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At least 1,423 records · Page 79Linked to original sources
PubMed2000

Regulation of the tinman homologues in Xenopus embryos.

Vertebrate homologues of the Drosophila tinman transcription factor have been implicated in the processes of specification and differentiation of cardiac mesoderm. In Xenopus three members of this family have been isolated to date. Here we show that the XNkx2-3, Xnkx2-5, and XNkx2-10 genes are expressed in increasingly distinctive patterns in endodermal and mesodermal germ layers through early development, suggesting that their protein products (either individually or in different combinations) perform distinct functions. Using amphibian transgenesis, we find that the expression pattern of one of these genes, XNkx2-5, can be reproduced using transgenes containing only 4.3 kb of promoter sequence. Sequence analysis reveals remarkable conservation between the distalmost 300 bp of the Xenopus promoter and a portion of the AR2 element upstream of the mouse and human Nkx2-5 genes. Interestingly, only the 3' half of this evolutionarily conserved sequence element is required for correct transgene expression in frog embryos. Mutation of conserved GATA sites or a motif resembling the dpp-response element in the Drosophila tinman tinD enhancer dramatically reduces the levels of transgene expression. Finally we show that, despite its activity in Xenopus embryos, in transgenic mice the Xenopus Nkx2-5 promoter is able to drive reporter gene expression only in a limited subset of cells expressing the endogenous gene. This intriguing result suggests that despite evolutionary conservation of some cis-regulatory sequences, the regulatory controls on Nkx2-5 expression have diverged between mammals and amphibians.

Animals↗
PubMed1995

Identification and chromosomal mapping of the mouse inositol polyphosphate 1-phosphatase gene.

A mouse inositol polyphosphate 1-phosphatase (Inpp1) cDNA fragment (348 bp) was amplified by means of the polymerase chain reaction using a mouse cDNA library as template with primers designed from published human and bovine cDNA sequences. We isolated a 1623-bp full-length Inpp1 cDNA from a mouse brain cDNA library using this amplified cDNA fragment as probe. Amino acid sequences of mouse, human, and bovine inositol polyphosphate 1-phosphatase are highly conserved. Northern blot analysis shows a major transcript of 1.65-kb mRNA and several higher molecular weight mRNAs that are expressed in a variety of mouse tissues. Utilizing the Jackson Lab backcross DNA panel map service, we mapped Inpp1 to chromosome 1, 1.06 cM proximal to Ctla4.

Amino Acid Sequence↗
PubMed1995

Human genomic characterization of a novel locus-specific repetitive sequence.

A novel human chromosome locus-specific repetitive sequence was identified and characterized using arbitrary PCR. The repeat monomer consensus sequence is 100 bp long, and there are a minimum of 140 to 160 copies of the repetitive sequence per haploid human genome. The repetitive sequence is highly clustered on 20q12 within a 200- to 400-kb region. The highly polymorphic repeat array is inherited in a stable Mendelian fashion. Hybridization analysis revealed detectable conservation of the repeated element only among hominoids and Old World monkeys, where repeat arrangements are also polymorphic.

Animals↗
PubMed1996

A novel ribosomal protein L3-like gene (RPL3L) maps to the autosomal dominant polycystic kidney disease gene region.

A full-length cDNA encoding a novel ribosomal protein L3 gene was isolated and sequenced. The deduced protein sequence is 407 amino acids long and shows 77% identity to other known mammalian ribosomal protein L3 genes, which are themselves highly conserved. Southern blot analysis of human genomic DNA suggests that this novel gene is single copy. While the previously identified human ribosomal protein L3 gene has ubiquitous expression in all tissues surveyed, the novel gene described herein is strongly expressed in skeletal muscle and heart tissue, with low levels of expression in the pancreas. This novel gene, RPL3L, is located in a gene-rich region near the PKD1 and TSC2 genes on chromosome 16p13.3.

Amino Acid Sequence↗
PubMed1996

Molecular cloning and characterization of the mouse Kin17 gene coding for a Zn-finger protein that preferentially recognizes bent DNA.

