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At least 253 records · Page 14Linked to original sources
PubMed2000

Genomic characterization of the human heterotrimeric G protein alpha, beta, and gamma subunit genes.

Heterotrimeric guanine nucleotide binding proteins (G proteins) transduce extracellular signals received by transmembrane receptors to effector proteins. Each subunit of the G protein complex is encoded by a member of one of three corresponding gene families. Currently, 16 different members of the alpha subunit family, 5 different members of the beta subunit family, and 11 different members of the gamma subunit family have been described in mammals. Here we have identified and characterized Bacterial Artificial Chromosomes (BACs) containing the human homologs of each of the alpha, beta, and gamma subunit genes as well as a G alpha11 pseudogene and a previously undiscovered G gamma5-like gene. The gene structure and chromosome location of each gene was determined, as were the orientations of paired genes. These results provide greater insight into the evolution and functional diversity of the mammalian G protein subunit genes.

Amino Acid Sequence↗
PubMed2000

Genomic characterization of a liberibacter present in an ornamental rutaceous tree, Calodendrum capense, in the Western Cape Province of South Africa. Proposal of 'Candidatus Liberibacter africanus subsp. capensis'.

In 1994, the uncultured phloem-restricted bacteria of citrus huanglongbing (ex-greening) disease in Asia and Africa were characterized as 'Candidatus Liberobacter asiaticum' and 'Candidatus Liberobacter africanum', respectively. Following the rules of the International Code of Nomenclature of Bacteria, the two bacterial species have now been renamed 'Candidatus Liberibacter asiaticus' and 'Candidatus Liberibacter africanus'. A third liberibacter was detected by PCR in an ornamental rutaceous tree, Cape chestnut (Calodendrum capense), in South Africa. The new liberibacter was characterized by serology and from the sequences of its 16S rDNA, intergenic 16S/23S rDNA and ribosomal protein genes of the beta operon. Phylogenetic analysis showed that the liberibacter present in C. capense differed from the two previously described liberibacter species from citrus and that it was more closely related to 'Candidatus Liberibacter africanus' than to 'Candidatus Liberibacter asiaticus'. It is proposed that the liberibacter from C capense be assigned a subspecies status, 'Candidatus Liberibacter africanus subsp. capensis'.

Alphaproteobacteria↗
PubMed1980

Regeneration of DI particles of virulent and attenuated rabies virus: genome characterization and lack of correlation with virulence phenotype.

Two strains of fixed rabies virus were examined for their ability to regenerate defective interfering (DI) particles and for possible correlation of DI particle production with the expression of virulence. A plaque-purified stock of the attenuated ERA strain (ERApp), which characteristically caused an auto-interfering death response in adult mice inoculated i.c., was serially passed at a high m.o.i. inBHK-21 cells. By the sixth passage, DI particles were regenerated that corresponded in sedimentation velocity and DI/RNA size to the smallest of three sizes of DI particles produced by the parental stock virus. The regeneration of ERA DI particles in vivo was not detected during 15 serial high or low m.o.i. passages of infected newborn mouse brain, though the passaged virus consistently elicited an auto-interfering-type death response when assayed in adult mice. The attenuated Flury HEPpp strain regenerated up to three unique size classes of DI particles during serial passage in BHK-21 or murine neuroblastoma C1300 clone NA cells compared with the one band of DI particles produced by the parental Flury HEP stock virus. The BHK-21 cell-adapted Flury HEPpp virus failed to kill adult mice when inoculated at high concentrations after two serial passages in NA cells. However, the virus became fully virulent and a single band of regenerated DI particles was visible. Additional bands of defective particles were visible following the third serial passage in NA cells. Single-stranded RNA with a mol. wt. of 0.62 x 10(6) was extracted from the first DI particle population to be regenerated. This corresponded in mol. wt. to the DI/ssRNA characteristic of the parental attenuated Flury HEP virus. However, in the parental type DI/RNA, partially dsRNA could be isolated in addition to ssRNA. Double-stranded RNA could not be detected in the regenerated DI particles derived from the virulent NA cell-propagated Flura HEPpp virus. These results suggest that the virulence phenotype of fixed rabies viruses does not depend on the presence or absence of DI particles.

