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At least 145 records · Page 8Linked to original sources

Functional conservation of the fruitless male sex-determination gene across 250 Myr of insect evolution.

Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the muscle of Lawrence (MOL), an abdominal muscle that develops in males but not in females. We have isolated the fru ortholog from the malaria mosquito Anopheles gambiae and show the gene's conserved genomic structure. We demonstrate that male-specific mosquito fru protein isoforms arise by conserved mechanisms of sex-specifically activated and alternative exon splicing. A male-determining function of mosquito fru is revealed by ectopic expression of the male mosquito isoform FRUMC in fruit flies; this results in MOL development in both fru-mutant males and fru+ females who otherwise develop no MOL. In parallel, we provide evidence of a unique feature of muscle differentiation within the fifth abdominal segment of male mosquitoes that strongly resembles the fruit fly MOL. Given these conserved features within the context of 250 Myr of evolutionary divergence between Drosophila and Anopheles, we hypothesize that fru is the prototypic gene of male sexual behavior among dipteran insects.

Abdomen↗

Iroquois genes: genomic organization and function in vertebrate neural development.

We review recent work that shows that the iroquois (Iro/Irx) homeobox genes have conserved genomic organization in Drosophila and vertebrates. In addition, these genes play pivotal functions in the initial specification of the vertebrate neuroectoderm, and, in collaboration with other transcription factors, later subdivision of the anterior-posterior and dorso-ventral axis of the neuroectoderm.

Animals↗

Assembly and Characterization of the First Complete Mitochondrial Genome of Tussilago farfara L.: Insights into Biological Functions and Phylogenetic Relationships within the Asteraceae Family.

Tussilago farfara L., a member of the Asteraceae family, is an economically valuable species due to its edible and medicinal properties. To elucidate the structural characteristics, genetic mechanisms, and evolutionary pathways of the organelle genomes of T. farfara, we sequenced, assembled, and annotated its mitochondrial genome for the first time. The complete mitochondrial genome of T. farfara spans 306,024 bp and contains 33 mitochondrial protein-coding genes (PCGs), 3 rRNAs, and 22 tRNAs. Analysis of the nucleotide substitution rate and genetic diversity revealed that most mitochondrial genome genes may have undergone purifying selection, indicating a slow evolutionary rate and a relatively conserved genomic structure. We further identified 13 fragments of chloroplast-derived DNA integrated into the mitochondrial genome, evidencing intracellular gene transfer. Collinearity analysis showed that Arctium lappa shares the most extensive mitochondrial homologous sequences and the highest sequence similarity with T. farfara. Phylogenetic analysis based on the mitochondrial genome helped to clarify the evolutionary and taxonomic position of T. farfara within the Asteraceae family. The mitochondrial genome sequence of T. farfara provides a valuable genomic resource for species identification and for evolutionary studies within the Asteraceae family.

Genome, Mitochondrial↗

Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments.

A power-law distribution of the length of perfectly conserved sequence from mouse/human whole-genome intersection and alignment is exhibited. Spatial correlations of these elements within the mouse genome are studied. It is argued that these power-law distributions and correlations are comprised in part by functional noncoding sequence and ought to be accounted for in estimating the statistical significance of apparent sequence conservation. These inter-genomic correlations of conservation are placed in the context of previously observed intra-genomic correlations, and their possible origins and consequences are discussed.

Animals↗

Sequence analysis of the porcine IFNAR1 and IFNGR2 genes.

A porcine BAC clone harboring the tightly linked IFNAR1 and IFNGR2 genes was identified by comparative analysis of the publicly available porcine BAC end sequences. The complete 168,835 bp insert sequence of this clone was determined. Sequence comparisons of the genomic sequence with EST sequences from public databases were performed and allowed a detailed annotation of the IFNAR1 and IFNGR2 genes. The analyzed genes showed a conserved genomic organization with their known mammalian orthologs, however the sequence conservation of these genes across species was relatively low. In addition to the IFNAR1 and IFNGR2 genes, which were completely sequenced, the analyzed BAC clone also contained parts of an orphan gene encoding a putative transmembrane protein (TMEM50B). In contrast to the IFNAR1 and IFNGR2 genes the sequence conservation of the TMEM50B gene across different mammalian species was extremely high.

