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At least 343 records · Page 19Linked to original sources
PubMed1999

Class VI unconventional myosin is required for spermatogenesis in Drosophila.

We have identified partial loss of function mutations in class VI unconventional myosin, 95F myosin, which results in male sterility. During spermatogenesis the germ line precursor cells undergo mitosis and meiosis to form a bundle of 64 spermatids. The spermatids remain interconnected by cytoplasmic bridges until individualization. The process of individualization involves the formation of a complex of cytoskeletal proteins and membrane, the individualization complex (IC), around the spermatid nuclei. This complex traverses the length of each spermatid resolving the shared membrane into a single membrane enclosing each spermatid. We have determined that 95F myosin is a component of the IC whose function is essential for individualization. In wild-type testes, 95F myosin localizes to the leading edge of the IC. Two independent mutations in 95F myosin reduce the amount of 95F myosin in only a subset of tissues, including the testes. This reduction of 95F myosin causes male sterility as a result of defects in spermatid individualization. Germ line transformation with the 95F myosin heavy chain cDNA rescues the male sterility phenotype. IC movement is aberrant in these 95F myosin mutants, indicating a critical role for 95F myosin in IC movement. This report is the first identification of a component of the IC other than actin. We propose that 95F myosin is a motor that participates in membrane reorganization during individualization.

Actins↗
PubMed2006

Spoligotype signatures in the Mycobacterium tuberculosis complex.

Evolution of the direct repeat region in Mycobacterium tuberculosis has created unique spoligotype signatures specifically associated with IS6110-defined strain families. Spoligotyping signatures may enable the analysis of the strain population structure in different settings and will enable the rapid identification of strain families that acquire drug resistance or escape protective immunity in drug and vaccine trials.

Bacterial Typing Techniques↗
PubMed2006

Rapid detection of Mycobacterium tuberculosis Beijing genotype strains by real-time PCR.

Mycobacterium tuberculosis strains of the Beijing genotype were first identified in China and neighboring countries and have attracted special attention due to their global emergence and association with drug resistance. To further analyze the spread and special characteristics of Beijing genotype strains, accurate, rapid and sensitive methods that overcome the drawbacks of the classical methods such as IS6110 DNA fingerprinting or spoligotyping for the identification of strains of this genotype are needed. Based on the nucleotide sequences of M. tuberculosis SAWC0780 and H37Rv, primers and fluorogenic 5' nuclease (TaqMan) probes for real-time PCR assays specific for Beijing and non-Beijing strains, respectively, were designed. The detection limits for the real-time PCR assays were about 5 and 10 copies of chromosomal DNA, respectively. In mixtures of Beijing and non-Beijing DNA, a multiplex assay was able to detect (i) one copy of Beijing DNA in approximately 1,000 copies of non-Beijing DNA and (ii) one copy of non-Beijing DNA in approximately 2,000 copies of Beijing DNA. In a blinded analysis of a collection of 103 multidrug-resistant strains isolated in Germany in 2001, all 62 Beijing and all 41 non-Beijing strains were correctly identified. In conclusion, the real-time assay allows for the rapid and specific detection of Beijing and non-Beijing strains. The major advantages of this test in comparison to other methods used for the identification of Beijing strains are its simplicity and sensitivity and the fact that amplification and detection occur within one reaction tube.

Bacterial Typing Techniques↗
PubMed1991

Position-effect variegation--an assay for nonhistone chromosomal proteins and chromatin assembly and modifying factors.

The past decade has brought us much information about gene regulation in eukaryotes and the importance of chromatin in gene expression. Clearly, we need to advance our understanding of chromatin assembly and modification. Hopefully, many Su(var) and E(var) loci will be cloned and their analysis will demonstrate that they are involved in this process. It will be interesting to see what classes of products they encode. Clearly, antibodies must be made against these proteins to determine: (1) the chromosomal distribution of those that encode chromatin structural proteins, (2) the tissue and temporal distribution of these proteins during development, and (3) the time of action during specific portions of the cell cycle for those genes encoding factors that regulate chromatin assembly or modifying proteins. In addition, it would be intriguing to identify and isolate those sequences or segments of DNA that serve as nucleation sites for the assembly of euchromatin and heterochromatin. The necessary materials for identifying these sequences are in place with the large number of variegating strains and revertants of those rearrangements and Su(var) and E(var) mutations that exist. From our current understanding of PEV, it appears that PEV provides a useful model for the study of determinative events that occur during development. This includes both the establishment of different lineages and the somatic memory or imprinting of the initial determinative decision. Clearly, PEV is more than a simple assay system for the identification of NHCPs, and ultimately the understanding of the mechanisms underlying PEV should lend insights into how such determinative events occur and are propagated.

