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 29.
Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny
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Homoplasy-free characters are a valuable and highly desired tool for molecular systematics. Nuclear sequences of mitochondrial origin (numts) are fragments of mitochondrial DNA that have been transferred into the nuclear genome. numts are passively captured into genomes and have no transposition activity, which suggests they may have utility as phylogenetic markers. Here, five fully sequenced primate genomes (human, chimpanzee, orangutan, rhesus macaque, and marmoset) are used to reconstruct the evolutionary dynamics of recent numt accumulation in a phylogenetic context. The status of 367 numt loci is used as categorical d...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Hazkani-Covo, E. Tags: Letters Source Type: journals
Linkage Disequilibrium Extends Across Putative Selected Sites in FOXP2Email this article to a colleague.
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Polymorphism data in humans suggest that the gene encoding the transcription factor FOXP2, which influences speech and language development, has been subject to a selective sweep within the last 260,000 years. It has been proposed that one or both of two substitutions that occurred on the human evolutionary lineage and changed amino acids were the targets for selection. In apparent contradiction to this is the observation that these substitutions are present in Neandertals who diverged from humans maybe 300,000–400,000 years ago. We have collected polymorphism data upstream and downstream of the substitutions. Contra...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Ptak, S. E., Enard, W., Wiebe, V., Hellmann, I., Krause, J., Lachmann, M., Paabo, S. Tags: Letters Source Type: journals
Comparative Evolutionary Analysis of the Major Structural Subunit of Vibrio vulnificus Type IV PiliEmail this article to a colleague.
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Type IV pili contribute to virulence in Vibrio vulnificus, the bacterium responsible for the majority of fatal seafood-related infections. Here, we performed within- and between-species evolutionary analysis of the gene that encodes the major structural subunit of the pilus, pilA, by comparing it with pilD and gyrB, the genes encoding the type IV prepilin peptidase and β subunit of DNA gyrase, respectively. Although the diversity in pilD and gyrB is similar to each other and likely to have accumulated after speciation of V. vulnificus, pilA is several times more diverse at both nonsynonymous and synonymous levels. Als...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Chattopadhyay, S., Paranjpye, R. N., Dykhuizen, D. E., Sokurenko, E. V., Strom, M. S. Tags: Research Articles Source Type: journals
Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic DonorsEmail this article to a colleague.
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The Uyghur (UIG) are a group of people primarily residing in Xinjiang of China, which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east, and northeast Asia about 40 kya. A recent study suggested that the UIG are ancestry donors of the East Asian (EAS) gene pool. However, an alternative hypothesis, that is, the UIG is an admixture population with both EAS and EUR ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype-sharing analysis (HSA) based on empirical and simulated data o...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Xu, S., Jin, W., Jin, L. Tags: Research Articles Source Type: journals
Application of the Isolation with Migration Model Demonstrates the Pleistocene Origin of Geographic Differentiation in Cardamine nipponica (Brassicaceae), an Endemic Japanese Alpine PlantEmail this article to a colleague.
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The Pleistocene was characterized by a cyclic pattern of cold and warm climatic periods, or climatic oscillations, which caused fluctuations in the distributions of organisms. This resulted in drastic changes in demography, thereby accelerating the genetic divergence of populations. Phylogeographic studies have elucidated the history of populations during the Pleistocene. However, given the lack of model-based analysis of population histories, previous phylogeographic studies could not adequately evaluate the effect of these Pleistocene climatic oscillations on the genetic divergence and migration events between population...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Ikeda, H., Fujii, N., Setoguchi, H. Tags: Research Articles Source Type: journals
Sequence-Based Analysis of Protein Energy Landscapes Reveals Nonuniform Thermal Adaptation within the ProteomeEmail this article to a colleague.
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Thermal adaptation of individual proteins is often achieved through modulating protein stability, with proteins that are adapted to extreme cold environments having increased conformational flexibility when brought to mesophilic conditions. Conversely, proteins adapted to higher temperatures appear less dynamic and are found to be much more stable against thermal denaturation than their mesophilic counterparts. According to the current paradigm, the adaptation of an organism for survival at higher or lower temperatures is facilitated by the adaptation of the component proteins. We note, however, that these observations hav...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Gu, J., Hilser, V. J. Tags: Research Articles Source Type: journals
Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene DuplicationsEmail this article to a colleague.
