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At least 1,135 records · Page 63Linked to original sources
PubMed2005

Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system.

The BaeSR two-component regulatory system controls expression of exporter genes conferring drug resistance in Escherichia coli (S. Nagakubo, K. Nishino, T. Hirata, and A. Yamaguchi, J. Bacteriol. 184:4161-4167, 2002; N. Baranova and H. Nikaido, J. Bacteriol. 184:4168-4176, 2002). To understand the whole picture of BaeSR regulation, a DNA microarray analysis of the effect of BaeR overproduction was performed. BaeR overproduction activated 59 genes related to two-component signal transduction, chemotactic responses, flagellar biosynthesis, maltose transport, and multidrug transport, and BaeR overproduction also repressed the expression of the ibpA and ibpB genes. All of the changes in the expression levels were also observed by quantitative real-time reverse transcription-PCR analysis. The expression levels of 15 of the 59 BaeR-activated genes were decreased by deletion of baeSR. Of 11 genes induced by indole (a putative inducer of the BaeSR system), 10 required the BaeSR system for induction. Combination of the expression data sets revealed a BaeR-binding site sequence motif, 5'-TTTTTCTCCATDATTGGC-3' (where D is G, A, or T). Several genes up-regulated by BaeR overproduction, including genes for maltose transport, chemotactic responses, and flagellar biosynthesis, required an intact PhoBR or CreBC two-component regulatory system for up-regulation. These data indicate that there is cross-regulation among the BaeSR, PhoBR, and CreBC two-component regulatory systems. Such a global analysis should reveal the regulatory network of the BaeSR system.

Chemotaxis↗
PubMed2001

Sex- and age-of-onset-based locus heterogeneity in asthma.

Asthma is a complex disease with a genetic component. The results of genome-wide linkage studies imply that locus heterogeneity is likely to be an important feature of the genetics of asthma. To attempt to reduce locus heterogeneity, we hypothesized that the following may form the bases for locus heterogeneity at some asthma susceptibility loci: sex of affected individuals, parental origin of alleles shared by affected sib pairs, and age of onset of wheeze. Analysis of such strata may assist in the identification of novel susceptibility loci, or reveal the basis for locus heterogeneity at previously identified loci. Genotype and phenotype data from genome-wide linkage searches for asthma susceptibility loci from three populations were analyzed. Some regions demonstrated evidence for linkage to affected individuals of a particular sex. There was evidence for excess maternal allele sharing at regions on chromosomes 9 and 11. Regions on chromosomes 2 and 6 were linked to late and early age at onset of wheeze in asthma, respectively. These analyses suggest that the bases that we selected for stratification may be appropriate at certain susceptibility loci for asthma, and may therefore assist in the fine mapping of such loci. Differences in such variables between studies may explain apparent nonreplication of linkage results.

Adolescent↗
PubMed1996

Framework for a physical map of the human 22q13 region using bacterial artificial chromosomes (BACs).

Detailed physical maps of entire chromosomes based on combined genetic, cytogenetic, and structural information are essential components for positional cloning and genomic sequencing. Despite the wealth of genetic information of the known diseases in the chromosome 22q13, the construction of a detailed physical map of the terminal region is difficult due to the sparsity of the genetic markers. We present here a map of bacterial artificial chromosome (BAC) contigs that cover a number of genetic loci in the 22q13 region. One hundred thirty-six BACs with an average insert size of 140 kb are assembled into 35 contigs defined by 64 markers in 22q13-qter. Twenty-three anonymous markers are now linked to the previously mapped genetic anchor points.

Chromosome Mapping↗
PubMed1991

Expression of a human cytomegalovirus glycoprotein multigene family.