Amino Acid Sequence↗

Analysis of the complete genome of indigenous swine hepatitis E virus isolated in Japan.

Using reverse transcription-polymerase chain reaction with primers derived from well-conserved genomic areas among all four hepatitis E virus (HEV) genotypes (I-IV), the HEV sequence was identified in serum samples obtained from 3 (3%) out of 95 60- to 90-day-old pigs in Japan and characterized molecularly. In the partial sequence of open reading frame (ORF) 2 of 421 nucleotides, the three swine isolates (swJ570, swJ681, and swJ791) showed the highest similarity of 83-87% to genotype III HEV representing human and swine strains (US1, US2, and swUS1) in the United States. The full-length nucleotide sequence of swJ570 consisted of 7225 nucleotides excluding the poly(A) tail and contained ORF 1 encoding 1703 amino acids (aa), ORF2 encoding 660 aa, and ORF3 encoding 122 aa. The swJ570 strain was most closely related to a Japanese strain (JRA1), which had been obtained from a hepatitis patient who had not traveled outside Japan. The overall nucleotide sequence identity between them was 89% and the deduced amino acid sequence identities of ORF1, ORF2, and ORF3 were 96, 99, and 98%, respectively. These results indicate that a certain proportion of pigs in Japan are HEV-viremic and may act as reservoirs of HEV infection, and that the presence of an indigenous strain(s) of HEV should be taken into consideration for the diagnosis of acute hepatitis in Japan.

3' Untranslated Regions↗

Strong phylogenetic signal from chloroplast genomes of three Barringtonia species provides the first genomic resources for their conservation.

BACKGROUND: The genus Barringtonia (Lecythidaceae) is a vital component of tropical coastal forests and mangrove ecosystems. Among its members, B. racemosa and B. fusicarpa are classified as Endangered and Vulnerable, respectively, due to habitat degradation and anthropogenic pressures, underscoring the urgent need for genetic studies to guide conservation. Chloroplast (cp.) genomes serve as essential resources for phylogenetic reconstruction and conservation genetics. However, the scarcity of cp. genome data for Barringtonia has limited comprehensive evolutionary and conservation-oriented investigations. RESULTS: We assembled and annotated the first complete cp. genomes of B. racemosa, B. fusicarpa, and B. acutangula. All three genomes exhibit the typical quadripartite structure, ranging from 158,959 bp (B. racemosa) to 159,837 bp (B. acutangula), and contain 132 genes (87 protein-coding, 37 tRNA, 8 rRNA) with a GC content of 36.68%-36.86%. Collinearity and IR boundary analyses revealed high structural conservation without large-scale rearrangements. Interspecific sequence-level variations were detected in simple sequence repeats (SSRs) and long repeats. Nucleotide diversity (π) analysis identified highly polymorphic regions, including rpl20 (π = 0.080), rpoA (π = 0.064), rps3 (π = 0.063), and ndhF (π = 0.060), which represent promising molecular markers for population genetics within the genus. Codon-based selection analyses (Ka/Ks) showed that all protein-coding genes are under strong purifying selection (mean Ka/Ks 0.32-0.37), with no evidence of positive selection. Pairwise genetic distances (p-distances) among Barringtonia species are extremely low (mean 0.0046), while distances to the related genus Bertholletia are ~ 6-fold higher, supporting their generic distinction. CONCLUSIONS: Phylogenetic analysis robustly supports Barringtonia as a monophyletic clade (bootstrap = 100%), with B. racemosa and B. fusicarpa forming a sister lineage to B. acutangula. This study provides the first high-quality cp. genome resources for the two threatened Barringtonia species, revealing strong structural and sequence conservation but no direct chloroplast genomic correlates of endangerment. The identified polymorphic regions and repeat markers lay a foundation for future population genetics, phylogeographic studies, and conservation-oriented genetic management of these ecologically important coastal plants.

