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PubMed2001

Molecular characterisation of the tammar wallaby (Macropus eugenii) CD3 epsilon chain cDNA.

The cDNA encoding the epsilon chain of the tammar wallaby CD3 complex (CD3epsilon) was isolated by PCR. This is the first CD3 component to be cloned in a marsupial. The tammar wallaby cDNA coding region was 61.7 and 63.0% identical to the human and mouse cDNA coding sequences, respectively. Similarly, the predicted amino acid sequence was 56.5 and 52.9% identical to the human and mouse sequences. When compared with other known CD3epsilon peptide sequences, the most conserved region of the tammar wallaby CD3epsilon chain peptide was the cytoplasmic domain and the least conserved was the extracellular portion. Phylogenetic reconstruction based on the deduced amino acid sequence placed the tammar wallaby sequence in its expected position outside of all the eutherian mammals.

Amino Acid Sequence↗

PubMed1999

TGF-beta3 exists in bony fish.

A partial nucleotide sequence of transforming growth factor-beta3 (TGF-beta3) has been isolated from the Siberian sturgeon (Acipenser baeri), rainbow trout (Oncorhynchus mykiss) and European eel (Anguilla anguilla), confirming a ubiquitous presence in the ray-finned (Actinopterygian) bony fish. The bony fish TGF-beta3 is highly conserved, with some 83-84% nucleotide identity (coding region) and 90-95% predicted amino acid identity to known homeotherm TGF-beta3's. Far lower homologies are apparent with other known TGF-beta isoforms in fish (e.g. 64-66% and 81-82% amino acid identity to trout TGF-beta 1/5 and carp TGF-beta2 respectively). Phylogenetic tree analysis showed that the fish TGF-beta3's clustered with the known homeotherm TGF-beta3's. The relatively tight clustering of TGF-beta1, TGF-beta2 and TGF-beta3 was in contrast to the TGF-beta5's, which are clearly a more heterogenous group.

Amino Acid Sequence↗

PubMed2000

Characterization of gonadal and extra-gonadal forms of the cDNA encoding the Atlantic stingray (Dasyatis sabina) cytochrome P450 aromatase (CYP19).

Cytochrome P450 aromatase (P450arom; CYP19) mediates the conversion of androgens to estrogens and its activity has been found in all vertebrates studied to date. This study describes the full-length cDNA encoding the ovarian form of P450arom and the differences in the 5'-untranslated region (5'-UTR) of the extra-gonadal P450arom transcript expressed by the Atlantic stingray (Dasyatis sabina). Elasmobranchs (cartilaginous fishes such as sharks, rays and skates) diverged from the other vertebrates more than 350 million years ago, therefore the stingray P450arom cDNA may represent an ancient form of this gene. Northern blot analysis showed that the ovarian follicle expressed transcripts of 3.1 and 1.7 kb in size which correspond to the clones isolated from a stingray ovarian follicle cDNA library. Both transcripts consisted of an identical 1.5 kb coding region and a 41 bp 5'-UTR, however the 3'-UTRs differed in the use of the most proximate and the most distal of four polyadenylation signals. COS cells transfected with the 1.7 kb cDNA had twice the aromatase activity as cells transfected with the 3.1 kb cDNA. The coding region of the cDNA predicted a 58.5 kDa protein which consisted of 511 residues. Alignment of the stingray protein indicates that the P450arom is equally identical (53-59%) to all other vertebrate forms of P450arom characterized to date, thus indicating a common ancestry. The evolutionary relationship of the stingray form of P450arom clearly predates the other forms and belongs to a unique lineage. Transcripts of P450arom were expressed in ovarian follicles (of all sizes), the testis, the pituitary, in all sections of the brain, and in the kidney. The extra-gonadal transcripts appear to encode a protein identical to the ovarian form, however, the 5'-UTR was 657 bp longer presumably due to the transcription of an untranslated 'first exon' as seen in the mammalian form of this gene.

Amino Acid Sequence↗

PubMed2002

Molecular cloning and tissue distribution of the ovine somatostatin receptor subtype 5: osst5.