We report the isolation of the mouse Kin17 gene, located on chromosome 2, coding a nuclear Zn-finger protein that has a 39-residue region homologous to Escherichia coli RecA protein and that is recognized by anti-RecA antibodies. Kin17 protein preferentially binds to curved DNA in vitro and in vivo, suggesting a role in illegitimate recombination and in regulation of gene expression. We have shown that the Kin17 gene is about 8 kb in length and displays three exons and two introns. The 5' flanking region lacks a canonical TATAA box but presents several putative regulatory domains. A major transcription initiation site is located 322 nucleotides upstream of the translation start site. The 1.7-kb transcript of the Kin17 gene is weakly and ubiquitously expressed in murine tissues and cell lines as determined by Northern analysis. The cross-hybridization of Kin17 cDNA with the genomic DNA of other species in Southern analysis indicates the conservation of the gene among mammals and suggests that the Kin17 gene plays a conserved role in DNA metabolism.

Animals↗
PubMed2000

DXS6673E encodes a predominantly nuclear protein, and its mouse ortholog DXHXS6673E is alternatively spliced in a developmental- and tissue-specific manner.

DXS6673E is a candidate gene for nonspecific X-linked mental retardation and encodes a novel Zn-finger protein. The ortholog murine gene DXHXS6673E in XC-D was isolated and characterized. It is ubiquitously expressed in all embryonic stages and adult tissues. Two different transcription start sites exist that result in two major transcripts of 6055 and 5352 nucleotides, each composed of 25 exons. Exon 1A is tissue specific, whereas exon 1B is transcribed constitutively. Both variants are translated into the same 1370-amino-acid protein. Transcripts are subject to alternative splicing at the 5'-end. Some of the isoforms are developmental stage and tissue specific. Among them, one was present only in embryos and adult brain. Sequence analysis demonstrated evolutionary conservation down to the arthropods and defined several conserved protein motifs. Subcellular localization studies with green fluorescent protein as a reporter showed that DXS6673E is predominantly located in the nucleus due to several functional nuclear localization signals. Three distinct protein distribution patterns in COS-7 cells could be identified.

Alternative Splicing↗
PubMed1993

Distribution of surface-exposed and non-accessible amino acid sequences among the two major structural domains of the S-layer protein of Aeromonas salmonicida.

The tetragonally arranged crystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor. Circular dichroism studies in the presence or absence of 0.1% sodium dodecyl sulfate showed that the secondary structure of A-protein, and its 39,439 molecular weight amino-terminal trypsin-resistant peptide, were altered. In both cases alpha-helix was increased significantly at the expense of beta-structure when SDS was added. Western and dot immunoblotting, immuno-microscopy and enzyme-linked immunosorbent assay with monospecific polyclonal antiserum and eight monoclonal antibodies specific for epitopes exposed on the surface of native A-layer showed that the 481 residue A-protein subunit and the surface of A-layer were conserved antigenically. Mimeotope analysis of nonapeptides representing the sequence of A-protein allowed identification of 146 residues in presumed linear epitopes accessible on the surface of A-layer. Inaccessible or non-epitopic residues accounted for 70% of the protein. The majority of inaccessible residues were in the N-terminal 301 residues of A-protein. Dispersed among these were 65 surface-accessible residues in five linear epitope clusters illustrating the complex folding of this major structural domain of A-protein. The C-terminal 180 residues carried fewer linear epitopes but contained the major region of A-layers surface-accessible sequence, including four linear epitopes in predominantly hydrophobic sequence. Four A-layer surface-binding monoclonal antibodies also bound to this minor structural domain, although the epitopes of only two were identified by mimeotope analysis. The epitopes of six A-layer surface-binding monoclonals could not be identified, suggesting that A-layer may also contain conformation dependent surface epitopes.

Aeromonas↗
PubMed1996

Identification of a human endogenous LTR-like sequence using HIV-1 LTR specific primers.