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Phylogenomic analyses show that gene and genome duplication events have led to the diversification of transcription factor gene families throughout the evolutionary history of land plants and that gene duplications have played an important role in shaping regulatory networks influencing key phenotypic characters including floral development and flowering time. A molecular evolutionary investigation of the mode and tempo of selection acting on the angiosperm MADS box AP1/SQUA, AP3/PI, AG/AGL11, and SEP gene subfamilies revealed site-specific patterns of shifting evolutionary constraint throughout angiosperm history. Specifi...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Shan, H., Zahn, L., Guindon, S., Wall, P. K., Kong, H., Ma, H., dePamphilis, C. W., Leebens-Mack, J. Tags: Research Articles Source Type: journals
The Unique Morgue Ubiquitination Protein Is Conserved in a Diverse but Restricted Set of InvertebratesEmail this article to a colleague.
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In this study, we address the evolutionary origins of this distinctive protein utilizing a combination of bioinformatics and molecular biology approaches. We find that Morgue exhibits widespread but restricted phylogenetic distribution among metazoans. Morgue proteins were identified in a wide range of Protostome phyla, including Arthropoda, Annelida, Mollusca, Nematoda, and Platyhelminthes. However, with one potential exception, Morgue was not detected in Deuterostomes, including Chordates, Hemichordates, or Echinoderms. Morgue was also not found in Ctenophora, Cnidaria, Placozoa, or Porifera. Characterization of Morgue s...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Zhou, Y., Carpenter, Z. W., Brennan, G., Nambu, J. R. Tags: Research Articles Source Type: journals
Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of EumetazoaEmail this article to a colleague.
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The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data ...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Sperling, E. A., Peterson, K. J., Pisani, D. Tags: Research Articles Source Type: journals
Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence LevelEmail this article to a colleague.
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In detecting natural selection operating at the amino acid sequence level by comparing the rates of synonymous (rS) and nonsynonymous (rN) substitutions, the rates of synonymous and nonsynonymous mutations are assumed to be approximately the same. In reality, however, these rates may not be the same if different proportions of synonymous and nonsynonymous sites overlap with CpG dinucleotides, which are known to be hypermutable in some organisms. Here, we develop the evolutionary pathway methods for comparing rS and rN at multiple codon sites (all-sites analysis) and at single codon sites (single-site analysis) that take in...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Suzuki, Y., Gojobori, T., Kumar, S. Tags: Research Articles Source Type: journals
Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human PopulationsEmail this article to a colleague.
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Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs in chimpanzee, mouse, rat, and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes was...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Moreno-Estrada, A., Tang, K., Sikora, M., Marques-Bonet, T., Casals, F., Navarro, A., Calafell, F., Bertranpetit, J., Stoneking, M., Bosch, E. Tags: Research Articles Source Type: journals
Genes within Genes: Multiple LAGLIDADG Homing Endonucleases Target the Ribosomal Protein S3 Gene Encoded within an rnl Group I Intron of Ophiostoma and Related TaxaEmail this article to a colleague.
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In some ascomycete fungi, ribosomal protein S3 (Rps3) is encoded within a group I intron (mL2449) that is inserted in the U11 region of the mitochondrial large subunit rDNA (rnl) gene. Previous characterization of the mL2449 intron in strains of Ophiostoma novo-ulmi subspecies americana (Dutch Elm Disease) revealed a complex genes-within-genes arrangement whereby a LAGLIDADG homing endonuclease gene (HEG) is inserted into the RPS3 gene near the 3' terminus, creating a hybrid Rps3–LAGLIDADG fusion protein. Here, we examined 119 additional strains of Ophiostoma and related taxa representing 85 different species by a po...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Sethuraman, J., Majer, A., Friedrich, N. C., Edgell, D. R., Hausner, G. Tags: Research Articles Source Type: journals
The Chloroplast Genomes of the Green Algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria Reveal a Shared Ancestry between the Pedinomonadales and ChlorellalesEmail this article to a colleague.
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The green algae belonging to the Chlorophyta—the lineage sister to that comprising the land plants and their charophycean green algal relatives (Streptophyta)—have been subdivided into four classes (Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae). Yet the Pedinomonadales, an assemblage consisting of tiny, naked uniflagellates with a second basal body, has no clear affiliation with these classes and the branching order of the crown chlorophytes remains unknown. To gain an insight into the phylogenetic position of the Pedinomonadales and the relationships among the recognized chlorophyte classes...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Turmel, M., Otis, C., Lemieux, C. Tags: Research Articles Source Type: journals
A Profound Role for the Expansion of Trypsin-Like Serine Protease Family in the Evolution of Hematophagy in MosquitoEmail this article to a colleague.