The sheep is a valuable model to study growth hormone (GH) neuroregulation since its GH secretion pattern is close to that in humans and an integrated physiological approach is possible in this species. Somatostatin receptor subtype 5 (sst5) appears to be important in GH regulation but the ovine sst5 gene (osst5) has not yet been cloned. We report here the cloning of sst5 in that species. We screened a cDNA sheep library and isolated a 1.24 kb cDNA, which includes the whole coding region of osst5. The predicted protein consists of 367 amino acids exhibiting a putative seven transmembrane domain topology typical of G protein-coupled receptors. Nucleotide sequence comparisons with that of other species sst5 showed that osst5 displays 83.8, 81 and 79.7% homology with human, rat, and mice sst5, respectively. Southern blot analysis of ovine cortex DNA demonstrated that osst5 is encoded by a single gene. Osst5 transiently expressed in Chinese Hamster ovary (CHO) cells exhibit a high affinity for somatostatin-14. Reverse transcriptase-polymerase chain reaction (RT-PCR) studies demonstrated that osst5 mRNAs are present in pituitary, cortex, hypothalamus, hippocampus, colon and adrenal gland. The cloning of osst5 should provide a useful tool to study the mechanisms through which somatostatin inhibits hormone secretion in the sheep.

Adrenal Glands↗

PubMed1996

Model calculations of the radiation dose and LET spectra on LDEF and comparisons with flight data.

Ionizing radiation environment models, a 3-D spacecraft mass model, and radiation transport codes have been used to predict the radiation dose and linear energy transfer (LET) spectra measured at various locations on the LDEF satellite. The predictions are compared with thermoluminescent dosimeter measurements of the trapped proton and electron doses and with LET spectra measured by plastic nuclear track detectors. The predicted vs observed comparisons indicate some of the uncertainties of present ionizing radiation environment models for low Earth-orbit missions.

Anisotropy↗

PubMed1999

Human Nop5/Nop58 is a component common to the box C/D small nucleolar ribonucleoproteins.

We have identified an apparent human homolog of the yeast Nop5/Nop58 protein. hNop5/Nop58 codes for a protein of predicted molecular weight 59.6 kDa and is 46.8% identical to Saccharomyces cerevisiae Nop5/Nop58. Immunofluorescent staining with antibodies against hNop5/Nop58 indicate that it is localized primarily to the nucleolus, and coimmunoprecipitation from nuclear extracts demonstrates that hNop5/Nop58 interacts with the box C/D family of snoRNAs. Thus, hNop5/Nop58 is a common component of the box C/D snoRNPs, and joins fibrillarin as the second such component identified and characterized in metazoans.

Amino Acid Sequence↗

PubMedDate not supplied

The ROBIA program for predicting organic reactivity.

A program to predict organic reactions, ROBIA, has been developed. It achieves reaction prediction on the basis of coded rules and molecular modeling calculations, generating possible transition states, intermediates, and products given the starting material and reaction conditions. The program generates all possible reaction pathways, on the basis of the selected transformations within its database, and evaluates them selecting the most feasible ones. The program has been successfully tested against several examples.

Algorithms↗

PubMed2025

Chromosome-level genome assembly of Triplophysa scleroptera.

Triplophysa scleroptera is an endemic fish species in Qinghai Lake and the upper reaches of the Yellow River. However, studies on conservation and evolutionary genetics were seriously impeded by the absence of a reference genome. Here, by using PacBio HiFi sequencing and Hi-C assembly technology, we assembled a chromosome-level genome of T. scleroptera, with a total length of 660.22 Mb and 99.82% of the sequence anchored to 25 chromosomes. The contig N50 and scaffold N50 were 9.09 Mb and 24.38 Mb, respectively. The evaluation using BUSCO indicated the genome assembly to be 96.40% complete. About 33.41% of the genome consists of repeat elements. We predicted 26,168 protein-coding genes in the genome, and 99.02% of them were functionally annotated. This high-quality reference genome would serve as a valuable genomic resource for advancing evolutionary conservation genetics studies in this species.

Animals↗

PubMed2025

Near-complete reference genome assembly of Hoya carnosa.

