defined. Herein, we assessed silibinin activity on prime endpoints and key molecular targets such as cell number, cell-cycle progression, and cell-cycle regulatory molecules in three cell lines representing different NSCLC subtypes, namely large cell carcinoma cells (H1299 and H460) and a bronchioalveolar carcinoma cell line (H322). Silibinin treatment (10-75 µM) inhibited cell growth and targeted cell-cycle progress...
Source: Molecular Carcinogenesis - November 11, 2009 Category: Molecular Biology Authors: Samiha Mateen, Alpna Tyagi, Chapla Agarwal, Rana P. Singh, Rajesh Agarwal Source Type: journals

The tumor suppressor parafibromin is required for posttranscriptional processing of histone mRNAEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we identify a novel role of parafibromin in the regulation of replication-dependent histones. Both in vitro and in vivo analyses reveal a posttranscriptional role of parafibromin in histone mRNA processing. Downregulation of parafibromin through RNA interference or in vivo mutations lead to uncleaved histone mRNA with polyadenylated tails. These results indicate that parafibromin regulates the 3[prime] processing of histone RNA, an essential component of the cell cycle. © 2009 Wiley-Liss, Inc.
Source: Molecular Carcinogenesis - November 11, 2009 Category: Molecular Biology Authors: Leslie J. Farber, Eric J. Kort, PengFei Wang, Jindong Chen, Bin T. Teh Source Type: journals

The role of astrocyte-secreted matricellular proteins in central nervous system development and function.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Matricellular proteins, such as thrombospondins (TSPs1-4), SPARC, SPARC-like1 (hevin) and tenascin C are expressed by astrocytes in the central nervous system (CNS) of rodents. The spatial and temporal expression patterns of these proteins suggest that they may be involved in important developmental processes such as cell proliferation and maturation, cell migration, axonal guidance and synapse formation. In addition, upon injury to the nervous system the expression of these proteins is upregulated, suggesting that they play a role in tissue remodeling and repair in the adult CNS. The genes encoding these proteins have...
Source: Journal of Cell Communication and Signaling - November 11, 2009 Category: Molecular Biology Authors: Eroglu C Tags: J Cell Commun Signal Source Type: journals

Apoptosis Induction in Human Leukemic Cells by a Novel Protein Bengalin, Isolated from Indian Black Scorpion Venom: through Mitochondrial Pathway and Inhibition of Heat Shock Proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Scorpion venom possesses protein toxins having numerous biological activities, some of which are potentially anticancerous. Previously we had reported antiproliferative activity of the venom of Indian black scorpion, Heterometrus bengalensis Koch. Here we have isolated and purified a novel protein named Bengalin (72kD) from the venom, responsible for antiproliferative and apoptogenic activities against human leukemic cells U937 (histiocytic lymphoma) and K562 (chronic myelogenous leukemia). N-terminal sequence of first 20 amino acids of Bengalin was G-P-L-T-I-L-H-I-N-D-V-H-A-A/R-F-E-Q/G-F/G-N-T. Bengalin induced cell g...
Source: Chemico-Biological Interactions - November 11, 2009 Category: Molecular Biology Authors: Gupta SD, Gomes A, Debnath A, Saha A, Gomes A Tags: Chem Biol Interact Source Type: journals

Benzene-Initiated Oxidative Stress: Effects on Embryonic Signaling Pathways.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Approximately 90% of childhood cancers are of unknown etiology; however, it is hypothesized that in utero carcinogen exposure may contribute. Epidemiological studies have correlated parental exposure to benzene with an increased incidence of childhood leukemias. However, mechanisms of benzene-induced carcinogenesis following in utero exposure remain unknown. We hypothesize that in utero exposure to benzene causes alterations in the redox sensitive signaling pathways involving c-Myb, Pim-1, AKT, ERK-MAPK, p38-MAPK, and NF-kappaB via the production of reactive oxygen species (ROS) as a possible mechanism of in utero init...
Source: Chemico-Biological Interactions - November 11, 2009 Category: Molecular Biology Authors: Badham HJ, Renaud SJ, Wan J, Winn L Tags: Chem Biol Interact Source Type: journals

