Allelic polymorphism of the tem(M) determinant in Mycoplasma hominis and Ureaplasma urealyticum clinical isolates resistant to tetracyclines

Of the 130 clinical isolates of Mycoplasma hominis from patients with nonspecific inflammatory diseases of the urogenital tract (UGT), approximately 10% contained the tet(M) gene after the course of treatment with tetracyclines. This gene was found in nine (25%) of the 36 Ureaplasma urealyticum clinical isolates. The nucleotide sequence of 13 tet(M) genes in TcR clinical isolates of M. hominis and five genes in U. urealyticum TcR clinical isolates was determined. A comparison of nucleotide sequences of eight tetM genes of different origin and tet(M) genes of Gardnerella vaginalis and M. hominis and U. urealyticum clinical isolates showed that the mosaic structure of the tet(M) gene is completely identical in 11 of 13 M. hominis TcR isolates but belongs to an unidentified allele different from those described earlier, Another new allelic variant of tet(M) was found in two isolates. In three of five TcR clinical isolates of U. urealyticum, a tet(M) gene, whose mosaic structure was identical to that of tet(M) reported previously for ureaplasmas, and also two new allelic variants, which have not been described so far, were found.     

Indiscriminate representation of VH-gene families in the murine B lymphocyte responses to Trypanosoma cruzi

The utilization of the nine major homology families of VH-genes was quantitated in the B lymphocyte response to Trypanosoma cruzi infection of C57BL/6 mice. Normal and infected mice at various times after parasite inoculation were compared for VH-gene distribution of CFU-B produced by activated blasts recovered from spleen and lymph nodes, and for relative hybridization of total spleen RNA with each of the family probes. T. cruzi infection results in large increases of splenic RNA in the various homology families, and the numbers of activated CFU-B, reflecting the massive B lymphocyte responses. In acute phase, all nine families are expressed in roughly the same proportions as in normal mice, whereas in chronic infection, B cells expressing S107 and 7183 VH-genes might be preferentially stimulated. These results establish the polyclonal nature of the host response to T. cruzi infection.     

On the structure and chromosome location of the 72- and 92-kDa human type IV collagenase genes.

The 72- and 92-kDa type IV collagenases are members of a group of secreted zinc metalloproteases. Two members of this family, collagenase and stromelysin, have previously been localized to the long arm of chromosome 11. Here we assign both of the two type IV collagenase genes to human chromosome 16. By sequencing, the 72-kDa gene is shown to consist of 13 exons, 3 more than have been reported for the other members of this gene family. The extra exons encode the amino acids of the fibronectin-like domain which has so far been found in only the 72- and 92-kDa type IV collagenase. The evolutionary relationship among the members of this gene family is discussed.     

Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity

SARS-CoV-2 belongs to the coronavirus family. Comparing genomic features of viral genomes of coronavirus family can improve our understanding about SARS-CoV-2. Here we present the first pan-genome analysis of 3,932 whole genomes of 101 species out of 4 genera from the coronavirus family. We found that a total of 181 genes in the pan-genome of coronavirus family, among which only 3 genes, the S gene, M gene and N gene, are highly conserved. We also constructed a pan-genome from 23,539 whole genomes of SARS-CoV-2. There are 13 genes in total in the SARS-CoV-2 pan-genome. All of the 13 genes are core genes for SARS-CoV-2. The pan-genome of coronaviruses shows a lower level of diversity than the pan-genomes of other RNA viruses, which contain no core gene. The three highly conserved genes in coronavirus family, which are also core genes in SARS-CoV-2 pan-genome, could be potential targets in developing nucleic acid diagnostic reagents with a decreased possibility of cross-reaction with other coronavirus species.     

Nucleotide sequences and three-dimensional modelling of the VH and VL domains of two human monoclonal antibodies specific for the D antigen of the human Rh-blood-group system.