Genome, Chloroplast↗

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Animals↗

Genomic organisation of the mouse Ret proto-oncogene.

The RET proto-oncogene is involved in the development of both kidney and neural crests derived tissues. RET deleterious mutations cause hereditary neuroendocrine tumours and congenital intestinal aganglionosis. Ongoing efforts aimed at elucidating the function of this gene include expression studies in different species and in transgenic mice. As first step in the study of Ret expression in mouse, we obtained the mouse Ret genomic structure. Intron-exon boundaries were determined and sequenced, all introns but the first one were amplified and cloned, and exons positioned in a restriction map. Mouse and human genes comparison indicates a highly conserved genomic organisation, except for exon 21 which is not conserved in mouse. A region extending 386 bp 5' to the first exon was sequenced and compared with its human counterpart. Some features, reported for the human promoter, like the absence of TATA or CAAT boxes and a high GC content, are conserved.

Animals↗

MFASAT: a new alphoid DNA sequence isolated from Macaca fascicularis (Cercopithecidae, Primates).

A new highly repeated DNA fragment isolated from Macaca fascicularis (MFASAT) is described. Our findings obtained by sequencing, Southern blot analysis, and fluorescent in situ hybridization (FISH) on metaphasic chromosomes strongly suggest that MFASAT can be considered as a member of the alphoid DNA family characteristic of Old World monkeys. The chromosomal localization of MFASAT, obtained by FISH, showed that this alphoid DNA is present in the peri-centromeric area of all the chromosomes. MFASAT showed a high degree of conservation when compared, by sequence alignment, to other Macaca species and Papio papio as expected for species with considerable genome conservation. A low degree of homology has been found comparing M. fascicularis alphoid DNA with a more distantly related Cercopithecidae species such as Cercopithecus aethiops.

Animals↗

[Genomic characterization of SARS coronavirus: a novel member of coronavirus].

In March 2003, SARS-CoV, a novel coronavirus which has been proved to be a pathogen causing Severe Acute Respiratory Syndrome (SARS). The complete genome of SARS-CoV has been sequenced by international collaboration including China. In the present study, the genome sequences were collected from NCBI and genomic characterization was analyzed. SARS-CoV has a genome of 28-30 kb including 11 ORFs (Open Reading Frames), which is consistent with that of coronavirus family, and its genome organization is similar to those of other coronaviruses as well. SARS-CoV evolutionally closes to other coronavirus in their corresponding proteins, such as spike protein, small membrane protein and nucleocapsid protein. In some regions of the genome, the genomic sequence of SARS-CoV was significantly different from that of other coronavirus, and has a self-conservative genomic sequence. Moreover, its encoding protein sequences were greatly different from those of other coronavirus. The analysis indicated that SARS-CoV has lower redundancy, that is, it has a high variation possibility. It may not be a variant of other coronaviruses but a novel coronavirus, which existed independently in nature and was not recognized by human being before, although SARS-CoV is morphologically similar to other coronavirus and belongs to coronavirus family. The sequences of its genes and encoding proteins are substantially different from those of other coronavirus.

Coronavirus↗

Microsynteny between the Medicago truncatula SYM2-orthologous genomic region and another region located on the same chromosome arm.

