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https://www.readbyqxmd.com/read/29454026/adaptation-of-escherichia-coli-to-long-term-batch-culture-in-various-rich-media
#1
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee, Haixu Tang, Steven E Finkel, Karin E Kram
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms...
February 14, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29453418/periodic-reanalysis-of-whole-genome-sequencing-data-enhances-the-diagnostic-advantage-over-standard-clinical-genetic-testing
#2
Gregory Costain, Rebekah Jobling, Susan Walker, Miriam S Reuter, Meaghan Snell, Sarah Bowdin, Ronald D Cohn, Lucie Dupuis, Stacy Hewson, Saadet Mercimek-Andrews, Cheryl Shuman, Neal Sondheimer, Rosanna Weksberg, Grace Yoon, M Stephen Meyn, Dimitri J Stavropoulos, Stephen W Scherer, Roberto Mendoza-Londono, Christian R Marshall
Whole-genome sequencing (WGS) as a first-tier diagnostic test could transform medical genetic assessments, but there are limited data regarding its clinical use. We previously showed that WGS could feasibly be deployed as a single molecular test capable of a higher diagnostic rate than current practices, in a prospectively recruited cohort of 100 children meeting criteria for chromosomal microarray analysis. In this study, we report on the added diagnostic yield with re-annotation and reanalysis of these WGS data ~2 years later...
February 16, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29453410/molecular-characterization-of-colorectal-adenomas-with-and-without-malignancy-reveals-distinguishing-genome-transcriptome-and-methylome-alterations
#3
Brooke R Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth Slettedahl, Douglas Mahoney, Nikolaos Vasmatzis, Hang Xu, Minsoo Kim, Matthew Bockol, Daniel O'Brien, Diane Grill, Nathaniel Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas Smyrk, Ann Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David Ahlquist, Lisa A Boardman
The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29452566/near-tetraploid-cancer-cells-show-chromosome-instability-triggered-by-replication-stress-and-exhibit-enhanced-invasiveness
#4
Darawalee Wangsa, Isabel Quintanilla, Keyvan Torabi, Maria Vila-Casadesús, Amaia Ercilla, Gregory Klus, Zeynep Yuce, Claudia Galofré, Miriam Cuatrecasas, Juan José Lozano, Neus Agell, Daniela Cimini, Antoni Castells, Thomas Ried, Jordi Camps
A considerable proportion of tumors exhibit aneuploid karyotypes, likely resulting from the progressive loss of chromosomes after whole-genome duplication. Here, by using isogenic diploid and near-tetraploid (4N) single-cell-derived clones from the same parental cell lines, we aimed at exploring how polyploidization affects cellular functions and how tetraploidy generates chromosome instability. Gene expression profiling in 4N clones revealed a significant enrichment of transcripts involved in cell cycle and DNA replication...
February 8, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29452121/an-open-label-pilot-study-to-evaluate-the-efficacy-of-tofacitinib-in-moderate-to-severe-patch-type-alopecia-areata-totalis-and-universalis
#5
A Jabbari, F Sansaricq, J Cerise, J C Chen, A Bitterman, G Ulerio, J Borbon, R Clynes, A M Christiano, J Mackay-Wiggan
Alopecia areata (AA) is a common autoimmune disease, with a lifetime risk of ∼2%. In AA, the immune systems targets the hair follicle, resulting in clinical hair loss. AA prognosis is unpredictable, and currently there is no definitive treatment. Our previous whole genome expression studies identified active immune circuits in AA lesions, including common γ-chain cytokine and IFN pathways. Since these pathways are mediated through JAK kinases, we prioritized clinical exploration of small molecule JAK inhibitors...
February 13, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29451893/vegetative-compatibility-groups-partition-variation-in-the-virulence-of-verticillium-dahliae-on-strawberry
#6
Rong Fan, Helen M Cockerton, Andrew D Armitage, Helen Bates, Emma Cascant-Lopez, Laima Antanaviciute, Xiangming Xu, Xiaoping Hu, Richard J Harrison
Verticillium dahliae infection of strawberry (Fragaria x ananassa) is a major cause of disease-induced wilting in soil-grown strawberries across the world. To understand what components of the pathogen are affecting disease expression, the presence of the known effector VdAve1 was screened in a sample of Verticillium dahliae isolates. Isolates from strawberry were found to contain VdAve1 and were divided into two major clades, based upon their vegetative compatibility groups (VCG); no UK strawberry isolates contained VdAve1...
