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491 records returned

Analysis of ribosomal RNA transcription termination and 3' end processing in Leishmania amazonensis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The control of gene expression in the human parasite Leishmania occurs mainly at the post-transcriptional level. Nevertheless, basic cell processes such as ribosome biogenesis seem to be conserved. Mature ribosomal RNAs (rRNAs) are synthesized from typical RNA polymerase I (Pol I) promoters and processed by pathways analogous to other eukaryotes. To further understand Pol I transcription control in these parasites, we have analyzed transcription termination and processing of the rDNA in Leishmania amazonensis. 3'-end S1 mapping of rRNA precursors identified three termini, one corresponding to the mature 28S rRNA and tw...
Source: Gene - November 12, 2009 Category: Genetics & Stem Cells Authors: Abreu-Blanco MT, Ramírez JL, Pinto-Santini DM, Papadopoulou B, Guevara P Tags: Gene Source Type: journals

Heterogeneous nuclear ribonucleoprotein E3 modestly activates splicing of tau exon 10 via its proximal downstream intron, a hotspot for frontotemporal dementia mutations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The microtubule-associated protein tau is important to normal neuronal activity in the mammalian nervous system. Aggregated tau is the major component of neurofibrillary tangles (NFTs), structures present in the brains of people affected by neurodegenerative diseases called tauopathies. Tauopathies include Alzheimer's disease (AD), frontotemporal dementia with Parkinsonism (FTDP) and the early onset dementia observed in Down syndrome (DS; trisomy 21). Splicing misregulation of adult-specific exon 10 results in expression of abnormal ratios of tau isoforms, leading to FTDP. Positions +3 to +19 of the intron downstream o...
Source: Gene - November 12, 2009 Category: Genetics & Stem Cells Authors: Wang Y, Gao L, Tse SW, Andreadis A Tags: Gene Source Type: journals

Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of Squids and Cuttlefish.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Five tRNA-derived short interspersed repetitive elements (SINEs), named SepiaSINE, Sepioth-SINE1, Sepioth-SINE2A, Sepioth-SINE2B and OegopSINE, were isolated from the genomes of three decabrachian species [Sepia officinalis (order Sepiida), Sepiotheuthis lessoniana (suborder Myopsida), and Mastigoteuthis cordiformes (suborder Oegopsida)], by random sequencing and genome screening. In addition, two tRNA-derived SINEs, named IdioSINE1 and IdioSINE2, were further detected from EST (expressed sequence tag) data of Idiosepius paradoxus (order Idiosepiida), using a GenBank FASTA search with a conserved sequence of the SepiaS...
Source: Gene - November 12, 2009 Category: Genetics & Stem Cells Authors: Akasaki T, Nikaido M, Nishihara H, Tsuchiya K, Segawa S, Okada N Tags: Gene Source Type: journals

Transcriptional activation of the human Klotho gene by epidermal growth factor in HEK293 cells; Role of Egr-1.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we investigated the transcriptional regulation of the Klotho gene by epidermal growth factor (EGF) in HEK293 human embryonic kidney cells. By using serial deletion constructs of the promoter, we identified a proximal 45 bp (-90 to -45) region responsible for EGF-induced promoter activity. The Egr-1-binding motif is located within this region. Forced expression of Egr-1 stimulated Klotho gene promoter activity. A point mutation in the Egr-1-binding motif abrogated promoter inducibility by EGF or ectopic Egr-1 expression. Knockdown of Egr-1 by expression of small interfering RNA (siRNA) attenuated EGF-induced ...
Source: Gene - November 11, 2009 Category: Genetics & Stem Cells Authors: Choi BH, Kim CG, Lim Y, Lee YH, Shin SY Tags: Gene Source Type: journals

Cytokinin Overproduction-Caused Alteration of Flower Development Is Partially Mediated by CUC2 and CUC3 in Arabidopsis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cytokinin is an essential regulator of numerous plant growth and developmental processes. However, less is known about the mechanisms of cytokinin-regulated floral development. In the present study, we found that flower-specific elevation of cytokinin through transgenic expression of an Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene under the control of the APETALA1 (AP1) promoter lead to floral developmental alterations. These changes included promotion of the number of flowers, and abnormal development of flowers, which were correlated with enlarged inflorescence and flower meristems. Genome-wide expressi...
Source: Gene - November 10, 2009 Category: Genetics & Stem Cells Authors: Li XG, Su YH, Zhao XY, Li W, Gao XQ, Zhang XS Tags: Gene Source Type: journals

Comparative Genomics Identifies New Alpha Class Genes within the Avian Glutathione S-transferase Gene Cluster.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study identifies the alpha-class tGST gene clutster and genetic markers (SNPs, single nucleotide polymorphisms) that can be used to further examine AFB(1) susceptibility and resistance in turkeys. Functional characterization of heterologously-expressed proteins from these genes is currently underway. PMID: 19913078 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - November 10, 2009 Category: Genetics & Stem Cells Authors: Kim JE, Bauer MM, Mendoza KM, Reed KM, Coulombe RA Tags: Gene Source Type: journals

