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https://www.readbyqxmd.com/read/28110506/antibiotic-discovery-throughout-the-small-world-initiative-a-molecular-strategy-to-identify-biosynthetic-gene-clusters-involved-in-antagonistic-activity
#1
Elizabeth Davis, Tyler Sloan, Krista Aurelius, Angela Barbour, Elijah Bodey, Brigette Clark, Celeste Dennis, Rachel Drown, Megan Fleming, Allison Humbert, Elizabeth Glasgo, Trent Kerns, Kelly Lingro, MacKenzie McMillin, Aaron Meyer, Breanna Pope, April Stalevicz, Brittney Steffen, Austin Steindl, Carolyn Williams, Carmen Wimberley, Robert Zenas, Kristen Butela, Hans Wildschutte
The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production...
January 22, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28110461/the-emerging-role-of-liquid-biopsies-circulating-tumor-cells-and-circulating-cell-free-tumor-dna-in-lung-cancer-diagnosis-and-identification-of-resistance-mutations
#2
REVIEW
Angela Esposito, Carmen Criscitiello, Dario Trapani, Giuseppe Curigliano
Therapeutic advances in the treatment of lung cancer are in part due to a more complete understanding of its genomic portrait. The serial monitoring of tumor genotypes, which are instable and prone to changes under selective pressure, is becoming increasingly needed. Although tumor biopsies remain the reference standard for the diagnosis and genotyping of lung cancer, they are invasive and not always feasible. The "liquid biopsies" have the potential to overcome many of these hurdles, allowing a rapid and accurate identification of de novo and resistant genetic alterations and a real-time monitoring of treatment responses...
January 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28110292/biomartr-genomic-data-retrieval-with-r
#3
Hajk-Georg Drost, Jerzy Paszkowski
MOTIVATION: Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, biomartr, which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses...
January 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28110279/walking-the-c4-pathway-past-present-and-future
#4
REVIEW
Robert T Furbank
The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO2 pool was not understood for a number of years, and the nature of C4 as a biochemical CO2 pump then linked the unique Kranz anatomy of C4 plants to their biochemical specialization...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110275/traces-of-strong-selective-pressures-in-the-genomes-of-c4-grasses
#5
Pascal-Antoine Christin
C4 photosynthesis is nature's response to CO2 limitations, and evolved recurrently in several groups of plants. To identify genes related to C4 photosynthesis, Huang et al. looked for evidence of past episodes of adaptive evolution in the genomes of C4 grasses. They identified a large number of candidate genes that evolved under divergent selection, indicating that, besides alterations to expression patterns, the history of C4 involved strong selection on protein-coding sequences.
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110274/c4-photosynthesis-50-years-of-discovery-and-innovation
#6
EDITORIAL
Susanne von Caemmerer, Oula Ghannoum, Robert T Furbank
It is now over half a century since the biochemical characterization of the C4 photosynthetic pathway, and this special issue highlights the sheer breadth of current knowledge. New genomic and transcriptomic information shows that multi-level regulation of gene expression is required for the pathway to function, yet we know it to be one of the most dynamic examples of convergent evolution. Now, a focus on the molecular transition from C3-C4 intermediates, together with improved mathematical models, experimental tools and transformation systems, holds great promise for improving C4 photosynthesis in crops...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110245/bipartite-network-analysis-reveals-metabolic-gene-expression-profiles-that-are-highly-associated-with-the-clinical-outcomes-of-acute-myeloid-leukemia
#7
Fanfan Xie, Mingxiong He, Li He, Keqin Liu, Menglong Li, Guoquan Hu, Zhining Wen
Dysregulated and reprogrammed metabolism are one of the most important characteristics of cancer, and exploiting cancer cell metabolism can aid in understanding the diverse clinical outcomes for patients. To investigate the differences in metabolic pathways among patients with acute myeloid leukemia (AML) and differential survival outcomes, we systematically conducted microarray data analysis of the metabolic gene expression profiles from 384 patients available from the Gene Expression Omnibus and Cancer Genome Atlas databases...