2018: PloS One
https://www.readbyqxmd.com/read/29451780/using-i-in-vitro-i-evolution-and-whole-genome-analysis-iviewga-to-discover-next-generation-targets-for-antimalarial-drug-discovery
#7
Madeline R Luth, Purva Gupta, Sabine Ottilie, Elizabeth A Winzeler
Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA)...
February 16, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29451365/the-genome-of-the-freshwater-monogonont-rotifer-brachionus-calyciflorus
#8
Hui-Su Kim, Bo-Young Lee, Jeonghoon Han, Chang-Bum Jeong, Dae-Sik Hwang, Min-Chul Lee, Hye-Min Kang, Duck-Hyun Kim, Hee-Jin Kim, Spiros Papakostas, Steven A J Declerck, Ik-Young Choi, Atsushi Hagiwara, Heum Gi Park, Jae-Seong Lee
Monogononta is the most speciose class of rotifers, with more than 2000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex, and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole genome assembly of the freshwater species Brachionus calyciflorus...
February 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29451363/the-genome-of-the-marine-medaka-oryzias-melastigma
#9
Hui-Su Kim, Bo-Young Lee, Jeonghoon Han, Chang-Bum Jeong, Dae-Sik Hwang, Min-Chul Lee, Hye-Min Kang, Duck-Hyun Kim, Daehwan Lee, Jaebum Kim, Ik-Young Choi, Jae-Seong Lee
Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50=23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish, and zebrafish) were identified...
February 16, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29451114/molecular-tools-to-study-preharvest-food-safety-challenges
#10
Deepak Kumar, Siddhartha Thakur
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply...
February 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29449963/the-nsight1-randomized-controlled-trial-rapid-whole-genome-sequencing-for-accelerated-etiologic-diagnosis-in-critically-ill-infants
#11
Josh E Petrikin, Julie A Cakici, Michelle M Clark, Laurel K Willig, Nathaly M Sweeney, Emily G Farrow, Carol J Saunders, Isabelle Thiffault, Neil A Miller, Lee Zellmer, Suzanne M Herd, Anne M Holmes, Serge Batalov, Narayanan Veeraraghavan, Laurie D Smith, David P Dimmock, J Steven Leeder, Stephen F Kingsmore
Genetic disorders are a leading cause of morbidity and mortality in infants in neonatal and pediatric intensive care units (NICU/PICU). While genomic sequencing is useful for genetic disease diagnosis, results are usually reported too late to guide inpatient management. We performed an investigator-initiated, partially blinded, pragmatic, randomized, controlled trial to test the hypothesis that rapid whole-genome sequencing (rWGS) increased the proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days...
2018: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/29449781/whole-genome-sequencing-of-multidrug-resistant-salmonella-enterica-serovar-typhimurium-isolated-from-humans-and-poultry-in-burkina-faso
#12
Assèta Kagambèga, Taru Lienemann, Jonathan G Frye, Nicolas Barro, Kaisa Haukka
Background: Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods: Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method...
2018: Tropical Medicine and Health
https://www.readbyqxmd.com/read/29449679/tert-promoter-mutation-in-adult-granulosa-cell-tumor-of-the-ovary
#13
Jessica A Pilsworth, Dawn R Cochrane, Zhouchunyang Xia, Geraldine Aubert, Anniina E M Färkkilä, Hugo M Horlings, Satoshi Yanagida, Winnie Yang, Jamie L P Lim, Yi Kan Wang, Ali Bashashati, Jacqueline Keul, Adele Wong, Kevin Norris, Sara Y Brucker, Florin-Andrei Taran, Bernhard Krämer, Annette Staebler, Esther Oliva, Sohrab P Shah, Stefan Kommoss, Friedrich Kommoss, C Blake Gilks, Duncan M Baird, David G Huntsman
The telomerase reverse transcriptase (TERT) gene is highly expressed in stem cells and silenced upon differentiation. Cancer cells can attain immortality by activating TERT to maintain telomere length and telomerase activity, which is a crucial step of tumorigenesis. Two somatic mutations in the TERT promoter (C228T; C250T) have been identified as gain-of-function mutations that promote transcriptional activation of TERT in multiple cancers, such as melanoma and glioblastoma. A recent study investigating TERT promoter mutations in ovarian carcinomas found C228T and C250T mutations in 15...
