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‣ Molecular model of shikimate kinase from Mycobacterium tuberculosis

De Azevedo Jr., Walter Filgueira; Canduri, Fernanda; De Oliveira, Jaim Simões; Basso, Luiz Augusto; Palma, Mario Sergio; Pereihenrra, José Henrique; Santos, Diógenes Santiago
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 142-148
Português
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Tuberculosis (TB) resurged in the late 1980s and now kills approximately 3 million people a year. The reemergence of tuberculosis as a public health threat has created a need to develop new anti-mycobacterial agents. The shikimate pathway is an attractive target for herbicides and anti-microbial agents development because it is essential in algae, higher plants, bacteria, and fungi, but absent from mammals. Homologs to enzymes in the shikimate pathway have been identified in the genome sequence of Mycobacterium tuberculosis. Among them, the shikimate kinase I encoding gene (aroK) was proposed to be present by sequence homology. Accordingly, to pave the way for structural and functional efforts towards anti-mycobacterial agents development, here we describe the molecular modeling of M. tuberculosis shikimate kinase that should provide a structural framework on which the design of specific inhibitors may be based. © 2002 Elsevier Science (USA). All rights reserved.

‣ Taxonomic and phylogenetic relationships between neotropical species of ticks from genus Amblyomma (Acari: Ixodidae) inferred from second internal transcribed spacer sequences of rDNA

Marrelli, M. T.; Souza, L. F.; Marques, R. C.; Labruna, M. B.; Matioli, S. R.; Tonon, A. P.; Ribolla, P. E M; Marinotti, O.; Schumaker, T. T S
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 222-228
Português
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57.12743%
The accurate specific identification of ticks is essential for the study, control and prevention of tick-borne diseases. Herein, we determined ribosomal nucleotide sequences of the second internal transcribed spacer (ITS2) of 15 Neotropical hard tick species of the genus Amblyomma Koch found in Brazil. Most of the studied ticks accidentally parasite humans and potentially act as vectors of zoonoses. Lengths of the ITS2 sequences ranged from 956 to 1,207 bp, whereas GC content varied from 62.4 to 66.9%. A matrix of ITS2 divergence was calculated with the ITS2 sequence data obtained showing divergence levels varying from 1.5 to 28.8%. The analysis indicated that this molecular marker can be useful for Amblyomma-specific identification. Phylogenetic inferences based on the ITS2 sequences were used to assess some issues in subgenus taxonomy. © 2007 Entomological Society of America.

‣ Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Clemente-Carvalho, Rute B.G.; Klaczko, Julia; Ivan Perez, S.; Alves, Ana C.R.; Haddad, Célio F.B.; Dos Reis, Sérgio F.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 79-89
Português
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Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18. mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition...

‣ Molecular sequence accuracy and the analysis of protein coding regions.

States, D J; Botstein, D
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/07/1991 Português
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57.1519%
Molecular sequences, like all experimental data, have finite error rates. The impact of errors on the information content of molecular sequence data is dependent on the analytic paradigm used to interpret the data. We studied the impact of nucleic acid sequence errors on the ability to align predicted amino acid sequences with the sequences of related proteins. We found that with a simultaneous translation and alignment algorithm, identification of sequence homologies is resilient to the introduction of random errors. Proteins with greater than 30% sequence identity can be reliably recognized even in the presence of 1% frameshifting (insertion or deletion) error rates and 5% base substitution rates. Incorporation of prior knowledge about the location and characteristics of errors improves tolerance to error of amino acid sequence alignments. Similarly, inclusion of prior knowledge of biased codon utilization by yeast (Saccharomyces cerevisiae) allows reliable detection of correct reading frames in yeast sequences even in the presence of 5% substitution and 1% frameshift errors.

‣ Using matK sequence data to unravel the phylogeny of Casuarinaceae

Steane, D.; Wilson, K.; Hill, R.
Fonte: Academic Press Inc Publicador: Academic Press Inc
Tipo: Artigo de Revista Científica
Publicado em //2003 Português
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76.997896%
Casuarinaceae are a Gondwanic family with a unique combination of morphological characters not comparable to any other family. Until recently, the 96 species in the family were classified in a single genus, Casuarina s.l. A recent morphological revision of the family resulted in the splitting of Casuarina s.l. into four genera—Allocasuarina, Casuarina s.s., Ceuthostoma, and Gymnostoma. This study uses matK sequence data from 76 species of Casuarinaceae and eight outgroup taxa to examine the phylogenetic structure within the Casuarinaceae. The study demonstrates the monophyly of the four genera and examines the relationships within the family; it tests the validity of the infra-generic subdivision of Allocasuarina; it discovers geography-based infra-generic subdivisions within Gymnostoma and Casuarina; and, finally, provides a molecular framework on which to trace the evolution of xeromorphy in the Casuarinaceae.; http://www.elsevier.com/wps/find/journaldescription.cws_home/622921/description#description; Dorothy A. Steane, Karen L. Wilson and Robert S. Hill

