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Higuchi Hitoshi H Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, 53706, - - 2014
Understanding the normal aging process will help us determine the mechanisms of how age-related diseases are caused and progress. A/J inbred mice have been shown to exhibit accelerated aging phenotypes in the retina including increased inflammation and photoreceptor cell degeneration, which resemble human aging symptoms. C57BL/6J (B6) inbred mice are ...
Li Guangqi G National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, - - 2014
Shank color of domestic chickens varies from black to blue, green, yellow, or white, which is controlled by the combination of melanin and xanthophylls in dermis and epidermis. Dermal shank pigmentation of chickens is determined by sex-linked inhibitor of dermal melanin (Id), which is located on the distal end of ...
Schmid E - - 2012
The induction of chromosome aberrations in human lymphocytes irradiated in vitro with slow neutrons was examined to assess the maximum low-dose RBE (RBE(M)) relative to (60)Co γ-rays. For the blood irradiations, cold neutron beam available at the prompt gamma activation analysis facility at the Munich research reactor FRM II was ...
Devernay Marie - - 2012
Context:The parental origin of the intact X-chromosome has been reported to affect phenotype and response to GH treatment in Turner syndrome (TS).Objective:Our objective was to evaluate the influence of the parental origin of the X-chromosome on body growth and GH treatment effect in TS.Design and Setting:We conducted a population-based cohort ...
Camara-Quintana Joaquin Q - - 2012
The purpose of this article is to update the neurosurgical field on current molecular markers important to glioblastoma biology, treatment, and prognosis. The highlighted biologic markers in this article include epidermal growth factor receptor (EGFR), EGFR variant III (EGFRvIII), phosphatase and tensin homolog deleted on chromosome 10 (PTEN), and O6-methylguanine-DNA ...
Chen Juan J Department of Clinical Oncology, The University of Hong Kong, Hong Kong, PR - - 2012
Nasopharyngeal carcinoma (NPC) is among the most common malignancies in southern China. Deletion of genomic DNA, which occurs during the complex pathogenesis process for NPC, represents a pivotal mechanism in the inactivation of tumor suppressor genes (TSGs). In many circumstances, loss of TSGs can be detected as diagnostic and prognostic ...
Hsiao H-H - - 2012
Chromosome evolution is one of the major mechanisms of disease progression and resistance in chronic myeloid leukemia (CML) patients. However, the clinical significance of chromosomal evolution in the Philadelphia (Ph)-negative clone during therapy is not fully understood. We evaluated 94 CML patients in the chronic phase of CML during treatment ...
Swati D - - 2011
One of the fascinating properties of the DNA sequences of prokaryotic and eukaryotic chromosomes is that they possess long-range order. Computational methods like spectral analysis, mutual information and DNA random walks have been used to probe long-range order via-long range correlations. This work attempts to show the advantage of using ...
Pireddu Luca - - 2011
SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per ...
Verlaque Régine - - 2011
Hybridization processes can lead to evolutionary changes, particularly in co-introduced congeneric plant species, such as Carpobrotus spp. which are recognized as invasive in Mediterranean climate regions. Morphological and karyological comparisons have therefore been made between native Carpobrotus edulis and C. acinaciformis in South Africa and their invasive counterparts in Provence (C. edulis and ...
Feller L - - 2011
Potentially malignant oral leukoplakias arise within precancerized epithelial fields consisting of cytogenetically altered keratinocytes at various stages of transformation. The evolution of a clone of keratinocytes culminating in a precancerous phenotype is a function of the number of mutagenic events, rather than the sequential order in which they occur. The ...
Spano Giovanni - - 2011
Several reports described various mosaic chromosomal syndromes characterized by alterations originated by either an excess or deficit in the number of chromosomes. A case of mosaic trisomy 8 and monosomy 18 with significant involvement of the oral cavity is described, both in terms of general medicine and from a dental-oral ...
Waldor Matthew K MK Channing Laboratory/Brigham and Women's Hospital, Boston, MA, USA. - - 2010
Many bacterial chromosomes contain genomic islands, large DNA segments that became incorporated into the chromosome following their horizontal transmission. However, the mechanisms that mediate the lateral transfer of genomic islands are for the most part unknown. In this issue of Molecular Microbiology, Daccord et al. describe a new type of ...