February 15, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29449667/identification-of-g-quadruplex-clusters-by-high-throughput-sequencing-of-whole-genome-amplified-products-with-a-g-quadruplex-ligand
#14
Wataru Yoshida, Hiroki Saikyo, Kazuhiko Nakabayashi, Hitomi Yoshioka, Daniyah Habiballah Bay, Keisuke Iida, Tomoko Kawai, Kenichiro Hata, Kazunori Ikebukuro, Kazuo Nagasawa, Isao Karube
G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449584/crispr-whole-genome-screening-identifies-new-necroptosis-regulators-and-ripk1-alternative-splicing
#15
Marinella G Callow, Colin Watanabe, Katherine E Wickliffe, Russell Bainer, Sarah Kummerfield, Julie Weng, Trinna Cuellar, Vasantharajan Janakiraman, Honglin Chen, Ben Chih, Yuxin Liang, Benjamin Haley, Kim Newton, Michael R Costa
The necroptotic cell death pathway is a key component of human pathogen defense that can become aberrantly derepressed during tissue homeostasis to contribute to multiple types of tissue damage and disease. While formation of the necrosome kinase signaling complex containing RIPK1, RIPK3, and MLKL has been extensively characterized, additional mechanisms of its regulation and effector functions likely remain to be discovered. We screened 19,883 mouse protein-coding genes by CRISPR/Cas9-mediated gene knockout for resistance to cytokine-induced necroptosis and identified 112 regulators and mediators of necroptosis, including 59 new candidate pathway components with minimal or no effect on cell growth in the absence of necroptosis induction...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449433/highly-similar-genomic-landscapes-in-monoclonal-b-cell-lymphocytosis-and-ultra-stable-chronic-lymphocytic-leukemia-with-low-frequency-of-driver-mutations
#16
Andreas Agathangelidis, Viktor Ljungström, Lydia Scarfò, Claudia Fazi, Maria Gounari, Tatjana Pandzic, Lesley-Ann Sutton, Kostas Stamatopoulos, Giovanni Tonon, Richard Rosenquist, Paolo Ghia
Despite the recent discovery of recurrent driver mutations in chronic lymphocytic leukemia, the genetic factors involved in disease onset remain largely unknown. To address this issue, we performed whole-genome sequencing in 11 individuals with monoclonal B-cell lymphocytosis, both of the low-count and high-count subtypes, and 5 patients with ultra-stable chronic lymphocytic leukemia (>10 years without progression from initial diagnosis). All three entities were indistiguishable at the genomic level exhibiting low genomic complexity and similar types of somatic mutations...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29449402/high-quality-draft-genome-sequences-of-five-xanthomonas-arboricola-pv-fragariae-isolates
#17
Michael Gétaz, Steve Baeyen, Jochen Blom, Martine Maes, Bart Cottyn, Joël F Pothier
Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight. We report here the first draft whole-genome sequences of five X. arboricola pv. fragariae isolates from Italy and France.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449380/annotated-genome-sequences-of-16-lineage-4-mycobacterium-tuberculosis-strains-from-guatemala
#18
Joseph W Saelens, Dalia Lau-Bonilla, Anneliese Moller, Ana M Xet-Mull, Narda Medina, Brenda Guzmán, Maylena Calderón, Raúl Herrera, Jason E Stout, Eduardo Arathoon, Blanca Samayoa, David M Tobin
Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449379/draft-genome-sequence-of-the-nitrogen-fixing-and-hormogonia-inducing-cyanobacterium-nostoc-cycadae-strain-wk-1-isolated-from-the-coralloid-roots-of-cycas-revoluta
#19
Yu Kanesaki, Masaki Hirose, Yuu Hirose, Takatomo Fujisawa, Yasukazu Nakamura, Satoru Watanabe, Shigeru Matsunaga, Hiroko Uchida, Akio Murakami
We report here the whole-genome sequence of Nostoc cycadae strain WK-1, which was isolated from cyanobacterial colonies growing in the coralloid roots of the gymnosperm Cycas revoluta It can provide valuable resources to study the mutualistic relationships and the syntrophic metabolisms between the cyanobacterial symbiont and the host plant, C. revoluta .
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29448938/comparative-genomic-analysis-of-ten-clinical-streptococcus-pneumoniae-collected-from-a-malaysian-hospital-reveal-31-new-unique-drug-resistant-snps-using-whole-genome-sequencing
#20
Hassan Mahmood Jindal, Babu Ramanathan, Cheng Foh Le, Ranganath Gudimella, Rozaimi Razali, Rishya Manikam, Shamala Devi Sekaran
BACKGROUND: Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. METHODS: In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics...
February 15, 2018: Journal of Biomedical Science
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