January 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28110208/inflammatory-pathway-genes-associated-with-inter-individual-variability-in-the-trajectories-of-morning-and-evening-fatigue-in-patients-receiving-chemotherapy
#8
Fay Wright, Marilyn Hammer, Steven M Paul, Bradley E Aouizerat, Kord M Kober, Yvette P Conley, Bruce A Cooper, Laura B Dunn, Jon D Levine, Gail DEramo Melkus, Christine Miaskowski
Fatigue, a highly prevalent and distressing symptom during chemotherapy (CTX), demonstrates diurnal and interindividual variability in severity. Little is known about the associations between variations in genes involved in inflammatory processes and morning and evening fatigue severity during CTX. The purposes of this study, in a sample of oncology patients (N=543) with breast, gastrointestinal (GI), gynecological (GYN), or lung cancer who received two cycles of CTX, were to determine whether variations in genes involved in inflammatory processes were associated with inter-individual variability in initial levels as well as in the trajectories of morning and evening fatigue...
January 19, 2017: Cytokine
https://www.readbyqxmd.com/read/28110206/an-epstein-barr-virus-susceptible-immature-t-cell-line-will4-established-from-a-patient-with-t-lymphoblastic-lymphoma-bearing-cd21-and-a-clonal-ebv-genome
#9
Hiroki Hosoi, Ken-Ichi Imadome, Shinobu Tamura, Kodai Kuriyama, Shogo Murata, Yusuke Yamashita, Toshiki Mushino, Takehiro Oiwa, Hiroshi Kobata, Akinori Nishikawa, Hideki Nakakuma, Nobuyoshi Hanaoka, Yasushi Isobe, Kouichi Ohshima, Takashi Sonoki
We managed a patient with an Epstein-Barr virus-associated T-cell lymphoblastic lymphoma. Mediastinal tumor cells at initial admission were positive for CD4, CD8, and TdT. Interestingly, a lymph node at necropsy was compatible for a CD4-positive peripheral T-cell lymphoma without CD8 and TdT expression, suggesting a different phenotype from the mediastinal tumor. Tumor cells in pleural effusion continued to proliferate in in vitro and were designated as WILL4. WILL4 cells were positive for CD3, CD4, CD8, CD21, T-cell receptor (TcR) αβ, and TdT, indicating a similar phenotype to thymocytes...
January 15, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28110140/occurrence-of-norovirus-in-raw-sewage-a-systematic-literature-review-and-meta-analysis
#10
Sorina E Eftim, Tao Hong, Jeffrey Soller, Alexandria Boehm, Isaac Warren, Audrey Ichida, Sharon P Nappier
Human noroviruses (NoV) are a leading cause of recreational waterborne illnesses and responsible for the majority of viral-associated gastrointestinal illnesses nationwide. We conducted a systematic literature review of published peer-reviewed publications to identify NoV density data in wastewater influent, and provided an approach for developing pathogen density distributions, using the NoV data. Literature review inclusion criteria included scope, study quality, and data availability. A non-parametric bootstrap statistical model was used to estimate the NoV distribution in wastewater influent...
January 9, 2017: Water Research
https://www.readbyqxmd.com/read/28110091/genome-wide-association-analyses-reveal-the-genetic-basis-of-stigma-exsertion-in-rice
#11
Hao Zhou, Pingbo Li, Weibo Xie, Saddam Hussain, Yibo Li, Duo Xia, Hu Zhao, Shengyuan Sun, Junxiao Chen, Hong Ye, Jun Hou, Da Zhao, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Xingming Lian, Jinghua Xiao, Sibin Yu, Xianghua Li, Yuqing He
Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. As few QTLs have been fine mapped or cloned, the genetic architecture of stigma exsertion is quite unclear. We performed genome-wide association study of stigma exsertion and related traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 loci significantly associated with stigma exsertion and related traits, three of which were co-located with three major grain size genes GS3, GW5 and GW2...
