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https://www.readbyqxmd.com/read/28810737/identification-of-the-colicin-v-bacteriocin-gene-cluster-by-functional-screening-of-a-human-microbiome-metagenomic-library
#1
Louis Cohen, Sun Han, Yun-Han Huang, Sean F Brady
The forces that shape human microbial ecology are complex. It is likely, that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli...
August 15, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28783216/sensitive-quantitative-naked-eye-biodetection-with-polyhedral-cu-nanoshells
#2
Jae-Ho Kim, Jeong-Eun Park, Mouhong Lin, Sungi Kim, Gyeong-Hwan Kim, SungJun Park, GwangPyo Ko, Jwa-Min Nam
One of the most heavily used methods in chemical and biological labeling, detection, and imaging is based on silver shell-based enhancement on Au nanoparticles (AuNPs) that is useful for amplifying Rayleigh scattering, colorimetric signal, surface-enhanced Raman scattering, and electrical signal, but poor structural controllability and nonspecific growth of silver shells have limited its applications, especially with respect to signal reproducibility and quantification. Here, a highly specific, well-defined Cu nanopolyhedral shell overgrowth chemistry is developed with the aid of polyethyleneimine (PEI) on AuNPs, and the use of this PEI-mediated Cu polyhedral nanoshell (CuP) chemistry is shown as a means of light-scattering signal enhancement for the development of naked-eye-based highly sensitive and quantitative detections of DNA and viruses...
August 7, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28780245/prevalence-and-virulence-gene-profiling-of-enteroaggregative-escherichia-coli-in-malnourished-and-nourished-brazilian-children
#3
Alexandre Havt, Ila Fn Lima, Pedro Hqs Medeiros, Marco Af Clementino, Ana Ks Santos, Marília Smg Amaral, Herlice N Veras, Mara Mg Prata, Noélia L Lima, Alessandra Di Moura, Álvaro M Leite, Alberto M Soares, José Q Filho, Eric R Houpt, James P Nataro, Richard L Guerrant, Aldo Am Lima
The impact of enteroaggregative E. coli (EAEC) infection on childhood malnutrition and inflammation has been suggested, regardless of diarrhea. We investigated whether EAEC and its virulence-related genes (VRGs) are associated with malnutrition in a case-control study. Children aged 6-24 months from Brazil were enrolled as malnourished if weight-for-age Z-score (WAZ) ≤ -2 and nourished if WAZ > -1. Stools were cultured and examined for E. coli. DNA was extracted from fecal isolates and tested for EAEC by polymerase chain reaction (PCR)...
July 4, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28777432/comparison-of-a-prototype-reverse-hybridization-assay-and-methylight-for-detection-of-sfrp2-promotor-methylation-in-fecal-dna
#4
Gernot Kriegshäuser, Dietmar Enko, Matthias Zitt, Michael Oberwalder, Christian Oberkanins, Dietmar Öfner, Robert Zeillinger, Hannes Maximilian Müller
BACKGROUND: This study aimed to evaluate the diagnostic performance of a novel nonquantitative methylation-specific reverse hybridization (MSRH) assay to detect secreted frizzled-related protein 2 (SFRP2) promotor methylation in fecal DNA. METHODS: SFRP2 promoter methylation was investigated in stool DNA isolated from 18 colorectal cancer (CRC) patients and 22 healthy controls using the MSRH assay based on methylation-specific DNA amplification followed by reverse hybridization of biotinylated amplicons to sequence-specific methylation detection probes, with MethyLight serving as a reference method...