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The trypsin-like serine protease (Tryp_SPc) family is ubiquitous in animals and plays diverse roles, especially in the digestive system, in different phyla. In the mosquito, some Tryp_SPc proteases make important contributions to the digestion of the blood meal. Here, we have defined the complete Tryp_SPc gene repertoire in the genome of the malaria mosquito, a repertoire that has expanded remarkably compared with that of Drosophila. Phylogenetic analysis also indicates that the large-scale lineage-specific expansion occurred leading to mosquitoes. Expression of Tryp_SPc genes elevates after a blood meal, and the expressio...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Wu, D.-D., Wang, G.-D., Irwin, D. M, Zhang, Y.-P. Tags: Research Articles Source Type: journals
Slcyt, a Newly Identified Sex-Linked Gene, Has Recently Moved onto the X Chromosome in Silene latifolia (Caryophyllaceae)Email this article to a colleague.
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The sex chromosomes of the plant species Silene latifolia (white campion) are very young (only 5–10 My old), and all 11 X-linked genes so far described have Y-linked homologues. Theory predicts that X chromosomes should accumulate a nonrandom set of genes. However, little is known about the importance of gene movements between the X and the autosomes in plants, or in any very young sex chromosome system. Here, we isolate from cDNA a new gene, Slcyt, on the S. latifolia X, which encodes a cytochrome B protein. We genetically mapped SlCyt and found that it is located ~1 cM from the pseudoautosomal region. Genes in this...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Kaiser, V. B., Bergero, R., Charlesworth, D. Tags: Research Articles Source Type: journals
Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in BacteriaEmail this article to a colleague.
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In this study, we conducted a systematic survey for the association in 262 complete genomes from 73 bacterial species. In these bacteria, the level of nucleotide diversity was negatively correlated with the distance from the closest indel, which is consistent with the eukaryote data. The same pattern was observed even after excluding noncoding sequences, indicating that the difference in functional constraints among genomic regions is not a primary cause of the correlation. In addition, the increase of nucleotide substitution rate was detected disproportionally on a lineage carrying a derived indel mutation, confirming the...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Zhu, L., Wang, Q., Tang, P., Araki, H., Tian, D. Tags: Research Articles Source Type: journals
A Phylogenetic Mixture Model for the Evolution of Gene ExpressionEmail this article to a colleague.
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Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly account for predicted nonindependence due to phylogenetic associations between measurements. In the interest of parsing the effects of selection: we introduce a mixture model for the comparative analysis of variation in gene expression across multiple taxa. This class of models isolates the phylogenetic signal fro...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Eng, K. H., Bravo, H. C., Keles, S. Tags: Research Articles Source Type: journals
Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in CaenorhabditisEmail this article to a colleague.
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Whether phenotypic evolution proceeds predominantly through changes in regulatory sequences is a controversial issue in evolutionary genetics. Ample evidence indicates that the evolution of gene regulatory networks via changes in cis-regulatory sequences is an important determinant of phenotypic diversity. However, recent experimental work suggests that the role of transcription factor (TF) divergence in developmental evolution may be underestimated. In order to help understand what levels of constraints are acting on the coding sequence of developmental regulatory genes, evolutionary rates were investigated among 48 TFs r...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Jovelin, R. Tags: Research Articles Source Type: journals
Structural Determinants of Protein Evolution Are Context-Sensitive at the Residue LevelEmail this article to a colleague.
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Structural properties of a protein residue's microenvironment have long been implicated as agents of selective constraint. Although these properties are inherently quantitative, structure-based studies of protein evolution tend to rely upon coarse distinctions between "surface" and "buried" residues and between "interfacial" and "noninterfacial" residues. Using homology-mapped yeast protein structures, we explore the relationships between residue evolution and continuous structural properties of the residue microenvironment, including solvent accessibility, density and distribution of residue–residue contacts, and bu...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Franzosa, E. A., Xia, Y. Tags: Research Articles Source Type: journals
Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal AcoelomorphaEmail this article to a colleague.
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During the past decade, great progress has been made in clarifying the relationships among bilaterian animals. Studies based on a limited number of markers established new hypotheses such as the existence of three superclades (Deuterostomia, Ecdysozoa, and Lophotrochozoa) but left major questions unresolved. The data sets used to the present either bear few characters for many taxa (i.e., the ribosomal genes) or present many characters but lack many phyla (such as recent phylogenomic approaches) failing to provide definitive answers for all the regions of the bilaterian tree. We performed phylogenetic analyses using a mole...
Source: Molecular Biology and Evolution - September 3, 2009 Category: Molecular Biology Authors: Paps, J., Baguna, J., Riutort, M. Tags: Research Articles Source Type: journals
Plasma membrane rafts engaged in T cell signalling: new developments in an old conceptEmail this article to a colleague.