January 18, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28110021/the-application-of-crispr-technology-to-high-content-screening-in-primary-neurons
#12
Ben L Callif, Brian Maunze, Nick L Krueger, Matthew T Simpson, Murray G Blackmore
Axon growth is coordinated by multiple interacting proteins that remain incompletely characterized. High content screening (HCS), in which manipulation of candidate genes is combined with rapid image analysis of phenotypic effects, has emerged as a powerful technique to identify key regulators of axon outgrowth. Here we explore the utility of a genome editing approach referred to as CRISPR (Clustered Regularly Interspersed Palindromic Repeats) for knockout screening in primary neurons. In the CRISPR approach a DNA-cleaving Cas enzyme is guided to genomic target sequences by user-created guide RNA (sgRNA), where it initiates a double-stranded break that ultimately results in frameshift mutation and loss of protein production...
January 18, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28110013/dna-damage-and-translational-response-during-detoxification-from-copper-exposure-in-a-wild-population-of-chironomus-riparius
#13
Paola Bernabò, Matteo Gaglio, Francesco Bellamoli, Gabriella Viero, Valeria Lencioni
Copper is one of the predominant components of pesticides employed in agriculture and known to be highly toxic once it reaches aquatic organisms. The impact of sublethal concentrations of this metal on wild insects is not yet completely understood. Studies addressing alterations in different levels of gene expression are still lacking. We previously demonstrated that in a wild population of Chironomus riparius, HSP and CYP families of genes were up-regulated at the transcriptional level after copper exposure...
January 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28109959/crispr-cas9-mediated-genome-editing-as-a-therapeutic-approach-for-leber-congenital-amaurosis-10
#14
Guo-Xiang Ruan, Elizabeth Barry, Dan Yu, Michael Lukason, Seng H Cheng, Abraham Scaria
As the most common subtype of Leber congenital amaurosis (LCA), LCA10 is a severe retinal dystrophy caused by mutations in the CEP290 gene. The most frequent mutation found in patients with LCA10 is a deep intronic mutation in CEP290 that generates a cryptic splice donor site. The large size of the CEP290 gene prevents its use in adeno-associated virus (AAV)-mediated gene augmentation therapy. Here, we show that targeted genomic deletion using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system represents a promising therapeutic approach for the treatment of patients with LCA10 bearing the CEP290 splice mutation...
January 18, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28109869/outcomes-infectiousness-and-transmission-dynamics-of-patients-with-extensively-drug-resistant-tuberculosis-and-home-discharged-patients-with-programmatically-incurable-tuberculosis-a-prospective-cohort-study
#15
Keertan Dheda, Jason D Limberis, Elize Pietersen, Jody Phelan, Aliasgar Esmail, Maia Lesosky, Kevin P Fennelly, Julian Te Riele, Barbara Mastrapa, Elizabeth M Streicher, Tania Dolby, Abdallah M Abdallah, Fathia Ben-Rached, John Simpson, Liezel Smith, Tawanda Gumbo, Paul van Helden, Frederick A Sirgel, Ruth McNerney, Grant Theron, Arnab Pain, Taane G Clark, Robin M Warren
BACKGROUND: The emergence of programmatically incurable tuberculosis threatens to destabilise control efforts. The aim of this study was to collect prospective patient-level data to inform treatment and containment strategies. METHODS: In a prospective cohort study, 273 South African patients with extensively drug-resistant tuberculosis, or resistance beyond extensively drug-resistant tuberculosis, were followed up over a period of 6 years. Transmission dynamics, infectiousness, and drug susceptibility were analysed in a subset of patients from the Western Cape using whole-genome sequencing (WGS; n=149), a cough aerosol sampling system (CASS; n=26), and phenotypic testing for 18 drugs (n=179)...