Hoya R. Br. is the largest genus in the tribe Marsdenieae (Apocynaceae), comprising 350-450 species. Hoya species are popular in horticulture for their distinctive floral traits and fragrances, primarily sourced from domestication and mutation breeding. However, the lack of molecular analysis for floral morphological traits has limited their cultivation and application. In this study, we assembled a near-complete reference genome for H. carnosa, the model species of the genus, using PacBio HiFi reads and Hi-C method. The genome size was approximately 465.7 Mb with a contig N50 of 39.3 Mb. 99.7% of the sequences were anchored to 11 pseudochromosomes, and the assembly achieved a BUSCO score of 98.5%. We predicted 24,309 protein-coding genes, of which 90.2% (21,927) were functionally annotated. This high-quality genome provides a valuable reference for the research of evolution, conservation and molecular breeding in Hoya.

Genome, Plant↗

PubMed2026

Chromosome-level genome assembly of Manglietia pachyphylla.

Manglietia pachyphylla, an endangered evergreen tree within the Magnoliaceae family, is renowned for its exceptional ornamental value in landscape horticulture. Despite its classification as a Category II nationally protected plant species in China, the genetic basis of its adaptive traits and conservation priorities remains poorly understood. To address this, we present the first chromosome-scale genome assembly of M. pachyphylla utilizing an integrated approach combining PacBio HiFi long-read and Hi-C chromosome conformation capture sequencing technologies. The assembled genome spans 2.15 Gb (contig N50 = 43.57 Mb), exhibiting a heterozygosity rate of 0.78% and repeat content of 78.64%, predominantly comprising long terminal repeat (LTR) retrotransposons (52.86%). Hi-C scaffolding anchored 99.57% of the assembly to 19 pseudochromosomes, achieving a BUSCO completeness score of 96.4%. Annotation revealed 42,505 putative protein-coding genes, with 84.46% of predicted genes were functionally annotated. Phylogenomic analysis positioned M. pachyphylla and Oyama sieboldii clustered together in a well-supported group. This high-contiguity genome assembly enables future investigations into adaptive evolution, functional genomics, and evidence-based conservation strategies for this endangered species.

Chromosomes, Plant↗

PubMed2026

A gap-free, telomere-to-telomere chromosome-scale genome assembly of the mangrove red snapper, Lutjanus argentimaculatus.

The mangrove red snapper (Lutjanus argentimaculatus) is a commercially important marine fish species in the Indo-Pacific region. Despite its significant economic value for aquaculture, existing genomic resources remain fragmented, limiting the advancement of molecular breeding and functional genomic studies. Here, we present a gap-free, telomere-to-telomere (T2T) genome assembly of L. argentimaculatus, generated using a hybrid approach combining PacBio HiFi, Oxford Nanopore ultra-long reads and Hi-C technology. The resulting assembly comprises exactly 24 scaffolds spanning 1.03 Gb, perfectly matching the haploid chromosome number with a contig N50 of 46.17 Mb. Notably, this assembly resolves all physical gaps present in previous versions, achieving a BUSCO completeness score of 98.2%. Comprehensive genome annotation successfully predicted 23,167 protein-coding genes. Among these, 22,067 genes (95.25%) were functionally annotated across major public databases, including eggNOG, InterPro, and Swiss-Prot. Furthermore, structural analysis successfully identified 19 telomeres and 20 centromeres, validating the chromosomal integrity. This high-fidelity, gap-free reference genome provides a robust foundation for comparative genomics, population genetics, and the genetic improvement of Lutjanidae species.

Animals↗

PubMed2002

Low frequency of MECP2 mutations in mentally retarded males.

A high frequency of mutations in the methyl CpG-binding protein 2 (MECP2) gene has recently been reported in males with nonspecific X-linked mental retardation. The results of this previous study suggested that the frequency of MECP2 mutations in the mentally retarded population was comparable to that of CGG expansions in FMR1. In view of these data, we performed MECP2 mutation analysis in a cohort of 475 mentally retarded males who were negative for FMR1 CGG repeat expansion. Five novel changes, detected in seven patients, were predicted to change the MECP2 coding sequence. Except for one, these changes were not found in a control population. While this result appeared to suggest a high mutation rate, this conclusion was not supported by segregation studies. Indeed, three of the five changes could be traced in unaffected male family members. For another change, segregation analysis in the family was not possible. Only one mutation, a frameshift created by a deletion of two bases, was found to be de novo. This study clearly shows the importance of segregation analysis for low frequency mutations, in order to distinguish them from rare polymorphisms. The true frequency of MECP2 mutations in the mentally retarded has probably been overestimated. Based on our data, the frequency of MECP2 mutations in mentally retarded males is 0.2% (1/475).