Epigenetic Regulation of Caspase-3 Gene Expression in Rat Brain Development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The expression levels of caspase-3, a major contributor to the execution of neuronal apoptosis, markedly decrease in the process of brain maturation. We have previously cloned the rat caspase-3 gene promoter and identified its essential regulatory elements. In the present study, we extended previous findings by examining transcriptional regulation of caspase-3 expression in the rat brain of two different ages, corresponding to the immature and mature brain. In particular, we determined that the rate of transcription initiation substantially declines during brain maturation. Furthermore, we established that mRNA levels ...
Source: Gene - November 9, 2009 Category: Genetics & Stem Cells Authors: Yakovlev A, Khafizova M, Abdullaev Z, Loukinov D, Kondratyev A Tags: Gene Source Type: journals

Dual transcriptional regulation by runx2 of matrix Gla protein in Xenopus laevis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Matrix Gla protein (MGP) is an extracellular mineral-binding protein expressed in several tissues but it only accumulates in bone and calcified cartilage under physiological conditions. Available evidence indicates that it acts as a physiological inhibitor of mineralization. Runx2 is a transcription factor essential for bone formation in mammals, affecting osteoblast and chondrocyte differentiation by regulating key genes crucial for bone and cartilage development. Being an important cartilage-associated gene, MGP is a potential target for Runx2, and thus we have investigated the possible functional interactions betwee...
Source: Gene - November 4, 2009 Category: Genetics & Stem Cells Authors: Fazenda C, Simões B, Kelsh RN, Cancela ML, Conceição N Tags: Gene Source Type: journals

Expression and regulation of IL-22 by bovine peripheral blood gamma/delta T cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
IL-22 is a novel T and NK cell cytokine that belongs to the IL-10 cytokine family. Here we report the identification of a bovine IL-22 ortholog that is expressed by mitogen activated bovine peripheral blood gamma/delta T cells. The full-length bovine IL-22 cDNA contained a 68 bp 5'-untranslated region (UTR), a 570 bp open reading frame, and a 480 bp 3'-UTR. The deduced pre-IL-22 has 190 amino acid residues containing a secretory signal peptide from amino acids 1-33 and several potential N-glycosylation sites. The mature protein is predicted to be a secreted, alpha-helical molecule. The bovine IL-22 gene is ~7.5 kb in l...
Source: Gene - October 28, 2009 Category: Genetics & Stem Cells Authors: Ma SD, Lancto CA, Enomoto S, Abrahamsen MS, Rutherford MS Tags: Gene Source Type: journals

Phylogenesis of Brain Derived Neurotrophic Factor (BDNF) in Vertebrates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Brain-Derived Neurotrophic Factor (BDNF) belongs to neurotrophin family, a class of molecules playing key roles in neuronal development, survival and regeneration, neurite growth and plasticity: memory processes are mainly affected, and mutations of the human BDNF gene are associated to cognitive and behavioural disturbances. All neurotrophins contain a highly conserved C-terminal domain and bind to the same receptor family. Both correct folding and post-translational processing of the entire preproprotein are pivotal for sorting to the extra cellular space, dimerization and receptor binding. Evolutionary studies condu...
Source: Gene - October 28, 2009 Category: Genetics & Stem Cells Authors: Tettamanti G, Cattaneo AG, Gornati R, de Eguileor M, Bernardini G, Binelli G Tags: Gene Source Type: journals

Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5'- and 3'- ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1,316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups set up by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally S. ...
Source: Gene - October 23, 2009 Category: Genetics & Stem Cells Authors: Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A Tags: Gene Source Type: journals

Molecular mechanisms of turtle anoxia tolerance: A role for NF-kappaB.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The transcription factor NF-kappaB has recently emerged as a central regulator of the vertebrate stress response, controlling hundreds of different effector genes. We hypothesized that this transcription factor would be activated during oxygen deprivation in the anoxia-tolerant freshwater turtle, Trachemys scripta elegans. Western immunoblotting was used to examine the relative expression levels of the phosphorylated NF-kappaB inhibitor, IkappaBalpha, under normoxic and anoxic conditions in turtle tissues. Elevated levels of the phosphorylated IkappaB were found in the liver in response to 5 h of anoxia, suggesting a p...
Source: Gene - October 23, 2009 Category: Genetics & Stem Cells Authors: Krivoruchko A, Storey KB Tags: Gene Source Type: journals

A Genome-wide Linkage Scan in German Shepherd Dogs Localizes Canine Platelet Procoagulant Deficiency (Scott Syndrome) to Canine Chromosome 27.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Scott syndrome is a rare hereditary bleeding disorder associated with an inability of stimulated platelets to externalize the negatively charged phospholipid, phosphatidylserine (PS). Canine Scott syndrome (CSS) is the only naturally-occurring animal model of this defect and therefore represents a unique tool to discover a disease gene capable of producing this platelet phenotype. We undertook platelet function studies and linkage analyses in a pedigree of CSS-affected German shepherd dogs. Based on residual serum prothrombin and flow cytometric assays, CSS segregates as an autosomal recessive trait. An initial genome ...
Source: Gene - October 22, 2009 Category: Genetics & Stem Cells Authors: Brooks M, Etter K, Catalfamo J, Brisbin A, Bustamante C, Mezey J Tags: Gene Source Type: journals