Dual oxidases and hydrogen peroxide in a complex dialogue between host mucosae and bacteria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Among the host defense mechanisms against bacteria, leukocyte phagocytosis leads to their hydrogen peroxide (H(2)O(2))-mediated destruction. The recent discovery of dual oxidase (DUOX)-dependent H(2)O(2) generation associated with peroxidase and thiocyanate secretion at the apex of mucosal cells has been similarly interpreted as a killing mechanism. However, the rapid degradation of H(2)O(2) would be expected to reduce the efficiency of this system. It has been demonstrated that H(2)O(2) acts as a chemorepellent for bacteria, and such an effect might be sufficient to block cellular infection. Therefore, H(2)O(2) genera...
Source: Trends in Molecular Medicine - November 11, 2009 Category: Molecular Biology Authors: Allaoui A, Botteaux A, Dumont JE, Hoste C, De Deken X Tags: Trends Mol Med Source Type: journals

The cardiovascular unit as a dynamic player in disease and regeneration.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cell-mediated cardiac regeneration remains a challenge as a therapeutic option in heart failure, but modest success using experimental models suggests that a better understanding of normal histogenesis will be needed to make progress towards cardiac regeneration. Recent studies of the heart show that the interstitium informs organogenesis and responsiveness to pathological stimuli through continuous bidirectional cross-talk between cardiomyocytes and non-cardiac cells. Here, we introduce the concept of the "cardiovascular unit" (CVU) as a building block of the heart, which includes cardiomyocytes and adjacent capillari...
Source: Trends in Molecular Medicine - November 11, 2009 Category: Molecular Biology Authors: Ausoni S, Sartore S Tags: Trends Mol Med Source Type: journals

Hyaluronan oligosaccharides promote excisional wound healing through enhanced angiogenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we prepared a special slow-releasing gel that contains a mixture of defined size of o-HA and studied the healing effects of o-HA by topical application to an acute wound model. We report that o-HA complex promotes the repair of tissue injury of a murine excisional dermal wound. The therapy by o-HA was compared with high molecular weight HA (HMW-HA) and the known angiogenesis stimulator, VEGF. At days 6 to 8 after treatment, significant differences were seen in wound closure rates between o-HA and control or HMW-HA groups, in which o-HA showed an increased wound recovery. Histological analysis revealed that i...
Source: Matrix Biology - November 11, 2009 Category: Molecular Biology Authors: Gao F, Liu Y, He Y, Yang C, Wang Y, Shi X, Wei G Tags: Matrix Biol Source Type: journals

The human alpha11 integrin promoter drives fibroblast-restricted expression in vivo and is regulated by TGF-beta1 in a Smad- and Sp1-dependent manner.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Integrin alpha11beta1 is expressed by ectomesenchymally- and mesodermally- derived fibroblasts and is the major collagen receptor on embryonic fibroblasts. We have previously characterized a 3kb human alpha11 promoter region in vitro. In the current study we generated promoter-LacZ reporter transgenic mice to examine the ability of the 3kb alpha11 promoter to drive tissue-specific expression also in vivo. Our data show that the alpha11 promoter region that we have characterized contains most of the regulatory elements that direct ectomesenchymal and mesodermal fibroblast-specific expression. Not much is known about int...
Source: Matrix Biology - November 11, 2009 Category: Molecular Biology Authors: Lu N, Ranta J, Heuchel R, Soininen R, Gullberg D Tags: Matrix Biol Source Type: journals

Inhibition of peptidyl–prolyl cis/trans isomerase Pin1 induces cell cycle arrest and apoptosis in vascular smooth muscle cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study was undertaken to determine the in vitro effect of lentivirus-mediated siPin1 on cell cycle and apoptosis of vascular smooth muscle cells (VSMCs). Further we sought to provide insight into the mechanisms behind these processes. Human umbilical artery smooth muscle cells (HUASMCs) were transfected with lentiviral siPin1. Real-time RT–PCR and Western blotting were used to examine Pin1 mRNA and protein expression. MTT and [3H]thymidine incorporation assays were employed to observe cell proliferation status. The apoptotic rate and cell cycle were analyzed by Hoechst33258 staining and flow cytometry. Final...
Source: Apoptosis - November 10, 2009 Category: Molecular Biology Tags: Apoptosis Source Type: journals