July 26, 2017: International Journal of Biological Markers
https://www.readbyqxmd.com/read/28763566/metabolites-and-microbial-composition-of-stool-of-women-with-fecal-incontinence-study-design-and-methods
#5
Lily A Arya, Holly E Richter, Eric Jelovsek, Marie Gantz, Sara Cichowski, Halina Zyczynski, Keisha Dyer, Nazema Siddiqui, Cassandra Carberry, Corey Broeckling, Casey Morrow, Purna Kashyap, Susie Meikle
AIMS: This paper aims to report the rationale, design, and the specific methodology of an ongoing nested observational study that will determine the association of the metabolite and microbial composition of stool with fecal incontinence (FI). METHODS: Eligible cases are participants with FI enrolled in the Controlling Anal Incontinence in women by Performing Anal Exercises with Biofeedback or Loperamide (CAPABLe) trial, a Pelvic Floor Disorders Network trial across eight clinical centers in the United States...
August 1, 2017: Neurourology and Urodynamics
https://www.readbyqxmd.com/read/28761489/the-impact-of-different-copro-preservation-conditions-on-molecular-detection-of-cryptosporidium-species
#6
Iman Moawad Abdelsalam, Rania Mohammad Sarhan, Marmar Ahmed Hanafy
BACKGROUND: We aimed to evaluate different copro-preservation conditions along the duration of one month for a better outcome of molecular diagnosis of Cryptosporidium species. METHODS: Ten samples out of 380 fresh stool samples collected from patients with diarrhea proved positive after direct examination, concentration, staining and confirmed by immunochromatographic test. The study was conducted at the Diagnostic and Research Unit of Parasitic diseases, Faculty of Medicine, Ain Shams University at the time interval from July 2014 to December 2015...
April 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28761464/genetic-variation-of-giardia-lamblia-isolates-from-food-handlers-in-kashan-central-iran
#7
Hossein Hooshyar, Shahrbanou Ghafarinasab, Mohsen Arbabi, Mahdi Delavari, Sima Rasti
BACKGROUND: Based on genotyping study of human isolates of Giardia lamblia; humans are mainly infected by two assemblages A and B. The present study was carried out to determine the sub-assemblages of G. lamblia isolated from food handlers referred to Kashan health centers, central Iran, 2015. METHODS: In this cross-sectional study, 3653 stool samples collected from food-handlers that annually refer to health center for getting a health certification and examined microscopically for G...
January 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28761462/subtypes-distribution-and-frequency-of-blastocystis-sp-isolated-from-diarrheic-and-non-diarrheic-patients
#8
Nahid Jalallou, Shahrokh Iravani, Mostafa Rezaeian, Atefe Alinaghizade, Hamed Mirjalali
BACKGROUND: Blastocystis is one of the most common parasites, reported from both human and animals. This parasite is more prevalent in regions with low levels of hygiene, close contact with animal and unsuitable disposal systems. The aim of the study was to subtype Blastocystis sp., isolated from diarrheic and non-diarrheic patients using sequencing of 18S ribosomal DNA. METHODS: Totally, 300 stool samples were collected from diarrheic and nondiarrheic patients referred to Imam Reza Hospital, Tehran from Apr to Aug 2015...
January 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28761377/fecal-occult-blood-versus-dna-testing-indirect-comparison-in-a-colorectal-cancer-screening-population
#9
Hermann Brenner, Hongda Chen
BACKGROUND: A multitarget stool DNA test (MSDT) that showed higher sensitivity but lower specificity than a fecal immunochemical test (FIT) for hemoglobin in one recent study from the US and Canada, is increasingly used for colorectal cancer (CRC) screening, despite its ~20-fold higher costs compared to FITs. We aimed to assess diagnostic performance of a quantitative FIT in an independent study among participants of screening colonoscopy and to compare it with the previously reported performance of MSDT...
2017: Clinical Epidemiology
https://www.readbyqxmd.com/read/28760481/molecular-identification-and-phylogenetic-analysis-of-human-trichostrongylus-species-from-an-endemic-area-of-iran
#10
Meysam Sharifdini, Sedigheh Drakhshani, Safar Ali Alizadeh, Laleh Ghanbarzadeh, Hamed Mirjalali, Mehrzad Saraei
Human infections with Trichostrongylus species have been reported in most parts of Iran. The aim of this study was the identification, molecular characterization and phylogenetic analysis of human Trichostrongylus species based on ITS2 region of ribosomal DNA from Guilan Province, northern Iran. Stool samples were collected from rural inhabitants and examined by formalin-ether concentration and agar plate culture techniques. After anthelmintic treatment, male adult worms were collected from five infected cases...