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Considerable controversy arose over the concept that cholesterol/sphingolipid-rich rafts in the T cell plasma membrane serve as a platform for TCR signalling reactions. This controversy was founded on the initial definition of rafts as detergent resistant membranes which later turned out to misrepresent many features of cell membrane organisation under physiological conditions. Raft-organisation was subsequently studied using a number of detergent-free experimental approaches. The results led to a refined perception of membrane rafts which resolves the controversies. Here we review new biophysical and biochemical data whic...
Source: Cell Communication and Signaling - September 3, 2009 Category: Molecular Biology Authors: Thomas HarderDhaval Sangani Source Type: journals
Molecular cloning and expression analysis of Bmrbp1, the Bombyx mori homologue of the Drosophila gene rbp1.Email this article to a colleague.
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RBP1 is an important splicing factor involved in alternative splicing of the pre-mRNA of Drosophila sex-determining gene dsx. In this work, the Bombyx mori homologue of the rbp1 gene, Bmrbp1, was cloned. The pre-mRNA of Bmrbp1 gene is alternatively spliced to produce four mature mRNAs, named Bmrbp1-PA, Bmrbp1-PB, Bmrbp1-PC and Bmrbp1-PD, with nucleotide lengths of 799 nt, 1,316 nt, 894 nt and 724 nt, coding for 142 aa, 159 aa, 91 aa and 117 aa, respectively. BmRBP1-PA and BmRBP1-PD contain a N terminal RNA recognization motif (RRM) and a C terminal arginine/serine-rich domain, while BmRBP1-PB and BmRBP1-PC only share a...
Source: Molecular Biology Reports - September 3, 2009 Category: Molecular Biology Authors: Wang Z, Zha X, He N, Xiang Z, Xia Q Tags: Mol Biol Rep Source Type: journals
The unsung reviewerEmail this article to a colleague.
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Nature Structural & Molecular Biology 16, 899 (2009). doi:10.1038/nsmb0909-899
Manuscript peer reviewing is at the heart of the scientific system, but it seems that these duties are often not properly (if at all) recognized by universities, funding agencies or even the rest of the scientific community.
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Tags: Editorial Source Type: journals
The p53 transcriptional synapse: activation on demandEmail this article to a colleague.
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eppert
The adequate and on-time response of cellular transcription to internal needs and external stimuli is a delicate task. Is the transcriptional regulator p53 on call to permit rapid activation of its target genes? A new study reports interplay of p53 with a previously unidentified regulator, calcineurin-binding protein 1 (Cabin1), and provides evidence for such a mechanism.
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Authors: Genrich V TolstonogWolfgang Deppert Tags: News and Views Source Type: journals
When chromatin meets splicingEmail this article to a colleague.
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J Blencowe
Using bioinformatics analysis of previously published global genome deep-sequencing data, two papers now show that DNA sequences associated with nucleosomes are preferentially located in exons. The correlation between nucleosome distribution and the exon-intron organization of genes may have a key role in exon recognition at the pre-mRNA level during co-transcriptional splicing, consistent with previous findings indicating chromatin-mediated regulation of alternative splicing.
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Authors: Alberto R KornblihttIgnacio E SchorMariano AlloBenjamin J Blencowe Tags: News and Views Source Type: journals
New functions for an ancient domainEmail this article to a colleague.
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Nature Structural & Molecular Biology 16, 904 (2009). doi:10.1038/nsmb0909-904
Author: W Lee Kraus
Macrodomains function as binding modules for metabolites of NAD+, including poly(ADP-ribose). Three new studies explore how binding of poly(ADP-ribose) by the macrodomains of histone variant macroH2A1.1 and the ATP-dependent chromatin-remodeling protein ALC1 (also called CHD1L) leads to the modulation of chromatin structure, regulating nuclear functions such as DNA-damage detection and repair.
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Authors: W Lee Kraus Tags: News and Views Source Type: journals
Dangerous play—splitting the message may leave you empty handedEmail this article to a colleague.
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Dangerous play—splitting the message may leave you empty handed
Nature Structural & Molecular Biology 16, 907 (2009). doi:10.1038/nsmb0909-907
Authors: Yvonne Klaue & Klemens J Hertel
An important aspect of eukaryotic gene expression is the efficient integration of transcription, pre-mRNA processing and nuclear export. A new study demonstrates that pre-mRNA transcript continuity is an essential component for maintaining productive coupling of transcription and RNA processing events.
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Authors: Yvonne KlaueKlemens J Hertel Tags: News and Views Source Type: journals
Research highlightsEmail this article to a colleague.
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Nature Structural & Molecular Biology 16, 909 (2009). doi:10.1038/nsmb0909-909
Source: Nature Structural and Molecular Biology - September 3, 2009 Category: Molecular Biology Tags: Research Highlights Source Type: journals
Cosmetic textiles with biological benefits: Gelatin microcapsules containing Vitamin C.Email this article to a colleague.