Serum deprivation-induced reactive oxygen species production is mediated by Romo1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract Serum deprivation-triggered increases in reactive oxygen species (ROS) are known to induce apoptotic cell death. However, the mechanism by which serum deprivation causes ROS production is not known. Since mitochondria are the main source of ROS and since mitochondrial ROS modulator 1 (Romo1) is involved in ROS production, we sought to determine if serum deprivation triggered ROS production through Romo1. To examine the relationship between Romo1 and the serum deprivation-triggered increase in ROS, we transfected Romo1 siRNA into various cell lines and looked for inhibition of mitochondrial ROS gener...
Source: Apoptosis - November 10, 2009 Category: Molecular Biology Tags: Apoptosis Source Type: journals

Structural traces of past experience in the cerebral cortexEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract It is widely assumed that changes in the connections between neurons mediate the integration and storage of information in the brain and thereby underlie our ability to learn and remember. In particular, long-term memory is thought to rely on a structural reorganisation of neuronal circuits, but the proof for such a mechanism in the complex mammalian brain remains elusive. Recent advances in scientists' ability to follow structural dynamics of neuronal networks in the intact brain in vivo by means of 2-photon laser scanning microscopy has provided new insight into how information about new experienc...
Source: Journal of Molecular Medicine - November 10, 2009 Category: Molecular Biology Tags: Journal of Molecular Medicine Source Type: journals

AssociateEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals

EboardEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals

SubcriptionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals

CoverEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Cover Source Type: journals

Selection to Maintain Paralogous Amino Acid Differences Under the Pressure of Gene Conversion in the Heat-Shock Protein Genes in YeastEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A genome scan for the signatures of selection for paralogous functional amino acid differences was performed with yeast genomes. This recently developed method makes it possible to localize the target sites of selection under the pressure of gene conversion. We found that two gene pairs have strong signatures of selection. The two pairs of duplicated genes happened to be heat shock genes (Ssa1/ Ssa2 and Ssb1/Ssb2), which have similar protein structures to each other, although the amino acid sequence identity between Ssa and Ssb is not high (~60%). Interestingly, the two gene pairs exhibit signature of selection at almost i...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Takuno, S., Innan, H. Tags: Letter Source Type: journals

Transcription, Translation, and the Evolution of Specialists and GeneralistsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We used DNA microarrays to measure transcription and iTRAQ 2D liquid chromatography-mass spectrometry/mass spectrometry (a mass-tag labeling proteomic technique) to measure protein expression in 14 strains of Escherichia coli adapted for hundreds of generations to growth-limiting concentrations of either lactulose, methylgalactoside, or a 72:28 mixture of the two. The two ancestors, TD2 and TD10, differ only in their lac operons and have similar transcription and protein expression profiles. Changes in transcription and protein expression are observed at 30–250 genes depending on the evolved strain. Lactulose special...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Zhong, S., Miller, S. P., Dykhuizen, D. E., Dean, A. M. Tags: Research Articles Source Type: journals

Molecular Evolution of GYPC: Evidence for Recent Structural Innovation and Positive Selection in HumansEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
GYPC encodes two erythrocyte surface sialoglycoproteins in humans, glycophorin C and glycophorin D (GPC and GPD), via initiation of translation at two start codons on a single transcript. The malaria-causing parasite Plasmodium falciparum uses GPC as a means of invasion into the human red blood cell. Here, we examine the molecular evolution of GYPC among the Hominoidea (Greater and Lesser Apes) and also the pattern of polymorphism at the locus in a global human sample. We find an excess of nonsynonymous divergence among species that appears to be caused solely by accelerated evolution of GYPC in the human lineage. Moreover...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Wilder, J. A., Hewett, E. K., Gansner, M. E. Tags: Research Articles Source Type: journals

General Heterotachy and Distance Method AdjustmentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980–984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for eac...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Wu, J., Susko, E. Tags: Research Articles Source Type: journals

Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within OpisthokontaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The shared ancestry between Fungi and animals has been unequivocally demonstrated by abundant molecular and morphological data for well over a decade. Along with the animals and Fungi, multiple protists have been placed in the supergroup Opisthokonta making it exceptionally diverse. In an effort to place the cellular slime mold Fonticula alba, an amoeboid protist with aggregative, multicellular fruiting, we sequenced five nuclear encoded genes; small subunit ribosomal RNA, actin, beta-tubulin, elongation factor 1-alpha, and the cytosolic isoform of heat shock protein 70 for phylogenetic analyses. Molecular trees demonstrat...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Brown, M. W., Spiegel, F. W., Silberman, J. D. Tags: Research Articles Source Type: journals

Hemocyanin Suggests a Close Relationship of Remipedia and HexapodaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Remipedia are enigmatic crustaceans from anchialine cave systems, first described only 30 years ago, whose phylogenetic affinities are as yet unresolved. Here we report the sequence of hemocyanin from Speleonectes tulumensis Yager, 1987 (Remipedia, Speleonectidae). This is the first proof of the presence of this type of respiratory protein in a crustacean taxon other than Malacostraca. Speleonectes tulumensis hemocyanin consists of multiple distinct (at least three) subunits (StuHc1–3; Hc, hemocyanin). Surprisingly, the sequences are most similar to hexapod hemocyanins. Phylogenetic analyses showed that the S. tu...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Ertas, B., von Reumont, B. M., Wagele, J.-W., Misof, B., Burmester, T. Tags: Research Articles Source Type: journals

A Phylogenomic Approach to Resolve the Basal Pterygote DivergenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One of the most fascinating Bauplan transitions in the animal kingdom was the invention of insect wings, a change that also contributed to the success and enormous diversity of this animal group. However, the origin of insect flight and the relationships of basal winged insect orders are still controversial. Three hypotheses have been proposed to explain the phylogeny of winged insects: 1) the traditional Palaeoptera hypothesis (Ephemeroptera + Odonata, Neoptera), 2) the Metapterygota hypothesis (Ephemeroptera, Odonata + Neoptera), and 3) the Chiastomyaria hypothesis (Odonata, Ephemeroptera + Neoptera). Neither phylogeneti...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Simon, S., Strauss, S., von Haeseler, A., Hadrys, H. Tags: Research Articles Source Type: journals

Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary GenomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Next-generation sequencing has opened the door to genomic analysis of nonmodel organisms. Technologies generating long-sequence reads (200–400 bp) are increasingly used in evolutionary studies of nonmodel organisms, but the short-sequence reads (30–50 bp) that can be produced at lower cost are thought to be of limited utility for de novo sequencing applications. Here, we tested this assumption by short-read sequencing the transcriptomes of the tropical disease vectors Aedes aegypti and Anopheles gambiae, for which complete genome sequences are available. Comparison of our results to the reference genomes allowe...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Gibbons, J. G., Janson, E. M., Hittinger, C. T., Johnston, M., Abbot, P., Rokas, A. Tags: Research Articles Source Type: journals

Signal Conflicts in the Phylogeny of the Primary Photosynthetic EukaryotesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is widely accepted that the first photosynthetic eukaryotes arose from a single primary endosymbiosis of a cyanobacterium in a phagotrophic eukaryotic host, which led to the emergence of three major lineages: Chloroplastida (green algae and land plants), Rhodophyta, and Glaucophyta. For a long time, Glaucophyta have been thought to represent the earliest branch among them. However, recent massive phylogenomic analyses of nuclear genes have challenged this view, because most of them suggested a basal position of Rhodophyta, though with moderate statistical support. We have addressed this question by phylogenomic analysis...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Deschamps, P., Moreira, D. Tags: Research Articles Source Type: journals

Targets of Balancing Selection in the Human GenomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Balancing selection is potentially an important biological force for maintaining advantageous genetic diversity in populations, including variation that is responsible for long-term adaptation to the environment. By serving as a means to maintain genetic variation, it may be particularly relevant to maintaining phenotypic variation in natural populations. Nevertheless, its prevalence and specific targets in the human genome remain largely unknown. We have analyzed the patterns of diversity and divergence of 13,400 genes in two human populations using an unbiased single-nucleotide polymorphism data set, a genome-wide approa...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Andres, A. M., Hubisz, M. J., Indap, A., Torgerson, D. G., Degenhardt, J. D., Boyko, A. R., Gutenkunst, R. N., White, T. J., Green, E. D., Bustamante, C. D., Clark, A. G., Nielsen, R. Tags: Research Articles Source Type: journals