July 28, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28730505/stool-based-testing-for-colorectal-cancer-an-overview-of-available-evidence
#11
REVIEW
Kevin M Rank, Aasma Shaukat
PURPOSE OF REVIEW: The goal of this review is to summarize stool-based testing for colorectal cancer (CRC). The key questions answered in this review were the advantages and limitations of each available stool-based test for CRC and to examine their comparative efficacy. RECENT FINDINGS: Guaiac-based fecal occult blood testing (gFOBT) is no longer a relevant test for CRC screening. fecal immunochemical testing (FIT) tests, especially quantitative assays, are clearly a reliable stool-based test...
August 2017: Current Gastroenterology Reports
https://www.readbyqxmd.com/read/28728909/assessing-impacts-of-dna-extraction-methods-on-next-generation-sequencing-of-water-and-wastewater-samples
#12
Connie Walden, Franck Carbonero, Wen Zhang
Next Generation Sequencing (NGS) is increasingly affordable and easier to perform. However, standard protocols prior to the sequencing step are only available for few selected sample types. Here we investigated the impact of DNA extraction methods on the consistency of NGS results. Four commercial DNA extraction kits (QIAamp DNA Mini Kit, QIAamp DNA Stool Mini Kit, MO BIO Power Water Kit, and MO BIO Power Soil DNA Isolation Kit) were used on sample sources including lake water and wastewater, and sample types including planktonic and biofilm bacteria communities...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28723708/subclinical-herpesvirus-shedding-among-hiv-1-infected-men-on-antiretroviral-therapy
#13
Arcadio Agudelo-Hernandez, Yue Chen, Arlene Bullotta, William G Buchanan, Cynthia R Klamar-Blain, Luann Borowski, Sharon A Riddler, Charles R Rinaldo, Bernard Jc Macatangay
DESIGN: We evaluated the subclinical shedding of 6 different herpesviruses in antiretroviral drug-treated HIV(+) men who have sex with men (MSM), and determined how this is associated with markers of inflammation and immune activation. METHODS: We obtained blood, semen, throat washing, urine, and stool from 15 antiretroviral-treated HIV-1-infected MSM with CD4 T cell reconstitution, and 12 age-matched HIV(-) MSM from the Multicenter AIDS Cohort Study at 4 timepoints over 24 weeks to measure DNA levels of cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 and 2, human herpesvirus 6 (HHV6), and HHV8...
July 18, 2017: AIDS
https://www.readbyqxmd.com/read/28719952/molecular-phylogenetics-of-trichostrongylus-species-nematoda-trichostrongylidae-from-humans-of-mazandaran-province-iran
#14
Meysam Sharifdini, Zahra Heidari, Zahra Hesari, Sajad Vatandoost, Eshrat Beigom Kia
The present study was performed to analyze molecularly the phylogenetic positions of human-infecting Trichostrongylus species in Mazandaran Province, Iran, which is an endemic area for trichostrongyliasis. DNA from 7 Trichostrongylus infected stool samples were extracted by using in-house (IH) method. PCR amplification of ITS2-rDNA region was performed, and products were sequenced. Phylogenetic analysis of the nucleotide sequence data was performed using MEGA 5.0 software. Six out of 7 isolates had high similarity with Trichostrongylus colubriformis, while the other one showed high homology with Trichostrongylus axei registered in GenBank reference sequences...
June 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#15
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28707271/identification-and-genetic-characterization-of-a-novel-circular-single-stranded-dna-virus-in-a-human-upper-respiratory-tract-sample
#16
Lunbiao Cui, Binyao Wu, Xiaojuan Zhu, Xiling Guo, Yiyue Ge, Kangchen Zhao, Xian Qi, Zhiyang Shi, Fengcai Zhu, Lixin Sun, Minghao Zhou
Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR)...
