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pathogen dna enrichment

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https://www.readbyqxmd.com/read/29755676/genetic-heterogeneity-and-actionable-mutations-in-her2-positive-primary-breast-cancers-and-their-brain-metastases
#1
Leticia De Mattos-Arruda, Charlotte K Y Ng, Salvatore Piscuoglio, Maria Gonzalez-Cao, Raymond S Lim, Maria R De Filippo, Nicola Fusco, Anne M Schultheis, Carolina Ortiz, Santiago Viteri, Alexandra Arias, Gabriel S Macedo, Mafalda Oliveira, Patricia Gomez, Cristina Teixidó, Paolo Nuciforo, Vicente Peg, Cristina Saura, Santiago Ramon Y Cajal, Francesc Tresserra Casas, Britta Weigelt, Javier Cortes, Joan Seoane, Jorge S Reis-Filho
Brain metastases constitute a challenge in the management of patients with HER2-positive breast cancer treated with anti-HER2 systemic therapies. Here we sought to define the repertoire of mutations private to or enriched for in HER2-positive brain metastases. Massively parallel sequencing targeting all exons of 254 genes frequently mutated in breast cancers and/or related to DNA repair was used to characterize the spatial and temporal heterogeneity of HER2-positive breast cancers and their brain metastases in six patients...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29748565/genome-wide-and-high-density-crispr-cas9-screens-identify-point-mutations-in-parp1-causing-parp-inhibitor-resistance
#2
Stephen J Pettitt, Dragomir B Krastev, Inger Brandsma, Amy Dréan, Feifei Song, Radoslav Aleksandrov, Maria I Harrell, Malini Menon, Rachel Brough, James Campbell, Jessica Frankum, Michael Ranes, Helen N Pemberton, Rumana Rafiq, Kerry Fenwick, Amanda Swain, Sebastian Guettler, Jung-Min Lee, Elizabeth M Swisher, Stoyno Stoynov, Kosuke Yusa, Alan Ashworth, Christopher J Lord
Although PARP inhibitors (PARPi) target homologous recombination defective tumours, drug resistance frequently emerges, often via poorly understood mechanisms. Here, using genome-wide and high-density CRISPR-Cas9 "tag-mutate-enrich" mutagenesis screens, we identify close to full-length mutant forms of PARP1 that cause in vitro and in vivo PARPi resistance. Mutations both within and outside of the PARP1 DNA-binding zinc-finger domains cause PARPi resistance and alter PARP1 trapping, as does a PARP1 mutation found in a clinical case of PARPi resistance...
May 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29722810/genome-wide-detection-of-genes-under-positive-selection-in-worldwide-populations-of-the-barley-scald-pathogen
#3
Norfarhan Mohd-Assaad, Bruce A McDonald, Daniel Croll
Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host...
May 2, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29717009/an-attenuated-crispr-cas-system-in-enterococcus-faecalis-permits-dna-acquisition
#4
Karthik Hullahalli, Marinelle Rodrigues, Uyen Thy Nguyen, Kelli Palmer
Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis , since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E...
May 1, 2018: MBio
https://www.readbyqxmd.com/read/29712845/systematic-analysis-of-copy-number-variation-associated-with-congenital-diaphragmatic-hernia
#5
Qihui Zhu, Frances A High, Chengsheng Zhang, Eliza Cerveira, Meaghan K Russell, Mauro Longoni, Maliackal P Joy, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Caroline M Coletti, Pooja Bhayani, Regis Hila, Jay M Wilson, Patricia K Donahoe, Charles Lee
Congenital diaphragmatic hernia (CDH), characterized by malformation of the diaphragm and hypoplasia of the lungs, is one of the most common and severe birth defects, and is associated with high morbidity and mortality rates. There is growing evidence demonstrating that genetic factors contribute to CDH, although the pathogenesis remains largely elusive. Single-nucleotide polymorphisms have been studied in recent whole-exome sequencing efforts, but larger copy number variants (CNVs) have not yet been studied on a large scale in a case control study...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665884/factors-influencing-horizontal-gene-transfer-in-the-intestine
#6
Ximin Zeng, Jun Lin
Antibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensive in vitro studies; to date, there is still a significant knowledge gap regarding in situ HGT events as well as the factors that influence HGT in different ecological niches...
December 2017: Animal Health Research Reviews
https://www.readbyqxmd.com/read/29661159/active-dna-end-processing-in-micronuclei-of-ovarian-cancer-cells
#7
Zizhi Tang, Juan Yang, Xin Wang, Ming Zeng, Jing Wang, Ao Wang, Mingcai Zhao, Liandi Guo, Cong Liu, Dehua Li, Jie Chen
BACKGROUND: Ovarian cancer is one of the most deadly gynecological malignancies and inclined to recurrence and drug resistance. Previous studies showed that the tumorigenesis of ovarian cancers and their major histotypes are associated with genomic instability caused by defined sets of pathogenic mutations. In contrast, the mechanism that influences the development of drug resistance and disease recurrence is not well elucidated. Solid tumors are prone to chromosomal instability (CIN) and micronuclei formation (MN)...