Tracing the History of Goat Pastoralism: New Clues from Mitochondrial and Y Chromosome DNA in North AfricaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the first study combining results from mitochondrial DNA (mtDNA) and Y chromosome loci for the genetic characterization of a domestic goat population. Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East. It has been previously shown that goats have a weak phylogeographic str...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Pereira, F., Queiros, S., Gusmao, L., Nijman, I. J., Cuppen, E., Lenstra, J. A., Consortium, E., Davis, S. J.M., Nejmeddine, F., Amorim, A. Tags: Research Articles Source Type: journals

A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox GenesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron–exon structure and by unique codomain architectures. We identified many new genes belonging to previ...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Mukherjee, K., Brocchieri, L., Burglin, T. R. Tags: Research Articles Source Type: journals

A Broadscale Phylogenetic Analysis of Group II Intron RNAs and Intron-Encoded Reverse TranscriptasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we present a broadscale phylogenetic analysis of group II introns using sequence data from both the conserved RNA structure and the intron-encoded reverse transcriptase (RT). Two similar phylogenies are estimated for the RT open reading frame (ORF), based on either amino acid or nucleotide sequence, whereas one phylogeny is produced for the RNA. In making these estimates, we confronted nearly all the classic challenges to phylogenetic inference, including positional saturation, base composition heterogeneity, short internodes with low support, and sensitivity to taxon sampling. Although the major lineages ar...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Simon, D. M., Kelchner, S. A., Zimmerly, S. Tags: Research Articles Source Type: journals

Global Microsatellite Content Distinguishes Humans, Primates, Animals, and PlantsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microsatellites are highly mutable, repetitive sequences commonly used as genetic markers, but they have never been studied en masse. Using a custom microarray to measure hybridization intensities of every possible repetitive nucleotide motif from 1-mers to 6-mers, we examined 25 genomes. Here, we show that global microsatellite content varies predictably by species, as measured by array hybridization signal intensities, correlating with established taxonomic relationships, and particular motifs are characteristic of one species versus another. For instance, hominid-specific microsatellite motifs were identified despite al...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Galindo, C.L., McIver, L.J., McCormick, J.F., Skinner, M.A., Xie, Y., Gelhausen, R.A., Ng, K., Kumar, N.M., Garner, H.R. Tags: Research Articles Source Type: journals

Evolution of 7SK RNA and Its Protein Partners in MetazoaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
7SK RNA is a key player in the regulation of polymerase II transcription. 7SK RNA was considered as a highly conserved vertebrate innovation. The discovery of poorly conserved homologs in several insects and lophotrochozoans, however, implies a much earlier evolutionary origin. The mechanism of 7SK function requires interaction with the proteins HEXIM and La-related protein 7. Here, we present a comprehensive computational analysis of these two proteins in metazoa, and we extend the collection of 7SK RNAs by several additional candidates. In particular, we describe 7SK homologs in Caenorhabditis species. Furthermore, we de...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Marz, M., Donath, A., Verstraete, N., Nguyen, V. T., Stadler, P. F., Bensaude, O. Tags: Research Articles Source Type: journals

Genic Incompatibilities in Two Hybrid BacteriophagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Horizontal gene transfer and recombination play a major role in microbial evolution and have been detected in diverse groups, including many of medical relevance such as HIV and dengue virus. In the absence of mechanistic barriers, the evolutionary success of a particular recombination event is determined by whether the recombinant genotype suffers a fitness cost through the disruption of favorable epistatic interactions within the genome, and if so, the extent to which this fitness cost might be mitigated by subsequent compensatory evolution. To investigate the importance of epistatic interactions between genes and the ev...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Rokyta, D. R., Wichman, H. A. Tags: Research Articles Source Type: journals

Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary PatternsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological research. Yet, little is known about the natural function or evolution of this superfamily of proteins that originate from marine organisms. Using molecular phylogenetic analyses of 102 naturally occurring cyan fluorescent proteins, green fluorescent proteins, red fluorescent proteins, as well as the nonfluorescent (purple-blue) protein sequences (including new FPs from Lizard Island, Australia) derived from organisms with known geographic origin, we show that FPs consist of two distinct and novel regions that have evolved under opp...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Gruber, D. F., DeSalle, R., Lienau, E. K., Tchernov, D., Pieribone, V. A., Kao, H.-T. Tags: Research Articles Source Type: journals

mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous WolvesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence ...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Pang, J.-F., Kluetsch, C., Zou, X.-J., Zhang, A.-b., Luo, L.-Y., Angleby, H., Ardalan, A., Ekstrom, C., Skollermo, A., Lundeberg, J., Matsumura, S., Leitner, T., Zhang, Y.-P., Savolainen, P. Tags: Research Articles Source Type: journals

Evolutionary Trajectories of Primate Genes Involved in HIV PathogenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The current availability of five complete genomes of different primate species allows the analysis of genetic divergence over the last 40 million years of evolution. We hypothesized that the interspecies differences observed in susceptibility to HIV-1 would be influenced by the long-range selective pressures on host genes associated with HIV-1 pathogenesis. We established a list of human genes (n = 140) proposed to be involved in HIV-1 biology and pathogenesis and a control set of 100 random genes. We retrieved the orthologous genes from the genome of humans and of four nonhuman primates (Pan troglodytes, Pongo pygmaeus ab...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Ortiz, M., Guex, N., Patin, E., Martin, O., Xenarios, I., Ciuffi, A., Quintana-Murci, L., Telenti, A. Tags: Research Articles Source Type: journals

Lineage-Specific Adaptive Evolution of the Centromeric Protein CENH3 in Diploid and Allotetraploid Oryza SpeciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Centromeres in eukaryotic species are defined by the presence of a centromere-specific histone H3 variant, CENH3. CENH3 plays a key role in recruiting other centromeric proteins; thus, it is the central component in kinetochore formation and centromere function. The CENH3 proteins in several plant and animal species were found to be under positive selection, which was hypothesized to respond to the rapid changing of the repetitive DNA sequences associated with the centromeres. Here, we report the expression and evolution of the CenH3 genes in two allotetraploid rice species as well as their representative diploid progenito...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Hirsch, C. D., Wu, Y., Yan, H., Jiang, J. Tags: Research Articles Source Type: journals

Genotoxicity of a freshwater cyanotoxin, cylindrospermopsin, in two human cell lines: Caco-2 and HepaRGEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cylindrospermopsin (CYN), a cyanotoxin produced by certain freshwater cyanobacteria, causes human intoxications and animal mortalities. CYN is a potent inhibitor of protein- and glutathione-synthesis. Preliminary evidence for in vivo tumor initiation has been found in mice but the mechanism remains unclear. Several in vitro and in vivo studies demonstrate that CYN is genotoxic and requires metabolic activation. In the present study, the genotoxicity of CYN was assessed in human hepatocyte and enterocyte cell lines, which are models for CYN target organs. The cytokinesis-block micronucleus assay was conducted on liver-deriv...
Source: Environmental and Molecular Mutagenesis - November 10, 2009 Category: Molecular Biology Authors: Emmanuelle Bazin, Annick Mourot, Andrew R. Humpage, Valérie Fessard Source Type: journals

When monocytes and platelets compete: The effect of platelet count on the flow cytometric measurement of monocyte CD36Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Flow cytometric measurement of monocyte surface CD36 is relevant to several conditions including diabetes, cardiovascular disease, lipid disorders, platelet isoimmunization, and susceptibility to P falciparum malaria. CD36 is also strongly expressed on platelets where it is also known as platelet glycoprotein IV.Whole blood samples, containing identical monocyte concentrations, were adjusted to contain platelets ranging from 20,000/uL to 600,000/uL, were stained with fluorescent-labeled anti-CD36, and analyzed by flow cytometry.CD36 median fluorescent intensity (MFI) observed on monocytes decreased as the platelet concentr...
Source: Cytometry Part B: Clinical Cytometry - November 10, 2009 Category: Molecular Biology Authors: W.H. Dzik, C.M. Cserti-Gazdewich, I. Ssewanyana, M. DeLelys, F.I. Preffer Source Type: journals