The nucleotide sequences were determined for the VH and VL domains of two human IgG1 antibodies, Pag-1 and Fog-B, specific for the D antigen of the Rh-blood-group system. The VH-region genes of the two antibodies were derived from separate germ-line genes within the VH-IV gene family, but both antibodies used the same JH6 gene. The D-region genes differed from each other, and no similarity was found to known D regions. The light chain of Fog-B belongs to the V lambda-I subgroup and that of Pag-1 probably belongs to the V lambda-V subgroup; both light chains used the J2/3 gene. Three-dimensional models of the variable domains were made, based on those of known crystallographic structure. The surface contours at the combining sites are clearly different, consistent with the evidence that the antibodies recognize different but overlapping epitopes. Some details of the molecular modelling of hypervariable regions have been deposited as Supplementary Publication SUP 50155 (6 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1990) 265, 5.     

黑麂线粒体基因组序列分析

采用PCR产物直接测序方法测定了黑麂线粒体基因组全序列 ,初步分析了其基因组特点并定位了各基因的位置 .结果显示 :黑麂的线粒体基因组全序列长度为 1 6 35 7bp ,可编码 2 2种tRNA、2种rRNA、1 3种蛋白质 ,碱基组成及基因位置与小麂、赤麂和其它哺乳类动物的线粒体基因组相似 ;模拟电子酶切图谱与先前的报道基本一致 ;基于细胞色素b的全基因序列 ,分别以最大简约法、N J法、最大似然数法与其它 1 4种鹿类动物的相应序列进行了聚类分析 ,构建出相似的系统进化树 :初步确定了麂亚科动物在鹿科中处于与鹿亚科、北美鹿亚科并列的进化地位 .在此基础上 ,进一步以黑麂、赤麂、小麂的线粒体编码RNA和编码蛋白质的基因序列构建系统进化树 ,分析了三者的亲缘关系 .结果表明 :黑麂和赤麂亲缘关系较近 ,是较新的物种 ,而小麂是较为原始的物种     

Definition of a new alpha satellite suprachromosomal family characterized by monomeric organization.

We have analyzed more than 500 alphoid monomers either sequenced in our laboratory or available in the literature. Most of them belonged to the well studied suprachromosomal families 1, 2 and 3 characterized by dimeric (1 and 2) and pentameric (3) ancestral periodicities. The sequences that did not belong to the previously known families were subjected to further analysis. About a half of them formed a relatively homogenous family. Its members were on average 80.5% identical and 89.5% homologous to the M1 consensus sequence derived from this group (39 monomers). In the genome they do not form any ancestral periodicities other than a monomeric one, and are found at least in chromosomes 13, 14, 15, 21, 22 and Y. The newly defined family was termed suprachromosomal family 4. Comparison of all 10 alphoid monomeric groups identified so far showed that the M1 sequence is closely related to the J1-D2-W4-W5 homology grouping. Notably the African Green Monkey alpha satellite, also characterized by monomeric construction, appears to be a member of the same group.     

利用抑制消减杂交技术研究结核分支杆菌强毒株H37Rv和弱毒株H37Ra的基因差异

为了解结核病的致病分子机理和筛选结核病致病菌的毒力基因,利用抑制消减杂交（SSH）技术分析了结核分支杆菌强毒株H37Rv和弱毒株H37Ra间的基因组DNA间差异。通过Southern杂交验证及序列分析得到仅在强毒株H37Rv基因组中有的DNA片段8个,其中一个编码已知的毒力因子mce蛋白,1个编码PE家族蛋白,1个编码purC合成酶,和4个潜在蛋白,另一个为非编码区片段。其中有2个基因经PCR方法已证实在强毒株H37Rv和临床分离的强毒株中存在,而在H37Ra和临床弱毒株中无;仅在弱毒株H37Ra基因组中的DNA片段3个,其中2个为新基因片段,已被GenBank收录。     

High-multiplicity of chitinase genes in Streptomyces coelicolor A3(2).

Six different genes for chitinase from ordered cosmids of the chromosome of Streptomyces coelicolor A3(2) were identified by hybridization, using the chitinase genes from other Streptomyces spp. as probes, and cloned. The genes were sequenced and analyzed. The genes, together with an additional chitinase gene obtained from the data bank, can be classified into either family 18 or family 19 of the glycosyl hydrolase classification. The five chitinases that fall into family 18 show diversity in their multiple domain structures as well as in the amino acid sequences of their catalytic domains. The remaining two chitinases are members of family 19 chitinases, since their C-terminus shares more than 70% identity with the catalytic domain of ChiC of Streptomyces griseus, the sole gene for family 19 chitinase so far found in an organism other than higher plants.     