One-step identification of conserved miRNAs, their targets, potential transcription factors and effector genes of complete secondary metabolism pathways after 454 pyrosequencing of calyx cDNAs from the Labiate Salvia sclarea L.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The outermost floral whorl, composed of sepals, is generally thought to function in the protection of reproductive tissues. In the plant family Lamiaceae, sepals are fused into a tube that is densely covered by hairs for mechanical defence and contains secondary metabolites for chemical defence against insects and abiotic stresses. Despite the importance of this tissue in plant fitness, virtually no study has addressed the basic aspects of sepal development and functioning. Because of its large size and its impressive metabolic activity (both in terms of quantity and diversity of secondary metabolites), we have used cl...
Source: Gene - October 15, 2009 Category: Genetics & Stem Cells Authors: Legrand S, Valot N, Nicolé F, Moja S, Baudino S, Jullien F, Magnard JL, Caissard JC, Legendre L Tags: Gene Source Type: journals

Screening of human gene promoter activities using transfected-cell arrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Promoters are the best characterized transcriptional regulatory sequences in complex genomes because of their predictable location immediately upstream of transcription start sites. Despite a substantial body of literature describing transcriptional promoters, the identification of true start sites for all human transcripts is far from complete. The same is true of the key structural and functional elements responsible for promoter action in different cell types. In order to identify elements responsible for promoter activity, we applied transfected-cell array technology to functionally evaluate promoters for genes inv...
Source: Gene - October 15, 2009 Category: Genetics & Stem Cells Authors: Cheng X, Guerasimova A, Manke T, Rosenstiel P, Haas S, Warnatz HJ, Querfurth R, Nietfeld W, Vanhecke D, Lehrach H, Yaspo ML, Janitz M Tags: Gene Source Type: journals

Genetic Variation and Demographic History of the Haplochromis laparogramma Group of Lake Victoria-An Analysis Based on SINEs and Mitochondrial DNA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we examined the population structure and historical demography of 3 pelagic haplochromine cichlid species that resemble in morphology and have similar niche, Haplochromis (Yssichromis) laparogramma, H. (Y.) pyrrhocephalus and H. (Y.) sp. "glaucocephalus". We investigated the sequences of the mitochondrial DNA control region and the insertion patterns of short interspersed elements (SINEs) of 759 individuals. We show that sympatric forms are genetically differentiated in 4 of 6 cases, but we also found apparent weakening of the genetic differentiation in areas with turbid water. We estimated the timings of po...
Source: Gene - October 14, 2009 Category: Genetics & Stem Cells Authors: Mzighani SI, Nikaido M, Takeda M, Seehausen O, Budeba YL, Ngatunga BP, Katunzi EF, Aibara M, Mizoiri S, Sato T, Tachida H, Okada N Tags: Gene Source Type: journals

The Idefix enhancer-blocking insulator also harbors barrier activity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Chromatin insulators are cis-regulatory sequences participating to the regulation of gene expression. Their presence within the genome is associated with two main functions. One of them is an enhancer-blocking function that blocks enhancer-promoter communication when the insulator is located in between. The second is a boundary or barrier function that insulates independent units of transcription. This latter is observed when two insulators flanking a gene and its regulatory sequences block the regulatory influences of surrounding chromatin. Some years ago, we reported the presence of an insulator within the retrotrans...
Source: Gene - October 7, 2009 Category: Genetics & Stem Cells Authors: Brasset E, Hermand C, Jensen S, Vaury C Tags: Gene Source Type: journals

Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Phylogenetic analyses of several marker genes have previously shown that Asian primate Plasmodium species (malaria parasites) were monophyletic including Plasmodium vivax, one of the four malaria parasites that infect humans. However, except for the presence of a few established groupings, phylogenetic relationships among the Asian primate Plasmodium species + P. vivax group have neither been clearly resolved with confident statistical supports, nor the closest relative to P. vivax was elucidated. Since comparative biological studies between P. vivax and its closest relative would provide valuable information on immuno...
Source: Gene - October 6, 2009 Category: Genetics & Stem Cells Authors: Mitsui H, Arisue N, Sakihama N, Inagaki Y, Horii T, Hasegawa M, Tanabe K, Hashimoto T Tags: Gene Source Type: journals