The short unique component of the human cytomegalovirus genome contains several multigene families, one of which encodes glycoproteins in the virion envelope glycoprotein complex gcII (4). The HXLF glycoprotein multigene family was subcloned into pSP6 or pGEM transcription vectors. Gene products were expressed from the six open reading frames (designated HXLF1 through HXLF6) via in vitro transcription and translation in rabbit reticulocyte lysates. The HXLF gene products were analyzed by immunoprecipitation using virus-specific monoclonal antibodies or human convalescent-phase antisera. One of the anti-gcII monoclonal antibodies, designated 9E10, specifically immunoprecipitated each of the HXLF gene products. Four of the HXLF gene products were immunoprecipitated by human convalescent-phase antisera, but not preimmune sera. Southern blot analysis of genomic DNAs purified from 12 different virus isolates indicated the HXLF multigene family is present in wild-type strains of human cytomegalovirus.

Blotting, Southern↗
PubMed1996

Automating combinatorial chemistry: a primer on benchtop robotic systems.

Benchtop robotic systems are inexpensive, flexible automation tools with potential applications in a wide array of disciplines such as combinatorial chemistry, high-throughput screening, and genomics. We explain the basic components of a benchtop system and explore factors to consider when purchasing or customizing a robot, such as automation benefits, vendor selection, and current system limitations. Issues involving system specification, software design, and hardware customization are then discussed. Additionally, system optimization, validation, and support are detailed. Given a properly designed and implemented system, the combinatorial laboratory can markedly increase compound synthesis and purification.

Computers↗
PubMed2001

The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses.

Polymerase chain reaction (PCR) was applied to detect and establish provisional identity of begomoviruses through amplification of a approximately 575 bp fragment of the begomoviral coat protein gene (CP), referred to as the 'core' region of the CP gene (core CP). The core CP fragment contains conserved and unique regions, and was hypothesized to constitute a sequence useful for begomovirus classification. Virus relationships were predicted by distance and parsimony analyses using the A component (bipartite viruses) or full genome (monopartite viruses), CP gene, core CP, or the 200 5'-nucleotides (nt) of the CP. Reconstructed trees and sequence divergence estimates yielded very similar conclusions for all sequence sets, while the CP 5'-200 nt was the best strain discriminator. Alignment of the core CP region for 52 field isolates with reference begomovirus sequences permitted provisional virus identification based on tree position and extent of sequence divergence. Geographic origin of field isolates was predictable based on phylogenetic separation of field isolates examined here. A 'closest match' or genus-level identification could be obtained for previously undescribed begomoviruses using the BLAST program to search a reference core CP database located at our website and/or in GenBank. Here, we describe an informative molecular marker that permits provisional begomovirus identification and classification using a begomoviral sequence that is smaller than the presently accepted, but less accessible CP sequence.

Capsid↗
PubMed1978

Ribulose-1,5-biphosphate carboxylase-deficient plastome mutants of Oenothera.

In spite of only slightly subnormal pigment contents, two plastome mutants of Oenothera (Valpha, Isigma) were practically incapable of photosynthetic CO2 fixation and another one exhibited considerably reduced photosynthesis (IVbeta). While other photosynthetic enzymes were present as far as investigated, ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) activity was very low or missing altogether. As shown by gel electrophoresis, mutant IVbeta contained some, though little, fraction I protein. In the other two mutants fraction I protein could not be detected. Also, neither the small nor the large subunit of ribulose-1,5-biphosphate carboxylase could be found in these mutants. In immunodiffusion experiments with a monospecific antiserum against rye ribulose-1,5-bisphosphate carboxylase, only extracts from wild-type Oenothera produced visible precipitation lines. Still, the presence of very low levels of immunochemically reactive antigen was indicated for all three mutants. The highest level was observed in mutant IVbeta. The behaviour of the mutant extracts suggested that the antigens of mutant and wild type leaves reacting with the antiserum were not identical. All mutants appeared to have a coupled electron transport system as shown by ATP measurements, light scattering and 515 nm absorption changes. Linear electron transport was possible in the mutants. Still, the photoresponse of cytochrome f and fluorescence measurements suggested altered electron transport properties in the mutants. These are interpreted to be secondary lesions of the photosynthetic apparatus caused by primary deficiency in ribulose-1,5-bisphosphate carboxylase activity. From the absence in two mutants (Valpha, Isigna) of the small subunit of ribulose-1,5-bisphosphate carboxylase, which is known to be coded for by nuclear DNA and to be synthesized on cytoplasmic ribosomes, it appears that the genetic system of the plastids is capable of interfering with the genome-controlled synthesis of plastid components.