Complete mitochondrial genome of the Iberian Mole <Emphasis Type="Italic">Talpa occidentalis</Emphasis> (Talpidae,Insectivora) and comparison with <Emphasis Type="Italic">Talpa europaea</Emphasis>

The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.     

Evolutionary History of Eukaryotic α-Glucosidases from the α-Amylase Family

Although some α-glucosidases from the α-amylase family (glycoside hydrolase family GH13) have been studied extensively, their exact number, organization on the chromosome, and orthology/paralogy relationship were unknown. This was true even for important disease vectors where gut α-glucosidase is known to be receptor for the Bin toxin used to control the population of some mosquito species. In some cases orthologs from related species were studied intensively, while potentially important paralogs were omitted. We have, therefore, used a bioinformatics approach to identify all family GH13 α-glucosidases from the selected species from Metazoa (including three mosquito species: Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus) as well as from Fungi in an effort to characterize their arrangement on the chromosome and evolutionary relationships among orthologs and among paralogs. We also searched for pseudogenes and genes coding for enzymatically inactive proteins with a possible new function. We have found GH13 α-glucosidases mostly in Arthropoda and Fungi where they form gene families, as a result of multiple lineage-specific gene duplications. In mosquito species we have identified 14 α-glucosidase (Aglu) genes of which only five have been biochemically characterized so far, two are putative pseudogenes and the rest remains uncharacterized. We also revealed quite a complex evolutionary history of the eukaryotic α-glucosidases probably involving multiple losses of genes or horizontal gene transfer from bacteria.     

近亲结婚所致一遗传性非综合征型耳聋家系的调查

耳聋是一种最常见的人类感觉系统缺陷, 在已发现的遗传性耳聋中,有70％的属于非综合征型听力缺损。据估计非综合征型遗传性耳聋基因总数在100个以上,目前已经确定了近80个非综合征型遗传性耳聋的遗传位点,其中23个基因已经被成功克隆。文章报道一遗传性非综合征型耳聋家系。该家系中存在2代近亲结婚,共2代13人出现聋哑症状。经遗传分析,该家系的遗传方式与常染色体显性或隐性遗传均不符合,提示此家系中的非综合征型遗传性耳聋可能为线粒体突变所致。     

Nematode collagen genes

The collagen genes of nematodes encode proteins that have a diverse range of functions. Among their most abundant products are the cuticular collagens, which include about 80% of the proteins present in the nematode cuticle. The structures of these collagens have been found to be strikingly similar in the free-living and parasitic nematode species studied so far, and the genes that encode them appear to constitute a large multigene family whose expression is subject to developmental regulation. Collagen genes that may have a role in cell-cell interactions and collagen genes that correspond to the vertebrate type IV collagen genes have also been identified and studied in nematodes.     

A 4-Mb BAC/PAC contig and complete genomic structure of the GPC5/GPC6 gene cluster on chromosome 13q32.

The glypicans compose a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans that may play a role in the control of cell division and growth regulation. So far, six members (GPC1-6) of this family are known in vertebrates. We report the construction of a high-resolution 4 Mb sequence-ready BAC/PAC contig of the GPC5/GPC6 gene cluster on chromosome region 13q32. The contig indicates that, like the GPC3/GPC4 genes on Xq26, GPC5 and GPC6 are arranged in tandem array. Both GPC5 and GPC6 are very large genes, with sizes well over 1 Mb. With a size of approximately 2 Mb, GPC5 would be the second largest human gene identified to date. Comparison of the long range gene organisation on 13q and Xq, suggests that these chromosomes share several regions of homology. Mutations and deletions affecting GPC3 are associated with the Simpson-Golabi-Behmel overgrowth syndrome. Mutational analysis of GPC5 and GPC6 in 19 patients with somatic overgrowth failed to reveal pathologic mutations in either of these genes, but identified several coding region polymorphisms.     