The Origin of Peroxisome: Possibility of an Actinobacteria Symbiosis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Peroxisome is an organelle found in most eukaryotes crucial for lipid metabolism. The ability of peroxisome to divide themselves and to transport post-translational proteins suggest a hypothesis that peroxisome has an endosymbiont origin. However, the localization of peroxisomal proteins also in the endoplasmic reticulum (ER), and the similarity of some peroxisomal proteins to those localized in the ER suggest other hypothesis that peroxisome was developed from the ER. To study the evolutionary distance of peroxisome to ER and Prokaryotes, we have carried out a phylogenetic analysis of the CDC48 (cell division control ...
Source: Gene - October 5, 2009 Category: Genetics & Stem Cells Authors: Duhita N, Satoshi S, Kazuo H, Daisuke M, Takao S Tags: Gene Source Type: journals

Mitochondrial rRNA secondary structures and genome arrangements distinguish chelicerates: Comparisons with a harvestman (Arachnida: Opiliones: Phalangium opilio).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Arachnids are a highly diverse group of arthropods, and many of the mitochondrial genomes that have been sequenced from arachnids possess unusual features in their inferred gene structures and genome organization. The first complete sequence of a mitochondrial genome from the arachnid order Opiliones (harvestmen) is presented here. Secondary structures of the two mitochondrial ribosomal subunits of Phalangium opilio are inferred and compared to mitochondrial rRNA structures of a hexapod and a chelicerate. The large subunit rRNA of P. opilio is found to have more helices conserved than in other arthropods, while the sma...
Source: Gene - September 29, 2009 Category: Genetics & Stem Cells Authors: Masta SE Tags: Gene Source Type: journals

Identification of LATS transcriptional targets in HeLa cells using whole human genome oligonucleotide microarray.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Human LATS1 and LATS2) (LATS1/2) are tumor suppressors that have been shown to be mutated or downregulated in several human cancers including leukemia, lung, prostate and breast cancers. However, the precise mechanisms and the proteins modulated by LATS1/2 that are responsible for these events remain largely unknown. To elucidate potential signaling pathways, the current study investigated the expression profile in HeLa cells with reduced expression of LATS1/2. Using RNA-mediated interference, both LATS1 and LATS2 were substantially knocked-down, and accordingly, this lead to an increase in multiple phenotypes associat...
Source: Gene - September 28, 2009 Category: Genetics & Stem Cells Authors: Stacy Visser , Yang X Tags: Gene Source Type: journals

Clonal diversity in Giardia duodenalis isolates from Thailand: Evidences for intragenic recombination and purifying selection at the beta giardin locus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The beta giardin locus of Giardia duodenalis encodes a structural component of ventral disc and exhibits sequence variation among isolates rendering it a useful marker for genotypic analysis. To determine the distribution of genotypes of G. duodenalis in Thailand and to explore the extent of sequence variation in this locus, we deployed the PCR-RFLP method and sequence analysis of recombinant subclones from 30 clinical isolates. In total, assemblage B was more prevalent than assemblage A. Sequence analysis revealed that 13 isolates had clonal mixtures, comprising three to five distinct sequences per isolate. Nucleotide...
Source: Gene - September 27, 2009 Category: Genetics & Stem Cells Authors: Kosuwin R, Putaporntip C, Pattanawong U, Jongwutiwes S Tags: Gene Source Type: journals

The histone demethylase Dmel\Kdm4A controls genes required for lifespan and male-specific sex-determination in Drosophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Histone methylation plays an important role in regulating chromatin-mediated gene control and epigenetic-based memory systems that direct cell fate. Enzymes termed histone demethylases directly remove the methyl marks from histones, thus contributing to a dynamically regulated histone methylated genome, however the biological functions of these newly identified enzymes remains unclear. The JMJD2A-D family belongs to the JmjC domain-containing family of histone demethylases (JHDMs). Here, we report the cloning and functional characterization of the Drosophila HDM gene Dmel\Kdm4A that is a homolog of the human JMJD2 fami...
Source: Gene - September 24, 2009 Category: Genetics & Stem Cells Authors: Lorbeck MT, Singh N, Zervos A, Dhatta M, Lapchenko M, Yang C, Elefant F Tags: Gene Source Type: journals

Mutational Analysis of Drosophila Basigin Function in the Visual System.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Drosophila basigin is a cell-surface glycoprotein of the Ig superfamily and a member of a protein family that includes mammalian EMMPRIN/CD147/basigin, neuroplastin, and embigin. Our previous work on Drosophila basigin has shown that it is required for normal photoreceptor cell structure and normal neuron-glia interaction in the fly visual system. Specifically, the photoreceptor neurons of mosaic animals that are mutant in the eye for basigin show altered cell structure with nuclei, mitochondria and rER misplaced and variable axon diameter compared to wild-type. In addition, glia cells in the optic lamina that contact ...
Source: Gene - September 23, 2009 Category: Genetics & Stem Cells Authors: Munro M, Akkam Y, Curtin KD Tags: Gene Source Type: journals