Carboxy-Lyases↗
PubMed1983

Cytolytic T-cell mediated lysis of reovirus-infected cells: requirements for infectious virus, viral particles, and viral proteins in infected target cells.

The virological requirements for the recognition of infected target cells by cytolytic T lymphocytes (CTL), using reovirus, a nonenveloped, icosahedral virus has been investigated. Using mouse L cells infected at the nonpermissive temperature with ts (temperature-sensitive) mutants of reovirus in complementation groups C and G, it has been shown that the production of complete viral particles is not necessary for efficient lysis of infected cells by CTL. In addition, adsorption of purified viral particles and viral top component (TC), empty capsids lacking genome ds-RNA, to L cells just prior to use in cytolytic T cell assays is sufficient to produce target cells capable of being lysed, though target production is less efficient than with L cells infected with reovirus. Membrane fluorescence analysis of cells infected with reovirus ts mutants at the nonpermissive temperature and with adsorbed viral particles revealed the presence of the viral sigma 1 protein on the cell surface. For adsorbed particles, the degree of membrane fluorescence paralleled the capacity of CTL to lyse target cells. It is concluded that cells infected with icosahedral, nonenveloped viruses, like cells infected with enveloped viruses, express viral antigens on the cell surface even in the absence of the production of complete viral particles; adsorbed viral particles can be incorporated into the cell membrane in a manner sufficient for recognition and lysis by CTL, in the absence of actual infection of the cells.

Adsorption↗
PubMed1986

A common plasmid of Chlamydia trachomatis.

A 7.4-kb plasmid is a common and perhaps essential component of the Chlamydia trachomatis genome. This plasmid occurs as 10 copies per chlamydial chromosomal equivalent. It is unable to replicate in Escherichia coli. Complete plasmid genomes from eight serovars of C. trachomatis have been isolated in E. coli as cloned sequences ligated to pBR322. Restriction enzyme cleavage site mapping indicates that these plasmids are closely related. Homologous plasmid sequences have also been detected by DNA hybridization in all of the 200 clinically isolated strains of C. trachomatis which have been examined. DNA sequences homologous to the C. trachomatis plasmid were not found in eucaryotic DNA nor in a plasmid of similar size isolated from C. psittaci. C. trachomatis plasmid genes are expressed in vivo and the plasmid encoded gene products may play a role in the intracellular growth of this organism. Plasmid encoded genes were also expressed from the cloned C. trachomatis plasmid in E. coli minicells and using an E. coli S-30 in vitro transcription translation extract.

Chlamydia trachomatis↗
PubMed1993

Evolution of genetic redundancy for advanced players.

An ever expanding database on the sequence organization and repetition of genic and non-genic components of nuclear and organelle genomes reveals that the vast majority of sequences are subject to one or other mechanism of DNA turnover (gene conversion, unequal crossing over, slippage, retrotransposition, transposition and others). Detailed studies, using novel methods of experimental detection and analytical procedures, show that such mechanisms can operate one on top of another and that wide variations in their unit lengths, biases, polarities and rates create bizarre and complex patterns of genetic redundancy. The ability of these mechanisms to operate both within and between chromosomes implies that realistic models of the evolutionary dynamics of redundancy, and of the potential interaction with natural selection in a sexual species, need to consider the diffusion of variant repeats across multiple chromosome lineages, in a population context. Recently, important advances in both experimental and analytical approaches have been made along these lines. There is increasing awareness that genetic redundancy and turnover induces a molecular co-evolution between functionally interacting genetic systems in order to maintain essential functions.

Animals↗
PubMed2004

Organization and regulation of the neurotoxin genes in Clostridium botulinum and Clostridium tetani.