Intronic U14 snoRNAs of Xenopus laevis are located in two different parent genes and can be processed from their introns during early oogenesis.

U14 is a member of the rapidly growing family of intronic small nucleolar RNAs (snoRNAs) that are involved in pre-rRNA processing and ribosome biogenesis. These snoRNA species are encoded within introns of eukaryotic protein coding genes and are synthesized via an intron processing pathway. Characterization of Xenopus laevis U14 snoRNA genes has revealed that in addition to the anticipated location of U14 within introns of the amphibian hsc70 gene (introns 4, 5 and 7), additional intronic U14 snoRNAs are also found in the ribosomal protein S13 gene (introns 3 and 4). U14 is thus far a unique intronic snoRNA in that it is encoded within two different parent genes of a single organism. Northern blot analysis revealed that U14 snoRNAs accumulate during early oocyte development and are rapidly expressed after the mid-blastula transition of developing embryos. Microinjection of hsc70 pre-mRNAs into developing oocytes demonstrated that oocytes as early as stages II and III are capable of processing U14 snoRNA from the pre-mRNA precursor. The ability of immature oocytes to process intronic snoRNAs is consistent with the observed accumulation of U14 during oocyte maturation and the developmentally regulated synthesis of rRNA during oogenesis.     

Allelic Polymorphism of the tet(M) Determinant in Mycoplasma hominis and Ureaplasma urealyticum Clinical Isolates Resistant to Tetracyclines

Of the 130 clinical isolates of Mycoplasma hominisfrom patients with nonspecific inflammatory diseases of the urogenital tract (UGT), approximately 10% contained the tet(M) gene after the course of treatment with tetracyclines. This gene was found in nine (25%) of the 36 Ureaplasma urealyticum clinical isolates. The nucleotide sequence of 13 tet(M) genes in Tc^R clinical isolates ofM. hominis and five genes in U. urealyticum Tc^R clinical isolates was determined. A comparison of nucleotide sequences of eight tetM genes of different origin and tet(M) genes ofGardnerella vaginalis and M. hominis and U. urealyticumclinical isolates showed that the mosaic structure of thetet(M) gene is completely identical in 11 of 13 M. hominis Tc^Risolates but belongs to an unidentified allele different from those described earlier. Another new allelic variant oftet(M) was found in two isolates. In three of five Tc^R clinical isolates of U. urealyticum, a tet(M) gene, whose mosaic structure was identical to that of tet(M) reported previously for ureaplasmas, and also two new allelic variants, which have not been described so far, were found.     

Evolution of the B7 family: co-evolution of B7H6 and NKp30, identification of a new B7 family member, B7H7, and of B7's historical relationship with the MHC

The B7 family of genes is essential in the regulation of the adaptive immune system. Most B7 family members contain both variable (V)- and constant (C)-type domains of the immunoglobulin superfamily (IgSF). Through in silico screening of the Xenopus genome and subsequent phylogenetic analysis, we found novel genes belonging to the B7 family, one of which is the recently discovered B7H6. Humans and rats have a single B7H6 gene; however, many B7H6 genes were detected in a single large cluster in the Xenopus genome. The B7H6 expression patterns also varied in a species-specific manner. Human B7H6 binds to the activating natural killer receptor, NKp30. While the NKp30 gene is single-copy and maps to the MHC in most vertebrates, many Xenopus NKp30 genes were found in a cluster on a separate chromosome that does not harbor the MHC. Indeed, in all species so far analyzed from sharks to mammals, the number of NKp30 and B7H6 genes correlates well, suggestive of receptor-ligand co-evolution. Furthermore, we identified a Xenopus-specific B7 homolog (B7HXen) and revealed its close linkage to B2M, which we have demonstrated previously to have been originally encoded in the MHC. Thus, our study provides further proof that the B7 precursor was included in the proto MHC. Additionally, the comparative analysis revealed a new B7 family member, B7H7, which was previously designated in the literature as an unknown gene, HHLA2.