Animals↗
PubMed1991

Serological and genomic characterization of L338, a novel equine group A rotavirus G serotype.

A group A rotavirus designated L338 was isolated from the faeces of a diarrhoeic foal and was compared to 11 standard G serotype strains of group A rotaviruses by cross-neutralization. It was clearly distinct from serotypes G1 to G11 and thus representative of a novel rotavirus G serotype tentatively designated G13. The nucleic acid sequence of the virion protein 7 (VP7) coding region was determined and the deduced amino acid sequence compared to published sequences. Within VP7 regions A and B, L338 was clearly distinct from serotypes G1 to G12 (excluding G7 which has not been sequenced), but region C was very similar to those of G3 and G8. This further questions the significance of region C in determining serotype specificity of at least three distinct rotavirus G serotypes.

Amino Acid Sequence↗
PubMed1994

Polydnavirus of the parasitic wasp Chelonus inanitus (Braconidae): characterization, genome organization and time point of replication.

Ultrastructural analysis of the polydnavirus of the braconid wasp Chelonus inanitus revealed that virions consist of one cylindrical nucleocapsid enveloped by a single unit membrane. Nucleocapsids have a constant diameter of 33.7 +/- 1.4 nm and a variable length of between 8 and 46 nm. Spreading of viral DNA showed that the genome consists of circular dsDNA molecules of variable sizes and measurement of the contour lengths indicated sizes of between 7 and 31 kbp. When virions were exposed to osmotic shock conditions to release the DNA, only one circular molecule was released per particle suggesting that the various DNA molecules are singly encapsidated in this bracovirus. The viral genome was seen to consist of at least 10 different segments and the aggregate genome size is in the order of 200 kbp. By partial digestion of viral DNA with HindIII or EcoRI in the presence of ethidium bromide and subsequent ligation with HindIII-cut pSP65 or EcoRI-cut pSP64 and transfection into Escherichia coli, libraries of 103 HindIII and 23 EcoRI clones were obtained. Southern blots revealed that complete and unrearranged segments were cloned with this approach, and restriction maps for five segments were obtained. Part of a 16.8 kbp segment was sequenced, found to be AT-rich (73%) and to contain six copies of a 17 bp repeated sequence. The development of the female reproductive tract in the course of pupal-adult development of the wasp was investigated and seen to be strictly correlated with the pigmentation pattern. By the use of a semiquantitative PCR, replication of viral DNA was observed to initiate at a specific stage of pupal-adult development.

Animals↗
PubMed2005

Genomic characterization of KIR2DL4 in families and unrelated individuals reveals extensive diversity in exon and intron sequences including a common frameshift variation occurring in several alleles.

The KIR2DL4 gene including a portion of exon 1 through exon 9 was sequenced from two families and eight cell lines from the International Histocompatibility Workshop (IHWS). Two known alleles and eight variants were detected. Overall, there were five synonymous and three non-synonymous changes when the variants were compared to the coding sequences of the most closely related known alleles plus a common frameshift change in five of the variant alleles. Alignment of the new variants with all known alleles showed that the regions encoding the extracellular region and the cytoplasmic tail were the most polymorphic. Two non-synonymous changes, P146H and L161V, occurred in an extracellular immunoglobulin-like domain. Five of the eight variants had a single adenine deletion in the exon encoding the transmembrane region, potentially resulting in a truncated protein lacking the cytoplasmic tail. The distribution of the deletion variant among many KIR2DL4 alleles may explain the high frequency of this variation in the population. Four of the eight consanguineous IHWS cell lines were found to be heterozygous for KIR2DL4 carrying two alleles that differed from one another by a few nucleotide substitutions. Analysis of intron sequences in the families revealed the nature and distribution of interspersed repeat elements which comprise 46% of the KIR2DL4 nucleotide sequence and consist of 12 elements including six SINEs (13.73% of the total length), one LINE (12.41%), and five LTR elements (19.51%). The results revealed the presence of extensive diversity in the KIR2DL4 gene. This is the first extensive report providing both exon and intron data in related individuals.