January 18, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28109755/construction-of-agrobacterium-tumefaciens-mediated-tomato-black-ring-virus-infectious-cdna-clones
#16
Aleksandra Zarzyńska-Nowak, Inmaculada Ferriol, Bryce W Falk, Natasza Borodynko-Filas, Beata Hasiów-Jaroszewska
Tomato black ring virus (TBRV, genus Nepovirus) infects a wide range of economically important plants such as tomato, potato, tobacco and cucumber. Here, a successful construction of infectious full-length cDNA clones of the TBRV genomic RNAs (RNA1 and RNA2) is reported for the first time. The engineered constructs consisting of PCR-amplified DNAs were cloned into binary vector pJL89 immediately downstream of a double Cauliflower mosaic virus (CaMV) 35S promoter, and upstream of the Hepatitis delta virus (HDV) ribozyme and nopaline synthase terminator (NOS)...
January 18, 2017: Virus Research
https://www.readbyqxmd.com/read/28109746/diversity-and-evolution-of-tir-domain-containing-proteins-in-bivalves-and-metazoa-new-insights-from-comparative-genomics
#17
Marco Gerdol, Paola Venier, Paolo Edomi, Alberto Pallavicini
The Toll/interleukin-1 receptor (TIR) domain has a fundamental role in the innate defence response of plants, vertebrate and invertebrate animals. Mostly found in the cytosolic side of membrane-bound receptor proteins, it mediates the intracellular signalling upon pathogen recognition via heterotypic interactions. Although a number of TIR-domain-containing (TIR-DC) proteins have been characterized in vertebrates, their evolutionary relationships and functional role in protostomes are still largely unknown. Due to the high abundance and diversity of TIR-DC proteins in bivalve molluscs, we investigated this class of marine invertebrates as a case study...
January 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28109725/6q12-and-11p14-variants-are-associated-with-postnatal-exhaled-nitric-oxide-and-respiratory-symptoms
#18
Oliver Fuchs, Olga Gorlanova, Philipp Latzin, Anne Schmidt, Maximilian Schieck, Antoaneta A Toncheva, Sven Michel, Vincent D Gaertner, Michael Kabesch, Urs Frey
BACKGROUND: Exhaled nitric oxide (eNO) is a biomarker of airway inflammation and seems to precede respiratory symptoms, such as asthma in childhood. Identifying genetic determinants of postnatal eNO may aid in unraveling the role of eNO in epithelial function or airway inflammation and disease. OBJECTIVE: To identify genetic determinants of early postnatal eNO and subsequent respiratory symptoms during the first year of life. METHODS: Within a population-based birth cohort, eNO was measured in healthy term infants aged 5 weeks during quiet tidal breathing in unsedated sleep...
January 18, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28109719/the-expanding-repertoire-of-g4-dna-structures
#19
Anna Varizhuk, Dmitry Ischenko, Vladimir Tsvetkov, Roman Novikov, Nikolay Kulemin, Dmitry Kaluzhny, Maria Vlasenok, Vladimir Naumov, Igor Smirnov, Galina Pozmogova
The definition of DNA and RNA G-quadruplexes (G4s) has recently been broadened to include structures with certain defects: bulges, G-vacancies or mismatches. Despite the striking progress in computational methods for assessing G4 folding propensity, predicting G4s with defects remains problematic, reflecting the enhanced sequential diversity of these motifs. "Imperfect" G4 motifs, i.e., those containing interrupted or truncated G-runs, are typically omitted from genomic analyses. We report here studies of G4s with defects and compare these structures with classical ("perfect") quadruplexes...
January 18, 2017: Biochimie
https://www.readbyqxmd.com/read/28109622/genetics-for-the-identification-of-lipid-targets-beyond-pcsk9
#20
REVIEW
Linda R Wang, Robert A Hegele
From studies of rare families to genome-wide associations in populations, understanding of human genetics has accelerated the search for new drug targets for the prevention of atherosclerotic cardiovascular disease. DNA sequencing and genome-wide analyses of DNA markers have illuminated rare as well as common variants in genes that regulate lipids and ultimately atherosclerosis risk. A recent innovative approach called Mendelian randomization can endorse specific genes and variants as causative not just for lipid disturbances, but also for clinical cardiovascular end points...
November 11, 2016: Canadian Journal of Cardiology
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