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This study discusses the development of cosmetic textiles and addresses microencapsulation technology with respect to its historical background, significant advantages, microencapsulation methods and recent applications in the textile industry. Gelatin microcapsules containing vitamin C were prepared using emulsion hardening technique. Both the optical microscopy and scanning electron microscopy demonstrated that the newly developed microcapsules were in the form of core-shell spheres with relatively smooth surface. The particle size of microcapsules ranged from 5.0 to 44.1 microm with the average particle size being 24.6 ...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Cheng SY, Yuen MC, Kan CW, Cheuk KK, Chui CH, Lam KH Tags: Int J Mol Med Source Type: journals
Identification of sex hormone binding globulin-interacting proteins in the brain using phage display screening.Email this article to a colleague.
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The present study reports the identification of human sex hormone binding globulin (SHBG)-interacting proteins in the brain using a phage display-based screening technology. Phage display is a system in which a foreign protein is displayed on the surface of a bacteriophage as a fusion protein with one of the coat proteins of the bacteriophage. T7 phage clones expressing normal human brain proteins (human normal brain phage-display cDNA expression library) were screened using SHBG as bait. The bound phage clones were then identified by DNA sequencing and by BLAST search analysis. Of the twenty binding proteins analyzed,...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Gnanasekar M, Suleman FG, Ramaswamy K, Caldwell JD Tags: Int J Mol Med Source Type: journals
A novel mutated cell line with characteristics of dedifferentiated chondrosarcoma.Email this article to a colleague.
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In this study, a novel dedifferentiated CS cell line, MS0812, was spontaneously established from mutated human embryonic muscle cells. Several features of the cell line were investigated, including growth characteristics, cytogenetics, electron microscopic features, expression of various antigenic markers and tumor formation. MS0812 has been cultured continuously for more than 3 years. The growth characteristics of MS0812 are similar to the immortalized cell lines as reported. The cell line exhibited complex karyotypes and hyperploidy, the chromosome number ranged from 50 to 158. MS0812 was positive for vimentin, desmin an...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Yang L, Chen Q, Zhang S, Wang X, Li W, Wen J, Huang X, Zheng J, Huang G, Huang T, Ju G Tags: Int J Mol Med Source Type: journals
In vitro preparation and characterization of the human CD3epsilonepsilon homodimer and CD3epsilongamma and CD3epsilondelta heterodimers.Email this article to a colleague.
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In this study we investigated whether interactions between each CD3epsilon subunit play a role in the formation of the CD3 molecular complex. Our results revealed that the human CD3epsilon subunit forms a homodimer structure, which is a crucial piece of information for the elucidation of cellular signaling following TCR receptor ligation, and provide insight into our understanding of the molecular assembly of the CD3 molecular complex.
PMID: 19724882 [PubMed - in process]
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Su Z, Wang H, Wan Y, Bi Z Tags: Int J Mol Med Source Type: journals
Notch1 induces enhanced expression of Delta-like-1 in the U251MG glioma cell line.Email this article to a colleague.
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The Notch signaling pathway takes part in coordinated regulation of cell growth, survival and differentiation. Previous findings have shown that Notch1 and Delta-like-1 (DLL1) are overexpressed in many glioma cell lines and primary human gliomas. Down-regulation of DLL1 by RNA interference inhibits proliferation and induces apoptosis in multiple glioma cell lines. Our studies showed that Notch1 expression plasmid induced more expression of DLL1 in the U251MG glioma cell line. Adversely, blocking Notch1 receptors down-regulated the expression of DLL1. Both down-regulating DLL1 and blocking Notch1 receptors induced U251M...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Qian CF, Yan W, Zhang JX, Shi L, Qian J, Fu Z, Kang CS, Liu N, You YP Tags: Int J Mol Med Source Type: journals
Interleukin-15 increases calcineurin expression in 3T3-L1 cells: Possible involvement on in vivo adipocyte differentiation.Email this article to a colleague.
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In this study we investigated the role of interleukin-15 (IL-15), a cytokine previously known to be involved in the control of fat accretion by adipose cells, in the differentiation of the 3T3-L1 preadipose cell line. We found that IL-15 is able to increase alpha-calcineurin mRNA content in white adipose tissue of rats chronically treated with the cytokine and also in the 3T3-L1 preadipose cell line. Moreover, IL-15 promoted a decrease in both leptin mRNA expression and lipid accumulation, as estimated by Red Oil O staining. Cotreatment with IL-15 and FK506 (a calcineurin inhibitor) resulted in no changes in lipid content ...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Almendro V, Fuster G, Ametller E, Costelli P, Pilla F, Busquets S, Figueras M, Argilés JM, López-Soriano FJ Tags: Int J Mol Med Source Type: journals
Cholesterol overloading leads to hepatic L02 cell damage through activation of the unfolded protein response.Email this article to a colleague.