‣ The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the β-helix domain; The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the beta-helix domain

Freiberg, A.; Morona, R.; Van Den Bosch, L.; Jung, C.; Behlke, J.; Carlin, N.; Seckler, R.; Baxa, U.
Fonte: Amer Soc Biochemistry Molecular Biology Inc Publicador: Amer Soc Biochemistry Molecular Biology Inc
Tipo: Artigo de Revista Científica
Publicado em //2003 Português
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66.979785%
Bacteriophage Sf6 tailspike protein is functionally equivalent to the well characterized tailspike of Salmonella phage P22, mediating attachment of the viral particle to host cell-surface polysaccharide. However, there is significant sequence similarity between the two 70-kDa polypeptides only in the N-terminal putative capsid-binding domains. The major, central part of P22 tailspike protein, which forms a parallel -helix and is responsible for saccharide binding and hydrolysis, lacks detectable sequence homology to the Sf6 protein. After recombinant expression in Escherichia coli as a soluble protein, the Sf6 protein was purified to homogeneity. As shown by circular dichroism and Fourier transform infrared spectroscopy, the secondary structure contents of Sf6 and P22 tailspike proteins are very similar. Both tailspikes are thermostable homotrimers and resist denaturation by SDS at room temperature. The specific endorhamnosidase activities of Sf6 tailspike protein toward fluorescence-labeled dodeca-, deca-, and octasaccharide fragments of Shigella O-antigen suggest a similar active site topology of both proteins. Upon deletion of the N-terminal putative capsid-binding domain, the protein still forms a thermostable, SDS-resistant trimer that has been crystallized. The observations strongly suggest that the tailspike of phage Sf6 is a trimeric parallel -helix protein with high structural similarity to its functional homolog from phage P22.; Alexander Freiberg...

‣ Further characterization of proteins associated with elastic fiber microfibrils including the molecular cloning of MAGP-2 (MP25)

Gibson, M.; Hatzinikolas, G.; Kumaratilake, J.; Sandberg, L.; Nicholl, J.; Sutherland, G.; Cleary, E.
Fonte: American Society for Biochemistry and Molecular Biology Publicador: American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
Publicado em //1996 Português
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67.100527%
Together with the 31-kDa microfibril-associated glycoprotein (MAGP), four polypeptides designated MP340 (340 kDa), MP78 (78 kDa), MP70 (70 kDa), and MP25 (25 kDa) have previously been identified in tissue extracts designed specifically to solubilize the microfibrillar component of elastic fibers. In the present study, both MP78 and MP70 were shown to be forms of a protein which is closely related to the human protein βig-h3, and MP340 was confirmed to be the bovine form of fibrillin-1. Peptide sequences from MP25 proved to be unique, and affinity-purified anti-MP25 antibodies were shown, by immunofluorescence and immunoelectron microscopy, to localize specifically to the elastin-associated microfibrils. This confirmed that MP25 was a distinct component of these structures. Expression screening of nuchal ligament cDNA libraries yielded a cDNA, cM10A (770 base pairs) which encodes amino acid sequences matching those of the MP25 peptides. Further library screening with cM10A identified cDNAs which encode the complete primary structures of bovine and human MP25. Bovine and human MP25 were found to be around 80% homologous and contain 170 and 173 amino acids, respectively. Data base searches revealed that MP25 had significant similarity of structure only with MAGP...