Browning Douglas F - - 2010
Bacterial nucleoid-associated proteins play a key role in the organisation, replication, segregation, repair and expression of bacterial chromosomes. Here, we review some recent progress in our understanding of the effects of these proteins on DNA and their biological role, focussing mainly on Escherichia coli and its chromosome. Certain nucleoid-associated proteins ...
Hassan Faizule F Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka-1212, - - 2010
Bacterial chromosomes often carry integrated genetic elements (for example plasmids, transposons, prophages and islands) whose precise function and contribution to the evolutionary fitness of the host bacterium are unknown. The CTXφ prophage, which encodes cholera toxin in Vibrio cholerae, is known to be adjacent to a chromosomally integrated element of ...
Shah Shiraz A - - 2011
CRISPR/Cas and CRISPR/Cmr immune machineries of archaea and bacteria provide an adaptive and effective defence mechanism directed specifically against viruses and plasmids. Present data suggest that both CRISPR/Cas and Cmr modules can behave like integral genetic elements. They tend to be located in the more variable regions of chromosomes and ...
Morissette Guillaume - - 2010
Herpesviruses are members of a diverse family of viruses that colonize all vertebrates from fish to mammals. Although more than one hundred herpesviruses exist, all are nearly identical architecturally, with a genome consisting of a linear double-stranded DNA molecule (100 to 225 kbp) protected by an icosahedral capsid made up ...
Nagata Yuji - - 2010
Sphingobium japonicum strain UT26 utilizes γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide that causes serious environmental problems due to its toxicity and long persistence, as a sole source of carbon and energy. Here, we report the complete genome sequence of UT26, which consists of two chromosomes and three plasmids. The 15 ...
Gong Shiaoching - - 2010
We report here a high-throughput method for the modification of bacterial artificial chromosomes (BACs) that uses a novel two-plasmid approach. In this protocol, a vector modified in our laboratory to hold an R6Kγ origin of replication and a marker recombination cassette is inserted into a BAC in a single recombination ...
Ohtani Naoto - - 2010
An extremely thermophilic bacterium, Thermus thermophilus HB8, is one of the model organisms for systems biology. Its genome consists of a chromosome (1.85 Mb), a megaplasmid (0.26 Mb) designated pTT27, and a plasmid (9.3 kb) designated pTT8, and the complete sequence is available. We show here that T. thermophilus is ...
Wirtz Christiane - - 2010
Temperate bacteriophages play a critical role in the pathogenicity of the human pathogen Staphylococcus aureus by mediating positive lysogenic conversion for different virulence factors such as Panton-Valentine leukocidin (PVL) or by interrupting chromosomal virulence genes. PVL-encoding phages are integrated in the S. aureus genome within a conserved ORF which is ...
Lozano Luis - - 2010
Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the ...
Doyle Timothy M - - 2010
OBJECTIVE: Pneumonic plague resulting from Yersinia pestis induces swiftly lethal sepsis and is a major concern as a weapon of bioterrorism. However, the role of specific plasmid-encoded vs. chromosomal Y. pestis virulence factors in the pathogenesis of acute lung injury, shock, and nonpulmonary dysfunction is unclear. We hypothesized that the ...
Marrero Vanessa A VA Department of Genetics and Development, Columbia University Medical Center, New York, New York, United States of - - 2010
Homology-dependent repair of DNA double-strand breaks (DSBs) by gene conversion involves short tracts of DNA synthesis and limited loss of heterozygosity (LOH). For DSBs that present only one end, repair occurs by invasion into a homologous sequence followed by replication to the end of the chromosome resulting in extensive LOH, ...
Diago-Navarro Elizabeth - - 2010
Toxin-antitoxin systems, as found in bacterial plasmids and their host chromosomes, play a role in the maintenance of genetic information, as well as in the response to stress. We describe the basic biology of the parD/kiskid toxin-antitoxin system of Escherichia coli plasmid R1, with an emphasis on regulation, toxin activity, ...
Manson Janet M - - 2010
The Enterococcus faecalis pathogenicity island (PAI) encodes known virulence traits and >100 additional genes with unknown roles in enterococcal biology. Phage-related integration and excision genes, and direct repeats flanking the island, suggest it moves as an integrative conjugative element (ICE). However, transfer was observed not to require these genes. Transfer ...