Amino Acid Sequence↗

PubMed1997

ERF: genomic organization, chromosomal localization and promoter analysis of the human and mouse genes.

ERF (Ets2 Repressor Factor) is a ubiquitously expressed ets-domain protein that exhibits strong transcriptional repressor activity, has been shown to suppress ets-induced transformation and has been suggested to be regulated by MAPK phosphorylation. We report here the sequence of the mouse gene, the genomic organization of the human and the mouse genes, their chromosomal position and the analysis of the promoter region. Genomic clones encompassing either the human ERF or the mouse Erf gene were isolated and utilized to define their molecular organization. The gene in both species consists of 4 exons over a 10 kb region. Utilizing FISH, somatic cell hybrids and linkage analysis, we identified the chromosomal position of ERF on human chromosome 19q13.1 and on its syntenic region in the mouse, on chromosome 7. Sequence analysis of the mouse gene indicated a 90% identity to the human gene within the coding and promoter regions. The predicted Erf protein is 98% identical to the human protein and all of the identifiable motifs are conserved between the two proteins. However, the mouse protein is three amino acids longer (551 versus 548 aa). The area surrounding the region that is homologous to the 5' end of the human cDNA can serve as a promoter in transfection into eukaryotic cells. This region is highly conserved between the mouse and the human genes. A number of conserved transcription factor binding sites can be identified in the region including an ets binding site (EBS). Interestingly, removal of a small segment that includes the EBS, seriously hampers promoter function, suggesting the ERF transcription may be regulated by ets-domain proteins.

Amino Acid Sequence↗

PubMed2004

A novel outer-membrane anion channel (porin) as part of a putatively two-component transport system for 4-toluenesulphonate in Comamonas testosteroni T-2.

Inducible mineralization of TSA (4-toluenesulphonate) by Comamonas testosteroni T-2 is initiated by a secondary transport system, followed by oxygenation and oxidation by TsaMBCD to 4-sulphobenzoate under the regulation of TsaR and TsaQ. Evidence is presented for a novel, presumably two-component transport system (TsaST). It is proposed that TsaT, an outer-membrane porin, formed an anion-selective channel that works in co-operation with the putative secondary transporter, TsaS, located in the inner membrane. tsaT was identified as a 1017-bp ORF (open reading frame) on plasmid pTSA upstream of the TSA-catabolic genes in the tsa operon. Expression of tsaT was regulated by TsaR, the transcriptional activator of the tsa regulon. The presence of tsaT was concomitant with the presence of the tsa operon in different TSA-degrading isolates. tsaT was expressed in Escherichia coli and was detected in the outer membrane. A 22-amino-acid leader peptide was identified. Purified protein reconstituted in lipid bilayer membranes formed anion-selective channels with a single-channel conductance of 3.5 nS in 1 M KCl. Downstream of tsaT, a constitutively expressed 720-bp ORF (tsaS) was identified. tsaS coded for a hydrophobic protein predicted to have six transmembrane helices and which is most likely localized in the cytoplasmic membrane. tsaS is adjacent to tsaT, but showed a different transcriptional profile.

Benzenesulfonates↗

PubMed2002

Cloning of hamster type XVII collagen cDNA, and pathogenesis of anti-type XVII collagen antibody and complement in hamster bullous pemphigoid.