Botulinum and tetanus neurotoxins are structurally and functionally related 150 kDa proteins that are potent inhibitors of neuroexocytosis. Botulinum neurotoxin associates with non-toxic proteins to form complexes of various sizes. The botulinum neurotoxin and non-toxic protein genes are clustered in a DNA segment called the botulinum locus. This locus is probably located on a mobile or degenerate mobile element, which accounts for the various genomic localizations (chromosome, plasmid, phage) in different Clostridium botulinum types. The botulinum neurotoxin and non-toxic protein genes are organized in two polycistronic operons (ntnh-bont and ha operons) transcribed in opposite orientations. The gene that separates the two operons of the botulinum locus in C. botulinum A encodes a 21 kDa protein BotR/A, which is a positive regulator of the expression of the botulinum locus genes. Similarly, in Clostridium tetani, the gene located immediately upstream of the tetanus toxin gene, encodes a positive regulatory protein, TetR. BotR and TetR are possibly alternative sigma factors related to TxeR and UviA, which regulate C. difficile toxin and C. perfringens bacteriocin production, respectively. TxeR and UviA define a new sub-group of the sigma(70) family of RNA polymerase initiation factors. In addition, the C. botulinum genome contains predicted two-component system genes, some of which are possibly involved in regulation of toxinogenesis.

Journal Article↗
PubMed2005

Fos expression in the vestibular brainstem: what one marker can tell us about the network.

Fos inducible transcription factor expression in rodent brains (rats and gerbils) during manipulations of vestibular input is reviewed. Stimuli included centripetal hypergravity, unilateral labyrinth lesion or semicircular canal plugging, rotational axis cross-coupling (Coriolis forces), high and low rotational vestibulo-ocular reflex gain adaptation, translabyrinth galvanic stimulation, pharmacological manipulation, and combinations thereof. Each type of stimulation elicited unique but partially redundant response patterns in the vestibulo-olivo-cerebellar (VOC) network that reflect the origin and interaction of the labyrinth inputs. On the basis of these patterns, a trained observer can predict what the animal experienced during testing; the patterns of VOC Fos expression reveal a trace of recent genomic activity. Based on principal component analysis, VOC network modules associated with lesion recovery, spatial representation and the calibration of gravity, and optokinetic influences are proposed. Probable and possible gene targets of the Fos protein are also reviewed.

Animals↗
PubMed2006

Globin genes transcriptional switching, chromatin structure and linked lessons to epigenetics in cancer: a comparative overview.

At the present time research situates differential regulation of gene expression in an increasingly complex scenario based on interplay between genetic and epigenetic information networks, which need to be highly coordinated. Here we describe in a comparative way relevant concepts and models derived from studies on the chicken alpha- and beta-globin group of genes. We discuss models for globin switching and mechanisms for coordinated transcriptional activation. A comparative overview of globin genes chromatin structure, based on their genomic domain organization and epigenetic components is presented. We argue that the results of those studies and their integrative interpretation may contribute to our understanding of epigenetic abnormalities, from beta-thalassemias to human cancer. Finally we discuss the interdependency of genetic-epigenetic components and the need of their mutual consideration in order to visualize the regulation of gene expression in a more natural context and consequently better understand cell differentiation, development and cancer.

Animals↗
PubMed2004

Gene silencing of selected calcium-signalling molecules in a Drosophila cell line using double-stranded RNA interference.

Using the Drosophila melanogaster S2 cell line, stably expressing a cloned muscarinic acetylcholine receptor (AChR), DM1, we have applied gene silencing by double-stranded RNA interference (RNAi) to knock down gene products involved in DM1-mediated calcium signalling. We have shown that RNAi knock down of either the inositol 1,4,5-trisphosphate receptor (Ins(1,4,5)P(3)R), or the SERCA calcium pump in the S2-DM1 cells blocks the increase in intracellular calcium concentration ([Ca(2+)](i)) resulting from activation of the DM1 receptor by 100 microM carbamylcholine (CCh). When RNAi designed to knock down the ryanodine receptor (RyR) was tested, there was no change in the calcium increase detected in response to CCh, consistent with a failure to detect RyRs in S2-DM1 cells using RT-PCR. A combination of RNAi and calcium imaging has provided a direct demonstration of key roles for the Ins(1,4,5)P(3)R and the SERCA pump in the response to DM1 receptor activation.Thus, we show that silencing of individual genes by RNAi in a well characterised Drosophila S2 cell line offers experimental opportunities for cell-signalling studies. Future investigations with RNAi libraries taking full advantage of the wealth of new information available from sequencing the Drosophila genome, may help identify novel components of cell-signalling pathways and functionally linked gene products.