July 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28700744/hypermethylated-dna-a-circulating-biomarker-for-colorectal-cancer-detection
#17
Simon Ladefoged Rasmussen, Henrik Bygum Krarup, Kåre Gotschalck Sunesen, Martin Berg Johansen, Mogens Tornby Stender, Inge Søkilde Pedersen, Poul Henning Madsen, Ole Thorlacius-Ussing
BACKGROUND: Colorectal cancer (CRC) is one of the most common cancers in the western world. Screening is an efficient method of reducing cancer-related mortality. Molecular biomarkers for cancer in general and CRC in particular have been proposed, and hypermethylated DNA from stool or blood samples are already implemented as biomarkers for CRC screening. We aimed to evaluate the performance of proven hypermethylated DNA promoter regions as plasma based biomarkers for CRC detection. METHODS: We conducted a cross-sectional case-control study of 193 CRC patients and 102 colonoscopy-verified healthy controls...
2017: PloS One
https://www.readbyqxmd.com/read/28700459/the-microbiome-in-posttraumatic-stress-disorder-and-trauma-exposed-controls-an-exploratory-study
#18
Sian M J Hemmings, Stefanie Malan-Muller, Leigh L van den Heuvel, Brittany A Demmitt, Maggie A Stanislawski, David G Smith, Adam D Bohr, Christopher E Stamper, Embriette R Hyde, James T Morton, Clarisse A Marotz, Philip H Siebler, Maarten Braspenning, Wim Van Criekinge, Andrew J Hoisington, Lisa A Brenner, Teodor T Postolache, Matthew B McQueen, Kenneth S Krauter, Rob Knight, Soraya Seedat, Christopher A Lowry
OBJECTIVE: Inadequate immunoregulation and elevated inflammation may be risk factors for posttraumatic stress disorder (PTSD), and microbial inputs are important determinants of immunoregulation; however, the association between the gut microbiota and PTSD is unknown. This study investigated the gut microbiome in a South African sample of PTSD-affected individuals and trauma-exposed (TE) controls, to identify potential differences in microbial diversity or microbial community structure...
July 11, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28698878/bacterial-community-profile-of-the-gut-microbiota-differs-between-hypercholesterolemic-subjects-and-controls
#19
Camilo Rebolledo, Alejandro Cuevas, Tomás Zambrano, Jacquelinne J Acuña, Milko A Jorquera, Kathleen Saavedra, Claudia Martínez, Fernando Lanas, Pamela Serón, Luis A Salazar, Nicolás Saavedra
The role of gut microbiota in the development of metabolic illnesses has been abundantly demonstrated. Recent studies suggest that gut microbiota alterations may also be related to the development of hypercholesterolemia. Therefore, we aimed to assess differences in the gut bacterial community profiles between hypercholesterolemic subjects and controls. Thirty cases diagnosed with hypercholesterolemia and 27 normocholesterolemic controls were included. A fasting whole blood sample was obtained to determine the lipid profile...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28692668/a-novel-species-specific-real-time-pcr-assay-for-the-detection-of-the-emerging-zoonotic-parasite-ancylostoma-ceylanicum-in-human-stool
#20
Marina Papaiakovou, Nils Pilotte, Jessica R Grant, Rebecca J Traub, Stacey Llewellyn, James S McCarthy, Alejandro J Krolewiecki, Rubén Cimino, Rojelio Mejia, Steven A Williams
BACKGROUND: Molecular-based surveys have indicated that Ancylostoma ceylanicum, a zoonotic hookworm, is likely the second most prevalent hookworm species infecting humans in Asia. Most current PCR-based diagnostic options for the detection of Ancylostoma species target the Internal Transcribed Spacer (ITS) regions of the ribosomal gene cluster. These regions possess a considerable degree of conservation among the species of this genus and this conservation can lead to the misidentification of infecting species or require additional labor for accurate species-level determination...
July 2017: PLoS Neglected Tropical Diseases
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