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831.
Watt RM Wang J Leong M Kung HF Cheah KS Liu D Danchin A Huang JD 《Nucleic acids research》2007,35(6):e37
To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for chromosomal tagging with one or more fluorescent protein genes (EGFP, EYFP, mRFP1, DsRed2). We used λ-Red recombination to precisely and efficiently position PCR-generated DNA targeting cassettes containing a fluorescent protein gene and an antibiotic resistance marker, at the C-termini of the CDSs of interest, creating in-frame fusions under the control of their native promoters. We incorporated cre/loxP and flpe/frt technology to enable multiple rounds of chromosomal tagging events to be performed sequentially with minimal disruption to the target locus, thus allowing sets of proteins to be co-localized within the cell. The visualization of labeled proteins in live E. coli cells using fluorescence microscopy revealed a striking variety of distributions including: membrane and nucleoid association, polar foci and diffuse cytoplasmic localization. Fifty of the fifty-two independent targeting experiments performed were successful, and 21 of the 23 selected CDSs could be fluorescently visualized. Our results show that E. coli has an organized and dynamic proteome, and demonstrate that this approach is applicable for tagging and (co-) localizing CDSs on a genome-wide scale. 相似文献
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834.
Jos F Muoz Rory M Welsh Terrance Shea Dhwani Batra Lalitha Gade Dakota Howard Lori A Rowe Jacques F Meis Anastasia P Litvintseva Christina A Cuomo 《Genetics》2021,218(1)
Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades. While Clades I, III, and IV are responsible for ongoing outbreaks of invasive and multidrug-resistant infections, Clade II, also termed the East Asian clade, consists primarily of cases of ear infection, is often susceptible to all antifungal drugs, and has not been associated with outbreaks. Here, we generate chromosome-level assemblies of twelve isolates representing the phylogenetic breadth of these four clades and the only isolate described to date from Clade V. This Clade V genome is highly syntenic with those of Clades I, III, and IV, although the sequence is highly divergent from the other clades. Clade II genomes appear highly rearranged, with translocations occurring near GC-poor regions, and large subtelomeric deletions in most chromosomes, resulting in a substantially different karyotype. Rearrangements and deletion lengths vary across Clade II isolates, including two from a single patient, supporting ongoing genome instability. Deleted subtelomeric regions are enriched in Hyr/Iff-like cell-surface proteins, novel candidate cell wall proteins, and an ALS-like adhesin. Cell wall proteins from these families and other drug-related genes show clade-specific signatures of selection in Clades I, III, and IV. Subtelomeric dynamics and the conservation of cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggest an explanation for the different phenotypes observed between clades. 相似文献
835.
836.
Moriah L. Szpara Derek Gatherer Alejandro Ochoa Benjamin Greenbaum Aidan Dolan Rory J. Bowden Lynn W. Enquist Matthieu Legendre Andrew J. Davison 《Journal of virology》2014,88(2):1209-1227
Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide. 相似文献
837.
Johannes Michiel Luteijn Helen Dolk Marie‐Claude Addor Larraitz Arriola Ingeborg Barisic Fabrizio Bianchi Elisa Calzolari Elizabeth Draper Ester Garne Miriam Gatt Martin Haeusler Babak Khoshnood Bob McDonnell Vera Nelen Mary O'Mahony Carmel Mullaney Annette Queisser‐Luft Judith Rankin David Tucker Christine Verellen‐Dumoulin Hermien de Walle Lyubov Yevtushok 《Birth defects research. Part A, Clinical and molecular teratology》2014,100(4):260-269
838.
Delia Projahn Sakine Simsekyilmaz Smriti Singh Isabella Kanzler Birgit K. Kramp Marcella Langer Alexandrina Burlacu Jürgen Bernhagen Doris Klee Alma Zernecke Tilman M. Hackeng Jürgen Groll Christian Weber Rory R. Koenen 《Journal of cellular and molecular medicine》2014,18(5):790-800
Myocardial infarction (MI) induces a complex inflammatory immune response, followed by the remodelling of the heart muscle and scar formation. The rapid regeneration of the blood vessel network system by the attraction of hematopoietic stem cells is beneficial for heart function. Despite the important role of chemokines in these processes, their use in clinical practice has so far been limited by their limited availability over a long time‐span in vivo. Here, a method is presented to increase physiological availability of chemokines at the site of injury over a defined time‐span and simultaneously control their release using biodegradable hydrogels. Two different biodegradable hydrogels were implemented, a fast degradable hydrogel (FDH) for delivering Met‐CCL5 over 24 hrs and a slow degradable hydrogel (SDH) for a gradual release of protease‐resistant CXCL12 (S4V) over 4 weeks. We demonstrate that the time‐controlled release using Met‐CCL5‐FDH and CXCL12 (S4V)‐SDH suppressed initial neutrophil infiltration, promoted neovascularization and reduced apoptosis in the infarcted myocardium. Thus, we were able to significantly preserve the cardiac function after MI. This study demonstrates that time‐controlled, biopolymer‐mediated delivery of chemokines represents a novel and feasible strategy to support the endogenous reparatory mechanisms after MI and may compliment cell‐based therapies. 相似文献
839.
Mark D. McDonnell ?mer Nebil Yavero?lu Brett A. Schmerl Nicolangelo Iannella Lawrence M. Ward 《PloS one》2014,9(12)
Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are ‘structural’ (induced subgraphs) and ‘functional’ (partial subgraphs). Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File. 相似文献
840.
Norah E. Palmateer Avril Taylor David J. Goldberg Alison Munro Celia Aitken Samantha J. Shepherd Georgina McAllister Rory Gunson Sharon J. Hutchinson 《PloS one》2014,9(8)