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This study suggests that cholesterol overloading in hepatic L02 cells induces ERS and activates the UPR which, in part, leads to the apoptotic damage of cells.
PMID: 19724885 [PubMed - in process]
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Li Q, Liu Z, Guo J, Chen J, Yang P, Tian J, Sun J, Zong Y, Qu S Tags: Int J Mol Med Source Type: journals
Establishment and characterization of the human SaTM-1 anal canal squamous cell carcinoma cell line derived from lymph node metastasis.Email this article to a colleague.
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Human anal canal squamous cell carcinoma (SCC) cell line has not yet been reported due to the rarity of this disease. Since cell lines to study this malignancy were not available, we attempted to establish and characterize anal canal SCC cell line from primary culture of lymph node metastasis. Six sublines were cloned and isolated from parental cells. They were designated as SaTM-1A, B, C, D, E and F. The features of the six sublines were characterized by reverse transcription-PCR, chemosensitivity test to 5-Fu and CDDP, immunohistochemistry, cDNA microarray analysis and tumorigenicity using immunodeficient mice. All s...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Takeda A, Maeda M, Iseki H, Hirooka E, Shinozuka N, Koyama I Tags: Int J Mol Med Source Type: journals
Laser capture microdissection: A tool for the molecular characterization of histologic subtypes of lung adenocarcinoma.Email this article to a colleague.
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The histologic heterogeneity of lung adenocarcinoma is well known. Many histologic subtypes have been described, and recently their prognostic and predictive value has emerged. Laser capture microdissection may aid in the isolation of cancer cells from distinct subtypes of lung adenocarcinoma, thus enabling the description of their specific molecular features. Characterization of epidermal growth factor receptor (EGFR) mutations in histologic subtypes of lung adenocarcinoma has become an important issue. The purpose of this study was to analyze EGFR mutations in exons 18-21 in single histologic subtypes of lung adenoca...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Donati V, Lupi C, Alì G, Corsi V, Viti A, Lucchi M, Mussi A, Fontanini G Tags: Int J Mol Med Source Type: journals
Low levels of soluble CD1d protein alters NKT cell function in patients with rheumatoid arthritis.Email this article to a colleague.
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This study focused on soluble CD1d (sCD1d) by generating recombinant sCD1d proteins and assaying them in plasma using a newly established ELISA method. The amount of sCD1d proteins in plasma was significantly decreased in rheumatoid arthritis (RA) patients (55.2+/-13.3 years, mean +/-SD) compared with healthy donors (31.2+/-7.4 years). Plasma sCD1d protein levels correlated with the number of NKT cells (TCR Valpha24+ Vbeta11+CD3+) in peripheral blood mononuclear cells (r(2)=0.061). Furthermore, sCD1d proteins induced IFN-gamma production from NKT cells, but neither IL-4 nor IL-10. These findings suggest that the low plasma...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Segawa S, Goto D, Yoshiga Y, Hayashi T, Matsumoto I, Ito S, Sumida T Tags: Int J Mol Med Source Type: journals
Evaluation of the effect of glucosamine administration on biomarkers for cartilage and bone metabolism in soccer players.Email this article to a colleague.
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In the present study, to investigate the effect of glucosamine, a component of glycosaminoglycans with a chondroprotective action, on articular cartilage in athletes, we looked at soccer players, who expose their joints to excessive motion and loading, and compared the levels of biomarkers for type II collagen degradation (CTX-II) and type II collagen synthesis (CPII) between soccer players and non-athlete controls, and in soccer players before and after glucosamine-administration. CTX-II (P<0.01) and CPII (P=0.08) levels were substantially elevated in soccer players compared with those in controls, indicating that ...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Yoshimura M, Sakamoto K, Tsuruta A, Yamamoto T, Ishida K, Yamaguchi H, Nagaoka I Tags: Int J Mol Med Source Type: journals
Induction of G1 arrest and apoptosis by schisandrin C isolated from Schizandra chinensis Baill in human leukemia U937 cells.Email this article to a colleague.