April 16, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29649445/chromatin-accessibility-based-characterization-of-the-gene-regulatory-network-underlying-plasmodium-falciparum-blood-stage-development
#8
Christa Geeke Toenhake, Sabine Anne-Kristin Fraschka, Mahalingam Shanmugiah Vijayabaskar, David Robert Westhead, Simon Jan van Heeringen, Richárd Bártfai
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29648630/identification-of-prosthetic-joint-infection-pathogens-using-a-shotgun-metagenomics-approach
#9
Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwood-Quaintance, Janet Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel
Background: Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult to culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods: 408 sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection...
April 10, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29648586/direct-loop-mediated-isothermal-amplification-assay-for-on-site-detection-of-staphylococcus-aureus
#10
Xiaolan Tian, Junli Feng, Yi Wang
Staphylococcus aureus (S. aureus) is a major human pathogen which may produce a variety of toxins and cause staphylococcal food poisoning. In the present study, a direct loop-mediated isothermal amplification (LAMP) assay was developed and validated to detect S. aureus in food samples. Without prior cultural enrichment and DNA extraction steps, bacterial DNA was released by heating at 100°C for 5 min and directly subjected to LAMP assay. Using a set of LAMP primers recognizing six distinct regions of nuc gene, the developed direct LAMP assay was highly specific, and the analytical sensitivity was determined to be 7...
April 10, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29609164/aptamer-selection-and-application-in-multivalent-binding-based-electrical-impedance-detection-of-inactivated-h1n1-virus
#11
Chenjun Bai, Zhangwei Lu, Hua Jiang, Zihua Yang, Xuemei Liu, Hongmei Ding, Hui Li, Jie Dong, Aixue Huang, Tao Fang, Yongqiang Jiang, Lingling Zhu, Xinhui Lou, Shaohua Li, Ningsheng Shao
The type A influenza viruses are the most virulent and variable human pathogens with epidemic or even pandemic threat. The development of sensitive, specific and safe field testing methods is in particular need and quite challenging. We report here the selection and practical utilization of the inactivated influenza virus-specific aptamers. The DNA aptamers against inactivated intact H1N1 virus particles were identified through the systematic evolution of ligands by exponential enrichment (SELEX) procedure...
March 22, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29588600/identification-of-differentially-expressed-genes-and-signaling-pathways-in-ovarian-cancer-by-integrated-bioinformatics-analysis
#12
Xiao Yang, Shaoming Zhu, Li Li, Li Zhang, Shu Xian, Yanqing Wang, Yanxiang Cheng
Background: The mortality rate associated with ovarian cancer ranks the highest among gynecological malignancies. However, the cause and underlying molecular events of ovarian cancer are not clear. Here, we applied integrated bioinformatics to identify key pathogenic genes involved in ovarian cancer and reveal potential molecular mechanisms. Results: The expression profiles of GDS3592, GSE54388, and GSE66957 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 115 samples, including 85 cases of ovarian cancer samples and 30 cases of normal ovarian samples...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29566657/germline-breast-cancer-susceptibility-gene-mutations-and-breast-cancer-outcomes
#13
Yong Alison Wang, Jhih-Wei Jian, Chen-Fang Hung, Hung-Pin Peng, Chi-Fan Yang, Hung-Chun Skye Cheng, An-Suei Yang
BACKGROUND: It is unclear whether germline breast cancer susceptibility gene mutations affect breast cancer related outcomes. We wanted to evaluate mutation patterns in 20 breast cancer susceptibility genes and correlate the mutations with clinical characteristics to determine the effects of these germline mutations on breast cancer prognosis. METHODS: The study cohort included 480 ethnic Chinese individuals in Taiwan with at least one of the six clinical risk factors for hereditary breast cancer: family history of breast or ovarian cancer, young age of onset for breast cancer, bilateral breast cancer, triple negative breast cancer, both breast and ovarian cancer, and male breast cancer...
March 22, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29558886/divergent-transcriptomic-responses-underlying-the-ranaviruses-amphibian-interaction-processes-on-interspecies-infection-of-chinese-giant-salamander
#14
Fei Ke, Jian-Fang Gui, Zhong-Yuan Chen, Tao Li, Cun-Ke Lei, Zi-Hao Wang, Qi-Ya Zhang
BACKGROUND: Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio with a genome of 105.79 kb and Andrias davidianus ranavirus (ADRV), from diseased Chinese giant salamander (CGS) with a genome of 106.73 kb, contains 99% homologous genes. RESULTS: To uncover the differences in virus replication and host responses under interspecies infection, we analyzed transcriptomes of CGS challenged with RGV and ADRV in different time points (1d, 7d) for the first time...