‣ Molecular, genetic and topological characterization of O-antigen chain length regulation in Shigella flexneri

Morona, R.; Van Den Bosch, L.; Manning, P.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em //1995 Português
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57.10856%
The rfb region of Shigella flexneri encodes the proteins required to synthesize the O-antigen component of its cell surface lipopolysaccharides (LPS). We have previously reported that a region adjacent to rfb was involved in regulating the length distribution of the O-antigen polysaccharide chains (D. F. Macpherson et al., Mol. Microbiol. 5:1491-1499, 1991). The gene responsible has been identified in Escherichia coli O75 (called rol [R. A. Batchelor et al., J. Bacteriol. 173:5699-5704, 1991]) and in E. coli O111 and Salmonella enterica serovar typhimurium strain LT2 (called cld [D. A. Bastin et al., Mol. Microbiol. 5:2223-2231, 1991]). Through a combination of subcloning, deletion, and transposon insertion analysis, we have identified a gene adjacent to the S. flexneri rfb region which encodes a protein of 36 kDa responsible for the length distribution of O-antigen chains in LPS as seen on silver-stained sodium dodecyl sulfate-polyacrylamide gels. DNA sequence analysis identified an open reading frame (ORF) corresponding to the rol gene. The corresponding protein was almost identical in sequence to the Rol protein of E. coli O75 and was highly homologous to the functionally identical Cld proteins of E. coli O111 and S. enterica serovar typhimurium LT2. These proteins...

‣ Contrasting rates of mitochondrial molecular evolution in parasitic diptera and hymenoptera

Castro, L.; Austin, A.; Dowton, M.
Fonte: Soc Molecular Biology Evolution Publicador: Soc Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Publicado em //2002 Português
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66.844077%
We investigated the putative association between the parasitic lifestyle and an accelerated rate of mt genetic divergence, compositional bias, and gene rearrangement, employing a range of parasitic and nonparasitic Diptera and Hymenoptera. Sequences were obtained for the cox1, cox2, 16S, 28S genes, the regions between the cox2 and atp8 genes, and between the nad3 and nad5 genes. Relative rate tests indicated generally that the parasitic lifestyle was not associated with an increased rate of genetic divergence in the Diptera but reaffirmed that it was in the Hymenoptera. Similarly, a departure from compositional stationarity was not associated with parasitic Diptera but was in parasitic Hymenoptera. Finally, mitochondrial (mt) gene rearrangements were not observed in any of the dipteran species examined. The results indicate that these genetic phenomena are not accelerated in parasitic Diptera compared with nonparasitic Diptera. A possible explanation for the differences in the rate of mt molecular evolution in parasitic Diptera and Hymenoptera is the extraordinary level of radiation that has occurred within the parasitic Hymenoptera but not in any of the dipteran parasitic lineages. If speciation events in the parasitic Hymenoptera are associated with founder events...

‣ Phylogenetic relationships among the microgastroid wasps (Hymenoptera: Braconidae): combined analysis of 16S and 28S rDNA genes and morphological data

Dowton, M.; Austin, A.
Fonte: ACADEMIC PRESS INC Publicador: ACADEMIC PRESS INC
Tipo: Artigo de Revista Científica
Publicado em //1998 Português
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66.99476%
Relationships among the microgastroid complex of braconid wasps were investigated using sequence data from the 16S mitochondrial rDNA and 28S (D2 expansion region) nuclear rDNA genes, as well as morphological data. Parsimony analysis of these gene fragments, both separately and combined, indicated that Neoneurus (Neoneurinae) and Ichneutes (Ichneutinae) were no more closely related to the microgastroids than were a range of helconoid taxa. Combined parsimony analysis of the microgastroids indicated the relationships ((Cardiochilinae + Microgastrinae) + Miracinae) + Cheloninae, with Adeliinae falling inside the Cheloninae. Bootstrap proportions for each of these nodes were greater than 70%. Character reweighting (sensu Farris), using the rescaled consistency index, also recovered these relationships. Mapping of lifestyle traits onto this relatively well supported phylogeny indicated that solitary endoparasitism is ancestral for the microgastroids, with a single origin for egg-larval endoparasitism in the Cheloninae + Adeliinae. Mapping of the radiation of the microgastroids into lepidopteran hosts was less clear, due to the specialized biology of the most basal microgastroid clade, the Cheloninae + Adeliinae. Our data are consistent with attack of concealed lepidopteran hosts as the plesiomorphic lifestyle...