Animals↗
PubMed2003

Developmental retinal apoptosis in Ku86-/- mice.

The nonhomologous DNA end-joining pathway (NHEJ), a major pathway for repairing DNA double-strand breaks (DSBs), is essential for maintaining genomic stability. Knockout animals for components in this pathway demonstrate a distinct pattern of cell death in the developing brain. Here we demonstrate that cell death is also present in the developing retina of E14.5 Ku86-deficient mouse embryos, suggesting that the increase in cell death in the retina is associated with chromosome breaks. In the adult retina, we do not find continuing apoptosis, but interestingly, we find decreased numbers of total neuronal cells. This suggests that the increased retinal apoptosis during embryogenesis causes the reduction in cell numbers observed in the adult retina. This analysis of the retina provides the first opportunity to formally test the hypothesis that embryonic apoptosis accounts for reduced total cell numbers in adult Ku86-/- mice.

Animals↗
PubMed2005

Archaeal cell cycle progress.

The discovery of multiple chromosome replication origins in Sulfolobus species has added yet another eukaryotic trait to the archaea, and brought new levels of complexity to the cell cycle in terms of initiation of chromosome replication, replication termination and chromosome decatenation. Conserved repeated DNA elements--origin recognition boxes--have been identified in the origins of replication, and shown to bind the Orc1/Cdc6 proteins involved in cell cycle control. The origin recognition boxes aid in the identification and characterization of new origins, and their conservation suggests that most archaea have a similar replication initiation mechanism. Cell-cycle-dependent variation in Orc1/Cdc6 levels has been demonstrated, reminiscent of variations in cyclin levels during the eukaryotic cell cycle. Information about archaeal chromosome segregation is also accumulating, including the identification of a protein that binds to short regularly spaced repeats that might constitute centromere-like elements. In addition, studies of cell-cycle-specific gene expression have potential to reveal, in the near future, missing components in crenarchaeal chromosome replication, genome segregation and cell division. Together with an increased number of physiological and cytological investigations of the overall organization of the cell cycle, rapid progress of the archaeal cell cycle field is evident, and archaea, in particular Sulfolobus species, are emerging as simple and powerful models for the eukaryotic cell cycle.

Archaea↗
PubMed2005

Rotting softly and stealthily.

The soft rot erwiniae, which are plant pathogens on potato and other crops world-wide, synthesize and secrete large quantities of plant cell wall degrading enzymes that are responsible for the soft rot phenotype, earning them the epithet 'brute force' pathogens. They have been distinguished from classic 'stealth' pathogens, such as Pseudomonas syringae, which possesses an extensive battery of Type III secreted effector proteins and phytotoxins to manipulate and suppress host defences. However, recent studies, including whole-genome sequencing, are revealing many components of stealth pathogenesis within the soft rot erwiniae (SRE), suggesting that 'stealth' and 'brute force' should not be regarded as mutually exclusive modes of pathogenesis.

Cell Wall↗
PubMed2004

Antigen receptor genes and the evolution of a recombinase.

Antigen receptor genes exist in the germline in a "split" configuration and are assembled in developing B and T lymphocytes by V(D)J recombination. This site-specific recombination reaction is initiated by a complex containing the RAG1 and RAG2 proteins and completed by general DNA repair factors. RAG1 and RAG2, like the adaptive immune system itself, are found exclusively in jawed vertebrates, and are thought to have entered the vertebrate genome by horizontal transmission as components of a transposable element. This review discusses the structure of antigen receptor genes and the mechanisms by which they are assembled and diversified, and then goes on to consider the evolutionary implications of the arrival of the hypothetical "RAG transposon".

Animals↗