High divergence across the whole mitochondrial genome in the "pan-Antarctic" springtail Friesea grisea: evidence for cryptic species?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Collembola are one of the few hexapod groups adapted to live in the harsh environmental conditions of Antarctic terrestrial ecosystems. Diversity is limited to a few species which can be very abundant in coastal deglaciated sites. A remarkable lack of overlap in Collembola species composition is evident between Western and Eastern Antarctica, and Friesea grisea is currently the only species whose distribution is thought to span these two main regions of the continent. However, our analysis of the complete sequences of the mitochondrial genomes from specimens obtained from each of the two regions showed unexpected genet...
Source: Gene - September 23, 2009 Category: Genetics & Stem Cells Authors: Torricelli G, Carapelli A, Convey P, Nardi F, Boore JL, Frati F Tags: Gene Source Type: journals

Genomic organization and embryonic expression of miR-430 in medaka (Oryzias latipes): insights into the post-transcriptional gene regulation in early development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs, miRs) are short noncoding RNA molecules that negatively control the target mRNAs by binding to the 3' untranslated region (UTR). Previous studies have demonstrated that miR-430 is encoded by a clustered multigene family and is abundantly expressed in early development. In zebrafish, miR-430 is needed to suppress primordial germ cell (PGC)-specific genes, such as nanos1, in somatic cells. However, the molecular characteristics of the miR-430 family in other teleost species have not been reported, and it is unclear whether such a function of miR-430 in PGC specification is a conserved feature of animal...
Source: Gene - September 17, 2009 Category: Genetics & Stem Cells Authors: Tani S, Kusakabe R, Naruse K, Sakamoto H, Inoue K Tags: Gene Source Type: journals

Identification of Wnt4 as the ovary pathway gene and temporal disparity of its expression vis-a-vis testis genes in the garden lizard, Calotes versicolor.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sex determination in the Indian garden lizard, Calotes versicolor, which lacks sex-chromosomes and temperature dependent sex determination, appears to be genically controlled, and previous studies have identified orthologues of Sox9, Dmrt1 and Androgen receptor (AR) as genes involved in testis differentiation in genetic males. In the pursuit of female pathway genes in this species, the present paper deals with the identification of Wnt4 and Dax1 genes in C. versicolor and their expression in embryonic gonad. CvDax1 is expressed throughout the development in certain embryos from day 5 onwards but shows no clear associat...
Source: Gene - September 10, 2009 Category: Genetics & Stem Cells Authors: Tripathi V, Raman R Tags: Gene Source Type: journals

Clan CD of cysteine peptidases as an example of evolutionary divergences in related protein families across plant clades.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Comparative genomic analyses are powerful tools that can be used to analyze the presence, conservation and evolution of protein families and to elucidate issues concerning their function. To deal with these questions, we have chosen the clan CD of cysteine peptidases, which is formed by different protein families that play key roles in plants. An evolutionary comparative analysis of clan CD cysteine peptidases in representative species of different taxonomic groups that appeared during the evolution of the Viridiplantae was performed. The results obtained indicates: i) C13 GPI:protein transamidases, C14 metacaspases I ...
Source: Gene - September 10, 2009 Category: Genetics & Stem Cells Authors: Cambra I, Garcia FJ, Martinez M Tags: Gene Source Type: journals

Independent and parallel lateral transfer of DNA transposons in tetrapod genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In animals, the mode of transmission of transposable elements is generally vertical. However, recent studies have suggested that lateral transfer has occurred repeatedly in several distantly related tetrapod lineages, including mammals. Using transposons extracted from the genome of the lizard Anolis carolinensis as probes, we identified four novel families of hAT transposons that share extremely high similarity with elements in other genomes including several mammalian lineages (primates, chiropters, marsupials), one amphibian and one flatworm, the planarian Schmidtea mediterranea. The discontinuous phylogenetic distr...
Source: Gene - September 8, 2009 Category: Genetics & Stem Cells Authors: Novick P, Smith J, Ray D, Boissinot S Tags: Gene Source Type: journals

Unique genome of dicyemid mesozoan: highly shortened spliceosomal introns in conservative exon/intron structure.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dicyemids are enigmatic endoparasites, or endosymbionts, living in the renal sac of benthic cephalopod molluscs. The body of dicyemids consists of only 9-41cells, with neither extracellular matrices nor differentiated tissues. Due to the unusually simple body organization, dicyemids have long been the subject of phylogenetic controversy. Molecular evidences suggest dicyemids are lophotrochozoans that have secondarily lost many morphological characters. We studied 40 genes of the dicyemid Dicyema japonicum, and found that their spliceosomal introns are very short (mean length=26bp). This size was shorter than that of in...
Source: Gene - September 7, 2009 Category: Genetics & Stem Cells Authors: Ogino K, Tsuneki K, Furuya H Tags: Gene Source Type: journals

Rotifer rDNA-Specific R9 Retrotransposable Elements Generate an Exceptionally Long Target Site Duplication upon Insertion.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ribosomal DNA genes in many eukaryotes contain insertions of non-LTR retrotransposable elements belonging to the R2 clade. These elements persist in the host genomes by inserting site-specifically into multicopy target sites, thereby avoiding random disruption of single-copy host genes. Here we describe R9 retrotransposons from the R2 clade in the 28S RNA genes of bdelloid rotifers, small freshwater invertebrate animals best known for their long-term asexuality and for their ability to survive repeated cycles of desiccation and rehydration. While the structural organization of R9 elements is highly similar to that of o...
Source: Gene - September 6, 2009 Category: Genetics & Stem Cells Authors: Gladyshev EA, Arkhipova IR Tags: Gene Source Type: journals