‣ Molecular and functional analyses of the human and mouse genes encoding AFG3L1, a mitochondrial metalloprotease homologous to the human spastic paraplegia protein

Kremmidiotis, G.; Gardner, A.; Settasatian, C.; Savoia, A.; Sutherland, G.; Callen, D.
Fonte: Academic Press Inc Publicador: Academic Press Inc
Tipo: Artigo de Revista Científica
Publicado em //2001 Português
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57.08445%
The identification of SPG7 as the gene defective in a recessive form of spastic paraplegia has drawn attention to the yeast protein family of ATP-dependent zinc metalloproteases. The protein encoded by SPG7, paraplegin, shows high homology to members of this protein family. Recently, many mammalian ATP-dependent zinc metalloproteases have been identified and considered as possible candidates for defects in other forms of hereditary spastic paraplegia and possibly other neurodegenerative disorders. So far only a partial sequence has been available for one of those genes, ATPase family gene-3, yeast-like-1 (AFG3L1). We have carried out detailed molecular analysis of this gene and identified and characterized its mouse orthologue, Afg3l1. Our data indicate that AFG3L1 is transcribed into four mRNA isoforms that are not translated in humans. Afg3l1 encodes a protein with high homology to paraplegin and the other members of the ATP-dependent zinc metalloprotease family. Like the other ATP-dependent zinc metalloproteases, Afg3l1 localizes to the mitochondria.; Gabriel Kremmidiotis, Alison E. Gardner, Chatri Settasatian, Anna Savoia, Grant R. Sutherland, and David F. Callen; © 2001 by Academic Press. All rights of reproduction in any form reserved.

‣ Molecular phylogenetics of Puffinus shearwaters: preliminary evidence from mitochondrial cytochrome b gene sequences

Austin, J.
Fonte: ACADEMIC PRESS INC ELSEVIER SCIENCE Publicador: ACADEMIC PRESS INC ELSEVIER SCIENCE
Tipo: Artigo de Revista Científica
Publicado em //1996 Português
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Puffinus shearwaters (Family Procellariidae) are a diverse genus of pelagic seabirds or petrels with a worldwide distribution. Five subgroups of species have been recognized on the basis of osteological and external morphological characters. However, phylogenetic relationships among extant taxa are poorly understood, and evolutionary scenarios to explain the current overlapping distribution of the species subgroups are speculative. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences were used to examine the relationships among 19 species and subspecies of Puffinus shearwaters. In general, the molecular data support previous morphologically based phylogenetic hypotheses. However, the subgroup Neonectris appears to be polyphyletic with Puffinus nativitatis more closely related to species in the subgroup Puffinus. In addition the molecular data revealed a phylogenetic split between the Puffinus subgroup, with a worldwide distribution, and the remaining four subgroups which have an essentially southern hemisphere distribution. This suggests an evolutionary history in which the Puffinus ancestor was split between two geographic regions, from which dispersal and vicariant events resulted in the evolution and distribution of extant taxa.; Jeremy J. Austin

‣ Factor Inhibiting HIF (FIH) recognizes distinct molecular features within hypoxia-inducible factor-α (HIF-α) versus ankyrin repeat substrates; Factor Inhibiting HIF (FIH) recognizes distinct molecular features within hypoxia-inducible factor-alpha (HIF-alpha) versus ankyrin repeat substrates

Wilkins, S.; Karttunen, S.; Hampton-Smith, R.; Murchland, I.; Chapman-Smith, A.; Peet, D.
Fonte: Amer Soc Biochemistry Molecular Biology Inc Publicador: Amer Soc Biochemistry Molecular Biology Inc
Tipo: Artigo de Revista Científica
Publicado em //2012 Português
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67.023677%
Factor Inhibiting HIF (FIH) catalyzes the β-hydroxylation of asparagine residues in HIF-α transcription factors as well as ankyrin repeat domain (ARD) proteins such as Notch and Gankyrin. Although FIH-mediated hydroxylation of HIF-α is well characterized, ARDs were only recently identified as substrates, and less is known about their recognition and hydroxylation by FIH. We investigated the molecular determinants of FIH substrate recognition, with a focus on differences between HIF and ARD substrates. We show that for ARD proteins, structural context is an important determinant of FIH-recognition, but analyses of chimeric substrate proteins indicate that the ankyrin fold alone is not sufficient to explain the distinct substrate properties of the ARDs compared with HIF. For both substrates the kinetic parameters of hydroxylation are influenced by the amino acids proximal to the target asparagine. Although FIH tolerates a variety of chemically disparate residues proximal to the asparagine, we demonstrate that certain combinations of amino acids are not permissive to hydroxylation. Finally, we characterize a conserved RLL motif in HIF and demonstrate that it mediates a high affinity interaction with FIH in the presence of cell lysate or macromolecular crowding agents. Collectively...