Aneuploidy↗
PubMed1995

Ovarian carcinoma-associated TaqI restriction fragment length polymorphism in intron G of the progesterone receptor gene is due to an Alu sequence insertion.

Alu sequences, short, repetitive transposable DNA elements, are factors in a number of genetic diseases. We previously identified a germline TaqI RFLP, located in intron G of the human progesterone receptor gene, that showed an association with the incidence of sporadic ovarian carcinoma. Furthermore, the polymorphism was characterized as a small (approximately 300-bp) insertion that was inherited in a Mendelian fashion. Because of its insertional character, we named this polymorphism PROGINS. We report the identification of PROGINS as a 306-bp Alu element of the PV or HS-1 Alu subfamily.

Alleles↗
PubMed2004

Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae.

The recent availability of the genome of Anopheles gambiae offers an extraordinary opportunity for comparative studies of the diversity of transposable elements (TEs) and their evolutionary dynamics between two related species, taking advantage of the existing information from Drosophila melanogaster. To this goal, we screened the genome of A. gambiae for elements belonging to the Ty3/gypsy group of long-terminal repeat (LTR) retrotransposons. The A. gambiae genome displays a rich diversity of LTR retrotransposons, clearly greater than D. melanogaster. We have characterized in detail 63 families, belonging to five of the nine main lineages of the Ty3/gypsy group. The Mag lineage is the most diverse and abundant, with more than 30 families. In sharp contrast with this finding, a single family belonging to this lineage has been found in D. melanogaster, here reported for the first time in the literature, most probably consisting of old inactive elements. The CsRn1 lineage is also abundant in A. gambiae but almost absent from D. melanogaster. Conversely, the Osvaldo lineage has been detected in Drosophila but not in Anopheles. Comparison of structural characteristics of different families led to the identification of several lineage-specific features such as the primer-binding site (PBS), the gag-pol translational recoding signal (TRS), which is extraordinarily diverse within the Ty3/gypsy retrotransposons of A. gambiae, or the presence/absence of specific amino acid motifs. Interestingly, some of these characteristics, although in general well conserved within lineages, may have evolved independently in particular branches of the phylogenetic tree. We also show evidence of recent activity for around 75% of the families. Nevertheless, almost all families contain a high proportion of degenerate members and solitary LTRs (solo LTRs), indicative of a lower turnover rate of retrotransposons belonging to the Ty3/gypsy group in A. gambiae than in D. melanogaster. Finally, we have detected significant overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.

Amino Acid Motifs↗
PubMed2004

Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes.

A reverse probe hybridization method using two different Mycobacterium tuberculosis-specific rpoB DNA probes in combination was evaluated for the identification of M. tuberculosis culture isolates. Among the 384 isolates tested, 354 strains were identified as M. tuberculosis, which included 37 rifampin-resistant strains, and 30 were nontuberculous mycobacteria (NTM). This result was in accord with partial rpoB sequence analysis and IS6110 polymerase chain reaction (PCR) results, but not with the results of biochemical testing, which produced two false negative results. Because of its high level of sensitivity and specificity, we suggest that M. tuberculosis-specific rpoB probes immobilized on micro-titer well plates or on other solid matrixes can be used efficiently for the rapid and convenient identification of M. tuberculosis.

DNA Probes↗
PubMed1998

Ten novel 11q23 chromosomal partner sites. European 11q23 Workshop participants.

The MLL gene located at 11q23 has been described as a 'promiscuous' gene due its involvement with a large number of genetic partners. The EU Concerted Action Workshop on 11q23 provided 550 cases for study of which 82 showed abnormalities which did not involve the established translocations or deletion of 11q23. In these 'other' cases, which included inversions and duplications, 11q23 was found to be involved with 25 chromosome partners of which 10 had not been previously reported. These were 1q31, 4p11, 6q13, 8q21, 10q22, 10q25, 11q11, 11q21, 13q34 and 18q23. This study demonstrated the value of the Workshop, in confirming the diversity of chromosomal partner sites involved with 11q23 and in the identification of new partners.

Acute Disease↗
PubMed2003

Comparison of a multiplex-PCR assay with mycolic acids analysis and conventional methods for the identification of mycobacteria.