Esophageal cancer related gene 4 (ECRG4) is a marker of articular chondrocyte differentiation and cartilage destruction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
With the aim of identifying novel genes regulating cartilage development and degeneration, we screened a cartilage-specific expressed sequence tag database. Esophageal cancer related gene 4 (ECRG4) was selected, based on the criteria of 'chondrocyte-specific' and 'unknown function'. ECRG4 expression was particularly abundant in chondrocytes and cartilage, compared to various other mouse tissues. ECRG4 is a secreted protein that undergoes cleavage after secretion. The protein is specifically expressed in chondrocytes in a manner dependent on differentiation status. The expression is very low in mesenchymal cells, and dr...
Source: Gene - September 3, 2009 Category: Genetics & Stem Cells Authors: Huh YH, Ryu JH, Shin S, Lee DU, Yang S, Oh KS, Chun CH, Choi JK, Song WK, Chun JS Tags: Gene Source Type: journals

A potent enhancer element in the 5'-UTR intron is crucial for transcriptional regulation of the human ubiquitin C gene.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ubiquitin (Ub) plays a crucial role in almost every aspect of cellular functions. It is encoded by four genes, of which UbC is known to meet cell demand for ubiquitin in both basal and stressful conditions. To understand the molecular mechanisms regulating UbC gene expression, we performed a functional characterization of the UbC promoter. Deletion analyses on the 5' end of the -916/+878 promoter region, excluded the functional importance of nt -916/-371 in the transcriptional regulation of the gene, while 3' deletions revealed that intron removal (nt +65/+876) resulted in a marked reduction of promoter activity in all...
Source: Gene - September 1, 2009 Category: Genetics & Stem Cells Authors: Bianchi M, Crinelli R, Giacomini E, Carloni E, Magnani M Tags: Gene Source Type: journals

Alpha-fetoprotein related gene (ARG): A new member of the albumin gene family that is no longer functional in primates.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The serum albumin gene family is comprised of albumin, alpha-fetoprotein, alpha-albumin (afamin), and the more distantly related Vitamin D binding protein. These genes arose from a common ancestor through a series of duplication events, are expressed primarily in the liver and tightly linked in all species where this has been investigated. Here, we describe a fifth member of the albumin gene family that we have named Alpha-fetoprotein Related Gene (ARG) since it exhibits greatest similarity to this family member. ARG is activated in the liver perinatally, but is expressed at very low levels. The ARG gene is present and...
Source: Gene - September 1, 2009 Category: Genetics & Stem Cells Authors: Naidu S, Peterson ML, Spear BT Tags: Gene Source Type: journals

The intergenic region between the Mouse Recql4 and Lrrc14 genes functions as an evolutionary conserved bidirectional promoter.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mammalian genomes are highly complex, with neighbouring genes arranged in divergent, convergent, tandem, anti-sense, and interleaving fashions. Despite the vast genomic space, a substantial portion of human genes (10%) are arranged in a divergent, head-to-head fashion and controlled by bidirectional promoters. Here we define a small core bidirectional promoter that drives expression of the mouse genes Recql4, on one strand, and Lrrc14; a novel member of the LRR gene family, on the opposite strand. Regulation of Lrrc14 expression is highly complex, involving multiple promoters' and alternative splicing. Expression of th...
Source: Gene - August 27, 2009 Category: Genetics & Stem Cells Authors: Uwanogho DA, Yasin SA, Starling B, Price J Tags: Gene Source Type: journals

The hobo Transposon and hobo-Related Elements are Expressed as Developmental Genes in Drosophila.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Transposable elements comprise a significant part of genomes and are involved in their evolvability. The hobo element is found as an active Class II transposable element in Drosophila melanogaster that is able to induce gonadal dysgenesis. Some hobo-related sequences (hRSs) are thought to be relics of old "hobo" invasions, and are therefore ancient genomic constituents. However, some of these hRSs are still mobile. The present study analyzed the expression pattern of hobo and a particular type of hRSs, hobo(VAHS). Both elements were shown to be expressed as sense and antisense mRNA transcripts. Expression analysis in w...
Source: Gene - August 27, 2009 Category: Genetics & Stem Cells Authors: Deprá M, da Silva Valente VL, Margis R, da Silva Loreto EL Tags: Gene Source Type: journals