Alleles↗
PubMed2026

Screening, Physiological Characterization, Genomic Analysis and Optimization by Conjugated Linoleic Acid Bioconversion of Two Lactiplantibacillus plantarum Strains.

Conjugated linoleic acid (CLA) comprises a group of C18 fatty acids containing conjugated double bonds and has been associated with potential anti-obesity and antitumor effects. In this study, 116 presumptive lactic acid bacteria (LAB) isolates were recovered from homemade Sichuan pickles. Primary screening identified 28 CLA-producing isolates, among which strains 7# and 31# showed the highest absorbance at 233 nm (A233). CLA production by both strains was subsequently optimized and quantified using gas chromatography-quadrupole time-of-flight mass spectrometry (GC-Q-TOF). Under the optimized conditions, strain 31# produced 66.50 ± 3.80 μg/mL total CLA, including 52.70 ± 3.29 μg/mL c9,t11-CLA and 13.80 ± 0.51 μg/mL t10,c12-CLA. Strain 7# produced 26.79 ± 1.09 μg/mL total CLA, including 14.05 ± 0.49 μg/mL c9,t11-CLA and 12.74 ± 0.60 μg/mL t10,c12-CLA. Physiological, biochemical, and safety assessments showed that strain 31# outperformed strain 7# overall, supporting its use in further product development and mechanistic studies. Functional annotation using the COG database and pathway mapping with KEGG identified candidate genes encoding an enzyme associated with linoleic acid isomerization in both strains. Potential mechanisms underlying their different CLA-producing capacities were also examined, providing a basis for the selection and development of high-CLA-producing strains.

conjugated linoleic acid↗
PubMed2001

Genomic characterization of LIGHT reveals linkage to an immune response locus on chromosome 19p13.3 and distinct isoforms generated by alternate splicing or proteolysis.

LIGHT is a member of the TNF cytokine superfamily that signals through the lymphotoxin (LT)beta receptor and the herpesvirus entry mediator. LIGHT may function as a costimulatory factor for the activation of lymphoid cells and as a deterrent to infection by herpesvirus, which may provide significant selective pressure shaping the evolution of LIGHT. Here, we define the molecular genetics of the human LIGHT locus, revealing its close linkage to the TNF superfamily members CD27 ligand and 4-1BB ligand, and the third complement protein (C3), which positions LIGHT within the MHC paralog on chromosome 19p13.3. An alternately spliced isoform of LIGHT mRNA that encodes a transmembrane-deleted form is detected in activated T cells and gives rise to a nonglycosylated protein that resides in the cytosol. Furthermore, membrane LIGHT is shed from the cell surface of human 293 T cells. These studies reveal new mechanisms involved in regulating the physical forms and cellular compartmentalization of LIGHT that may contribute to the regulation and biological function of this cytokine.

4-1BB Ligand↗
PubMed2001

Cloning, characterization, and genomic structure of the mouse Ikbkap gene.

Our laboratory recently reported that mutations in the human I-kappaB kinase-associated protein (IKBKAP) gene are responsible for familial dysautonomia (FD). Interestingly, amino acid substitutions in the IKAP correlate with increased risk for childhood bronchial asthma. Here, we report the cloning and genomic characterization of the mouse Ikbkap gene, the homolog of human IKBKAP. Like its human counterpart, Ikbkap encodes a protein of 1332 amino acids with a molecular weight of approximately 150 kDa. The Ikbkap gene product, Ikap, contains 37 exons that span approximately 51 kb. The protein shows 80% amino acid identity with human IKAP. It shows very high conservation across species and is homologous to the yeast Elp1/Iki3p protein, which is a member of the Elongator complex. The Ikbkap gene maps to chromosome 4 in a region that is syntenic to human chromosome 9q31.3. Because no animal model of FD currently exists, cloning of the mouse Ikbkap gene is an important first step toward creating a mouse model for FD. In addition, cloning of Ikbkap is crucial to the characterization of the putative mammalian Elongator complex.