A synteny based positional cloning approach was started to clone the pea SYM2 gene by using locally conserved genome structure with the model plant Medicago truncatula. We reported that a pea marker tightly linked to SYM2 was used to screen a M. truncatula BAC library, and two contigs named C1/C2 and C3 were constructed that are both located on the long arm of M. truncatula chromosome 5 and separated by 9 cM. C1/C2 is highly microsyntenic to the pea SYM2 genomic region and corresponds to the M. truncatula SYM2-orthologous region, which is delimitated to 350 kbp. In this manuscript we analyze the distribution in the three contigs of 22 sequences and their homologues, including eight C1/C2 and two pea RFLP markers linked to SYM2. Among the analyzed sequences are several different (receptor) kinase-like gene sequences and two classes of LRR-containing resistance protein-like sequences. From all the studied sequences only four detected homologous sequences in C3, and their distribution is comparable in C1/C2 and C3, suggesting that a 70-kbp and a 120-kbp segments of these two contigs, respectively, arose through a duplication. The implications of these findings for the cloning of SYM2 are discussed.

Journal Article↗

Presence of a novel hamster oral papillomavirus in dysplastic lesions of hamster lingual mucosa induced by application of dimethylbenzanthracene and excisional wounding: molecular cloning and complete nucleotide sequence.

A combination of 9,10-dimethyl-1,2-benzanthracene (DMBA) application and excisional wounding on the lingual tips of Syrian Golden hamsters (Mesocricetus auratus) induces dysplastic and malignant mucosal lesions. Papillomavirus genus-specific antigen and viral particles, measuring 55 nm in diameter, were demonstrated in the nuclei of squamous cells of dysplastic lesions showing koilocytotic change. In this study, we cloned a circular genome at a single Kpnl site from one of these dysplastic lesions. The genomic sequence of this clone, consisting of 7647 bp, was shown to be that of a novel papillomavirus with a conserved genomic organization. We named the new virus hamster oral papillomavirus (HOPV). All dysplastic lesions induced by this combination of DMBA application and excisional wounding contained viral DNA. Although Southern blot hybridization analysis could not detect the HOPV genome, PCR analysis demonstrated the latent HOPV genome in the tongue and skin of an untreated hamster. These results suggest that latently present HOPV genome is reactivated by the DMBA/wounding procedures. Lingual HOPV infection may be an important model for gaining insight into the interactions between papillomavirus infection, chemical carcinogens and physical irritations in carcinogenesis or malignant transformation.

9,10-Dimethyl-1,2-benzanthracene↗

Simian immunodeficiency virus in which nef and U3 sequences do not overlap replicates efficiently in vitro and in vivo in rhesus macaques.

The nef genes of human immunodeficiency virus and simian immunodeficiency virus (SIV) overlap about 80% of the U3 region of the 3' long terminal repeat (LTR) and contain several essential cis-acting elements (here referred to as the TPI region): a T-rich region, the polypurine tract, and attachment (att) sequences required for integration. We inactivated the TPI region in the nef reading frame of the pathogenic SIVmac239 clone (239wt) by 13 silent point mutations. To restore viral infectivity, intact cis-regulatory elements were inserted just downstream of the mutated nef gene. The resulting SIV genome contains U3 regions that are 384 bp shorter than the 517-bp 239wt U3 region. Overall, elimination of the duplicated Nef coding sequences truncates the proviral genome by 350 bp. Nonetheless, it contains all known coding sequences and cis-acting elements. The TPI mutant virus expressed functional Nef and replicated like 239wt in all cell culture assays and in vivo in rhesus macaques. Notably, these SIVmac constructs allow us to study Nef function in the context of replication-competent viruses without the restrictions of overlapping LTR sequences and important cis-acting elements. The genomes of all known primate lentiviruses contain a large overlap between nef and the U3 region. We demonstrate that this conserved genomic organization is not obligatory for efficient viral replication and pathogenicity.

Animals↗

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org.

Animals↗

Chromosomal rearrangements differentiating the ryegrass genome from the Triticeae, oat, and rice genomes using common heterologous RFLP probes.