March 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29530467/tick-microbial-communities-within-enriched-extracts-of-amblyomma-maculatum
#15
A S Varela-Stokes, S H Park, J V Stokes, N A Gavron, S I Lee, G M Moraru, S C Ricke
Our objective of this study was to explore the bacterial microbiome in fresh or fresh-frozen adult Amblyomma maculatum (Gulf Coast ticks) using extracts enriched for microbial DNA. We collected 100 questing adult A. maculatum, surface disinfected them, and extracted DNA from individual ticks collected the same day or after storage at -80 °C. Because only extracts with microbial DNA concentrations above 2 ng/μL were considered suitable for individual analysis, we expected fewer samples to meet these requirements...
May 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29526210/rapid-and-sensitive-detection-of-viable-listeria-monocytogenes-in-food-products-by-a-filtration-based-protocol-and-qpcr
#16
Alejandro Garrido-Maestu, Sarah Azinheiro, Joana Carvalho, Marta Prado
Listeria monocytogenes continues to be one of the most important foodborne pathogens worldwide, either due to its incidence and/or to its high mortality rate. In the present study, a filtration-based protocol was applied for the screening of viable bacteria. Additionally, a complete method (enrichment, filtration, DNA extraction and real-time PCR detection) was evaluated in order to determine the capacity of this protocol to detect viable L. monocytogenes in food samples. A new multiplex qPCR detection system was designed, including an internal amplification control, both targets were detected with hydrolysis probes...
August 2018: Food Microbiology
https://www.readbyqxmd.com/read/29524216/recombinase-polymerase-amplification-combined-with-lateral-flow-strip-for-listeria-monocytogenes-detection-in-food
#17
Xin-Jun Du, Yu-Xuan Zang, Hai-Bin Liu, Ping Li, Shuo Wang
Listeria monocytogenes is an important food-borne pathogenic bacterium that causes human disease, resulting in economic losses worldwide. The current detection methods for L. monocytogenes are not well suited for direct field testing because they involve complicated, time-consuming operations. A simple, efficient method is vital for L. monocytogenes detection. In this study, we combined isothermal recombinase polymerase amplification (RPA) with a lateral flow (LF) strip to rapidly and reliably detect L. monocytogenes...
April 2018: Journal of Food Science
https://www.readbyqxmd.com/read/29478780/inherited-dna-repair-defects-in-colorectal-cancer
#18
Saud H AlDubayan, Marios Giannakis, Nathanael D Moore, G Celine Han, Brendan Reardon, Tsuyoshi Hamada, Xinmeng Jasmine Mu, Reiko Nishihara, Zhirong Qian, Li Liu, Matthew B Yurgelun, Sapna Syngal, Levi A Garraway, Shuji Ogino, Charles S Fuchs, Eliezer M Van Allen
Colorectal cancer (CRC) heritability has been estimated to be around 30%. However, mutations in the known CRC-susceptibility genes explain CRC risk in fewer than 10% of affected individuals. Germline mutations in DNA-repair genes (DRGs) have recently been reported in CRC, but their contribution to CRC risk is largely unknown. We evaluated the gene-level germline mutation enrichment of 40 DRGs in 680 unselected CRC individuals and 27,728 ancestry-matched cancer-free adults. Significant findings were then examined in independent cohorts of 1,661 unselected CRC individuals and 1,456 individuals with early-onset CRC...
March 1, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29467738/worlds-apart-transcriptome-profiles-of-key-oral-microbes-in-the-periodontal-pocket-compared-to-single-laboratory-culture-reflect-synergistic-interactions
#19
Zhi-Luo Deng, Helena Sztajer, Michael Jarek, Sabin Bhuju, Irene Wagner-Döbler
Periodontitis is a worldwide prevalent oral disease which results from dysbiosis of the periodontal microbiome. Some of the most active microbial players, e.g., Porphyromonas gingivalis, Treponema denticola , and Fusobacterium nucleatum , have extensively been studied in the laboratory, but it is unclear to which extend these findings can be transferred to in vivo conditions. Here we show that the transcriptional profiles of P. gingivalis, T. denticola , and F. nucleatum in the periodontal niche are distinct from those in single laboratory culture and exhibit functional similarities...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29467730/detection-of-shigella-in-milk-and-clinical-samples-by-magnetic-immunocaptured-loop-mediated-isothermal-amplification-assay
#20
Liding Zhang, Qiujiang Wei, Qinqin Han, Qiang Chen, Wenlin Tai, Jinyang Zhang, Yuzhu Song, Xueshan Xia
Shigella is an important human food-borne zoonosis bacterial pathogen, and can cause clinically severe diarrhea. There is an urgent need to develop a specific, sensitive, and rapid methodology for detection of this pathogen. In this study, loop-mediated isothermal amplification (LAMP) combined with magnetic immunocapture assay (IC-LAMP) was first developed for the detection of Shigella in pure culture, artificial milk, and clinical stool samples. This method exhibited a detection limit of 8.7 CFU/mL. Compared with polymerase chain reaction, IC-LAMP is sensitive, specific, and reliable for monitoring Shigella...
2018: Frontiers in Microbiology
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