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  • 1
    Language: English
    In: Nature, November 2018, Vol.563(7729), pp.121-125
    Description: Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
    Keywords: Antigenic Variation -- Genetics ; Chromatin -- Genetics ; DNA, Protozoan -- Metabolism ; Genome -- Genetics ; Trypanosoma Brucei Brucei -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 2
    In: Nature, 2016, Vol.540(7632), p.296
    Description: Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information1,2. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species3-8. Whether pairwise loops9-14 synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells. This approach captures chromosomal structure at varying scales. Inter-chromosomal contacts constitute only 7-10% of the pairs and are restricted by interfacing TADs. About half of the C-walks stay within one chromosome, and almost half of those are restricted to intra-TAD spaces. C-walks that couple 2-4 TADs indicate stochastic associations between transcriptionally active, early replicating loci. Targeted analysis of thousands of 3-walks anchored at highly expressed genes support pairwise, rather than hub-like, chromosomal topology at active loci. Polycomb-repressed Hox domains are shown by the same approach to enrich for synergistic hubs. Together, the data indicate that chromosomal territories, TADs, and intra-TAD loops are primarily driven by nested, possibly dynamic, pairwise contacts.
    Keywords: Chromosomes ; Binding Sites ; Deoxyribonucleic Acid–DNA ; Genomics ; Gene Loci;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 3
    Language: English
    In: Applied and environmental microbiology, 15 September 2017, Vol.83(18)
    Description: Shellfish-transmitted infections have recently increased from locations with historically low disease incidence, such as the Northeast United States. This change coincided with a bacterial population shift toward human-pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43, and ST636) to nearshore areas off the Atlantic coast of the Northeast United States. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human-pathogenic variant evolved independently through acquisition of distinct pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins or contained a chromosome I-inserted island we call VPaIβ that encodes a type 3 secretion system (T3SS2β) typical of Trh hemolysin producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaIγ that encodes both and and that was inserted in chromosome II. VPaIγ was derived from VPaIβ but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaIγ-type islands containing inserted adjacent to the cluster in the three introduced Pacific and most other emergent lineages that collectively cause 67% of infections in the Northeast United States as of 2016. The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in parallel from the same potentially benign lineage by independent VPaI acquisition is surprising considering the historically low prevalence of community members harboring VPaI in waters along the Northeast U.S. coast that could serve as the source of this material. This illustrates a possible predisposition of some lineages to not only acquire foreign DNA but also become human pathogens. Whereas the underlying cause for the expansion of lineages harboring VPaIγ along the U.S. Atlantic coast and spread of this element to multiple lineages that underlies disease emergence is not known, this work underscores the need to define the environment factors that favor bacteria harboring VPaI in locations of emergent disease.
    Keywords: Hgt ; Emerging Pathogen ; Genomics ; Molecular Epidemiology ; Pathogen Evolution ; Pathogenicity Islands ; Type III Secretion Systems ; Vibrio ; Whole-Genome Phylogeny
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 4
    Language: English
    In: Cell, 28 August 2014, Vol.158(5), pp.1187-1198
    Description: Programmed DNA rearrangements in the single-celled eukaryote completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains 〉3,500 scrambled genes, as well as 〉800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement. A draft assembly of the germline genome, including a comparison to the somatic genome, to present a global view of its massive scale of genome rearrangements.
    Keywords: Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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  • 5
    Language: English
    In: Cancer Research, 07/15/2016, Vol.76(14 Supplement), pp.848-848
    ISSN: 0008-5472
    E-ISSN: 1538-7445
    Source: CrossRef
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  • 6
    Language: English
    In: Clinical Lab Products, 2017, Vol.47(2), p.12(5)
    Keywords: Biomedical Laboratories – Technology Application ; Biomedical Laboratories – Management ; Medical Schools – Services ; DNA Sequencing – Research ; Genomics – Research
    ISSN: 0192-1282
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: Antimicrobial agents and chemotherapy, August 2016, Vol.60(8), pp.5068-71
    Description: The blaIMP-14 carbapenem resistance gene has largely previously been observed in Pseudomonas aeruginosa and Acinetobacter spp. As part of global surveillance and sequencing of carbapenem-resistant Escherichia coli, we identified a sequence type 131 strain harboring blaIMP-14 within a class 1 integron, itself nested within an ∼54-kb multidrug resistance region on an epidemic IncA/C2 plasmid. The emergence of blaIMP-14 in this context in the ST131 lineage is of potential clinical concern.