Genomic organization and functional characterization of the promoter for the human suppressor of cytokine signaling 6 gene.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we report the expression and genomic structure of the gene encoding human suppressor of cytokine signaling 6 (SOCS6), and the characterization of the functional promoter region. The human SOCS6 gene, spanning 40 kb on chromosome 18q22.2, is composed of two exons separated by an intron of 35 kb. Two transcripts are ubiquitously expressed, and both encode the full-length open reading frame of SOCS6. A primer extension assay revealed that the major transcription initiation site is located 469 bp upstream the ATG codon. Luciferase promoter analysis demonstrated that the 5'-flanking region is able to drive transc...
Source: Gene - August 26, 2009 Category: Genetics & Stem Cells Authors: Lai RH, Wang MJ, Yang SH, Chen JY Tags: Gene Source Type: journals

Multiple Chicken Repeat 1 (CR1) Lineages in the Genomes of Oestroid Flies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study was designed to identify lineages of CR1 elements in the genomes of forensically important oestroid flies and to further characterize one family, Sbul.CR1B. CR1 fragments from several taxa were amplified, cloned, sequenced and analyzed to identify different lineages of elements. A variety of retrotransposon families were recovered that exhibit similarity to known retrotransposon families. A number of these lineages may have given rise to taxon-specific subfamilies that have been recently active in oestroid fly genomes. One element from Sarcophaga bullata was analyzed in detail to reconstruct a partial Open Readi...
Source: Gene - August 26, 2009 Category: Genetics & Stem Cells Authors: Thompson ML, Gauna AE, Williams ML, Ray DA Tags: Gene Source Type: journals

Automatic Classification within families of transposable elements: application to the mariner family.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The higher levels of the classification of transposable elements (TEs) from Classes to Superfamilies or Families, is regularly updated, but the lower levels (below the Family) have received little investigation. In particular, this applies to the Families that include a large number of copies. In this article we propose an automatic classification of DNA sequences. This procedure is based on an aggregation process using a pairwise matrix of distances, allowing us to define several groups characterized by a sphere with a central sequence and a radius. This method was tested on the mariner Family, because this is probabl...
Source: Gene - August 25, 2009 Category: Genetics & Stem Cells Authors: Rouault JD, Casse N, Chénais B, Hua-Van A, Filée J, Capy P Tags: Gene Source Type: journals

Genome of a virulent bacteriophage Lb338-1 that lyses the probiotic Lactobacillus paracasei cheese strain.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is a lack of fundamental knowledge about the influence of bacteriophage on probiotic bacteria and other commensals in the gut. Here, we present the isolation and morphological and genetic characterization of a virulent narrow-host-range bacteriophage, phiLb338-1. This phage was isolated from fresh sewage and was shown to infect the probiotic cheese strain Lactobacillus paracasei NFBC 338. Electron microscopy studies revealed that phiLb338-1 is a member of the Myoviridae family, with an isometric head, a medium-size contractile tail and a complex base plate. Genome sequencing revealed a 142 kb genome with 199 open...
Source: Gene - August 23, 2009 Category: Genetics & Stem Cells Authors: Alemayehu D, Ross RP, O'Sullivan O, Coffey A, Stanton C, Fitzgerald GF, McAuliffe O Tags: Gene Source Type: journals

Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Close to 50 % of the human genome harbors repetitive sequences originally derived from mobile DNA elements, and in normal cells this sequence compartment is tightly regulated by epigenetic silencing mechanisms involving chromatin-mediated repression. In cancer cells, repetitive DNA elements suffer abnormal demethylation, with potential loss of silencing. We used a genome-wide microarray approach to measure DNA methylation changes in cancers of the head and neck, and to compare these changes to alterations found in adjacent non-tumor tissues. We observed specific alterations at thousands of small clusters of CpG dinucle...
Source: Gene - August 19, 2009 Category: Genetics & Stem Cells Authors: Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM Tags: Gene Source Type: journals

Initial characterization of a recombinant kynureninase from Trypanosoma cruzi identified from an EST database.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Kynureninase has been described in bacteria, fungi and animals as an enzyme involved in the catabolic degradation pathway of L-tryptophan. This pyridoxal 5'-phosphate (PLP)-dependent enzyme catalyzes the hydrolytic cleavage of L-kynurenine and 3-hydroxy-L-kynurenine to yield L-alanine and either anthranilic or 3-hydroxyanthranilic acid, respectively. We identified a putative kynureninase gene from a T. cruzi project aiming at the structural and functional characterization of more than 100 proteins differentially expressed during metacyclogenesis. This gene encodes a protein similar in size and sequence to kynureninases...
Source: Gene - August 18, 2009 Category: Genetics & Stem Cells Authors: Ecco G, Vernal J, Razzera G, Tavares C, Serpa VI, Arias S, Marchini FK, Krieger MA, Goldenberg S, Terenzi H Tags: Gene Source Type: journals

Identification of conserved Aquilegia coerulea microRNAs and their targets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides a phylogenetically important dataset for plant microRNA evolution studies. The current study is the first to identify miRNAs in a lower eudicot in which comprehensive genomic resources are becoming available. PMID: 19699282 [PubMed - as supplied by publisher] (Source: Gene)
Source: Gene - August 18, 2009 Category: Genetics & Stem Cells Authors: Puzey JR, Kramer EM Tags: Gene Source Type: journals