Using 'consensus' primers derived from the LTR region of 15 HIV-1 isolates, a fragment of 583 bp was amplified from human DNA. Even though specificity was confirmed by Southern blot analysis with a conserved LTR oligonucleotide probe, no significant homologies were detected to either retroviral regions or human or non-human published sequences. Nevertheless, when used as a probe, the 583-bp fragment identified a unique DNA sequence in the human genome on chromosome 1, and cross-reactive sequences in monkey, but not mouse, DNA. This novel, unique and conserved sequence of 583 bp was used to isolate a human HS-1 clone in which the structural property of a viral LTR could be identified.

Animals↗
PubMed1998

Organization of the simian hemorrhagic fever virus genome and identification of the sgRNA junction sequences.

SHFV is a member of the Arteriviridae family. Viruses within this family encode eight open reading frames (ORFs), two of which are translated from the full-length genome RNA. The remaining six ORFs are translated from a nested set of six or seven 3' co-terminal, subgenomic RNAs (sgRNAs). We have cloned and sequenced approximately 6000 nucleotides (nt) from the 3' end of the SHFV genome. Eleven ORFs, numbered ORFs 1a, 1b, 2a, 2b, 3, 4, 5, 6, 7, 8, and 9, were identified, three more than the other arteriviruses. The characteristics of the peptides encoded by ORFs 2a through 9 were determined from their computer-generated amino acid sequences. We also amplified the junction sequences from each of the SHFV subgenomic RNAs (sgRNAs) using RT-PCR analysis. Eight separate junction sequences were found which suggests that SHFV produces eight sgRNAs during replication. ORFs 2a and 2b appear to be encoded on the same sgRNA implying that RNA 2 is polycistronic. Sequence analysis identified the conserved SHFV junction sequence as 5'-(U/C)(C/U)N(U/C)(U/C)(A/C/G)AC(C/U)-3'. Since SHFV encodes additional ORFs and produces additional sgRNAs during replication, these data suggest that SHFV may be more complex than the other arteriviruses.

Animals↗
PubMed1990

Copper-induced expression, cloning, and regulatory studies of the plastocyanin gene from the cyanobacterium Synechocystis sp. PCC 6803.

Plastocyanin can be detected in Synechocystis sp. PCC 6803 when 3 microM copper is added to the growth medium, BG-11. The plastocyanin gene (petE) was cloned from a genomic lambda EMBL 3 library by screening with the petE gene from Anabaena sp. PCC 7937. The Synechocystis 6803 petE gene is present as a single copy and, as deduced from the DNA sequence, encodes a precursor protein of 126 amino acids. The predicted 29 amino acid transit peptide shows substantial homology to the Anabaena 7937 transit peptide, thought to direct the plastocyanin precursor to the thylakoid lumen. Putative promoter sites -16 and -38 base pairs from the start of the petE gene have been identified. The deduced amino acid sequence has the greatest homology (61%) to the green alga Scenedemus obliquus plastocyanin. Despite the lower homology, the copper binding residues and certain aromatic residues remain highly conserved. Northern hybridization analysis indicates that the Synechocystis sp. PCC 6803 petE gene is not transcriptionally regulated since the accumulation of petE mRNA appears to be independent of the copper concentration in the growth media. The possibility of an additional polypeptide needed to facilitate the electron transfer from plastocyanin to P700+ is also discussed.

Amino Acid Sequence↗
PubMed1991

Identification and structural characterization of further DNA elements in the potato and pepper genomes homologous to the transposable element-like insertion Tst1.

The molecular cloning and nucleotide sequence of elements from potato and pepper that are related to the recently identified Tst1 element are described. Sequence analysis reveals considerable conservation of sequences internal to both the Tst1 element and two of the related elements identified here. In six potato clones analysed, the 11 bp inverted repeat first identified in the Tst1 element is conserved. Several of the elements are flanked by an 8 bp direct repeat. DNA fragments which were amplified from several pepper genomes by polymerase chain reaction (PCR) amplification using the inverted repeat as sequence primers also display considerable conservation of sequences internal to the Tst1 element. These data further support the possibility that Tst1 is a non-autonomous transposable element and that Tst1 might be the first example of a transposable element which occurs in several genera of solanaceous plants.