    Keywords: Escherichia Coli -- Drug Effects ; Plasmids -- Genetics ; Beta-Lactamases -- Metabolism
    ISSN: 00664804
    E-ISSN: 1098-6596
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  • 8
    Language: English
    In: Journal of clinical microbiology, February 2017, Vol.55(2), pp.645-648
    Description: Vibrio parahaemolyticus is the leading seafood-transmitted bacterial pathogen worldwide where it causes gastroenteritis and rarely lethal septicemia.…
    Keywords: Vibrio Parahaemolyticus ; Core Genome Multilocus Sequence Type Analysis ; Emerging Pathogen ; Genomics ; Molecular Epidemiology ; Communicable Diseases, Emerging -- Microbiology ; Foodborne Diseases -- Microbiology ; Vibrio Infections -- Epidemiology ; Vibrio Parahaemolyticus -- Genetics
    E-ISSN: 1098-660X
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  • 9
    Language: English
    In: Analytical chemistry, 01 May 2006, Vol.78(9), pp.3144-51
    Description: A highly sensitive (pM), efficient (t 〈 20 min) detection assay was developed by designing surfaces with grafted antibodies. Through this approach, a short half-life antigen, glucagon, was rapidly detected in a biologically complex plasma/blood environment. Tailoring of graft composition eliminates the need for time-consuming blocking steps, significantly reducing antigen-antibody incubation times, while maintaining antibody specificity and activity toward target antigen. Grafted antibodies were bound through solvated, mobile polymer chains, thereby circumventing problems associated with antibody accessibility, analyte diffusion, and steric limitations. The efficiency of this assay is provided through grafting synthesized, acrylated antibodies in the presence of PEG monoacrylate. This procedure eliminates the need for blocking steps, due to a decrease in nonspecific protein interactions. These polymerizable antibodies were tethered with a range of densities while retaining biological activity. Moreover, biological activity of acrylated antibodies was compared to that of unmodified antibodies and remained comparable. The acrylated antibodies were grafted from substrate surfaces using controlled radical photopolymerization, maintaining the advantages of classical antibody immobilization techniques while providing improved detection. Through integrating this antibody conjugation chemistry and immunoassay approach with photolithographic techniques, construction of spatial patterns on a microfluidic device was demonstrated for efficient, parallel screening of multiple antigens.
    Keywords: Antibodies -- Chemistry ; Antigens -- Blood
    ISSN: 0003-2700
    E-ISSN: 15206882
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  • 10
    Language: English
    In: Sensors & Actuators: B. Chemical, 2006, Vol.119(1), pp.127-134
    Description: Here, we describe the construction of pH sensitive surfaces via the synthesis and controlled photografting of pH sensitive, fluorescent tethers from the surface of a reactive polymeric substrate. The living radical photografting technique presented makes use of dithiocarbamate-functionalized polymer to graft synthetic poly(ethylene glycol) acrylate succinyl fluorescein. Fluorescence intensity of grafted chains is analyzed as a function of photografting reaction time, graft length, buffer solution pH, and cycling sensors from acidic to basic conditions for optical switching. The graft fluorescence response occurs rapidly in a basic environment and grafted functionalities do not cleave or dramatically deplete (up to 72 h later) upon initial exposure to high or low pH buffers. This behavior is a result of the increased stability when introducing the PEG spacer into the structure of the fluorescein. Ultimately, the pH sensitive grafts developed here demonstrate rapid response times, are easy to produce, and are readily integrated onto a fully polymeric microfluidic device using photolithographic techniques and spatially controlled living radical photografting chemistry. Once integrated, sensors such as these could be useful in monitoring pH changes when mixing, reacting, or introducing new chemicals onto a microdevice like the one presented.
    Keywords: Grafting ; Photopolymerization ; Chemosensor ; Microfluidics ; Engineering
    ISSN: 0925-4005
    E-ISSN: 1873-3077
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