A fast, sensitive and cost-effective multiplex-PCR assay for Mycobacterium tuberculosis complex (MTC) and Mycobacterium avium (M. avium) identification for routine diagnosis was evaluated. A total of 158 isolates of mycobacteria from 448 clinical specimens from patients with symptoms of mycobacterial disease were analyzed. By conventional biochemical methods 151 isolates were identified as M. tuberculosis, five as M. avium and two as Mycobacterium chelonae (M. chelonae). Mycolic acid patterns confirmed these results. Multiplex-PCR detected only IS6110 in isolates identified as MTC, and IS1245 was found only in the M. avium isolates. The method applied to isolates from two patients, identified by conventional methods and mycolic acid analysis, one as M. avium and other as M. chelonae, resulted positive for IS6110, suggesting co-infection with M. tuberculosis. These patients were successfully submitted to tuberculosis treatment. The multiplex-PCR method may offer expeditious identification of MTC and M. avium, which may minimize risks for active transmission of these organisms and provide useful treatment information.

Bacterial Typing Techniques↗
PubMed1994

Genetic diversity of Schistosoma mansoni: quantifying strain heterogeneity using a polymorphic DNA element.

Intraspecific genetic variation among 14 geographic isolates of Schistosoma mansoni was quantified using a molecular marker to examine individual genotypes. Genetic crosses demonstrated maternal inheritance of S. mansoni DNA element pSM750. This element revealed diagnostic banding profiles, which allowed accurate strain identification. Most strains had similarity indices greater than 0.75 indicating that within-strain variation in these laboratory parasite populations was low. However, individual parasites from the NMRI strain were quite diverse (S = 0.40). Genetic heterogeneity among strains was quantified using a phenogram of mean genetic distance. Strain diversity between two geographic regions was quantified using a similarity index and was estimated to be substantial among isolates collected from a single local site.

Animals↗
PubMed2000

Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice.

A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice (Oryza sativa L.). The fragment (named RIRE9) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region. Northern blot hybridization indicated that this element was expressed in rice leaves and stems, suggesting that it is potentially active to transpose under normal growth conditions. Using dot-blot hybridization, the copy number of RIRE9 was estimated to be about 1600 copies per haploid rice genome. Five homologous copies of RIRE9 were assigned to five distinct positions of four chromosomes by restriction fragment length polymorphism (RFLP) mapping approach using an indica-japonica rice doubled-haploid (DH) population and its molecular linkage map.

Amino Acid Sequence↗
PubMed1993

Isolating plant genes.

The genetic transformation of most agriculturally important plant species is now possible. However, the application of this technology to rational plant-improvement is currently limited by a shortage of cloned genes for important traits. Recent technological advances in plant-gene isolation and identification, such as map-based cloning, insertional mutagenesis and large-scale cDNA sequencing, have accelerated the rate of gene isolation and significantly expanded the opportunities for genetic engineering of crop plants.

Biotechnology↗
PubMed2006

Forward genetic screening of insertional mutants.

Insertional mutagenesis has contributed to the success of forward genetics in Arabidopsis thaliana. The availability of large collections of lines mutagenized by either transposon or T-DNA insertions, in combination with the systematic sequencing of insertion/genome junctions, enables the identification of mutations for any given gene in the nuclear genome of this plant species. Protocols for the identification and confirmation of mutations by forward genetics, the isolation of insertion/genome junctions, and the stabilization of transposon-induced mutations are provided, together with an overview of available insertional mutant collections and of their characteristics.

Arabidopsis↗
PubMed2003

RescueMu protocols for maize functional genomics.

RescueMu is a modified Mu1 transposon transformed into maize to permit mutagenesis and subsequent recovery of mutant alleles by plasmid rescue. RescueMu elements insert late in the germline as well as in terminally dividing somatic (e.g., leaf) cells. Germinal insertions may result in a mutant phenotype, and RescueMu permits recovery of 5-25 kb of transposon-flanking genomic DNA without having to construct and screen genomic DNA libraries. Late somatic insertions of RescueMu do not result in a visible phenotype, but they are instead used to construct plasmid libraries of gene-enriched maize genomic DNA to facilitate the identification and sequencing of the euchromatic portion of the maize genome. This is because maize leaves contain abundant independent RescueMu somatic insertions, and 70-90% of these insertions occur preferentially into genes and not repetitive DNA. This chapter describes detailed protocols on how to obtain, generate, and use RescueMu for maize genomics, including resources developed by the Maize Gene Discovery Project (MGDP) consortium available online at ZmDB.

DNA Transposable Elements↗
PubMed1994

Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses.