Bullous pemphigoid is an inflammatory subepidermal blistering skin disease associated with an IgG autoimmune response to the type XVII collagen. The immunopathologic features of bullous pemphigoid can be reproduced in mice by the passive transfer of anti-type XVII collagen antibodies. In this model, it is thought that blister formation depends upon complement activation, neutrophil recruitment, and some proteolytic enzymes. In this study, we cloned hamster type XVII collagen cDNA, which contains a 4296 bp coding region and which is predicted to be a transmembrane protein with an extracellular collagenous domain, residing in type II orientation. Antipeptide antibodies (anti-1191 IgG) were obtained against a segment of hamster type XVII collagen homologous with the human type XVII collagen autoantibody-reactive site. The antipeptide antibodies were passively transferred to neonatal Syrian hamsters. The injected hamsters developed a microscopic subepidermal blister as seen previously in the mice. In order to test whether antigen-antibody complexes and complement initiate the subepidermal blister formation, we carried out experiments in vitro on condition that inflammatory cells were completely eliminated. Complement activation in sera was inhibited either by heating (at 56 degrees C for 30 min) or by preincubating with cobra venom factor. When the hamster skin was incubated with fresh anti-1191 antisera, separation of dermal-epidermal junction was observed. The anti-1191 IgG failed to induce C3 deposition and dermal-epidermal junction separation, however, if the anti-1191 IgG was added alone or complement activation in sera was inhibited. Under these conditions, IgG but not C3 was deposited on the basement membrane. These results strongly suggest that antigen-antibody complexes and complement initiate dermal-epidermal junction separation.

Amino Acid Sequence↗

PubMed2004

Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.

It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates. In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (approximately equal to 320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very few recently duplicated genes; hence, many human genes are much younger than fish genes. This lack of recent gene duplication, or, alternatively, the accelerated rate of gene loss, is possibly one reason for the drastic reduction of the genome size of Fugu observed during the past 100 million years or so, subsequent to the additional genome duplication that ray-finned fishes but not land vertebrates experienced.

Amino Acid Sequence↗

PubMed2004

Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins.

The rickettsia Anaplasma marginale is the most prevalent tick-borne livestock pathogen worldwide and is a severe constraint to animal health. A. marginale establishes lifelong persistence in infected ruminants and these animals serve as a reservoir for ticks to acquire and transmit the pathogen. Within the mammalian host, A. marginale generates antigenic variants by changing a surface coat composed of numerous proteins. By sequencing and annotating the complete 1,197,687-bp genome of the St. Maries strain of A. marginale, we show that this surface coat is dominated by two families containing immunodominant proteins: the msp2 superfamily and the msp1 superfamily. Of the 949 annotated coding sequences, just 62 are predicted to be outer membrane proteins, and of these, 49 belong to one of these two superfamilies. The genome contains unusual functional pseudogenes that belong to the msp2 superfamily and play an integral role in surface coat antigenic variation, and are thus distinctly different from pseudogenes described as byproducts of reductive evolution in other Rickettsiales.

Anaplasma marginale↗

PubMed2003

Why the kidney glomerulus does not clog: a gel permeation/diffusion hypothesis of renal function.

Current interpretations of kidney function in terms of a coarse filter followed by a fine filter have difficulty explaining why the glomerulus does not clog. I propose, as an alternative, a semiquantitative hypothesis that assumes that the size-selective property of the glomerulus is a consequence of the limited fraction of space in the glomerular basement membrane (a concentrated gel) into which macromolecules can permeate. The glomerular epithelial cell slits and slit diaphragms are assumed to impose substantial resistance to liquid flow across the glomerulus without acting as a molecular sieve. Calculations based on gel behavior show that proteins cross the glomerular basement membrane mainly by diffusion rather than by liquid flow, whereas water crosses entirely by flow. Thus, diffusion provides most of the protein, whereas flow provides the diluent. As a result, the single-nephron glomerular filtration rate (GFR) becomes a prime factor in (inversely) determining the concentration of proteins in early proximal tubular fluid. Because the reabsorption of proteins from the tubules is a saturable process, the gel permeationdiffusion hypothesis readily accounts for the albuminuria observed when single-nephron GFR is substantially reduced by severe pathological decreases in slit diaphragm length, such as occur in minimal-change nephrotic syndrome in humans, in animals treated with puromycin aminonucleoside, or in humans or animals with mutations in the gene coding for nephrin. My hypothesis predicts that albuminuria will ensue, even with a normal kidney, if the single-nephron GFR falls below approximately 50% of normal.

Animals↗