A short, chemoenzymatic route to chiral [small beta]-aryl-[gamma]-amino acids using reductases from anaerobic bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Anna Fryszkowska, Karl Fisher, John M. Gardiner, Gill M. Stephens (Communication from Org. Biomol. Chem.) Anna Fryszkowska, Org. Biomol. Chem., 2010, DOI: 10.1039/b919526b To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Organic Biomolecular Chemistry - November 10, 2009 Category: Molecular Biology Authors: Anna FryszkowskaKarl Fisher John M. Gardiner Gill M. Stephens Source Type: journals

Synthetic biologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ali Tavassoli (Emerging Area from Org. Biomol. Chem.) Ali Tavassoli, Org. Biomol. Chem., 2010, DOI: 10.1039/b913300n To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Organic Biomolecular Chemistry - November 10, 2009 Category: Molecular Biology Authors: Ali Tavassoli Source Type: journals

Stereoselective Syntheses of Pentose Sugars Under Realistic Prebiotic Conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Glycolaldehyde and DL: -glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL: -peptide catalysts, ribose was the only pentose sugar to have a significant D: -enantiomeric excess (ee) (</=44%), lyxose d...
Source: Origins of Life and Evolution of the Biosphere - November 10, 2009 Category: Molecular Biology Authors: Pizzarello S, Weber AL Tags: Orig Life Evol Biosph Source Type: journals

Dosage-dependent roles of the Cwt1 transcription factor for cell wall architecture, morphogenesis, drug sensitivity and virulence in Candida albicansEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Cwt1 transcription factor is involved in cell wall architecture of the human fungal pathogen Candida albicans. We demonstrate here that deficiency of Cwt1 leads to decreased [beta]1,6-glucan in the cell wall, while mannoproteins are increased in the cell wall of exponentially growing cells and are released into the medium of stationary phase cells. Hyphal morphogenesis of cwt1 mutants is reduced on the surfaces of some inducing media. Unexpectedly, the CWT1/cwt1 heterozygous strains shows some stronger in vitro phenotypes compared to the homozygous mutant. The heterozygous but not the homozygous strain is also strongly...
Source: Yeast - November 10, 2009 Category: Molecular Biology Authors: Inmaculada Moreno, María Martinez-Esparza, Leslie Carolina Laforet, Rafael Sentandreu, Joachim F. Ernst, Eulogio Valentin Source Type: journals

Isolation and characterization of Candida kefyr orotidine-5[prime]-phosphate decarboxylase (URA3) geneEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Candida kefyr is a common yeast species that can be found in fermented milk and cheeses. As a first step to developing a gene transfer system for C. kefyr, the orotidine-5[prime]-phosphate decarboxylase (URA3) gene was cloned, using degenerate PCR and genome walking. The uninterrupted open reading frame of the C. kefyr URA3 gene spans 801 bp, corresponding to 267 amino acid residues. The functionality of the gene was confirmed by complementation of ura3 auxotrophs of C. albicans and Saccharomyces cerevisiae. Phylogenetic analysis of the deduced amino acid sequence indicated that it shares a high degree of homology with oth...
Source: Yeast - November 10, 2009 Category: Molecular Biology Authors: Paul Wai-Kei Tsang, Kin-Sing Wong, Jennifer Ka-Man Chu Source Type: journals

Paracoccin from Paracoccidioides brasiliensis; purification through affinity with chitin and identification of N-acetyl-[beta]-D-glucosaminidase activityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The dimorphic fungus Paracoccidioides brasiliensis is the causative agent of paracoccidioidomycosis, the most frequent systemic mycosis in Latin America. Our group has been working with paracoccin, a P. brasiliensis lectin with MM 70 kDa, which is purified by affinity with immobilized N-acetylglucosamine (GlcNAc). Paracoccin has been described to play a role in fungal adhesion to extracellular matrix components and to induce high and persistent levels of TNF[alpha] and nitric oxide production by macrophages. In the cell wall, paracoccin colocalizes with the [beta]-1,4-homopolymer of GlcNAc into the budding sites of the P. ...
Source: Yeast - November 10, 2009 Category: Molecular Biology Authors: Fausto Bruno dos Reis Almeida, Leandro Licursi de Oliveira, Marcelo Valle de Sousa, Maria Cristina Roque Barreira, Ebert Seixas Hanna Source Type: journals