Zhou Fengfeng - - 2010
Huge amount of metagenomic sequence data have been produced as a result of the rapidly increasing efforts worldwide in studying microbial communities as a whole. Most, if not all, sequenced metagenomes are complex mixtures of chromosomal and plasmid sequence fragments from multiple organisms, possibly from different kingdoms. Computational methods for ...
Cuevas-Ramos Gabriel - - 2010
Escherichia coli is a normal inhabitant of the human gut. However, E. coli strains of phylogenetic group B2 harbor a genomic island called "pks" that codes for the production of a polyketide-peptide genotoxin, Colibactin. Here we report that in vivo infection with E. coli harboring the pks island, but not ...
Wei Xiao-Xing - - 2010
A method for construction of bacterial strains with multiple DNA inserted into their chromosomes has been developed based on the mini-Mu transposon and FLP/FRT recombination. Exogenous DNA can be integrated by Mu transposition with an FRT cassette containing selection marker and conditional replicative origin (R6Kgammaori). Subsequently, with the introduction of ...
Libby Elizabeth A - - 2010
Previously, an unexplained subcellular localization was reported for a functional fluorescent protein fusion to the response regulator OmpR in Escherichia coli. The pronounced regions of increased fluorescence, or foci, are dependent on OmpR phosphorylation and do not occupy fixed, easily identifiable positions, such as the poles or mid-cell. Here we ...
Cooper Tim F - - 2010
Toxin-antitoxin (TA) systems are commonly found on bacterial plasmids. The antitoxin inhibits toxin activity unless the system is lost from the cell. Then the shorter lived antitoxin degrades and the cell becomes susceptible to the toxin. Selection for plasmid-encoded TA systems was initially thought to result from their reducing the ...
Fiebig Aretha A Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. - - 2010
Toxin-antitoxin (TA) gene cassettes are widely distributed across bacteria, archaea and bacteriophage. The chromosome of the alpha-proteobacterium, Caulobacter crescentus, encodes eight ParE/RelE-superfamily toxins that are organized into operons with their cognate antitoxins. A systematic genetic analysis of these parDE and relBE TA operons demonstrates that seven encode functional toxins. The ...
Wang Lei - - 2010
The gene encoding resistance to methicillin and other beta-lactam antibiotics in staphylococci, mecA, is carried on a genomic island, SCCmec (for staphylococcal cassette chromosome mec). The chromosomal excision and integration of types I to IV SCCmec are catalyzed by the site-specific recombinases CcrA and CcrB, the genes for which are ...
Barale Jean-Christophe - - 2010
In this issue of Cell Host & Microbe, Iwanaga and colleagues (Iwanaga et al., 2010) report on the construction of plasmids and artificial chromosomes that are stably maintained throughout the Plasmodium life cycle. These new tools will have multiple applications, from episome-based genetic strategies to studies on telomere biology and ...
Iwanaga Shiroh S Mie University, School of Medicine, Tsu, - - 2010
The artificial chromosome represents a useful tool for gene transfer, both as cloning vectors and in chromosome biology research. To generate a Plasmodium artificial chromosome (PAC), we had to first functionally identify and characterize the parasite's centromere. A putative centromere (pbcen5) was cloned from chromosome 5 of the rodent parasite ...
Wiggins Paul A - - 2010
The stochasticity of chromosome organization was investigated by fluorescently labeling genetic loci in live Escherichia coli cells. In spite of the common assumption that the chromosome is well modeled by an unstructured polymer, measurements of the locus distributions reveal that the E. coli chromosome is precisely organized into a nucleoid ...
Hui Monica P MP Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, - - 2010
Most bacterial chromosomes contain homologs of plasmid partitioning (par) loci. These loci encode ATPases called ParA that are thought to contribute to the mechanical force required for chromosome and plasmid segregation. In Vibrio cholerae, the chromosome II (chrII) par locus is essential for chrII segregation. Here, we found that purified ...