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We isolated two phytochemical lignans, schisandrin and schisandrin C, from Schizandra chinensis Baill and investigated their anti-cancer effects in human leukemia U937 cells. Schisandrin C inhibited cell growth in a dose-dependent manner, which was associated with the induction of G1 arrest of the cell cycle and apoptosis; schisandrin did not inhibit growth. Schisandrin C induced G1 arrest was correlated with down-regulation of cyclin D1, cyclin E, cyclin-dependent kinase (Cdk) 4 and E2Fs expression, inhibition of phosphorylation of retinoblastoma protein (pRB), and up-regulation of the Cdk inhibitor p21(WAF1/CIP1). In...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Park C, Choi YW, Hyun SK, Kwon HJ, Hwang HJ, Kim GY, Choi BT, Kim BW, Choi IW, Moon SK, Kim WJ, Choi YH Tags: Int J Mol Med Source Type: journals
Effects of local vibrations on skeletal muscle trophism in elderly people: mechanical, cellular, and molecular events.Email this article to a colleague.
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Several studies have examined the effects of vibrations on muscle mass and performance in young healthy people. We studied the effects of vibrations on muscles of elderly male and female volunteers (65-85 years of age) diagnosed with sarcopenia. We applied mechanical vibrations locally (local vibrational training) to the thigh muscles at 300 Hz for a period of 12 weeks, starting with a session of 15 min stimulation once a week and increasing to three sessions of 15 min per week. Treated muscles displayed enhanced maximal isometric strength and increased content of fast MyHC-2X myosin. Single muscle fiber analysis did n...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Pietrangelo T, Mancinelli R, Toniolo L, Cancellara L, Paoli A, Puglielli C, Iodice P, Doria C, Bosco G, D'Amelio L, di Tano G, Fulle S, Saggini R, Fanò G, Reggiani C Tags: Int J Mol Med Source Type: journals
A polar extract of the Maya healing plant Anthurium schlechtendalii (Aracea) exhibits strong in vitro anticancer activity.Email this article to a colleague.
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In conclusion, we demonstrated that A. schlechtendalii root extract specifically targeted carcinogenic mechanisms, because Cdc25A and cyclin D1 are oncogenes that are frequently overexpressed in a variety of cancer entities and further, this extract affected microtubule function reminiscent of taxol.
PMID: 19724892 [PubMed - in process]
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Stark N, Gridling M, Madlener S, Bauer S, Lackner A, Popescu R, Diaz R, Tut FM, Vo TP, Vonach C, Giessrigl B, Saiko P, Grusch M, Fritzer-Szekeres M, Szekeres T, Kopp B, Frisch R, Krupitza G Tags: Int J Mol Med Source Type: journals
Production of sHLA-G molecules by in vitro matured cumulus-oocyte complex.Email this article to a colleague.
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This study investigated if soluble HLA-G molecules producted by the cumulus-oocyte complex (COC) are markers of oocyte maturation. sHLA-G molecule levels were analyzed using Bio-Plex assay in 152 COC supernatants obtained from 42 women and maturated by an 'in vitro maturation procedure'. The presence of sHLA-G molecules was confirmed by Western blotting technique. The results demonstrate detectable amounts of sHLA-G molecules ranging from 300 to 800 pg/ml in 14/73 (19%) COCs that generated mature oocytes and complete absence of detectable sHLA-G antigens in the supernatants of COCs that corresponded to immature oocytes. Th...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Rizzo R, Dal Canto MB, Stignani M, Fadini R, Fumagalli D, Renzini MM, Borgatti M, Gambari R, Baricordi OR Tags: Int J Mol Med Source Type: journals
Effect of insulin levels on the phosphorylation of specific amino acid residues in IRS-1: Implications for burn-induced insulin resistance.Email this article to a colleague.
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In this study, we performed in vitro experiments with 293 cells transfected with IRS-1. These studies demonstrated that there is a dramatic change in the phosphorylation pattern of Tyr, Ser and Thr residues in IRS-1 as a function of insulin levels. Specifically, Ser and Thr residues in the C-terminal region were phosphorylated only at high insulin levels. SILAC (stable isotope labeling with amino acids in cell culture) followed by sequencing of C-terminal IRS-1 fragments by tandem mass spectrometry demonstrated that there is significant protein cleavage at these sites. These findings suggest that one of the biological role...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Lu XM, Hamrahi VF, Tompkins RG, Fischman AJ Tags: Int J Mol Med Source Type: journals
Association of gene polymorphisms with chronic kidney disease in Japanese individuals.Email this article to a colleague.
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Chronic kidney disease (CKD) is recognized as a risk factor not only for end-stage renal disease but also for cardiovascular disease. Early detection and treatment of CKD is a likely key factor for prevention of its complications. Although genetic linkage analyses and association studies have implicated several loci and candidate genes in predisposition to CKD, the genes that underlie genetic susceptibility to this condition have remained largely unknown. The purpose of the present study was to identify genetic variants that confer susceptibility to CKD in Japanese individuals. The study population comprised 4,829 Japa...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Yoshida T, Kato K, Yokoi K, Oguri M, Watanabe S, Metoki N, Yoshida H, Satoh K, Aoyagi Y, Nozawa Y, Yamada Y Tags: Int J Mol Med Source Type: journals
Proteins and single nucleotide polymorphisms involved in apoptosis, growth control, and DNA repair predict cisplatin sensitivity in head and neck cancer cell lines.Email this article to a colleague.