Amino Acid Sequence↗
PubMed2002

Black rat ( Rattus rattus) genomic variability characterized by chromosome painting.

Black rats are of outstanding interest in parasitology and infective disease analysis. We used chromosome paints from both the mouse ( Mus musculus) and the Norway rat ( Rattus norvegicus) to characterize the genome of two Black rat subspecies from Italy. Both subspecies have two large metacentrics (n. 1, 4) not present in the Norway rat (2n = 42). Rattus rattus rattus has a diploid number of 2n = 38, while Rattus rattus frugivorous has two small metacentric "supernumerary" or B chromosomes for a diploid number of 2n = 38 + 2B. The 21 mouse paints gave 38 signals on the R. r. rattus karyotype and 39 signals in the R. r. frugivorous karyotype. The two metacentrics, not present in R. norvegicus, were hybridized by mouse 16/1/17 and mouse 4/10/15. These chromosomes are homologous to: RRA1 = RNO 5/7, and RRA4 = RNO 9/11 and not "4/7" and "11/12" as previously reported. Furthermore, the synteny of Chr 13 of the R. r. frugivorous with R. norvegicus Chr 16 and mouse Chrs 8/14 is not complete, because there is a small pericentromeric insertion of RNO Chr 18 (mouse Chr 18). If we consider only the two metacentrics, RRA1 and RRA4, the principal differences between R. norvegicus and R. rattus, then we can propose the derived synteny of 124 genes in the black rat. A comparison of the Z index between rats and mice shows an acceleration of genomic evolution among genus, species, and subspecies. The chromosomal differences between R. r. rattus x R. r. frugivorous suggest that they may be classified as different species because hybrids would produce 50% unbalanced gametes.

Animals↗
PubMed2006

Advancement in characterization of genomic alterations for improved diagnosis, treatment and prognostics in cancer.

Most human cancers are characterized by genetic instabilities. These instabilities manifest themselves as a series of genetic alterations, including discrete mutations and chromosomal aberrations. With the human genome deciphered, high-throughput technologies are rapidly advancing the field to generate genome-wide gene expression and mutation profiles that are highly correlative of biologic and disease phenotypes. While recent advancement in comprehensive genomic characterization presents an unprecedented opportunity for advancing the treatment of cancer, there are still many challenges that need to be overcome before we can fully utilize genomic markers and targets for cancer prediction, diagnostics, treatment and prognostics. This review describes recent advances in comprehensive genomic characterization at the DNA level, and considers some of the challenges that remain for defining the precise genomic portrait of tumors. Potential solutions that may help overcome these challenges are also offered.

Animals↗
PubMed1996

Isolation and characterization of genomic and cDNA clones encoding mouse senescence marker protein-30 (SMP30).

We isolated and characterized genomic and cDNA clones encoding mouse senescence marker protein-30 (SMP30), the protein amounts of which are known to decrease with aging in the livers of rats. This decrease in the expression of SMP30 is independent of androgen. SMP30 is a calcium binding protein also called regucalcin. The expression of SMP30 in aged mouse liver and 5' flanking sequence of the genome were also characterized. The cDNA contained an open reading frame encoding 299 amino acids with a calculated molecular weight of 33-404. The amino acid sequence of mouse SMP30 showed 94% similarity to rat SMP30 and 89% to human SMP30. Northern blot analysis specifically detected mouse SMP30 transcript in the liver and also confirmed its significant decrease with aging. Analysis of the murine genomic clone revealed that SMP30 was organized by seven exons and six introns, spanning approx. 17.5 kb. Primer extension analysis revealed that two major transcription initiation sites were localized at 101 bp and 102 bp upstream from ATG translation initiation codon. The nucleotide (nt) sequence of 5' flanking region showed a TATA-like sequence, a CAAT box, and SP-1 sites at nt -29, -72 and -169 in the promoter region, respectively. Interestingly, we found two classes of C/EBP sites which are highly and constantly expressed in the liver, in addition to AP-2, AP-1, GATA-1, AP-1/GRE and GAGA sites. These results provide important clues for understanding the regulatory mechanism of SMP30 gene expression and its relationship to aging.

Aging↗