Identification of novel LTR retrotransposons in the genome of Aedes aegypti.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have detected seventy-six novel LTR retrotransposons in the genome of the mosquito Aedes aegypti by a genome wide analysis using the LTR_STRUC program. We have performed a phylogenetic classification of these novel elements and a distribution analysis in the genome of A. aegypti. These mobile elements belong either to the Ty3/gypsy or to the Bel family of retrotransposons and were not annotated in the mosquito LTR retrotransposon database (TEfam). We have found that approximately 1.8% of the genome is occupied by these newly detected retrotransposons that are distributed predominantly in intergenic genomic sequences...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Minervini CF, Viggiano L, Caizzi R, Marsano RM Tags: Gene Source Type: journals

Special issue on phylogenomics and its future.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19374942 [PubMed - indexed for MEDLINE] (Source: Gene)
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Okada N Tags: Gene Source Type: journals

Characterization of the Haloarcula hispanica amyH gene promoter, an archaeal promoter that confers promoter activity in Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Archaea form a third domain of life that is distinct from Bacteria and Eukarya. According to the current knowledge, the basal transcription machinery of Archaea (including the core promoter architecture, the RNA polymerase, and the basal transcription factors) closely resembles that of Eukarya in structure and function, while differing considerably from the bacterial paradigm. In the present study, the promoter region of the halophilic archaeon Haloarcula hispanica's amyH gene was isolated and characterized, and it was surprisingly revealed that the amyH gene promoter could confer promoter activity (i.e., drive transcr...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Zeng C, Zhao YZ, Cui CZ, Zhang H, Zhu JY, Tang XF, Shen P, Huang YP, Chen XD Tags: Gene Source Type: journals

Identification of a minimal cis-element and cognate trans-factor(s) required for induction of Rac2 gene expression during K562 cell differentiation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study investigates the mechanisms responsible for increased Rac2 gene expression during myeloid cell differentiation. Treatment of K562 chronic myelogenous leukemia cells with phorbol-12-myristate-13-acetate (PMA) induces megakaryocytic differentiation and Rac2 gene transcription following a lag of 6-12 h. Promoter/luciferase reporter gene assays reveal that a 135 bp cis-element located between -4223 and -4008 bp upstream of the Rac2 transcription start site is necessary and sufficient for PMA-induced gene expression. The AP1 transcription factor binds to three cis-elements within the 135 bp Rac2 gene regulatory regio...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Muthukrishnan R, Skalnik DG Tags: Gene Source Type: journals

Activation of the brain-specific neurogranin gene in murine T-cell lymphomas by proviral insertional mutagenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report here on retroviral activation of the Nrgn gene in tumors induced by the T-cell lymphomagenic SL3-3 murine leukemia virus. We have performed a systematic expression analysis of Nrgn in various mouse tissues and SL3-3 induced T-cell tumors. This demonstrated that insertional activation of Nrgn increased RNA and protein expression levels to that observed in brain. Furthermore, elevated Nrgn expression was also observed in some T-cell tumors with no detected provirus integrations into this genomic region. The presented data demonstrate that Nrgn can be produced at high levels outside the brain, and suggest a novel on...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Nielsen AA, Kjartansdóttir KR, Rasmussen MH, Sørensen AB, Wang B, Wabl M, Pedersen FS Tags: Gene Source Type: journals

Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study we sequenced 10 mature chloroplast mRNAs, the chloroplast 16S rRNA and a partial chloroplast 23S rRNA from the dinoflagellate Heterocapsa triquetra, and found multiple types of substitutional editing, with A-to-G editing predominating. A-to-G editing of mRNAs converts two unusual AUA start codons into conventional AUG start codons, but three AUA start codons are not edited, showing that this dinoflagellate chloroplast has three possible start codons: AUG, AUA and UUG. To analyze the editing effects on rRNAs, we computationally predicted the secondary structure of the 16S rRNA based on the E. coli model. There...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Dang Y, Green BR Tags: Gene Source Type: journals

Purple acid phosphatase-like sequences in prokaryotic genomes and the characterization of an atypical purple alkaline phosphatase from Burkholderia cenocepacia J2315.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Purple acid phosphatases (PAP) are a group of dimetallic phosphohydrolase first identified in eukaryotes. Bioinformatics analysis revealed 57 prokaryotic PAP-like sequences in the genomes of 43 bacteria and 4 cyanobacteria species. A putative PAP gene (BcPAP) from the bacteria Burkholderia cenocepacia J2315 was chosen for further studies. Synteny analysis showed that this gene is present as an independent gene in most of the members of the genus Burkholderia. The predicted 561 a.a. polypeptide of BcPAP was found to harbour all the conserved motifs of the eukaryotic PAPs and an N-terminal twin-arginine translocation sig...
Source: Gene - June 28, 2009 Category: Genetics & Stem Cells Authors: Yeung SL, Cheng C, Lui TK, Tsang JS, Chan WT, Lim BL Tags: Gene Source Type: journals