Suzuki Keiichiro - - 2010
Chromosomal integration of exogenous DNA in mammalian cells allows stable gene expression for a variety of biological applications. Although it is presumably mediated by DNA repair machinery, little is known regarding site preferences and other characteristics. We isolated and analyzed 256 chromosomal-plasmid DNA integration junctions from 158 plasmid integrants after ...
Das Bhabatosh - - 2010
Cholera toxin is encoded in the genome of CTXvarphi, a lysogenic filamentous phage of Vibrio cholerae. CTXvarphi variants contribute to the genetic diversity of cholera epidemic strains. It has been shown that the El Tor variant of CTXvarphi hijacks XerC and XerD, two host-encoded tyrosine recombinases that normally function to ...
Harrison Peter W - - 2010
In addition to the main chromosome, approximately one in ten bacterial genomes have a 'second chromosome' or 'megaplasmid'. Here, we propose that these represent a single class of elements that have a distinct and consistent set of properties, and suggest the term 'chromid' to distinguish them from both chromosomes and ...
Kuhlman Thomas E - - 2010
We have developed an effective, easy-to-use two-step system for the site-directed insertion of large genetic constructs into arbitrary positions in the Escherichia coli chromosome. The system uses lambda-Red mediated recombineering accompanied by the introduction of double-strand DNA breaks in the chromosome and a donor plasmid bearing the desired insertion fragment. ...
Hüser Daniela - - 2010
Adeno-associated virus type 2 (AAV) is known to establish latency by preferential integration in human chromosome 19q13.42. The AAV non-structural protein Rep appears to target a site called AAVS1 by simultaneously binding to Rep-binding sites (RBS) present on the AAV genome and within AAVS1. In the absence of Rep, as ...
Bryda Elizabeth C - - 2010
Currently, most genetically engineered rat strains are created by methods that involve random integration of transgenes into the genome. The ability to identify the chromosomal location of the transgene insertion site enables the development of efficient genotyping assays, allows segregation of multiple transgene integration sites to be followed while breeding, ...
Albermann Christoph - - 2010
We report a method for the integration of expression cassettes into the Escherichia coli chromosome using rare and dispensable sugar degradation gene loci as sites for integration. Clones carrying successfully recombined DNA fragments in the chromosome are easily screened using a solid differential medium containing the respective sugar compound. As ...
Wong Ng Jérôme - - 2010
Plasmids are extra chromosomal DNA that can confer to their hosts' supplementary characteristics such as antibiotic resistance. Plasmids code for their copy number through their own replication frequency. Even though the biochemical networks underlying the plasmid copy number (PCN) regulation processes have been studied and modeled, no measurement of the ...
Gregory James A JA Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of - - 2010
We constructed a transposon (transposon assisted gene insertion technology, or TAGIT) that allows the random insertion of gfp (or other genes) into chromosomal loci without disrupting operon structure or regulation. TAGIT is a modified Tn5 transposon that uses Kan(R) to select for insertions on the chromosome or plasmid, beta-galactosidase to ...
Dubarry Nelly - - 2010
In bacteria, septum formation frequently initiates before the last steps of chromosome segregation. This is notably the case when chromosome dimers are formed by homologous recombination. Chromosome segregation then requires the activity of a double-stranded DNA transporter anchored at the septum by an integral membrane domain, FtsK. It was proposed ...
Lussier François-Xavier - - 2010
Streptomyces lividans is a Gram-positive bacterium known for its remarkable secretion efficiency and low extracellular protease activity. In the present work, we adapted the highly productive T7 expression system to S. lividans. A codon-optimized T7 RNA polymerase gene was chromosomally integrated, and a bifunctional T7 expression vector was constructed.
Yoshii Noriyo - - 2009
A total of 905 enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates that were recovered from experimentally infected cattle, in addition to the inoculated strain, were analyzed by pulsed-field gel electrophoresis (PFGE). Twelve PFGE profiles other than that of the inoculated strain were observed. We successfully identified five distinct chromosomal deletions that ...
Mellmann Alexander - - 2009
Bacterial chromosomes are not fixed molecules; they evolve over the course of infections in human beings. During infection, a variety of strong selective pressures are exerted on the pathogen. The resulting genetic changes that occur in intestinal pathogens might influence clinical outcome and have an impact on diagnosis and epidemiology. ...
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