The human c-fos and TNF[alpha] AU-rich elements show different effects on mRNA abundance and protein expression depending on the reporter in the yeast Pichia pastorisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, we illustrate that the analysis of ARE-mediated effects on mRNA abundance and protein expression of a reporter depends on the sequence of the reporter itself as well as the ARE-surrounding sequences within the 3[prime] UTR. For this reason, we question whether already established reporter constructs in other cellular systems display the true type of regulation of the tested AREs for its original host gene. Finally, we propose that AREs should be analysed in their native sequence context. Copyright © 2009 John Wiley & Sons, Ltd.
Source: Yeast - November 10, 2009 Category: Molecular Biology Authors: Thomas Lautz, Ulf Stahl, Christine Lang Source Type: journals

Nickel/magnesium-lanthanum mixed oxide catalyst in the Kumada-couplingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Arpad Kiss, Zoltan Hell, Maria Balint (Communication from Org. Biomol. Chem.) Arpad Kiss, Org. Biomol. Chem., 2010, DOI: 10.1039/b919246h To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
Source: RSC - Organic Biomolecular Chemistry - November 10, 2009 Category: Molecular Biology Authors: Arpad KissZoltan Hell Maria Balint Source Type: journals

Long-term prediction of fish growth under varying ambient temperatures using a multiscale dynamic modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We demonstrate that, despite thedifficulties involved, multiscale models in biology can yieldreasonable and useful results. The model predictions are reliableover several timescales and in the presence of strong temperaturefluctuations, which are crucial factors for modeling marine organismgrowth. The model provides important improvements over existingmodels.
Source: BMC Systems Biology - Latest articles - November 10, 2009 Category: Molecular Biology Authors: Nadav BarNicole Radde Source Type: journals

A possible correlation between the correction of endothelial dysfunction and normalization of high blood pressure levels by 1, 3, 4-oxadiazole derivative, an L-type Ca(2+) channel blocker in deoxycorticosterone acetate and N(G)-nitro L-arginine hypertensive rats.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have previously demonstrated the vasorelaxant activity of 1, 3, 4 oxadiazole derivative (NOX-1) through L-type Ca(2+) channel blockage. In the present study, we investigated whether the correction of endothelial dysfunction can be dependent of the normalization of high blood pressure levels by 1, 3, 4-oxadiazole derivative (NOX-1) in deoxycorticosterone acetate (DOCA-salt) and N(G)-nitro-L-arginine (L-NNA) hypertensive rats. In DOCA-salt and L-NNA hypertensive rats the mean systolic blood pressure (MSBB) was 185.3+/-4.7 and 170.2+/-4.1 mmHg, whereas after administration of NOX-1 to hypertensive rats, MSBB was 127.8+...
Source: Chemico-Biological Interactions - November 10, 2009 Category: Molecular Biology Authors: Bankar GR, Nampurath GK, Nayak PG, Bhattacharya S Tags: Chem Biol Interact Source Type: journals

Suppression of tumor necrosis factor receptor associated factor (TRAF)-2 attenuates the proinflammatory and proliferative effect of aggregated IgG on rat renal mesangial cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Immune-complex (IC) mediated glomerulonephritis (GN) is a common cause of chronic kidney disease associated with increased levels of tumor necrosis factor (TNF)-alpha in renal cells. TNF-alpha signaling pathways involve complicated interactions between multiple proteins including TNF-receptor-associated factor (TRAF)-2. We have previously found markedly up-regulated expression of TRAF-2 in renal tissues from IC mediated lupus nephritis patients. Here we investigated the effect of TRAF-2 on inflammatory response in rat mesangial cells (MCs). The results showed that treatment with soluble aggregated IgG (AIgG) resulted i...
Source: Cytokine - November 10, 2009 Category: Molecular Biology Authors: Zhu LJ, Yang X, Li XY, Liu QH, Tang XQ, Zhou SF, Kong QY, Axelsson J, Yu XQ Tags: Cytokine Source Type: journals

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