Tourist was originally described as a 128-bp insertion mutation in the maize wx-B2 allele. Subsequent analysis revealed that Tourist elements are in the introns or flanking sequences of 11 maize genes and a single barley gene. In this study we report that Tourist elements are frequently associated with the wild-type genes of two other grasses, rice and sorghum. Six of 35 rice and 5 of 8 sorghum complete gene sequences reported to date contain Tourist elements. Furthermore, 11 additional maize genes have been found to contain Tourist elements, bringing the current total of elements associated with maize genes to 23. Sequence comparison of Tourist elements has led to the identification of four subfamilies, designated A-D. Evidence is presented for the recent mobility of elements in three of these subfamilies and in three of the four grass species. These data suggest that Tourist elements are highly repetitive in the genomes of some and perhaps all members of the grasses.

Alcohol Dehydrogenase↗
PubMed2001

Construction of mini-Tn5cyaA' and its utilization for the identification of genes encoding surface-exposed and secreted proteins in Bordetella bronchiseptica.

A mini-Tn5 transposon derivative, mini-Tn5cyaA', has been constructed. It contains a promoter-less and ribosome binding site-deficient reporter gene, encoding the catalytic domain of Bordetella pertussis adenylate cyclase toxin (CyaA'). We used this system to mutagenize B. bronchiseptica and we developed a screen for identification of mutants containing cyaA' translational fusions. This system was used to identify B. bronchiseptica genes that encode surface-exposed and secreted proteins.

Adenylate Cyclase Toxin↗
PubMed1988

Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization.

A gene fusion library of Vibrio cholerae classical strain O395 was generated by using a broad host range vector for delivery of the transposon TnphoA. The insertion library was screened for colonies expressing alkaline phosphatase-positive (PhoA+) fusion proteins on LB agar at 30 degrees C in the presence of 0.2% glucose. Over 600 PhoA+ strains were isolated and then tested for regulation of their gene fusions in broth media that permitted high or low expression of cholera toxin. This strategy resulted in the isolation of 60 TnphoA (Tn5 IS50L::phoA) fusions to genes encoding secreted proteins that are apparently coordinately regulated with cholera toxin. Introduction of a toxR null mutation into 10 of these fusion strains confirmed that these TnphoA gene fusions are controlled either directly or indirectly by the cholera toxin transcriptional activator encoded by toxR. A combination of Southern and immunoblot analysis identified 17 distinct ToxR-regulated genes in V. cholerae O395. Many of these insertions were located in one of the two cholera toxin operon copies of strain O395, as well as a large gene cluster involved in the biogenesis of the toxin-coregulated pilus colonization factor. In addition, insertions were identified in genes that had no effect on either cholera toxin or toxin-coregulated pilus expression. Several of these insertions were localized to a cluster of four genes, the disruption of any of which by TnphoA reduced the ability of strain O395 to colonize the intestines of suckling mice. The product encoded by this second gene cluster was named accessory colonization factor to describe its possible role in cholera pathogenesis. These studies reinforce the contribution of ToxR-regulated genes to the virulence properties of V. cholerae. This report also demonstrates a new approach for the identification of bacterial virulence factors, based on the characterization of genes that are regulated by the same environmental signals that control the expression of a known virulence factor.

Animals↗
PubMed1989

Molecular analysis of a region of the group B streptococcus chromosome involved in type III capsule expression.

Type III group B streptococci (GBS) are the most common cause of neonatal sepsis and meningitis in the United States. The important role of the type III polysaccharide capsule and of the terminal sialic acid moiety of the capsule in the virulence of GBS has been demonstrated by using Tn916 mutagenesis. Several of the transposon insertion sites that resulted in defective type III capsule synthesis were located in a 30-kilobase (kb) region of the chromosome. Hybridization analysis of two other type III strains that differed in their relative virulence and of GBS serotypes Ia, Ib, Ic, and II showed that this region of the chromosome was highly conserved. A repetitive 1.4-kb sequence was found only in the 30-kb region of the more virulent type III strain, COH 1. The Escherichia coli maxicell in vivo expression system and an in vitro coupled transcription-translation system successfully identified the proteins expressed from the 30-kb region. Comparison of the proteins expressed from the same DNA fragments in these two assays indicated that some of these proteins may contain leader sequences that would ultimately result in their secretion to the cell surface. Identification and further characterization of the genes and their products will provide the foundation for understanding the genetic and biochemical events in GBS capsular polysaccharide production.

Blotting, Southern↗