‣ What lies beneath: Molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)

Abrams, K.; Guzik, M.; Cooper, S.; Humphreys, W.; King, R.; Cho, J.L.; Austin, A.
Fonte: Academic Press Inc Elsevier Science Publicador: Academic Press Inc Elsevier Science
Tipo: Artigo de Revista Científica
Publicado em //2012 Português
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67.07585%
The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally...

‣ Classification of taxonomic units for biology and conservation in the cases of Lathyrus pannonicus and Oxytropis pilosa - Evaluation of morphological and phytosociological studies integrating molecular genetic data

Schlee, Matthias
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Dissertação
Português
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66.63506%
In order to conserve biodiversity and develop taxon-specific conservation measures it is important to define and identify taxonomic units, which require protection. In this thesis, the differentiation processes in two species of the Fabaceae, the Hungarian Pea Lathyrus pannonicus (Jacq.) Garcke and the Wolly Milkvetch Oxytropis pilosa DC., are investigated using a combination of phytosociological surveys (using the Braun-Blanquet method) and molecular sequence data, and a set of analyses which include entirely novel approaches. Both species are relict species and elements of the Pontian-Pannonian floristic province. In the case of the generally more variable Lathyrus pannonicus correlations are found between ecological, morphological and genetic inter-stand distances. Mean Ellenberg indicator values calculated for stands (based on the Braun-Blanquet relevés) allowed to characterise the ecological properties of members of all subspecies, and to conclude that the genetic differentiation found in L. pannonicus is closely linked to Ellenberg’s moisture figure “F”. Lathyrus pannonicus and its subspecies fall into two major lineages in Europe: (1) a dry-adapted lineage (subspecies collinus, suevicus, and varius) thriving in habitats with mean “F” values of < 4...

‣ Analysis of the 5' portion of the type 19A capsule locus identifies two classes of cpsC, cpsD, and cpsE genes in Streptococcus pneumoniae

Morona, J.; Morona, R.; Paton, J.
Fonte: AMER SOC MICROBIOLOGY Publicador: AMER SOC MICROBIOLOGY
Tipo: Artigo de Revista Científica
Publicado em //1999 Português
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57.09806%
Analysis of the sequence data obtained from the 5' portion of the Streptococcus pneumoniae type 19A capsular polysaccharide biosynthesis locus (cps19a) revealed that the first seven genes are homologous to the first seven genes in the type 19F (cps19f) locus. The former genes were designated cps19aA to -G and were 70 to 90% identical to their cps19f counterparts. Southern hybridization analysis of the cps loci from various S. pneumoniae serotypes with probes specific for the cps19aC, cps19aD, and cps19aE genes indicated a hybridization pattern complementary to that previously reported for cps19fC, cps19fD, and cps19fE. That is, all serotypes tested contained high-stringency homologues of either the cps19aC to -E genes or the cps19fC to -E genes, but not both. On this basis S. pneumoniae cps loci can be divided into two distinct classes. Long-range PCR was used to amplify the cps regions between cpsB and aliA from a variety of pneumococcal serotypes. Direct sequencing of the 5' end of these PCR products, and phylogenetic analysis of the sequence data, confirmed the presence of the two distinct classes of cpsC. Whereas members within one class are greater than 95% identical to each other, the DNA sequence identity between the two classes is only approximately 70%.

‣ Isolation and characterization of ovine IGFBP-4: protein purification and cDNA sequence