An restriction fragment length polymorphism (RFLP)-based genetic map of ryegrass (Lolium) was constructed for comparative mapping with other Poaceae species using heterologous anchor probes. The genetic map contained 120 RFLP markers from cDNA clones of barley (Hordeum vulgare L.), oat (Avena sativa L.), and rice (Oryza sativa L.), covering 664 cM on seven linkage groups (LGs). The genome comparisons of ryegrass relative to the Triticeae, oat, and rice extended the syntenic relationships among the species. Seven ryegrass linkage groups were represented by 10 syntenic segments of Triticeae chromosomes, 12 syntenic segments of oat chromosomes, or 16 syntenic segments of rice chromosomes, suggesting that the ryegrass genome has a high degree of genome conservation relative to the Triticeae, oat, and rice. Furthermore, we found ten large-scale chromosomal rearrangements that characterize the ryegrass genome. In detail, a chromosomal rearrangement was observed on ryegrass LG4 relative to the Triticeae, four rearrangements on ryegrass LGs2, 4, 5, and 6 relative to oat, and five rearrangements on ryegrass LGs1, 2, 4, 5, and 7 relative to rice. Of these, seven chromosomal rearrangements are reported for the first time in this study. The extended comparative relationships reported in this study facilitate the transfer of genetic knowledge from well-studied major cereal crops to ryegrass.

Avena↗

Regulation of colony-stimulating factor production by normal and leukemic human cells.

Considerable progress has been made over the last 5 years in defining the exact factors which make up 'colony-stimulating activity', the cells that produce individual CSFs, and determining some of the stimuli that lead to secretion of specific CSFs. There is much to learn however about the mechanisms of CSF action, and also much to learn about the role these factors play in hematopoietic regulation in vivo. The role, if any, of marrow stromal cells in the production of CSFs is particularly important and needs much clearer definition. Much of our understanding of CSF activity has been previously dependent on in vitro bioassays which were sensitive but frequently imprecise. The availability of purified recombinant protein has alleviated the reliance on conditioned media. Previously used conditioned media frequently contained multiple growth factors and inhibitory factors. The cloning of the CSFs has revealed both structural homology and diversity. The conserved genomic structural schema between the majority of the CSFs suggest a common ancestral gene. However, M-CSF diverges from this schema. Conserved also is the 3' untranslated motif of AUUUA in the majority of CSFs. M-CSF is again divergent in this respect. However, where regulation of the mRNA transcript level has been characterized carefully, normal cells appear to regulate CSF mRNAs primarily in a post transcriptional manner. The regulation of CSF transcription in leukemia is complex. In retrovirally mediated leukemia, CSF production is due to increased transcription mediated by the retrovirus. In the few cases of human leukemias making CSFs which have been studied, evidence for both post-transcriptional regulation and structural rearrangements in the CSF genes has been presented. Due to the extreme rarity of normal hematopoietic progenitor cells that correspond to the same state of differentiation as that of the leukemic blast forms, several questions remain. Do normal progenitor cells also make CSFs at some stages of differentiation? What role, if any, do CSFs play in leukemogenesis? The rapid development of our understanding of CSFs over the past several years has led to a much better understanding of hematopoiesis. As we understand more of normal hematopoiesis we also begin to understand the complexities involved in the abnormal regulation as in myelogenous leukemias. With the powerful tools currently available we can be much more precise in our understanding of the intricacies involved.

Colony-Stimulating Factors↗

Repeat-modulated population genetic effects in fungal proteins.

A number of fungal lineages, notably N. crassa, have evolved a novel mechanism of processing genomic duplication events known as repeat-induced point (RIP) mutation. This mechanism appears, on the one hand, to act as a conservative genomic safeguard, by introducing stop codons into duplicated nucleotide sequences, thereby preempting consequences such as dosage effects. However, it also typically performs further nonsynonymous (i.e., amino acid-changing) nucleotide substitutions, the significance of which is unclear. We explore here the possibility that RIP-mutated genes which evade silencing may have some microevolutionary impact on functional sequences. Our approach focuses on structurally important hydrophobic/polar (HP) amino-acid substitutions effected by RIP. We exploit a simple generic protein folding model to predict the associated emergence of increased protein-structural stability and variance within a large population.

Amino Acids↗