Base Sequence↗
PubMed1995

Light-chain fibroin of Galleria mellonella L.

The posterior section of Galleria mellonella silk glands contains two abundant mRNAs that are identical except for the non-coding tail, which includes either two (1.1 kb mRNA) or three (1.2 kb mRNA) consensus sequences for polyadenylation sites. The transcripts are 40% homologous in the coding as well as non-coding regions with the mRNA encoding light-chain fibroin (L-fibroin) in Bombyx mori; the deduced translation product shows 43% identity with the Bombyx L-fibroin peptide, with all three cysteines conserved. Amino acid analysis of the N-termini of Galleria silk proteins revealed that L-fibroin (25 kDa) occurs in two isoforms, the shorter one lacking the Ala-Pro dipeptide residue at its N-terminus. The 29 and 30 kDa Galleria silk proteins appear to be homologs of Bombyx silk component P25. The results suggest that evolutionary diversification of Galleria and Bombyx L-fibroins involves alternative polyadenylation and proteolytic processing sites.

Alternative Splicing↗
PubMed1995

Variation in the fusion glycoprotein gene of human respiratory syncytial virus subgroup A.

Six different genotypes (designated lineages SHL1-6) of human respiratory syncytial (RS) virus have been defined by partial nucleotide sequence analysis of the variable SH and the hypervariable G membrane protein genes, and by restriction fragment analysis of the conserved N protein gene of viruses isolated in south Birmingham. Viruses of very similar genotype appear to be present worldwide at the present time. We have determined the nucleotide sequences of the fusion protein genes of five viruses isolated in south Birmingham in the same year, but belonging to different lineages, and have compared them with the sequences of four subgroup A viruses isolated at earlier times from diverse localities. The sequence diversity of the F genes of these five viruses, as measured by nucleotide (94.5-98.5%) and inferred amino acid (97.0-99.3%) identifies, is comparable with that of the nine subgroup A viruses considered as a whole. No sequence changes occur in any of the sites of known epitopes. Comparison of the nine subgroup A sequences with the published sequences of a subgroup B strain and three bovine RS viruses confirms that the F protein sequences are most divergent in the F2 region.

Amino Acid Sequence↗
PubMed1995

Sequence of the PV2 gene of rice hoja blanca tenuivirus RNA-2.

Comparison of a partial sequence of rice hoja blanca tenuivirus RNA-2 with 40% similarity to rice stripe tenuivirus RNA-2 revealed regions of high local sequence homology at the 5' terminus, within the coding region (the pv2 gene), and in the intergenic region separating this gene from the other protein (pc2) encoded by this ambisense RNA. Analysis of the conserved regions of the pv2 protein identified two motifs found principally in viral membrane glycoproteins and six motifs found each in a wide variety of proteins. The possible significance of these results is discussed.

Amino Acid Sequence↗
PubMed1995

Analysis of matrix protein gene nucleotide sequence diversity among Newcastle disease virus isolates demonstrates that recent disease outbreaks are caused by viruses of psittacine origin.

Nucleotide sequence analysis was completed for isolates of Newcastle disease virus (NDV; avian paramyxovirus 1) from 1992 outbreaks in cormorants and turkeys. These isolates were of the neurotropic velogenic type. The cormorant and turkey NDV isolates had the fusion protein cleavage sequence 109SRGRRQKR/FVG119, as opposed to the consensus sequence 109SGGRRQKR/FIG119 of most known velogenic NDV isolates. The R for G substitution at position 110 may be unique for the cormorant and turkey isolates. For comparative purposes, nucleotide sequencing and analysis of the conserved matrix protein gene coding region were completed for isolates representing all pathotypes. Phylogenetic relationships demonstrated that there are two major groups of NDV isolates. One group includes viruses found in North America and worldwide, such as B1, LaSota, Texas/GB, and Beaudette/C. The second group contains isolates, such as ulster/2C, Australia/Victoria, and Herts/33, considered exotic to North America. Within this second group are viruses of psittacine origin. The viruses from 1992 outbreaks of Newcastle disease in North America, and an isolate thought to have caused the major outbreak in southern California during the 1970s, are most closely related to an NDV isolate of psittacine origin.