CARR, J.M.; GRANT, P.A.; FRANCIS, G.L.; OWENS, J.A.; WALLACE, J.C.; WALTON, P.E.
Fonte: BioScientifica Publicador: BioScientifica
Tipo: Artigo de Revista Científica
Publicado em //1994 Português
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57.130225%
Three different molecular mass forms of IGF-binding proteins (IGFBPs) were purified from ovine plasma by IGF-I affinity chromatography and reverse-phase HPLC: a 46 kDa doublet and 29 kDa and 24 kDa forms. Amino-terminal sequence analysis confirmed that these proteins were ovine (o)IGFBP-3 (46 kDa) and two molecular size variants of oIGFBP-4. oIGFBP-3 and the 29 kDa form of oIGFBP-4 were shown to be N-glycosylated. Isoelectric points were determined to be at approximately pH 6 for oIGFBP-3 and at pH 7 and pH 7.5 for the 29 and 24 kDa forms of oIGFBP-4 respectively. The two different molecular mass variants of oIGFBP-4 had similar IGF-binding properties. Compared with human IGFBP-3 and oIGFBP-3, the two variants of oIGFBP-4 exhibited lower relative binding to amino-terminally modified IGF-I analogues in a competitive IGF-binding assay. The full protein sequence of oIGFBP-4, as deduced from the cDNA sequence, showed a high degree of identity with rat (90%), human (96%) and bovine (98%) IGFBP-4. The cDNA sequence also showed homology over regions of the 3' non-coding sequence, particularly in comparison with bovine IGFBP-4 (96%). Northern analysis of mRNA for oIGFBP-4 indicated a 2.6 kb major transcript and two minor transcripts of approximately 2.1 and 1.8 kb. oIGFBP-4 mRNA transcripts were detected in adult ewe liver > kidney > lung >> heart and also in several fetal tissues...

‣ Molecular cloning of the cDNA and chromosome localization of the gene for human ubiquitin-conjugating enzyme 9

Wang, Z.; Qiu, Q.; Seufert, W.; Taguchi, T.; Testa, J.; Whitmore, S.; Callen, D.; Welsh, D.; Shenk, T.; Deuel, T.
Fonte: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC Publicador: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Tipo: Artigo de Revista Científica
Publicado em //1996 Português
Relevância na Pesquisa
66.927593%
We report a novel human gene whose product specifically associates with the negative regulatory domain of the Wilms' tumor gene product (WT1) in a yeast two-hybrid screen and with WT1 in immunoprecipitation and glutathione S-transferase (GST) capture assays. The gene encodes a 17-kDa protein that has 56% amino acid sequence identity with yeast ubiquitin-conjugating enzyme (yUBC) 9, a protein required for cell cycle progression in yeast, and significant identity with other subfamilies of ubiquitin-conjugating enzymes. The human gene fully complements yeast that have a temperature-sensitive yUBC9 gene mutation to fully restore normal growth, indicating that we have cloned a functionally conserved human (h) homolog of yUBC9. Transcripts of hUBC9 of 4.4 kilobases (kb), 2.8 kb, and 1.3 kb were found in all human tissues tested. A single copy of the hUBC9 gene was found and localized to human chromosome 16p13.3. We conclude that hUBC9 retains striking structural and functional conservation with yUBC9 and suggest a possible link of the ubiquitin/proteosome proteolytic pathway and the WT1 transcriptional repressor system.

‣ Sequence, genomic organization and expression of the novel homeobox gene Hesx1

Thomas, P.; Johnson, B.; Rathjen, J.; Rathjen, P.
Fonte: The American Society for Biochemistry and Molecular Biology Inc Publicador: The American Society for Biochemistry and Molecular Biology Inc
Tipo: Artigo de Revista Científica
Publicado em //1995 Português
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66.955674%
Extensive analyses of homeobox gene expression and function during murine embryogenesis have demonstrated that homeobox gene products are key components in the establishment of pattern formation and regional identity during development. In this paper we report the molecular characterization and expression of a novel murine homeobox sequence, Hesx1, isolated from pluripotent embryonic stem cells. Hesx1 is expressed as two transcripts of 1.0 and 1.2 kilobases which encode an identical 185 amino acid open reading frame. The transcripts differ in the 3'-untranslated region due to the differential utilization of a weak splice donor site located immediately downstream of the translation termination codon. The Hesx1 homeodomain shared 80% identity with the Xenopus homeoprotein XANF-1 and was less than 50% related to other homeodomain sequences. Hesx1 and XANF-1 therefore constitute the founder members of a new homeodomain class. Hesx1 expression was down-regulated during embryonic stem cell differentiation and was detected in tissue-specific RNA samples derived from the embryonic liver, and at lower levels in viscera, amnion, and yolk sac. Expression in adult mice was not detected. These sites of expression are consistent with a role for Hesx1 in the regulation of developmental decisions in the early mouse embryo and during fetal hematopoiesis.; Paul Q. Thomas...

‣ A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

Penny, David; White, W.T.; Hendy, Mike D.; Phillips, Matthew
Fonte: Society for Molecular Biology Evolution Publicador: Society for Molecular Biology Evolution
Tipo: Artigo de Revista Científica
Português
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67.010664%
Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, th