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The present study was undertaken to evaluate the possibility of using a panel of proteins and single nucleotide polymorphisms (SNPs) involved in apoptosis, growth control, and DNA repair as predictive markers for cisplatin sensitivity. For this purpose the intrinsic cisplatin sensitivity (ICS) was determined in 39 cell lines derived from squamous cell carcinomas of the head and neck using a colony-forming assay. In these cell lines and in normal oral keratinocytes (NOK), the expression of epidermal growth factor receptor (EGFR), Hsp70, Bax, Bcl-2, Bcl-XL, survivin, and COX-2 was determined. Moreover, the p53, MDM2, FGF...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Farnebo L, Jedlinski A, Ansell A, Vainikka L, Thunell LK, Grénman R, Johansson AC, Roberg K Tags: Int J Mol Med Source Type: journals
Annexin A2 mediates anti-beta2GPI/beta2GPI-induced tissue factor expression on monocytes.Email this article to a colleague.
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In conclusion, these results indicate that ANX2 on cell surface functions as a mediator boosting TF expression on monocytes induced by anti-beta2GPI/beta2GPI complex, which is contributed to the thrombotic events in APS.
PMID: 19724897 [PubMed - in process]
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Zhou H, Wang H, Li N, Yu Y, Huang H, Yan Y, Wang T Tags: Int J Mol Med Source Type: journals
Effect of polymorphisms of IL-17A, -17F and MIF genes on CpG island hyper-methylation (CIHM) in the human gastric mucosa.Email this article to a colleague.
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CpG island hyper-methylation (CIHM) is one of the major events in the gastric carcinogenesis and also occurs in non-neoplastic gastric mucosa. IL-17A, -17F and MIF have a crucial role in the gastric inflammationand carcinogenesis. The CIHM status in the non-cancerous gastric mucosa, in relation to IL-17A (-197G>A, rs2275913), -17F (7488T>C, rs763780) and MIF (-173G>C and -794 tetranucleotide repeats) polymorphisms was investigated. Gastric mucosa samples were obtained from 121 cancer free subjects. CIHM of p14, p16, DAP-kinase and CDH1 genes were determined by methylation-specific polymerase chain reaction (MS...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Tahara T, Shibata T, Nakamura M, Yamashita H, Yoshioka D, Okubo M, Yonemura J, Maeda Y, Maruyama N, Kamano T, Kamiya Y, Fujita H, Nakagawa Y, Nagasaka M, Iwata M, Hirata I, Arisawa T Tags: Int J Mol Med Source Type: journals
Coptis chinensis inhibits hepatocellular carcinoma cell growth through nonsteroidal anti-inflammatory drug-activated gene activation.Email this article to a colleague.
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Conventional chemotherapy of liver cancer fails to provide satisfactory remission and may cause serious side effects, thus it is crucial to derive alternative treatments that effectively inhibit cancer cell growth with known mechanisms of action. In the present study, we investigated the anti-carcinogenic effects of Coptis chinensis and its major constituent, berberine, in HepG2 hepatocellular carcinoma (HCC) cells and attempted to elucidate the underlying mechanism, including involvement of the nonsteroidal anti-inflammatory drug (NSAID)-activated gene (NAG-1). Inhibition of cell proliferation, induction of apoptosis ...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Auyeung KK, Ko JK Tags: Int J Mol Med Source Type: journals
Pro- and anti-inflammatory cytokines increase hyaluronan production by rat synovial membrane in vitro.Email this article to a colleague.
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Synovial membrane consists of fibroblasts and macrophages forming the synovial lining supported by vascularized subsynovium. Each of these components may specifically react to a particular stimulus. Thus, reactions of isolated synovial cells may not correspond to that of intact tissue. We characterized the production of hyaluronan (HA) by rat synovial membrane exposed in vitro to pro- and anti-inflammatory cytokines and compared it with previous results obtained with isolated fibroblasts. Synovial membrane dissected from one knee joint served as a control to that from the opposite knee exposed to IL-1beta, TGF-beta1, T...
Source: International Journal of Molecular Medicine - September 3, 2009 Category: Molecular Biology Authors: Hyc A, Osiecka-Iwan A, Niderla-Bielinska J, Jankowska-Steifer E, Moskalewski S Tags: Int J Mol Med Source Type: journals