Amino Acid Sequence↗
PubMed1990

Ultrasonically guided percutaneous drainage of abdominal fluid collections: a long-term study of its therapeutic efficacy.

Fifty patients underwent ultrasonically guided percutaneous drainage (US-GPD) either with needle aspiration or catheter drainage. The procedures resulted in 70% complete recovery, 20% partial success and 10% of failures. The same patients were followed with clinical examination and sonography for a mean time of 36.3 months (minimum follow-up: 12 months). During the follow up period, 10 relapses occurred and one patient, considered for surgery after partial percutaneous treatment of a pyogenic liver abscess, recovered completely under conservative treatment. An analysis of the factors potentially related to the recurrence was made. It was found that one-step needle aspiration of abdominal abscesses and percutaneous treatment of chronic pancreatic pseudocysts are more prone to relapses. We conclude that US-GPD is an efficacious therapy for abdominal fluid collections, but an adequate drainage technique and a careful selection of the patients is crucial to avoid the possibility of relapse.

Adolescent↗
PubMed1991

Interspecific comparison of the unusually repetitive Drosophila locus mastermind.

The mastermind gene of Drosophila melanogaster encodes a novel, highly repetitive nuclear protein required for neural development. To identify functionally important regions we have initiated an interspecific comparison of the gene in Drosophila virilis. Mastermind transcription and genomic organization are similar in both species and sequence analysis reveals significant conservation in a major cluster of charged amino acids. In contrast, extensive variation is noted in homopolymer domains that immediately flank the acidic cluster. Distinct patterns of evolutionary change can be identified: the major difference between unique regions are occasional amino acid substitutions whereas the repetitive areas are characterized by numerous large in-frame insertions/deletions and a nearly threefold higher rate of amino acid replacement. Conservation of the acidic domain suggests that it has an important functional role whereas the hypervariable homopolymer regions appear to be under less selective constraints than adjacent unique areas.

Amino Acid Sequence↗
PubMed2005

Fat necrosis after conserving surgery and interstitial brachytherapy and/or external-beam irradiation in women with breast cancer.

PURPOSE: To investigate the incidence of fat necrosis, breast tissue fibrosis and breast pain after conserving surgery and accelerated partial-breast irradiation (APBI, group A), whole-breast external-beam irradiation (EBRT, group B), or EBRT combined with an interstitial boost (EBIB, group C) in women with breast cancer. PATIENTS AND METHODS: 85 patients who received breast-conserving therapy from 02/2000 to 03/2002 were analyzed. 30 patients received EBRT, 33 patients APBI, and 22 patients EBIB. Median follow-up was 35.5, 35.0, and 37.5 months, respectively. Fat necrosis was detected and rated by mammograms, fibrosis and pain were clinically rated with the LENT-SOMA scores. RESULTS: The incidence of fat necrosis was 15.3% for all patients; and 15.2%, 20.0%, and 9.0% for groups A, B, and C, respectively. The 3-year fat necrosis-free survival probability was 83%, 76%, and 95% (difference not significant). The mean time to first diagnosis of fat necrosis was 25.6, 26.2, and 26.0 months. No patient needed surgical intervention because of fat necrosis-related pain. Fibrosis was present in 27.3%, 63.3%, and 77.3% (p < 0.001), breast pain in 9.0%, 33.4%, and 18.1% (p < 0.05). CONCLUSION: Asymptomatic fat necrosis is a common finding after both percutaneous and interstitial irradiation after breast-conserving surgery. This analysis did not support the hypothesis that APBI with multicatheter implants leads to higher rates of fat necrosis, fibrosis, or pain.

Adipose Tissue↗