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fecal DNA extraction

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https://www.readbyqxmd.com/read/27910234/luminal-contents-from-the-gut-of-colicky-infants-induce-visceral-hypersensitivity-in-mice
#1
H Eutamène, C L Garcia-Rodenas, S Yvon, E d'Aldebert, F Foata, B Berger, J Sauser, V Theodorou, G Bergonzelli, E Mas
BACKGROUND: The pathophysiology of infantile colic is poorly understood, though various studies report gut microbiota dysbiosis in colicky infants. We aimed to test the hypothesis that colic-related dysbiosis is associated with visceral hypersensitivity triggered by an altered luminal milieu. METHODS: Fecal samples from seven colicky and seven non-colicky infants were studied. Fecal supernatants (FS) were infused into the colons of C57/Bl6 mice (n=10/specimen). Visceral sensitivity was subsequently assessed in the animals by recording their abdominal muscle response to colorectal distension (CRD) by electromyography (EMG)...
December 1, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27907225/informativeness-of-ngs-analysis-for-vaginal-fluid-identification
#2
Saverio Giampaoli, Elisabetta DeVittori, Federica Valeriani, Andrea Berti, Vincenzo Romano Spica
The identification of vaginal fluids in forensic examinations plays an important role in crime scene reconstruction. Molecular detection of vaginal bacterial communities can lead to the correct discrimination of body fluids. These kinds of studies can be performed through multiplex real-time PCR using primers for a specific selection of bacteria. The availability of next-generation sequencing (NGS) protocols provided for the extension of the analysis to evaluate the prokaryotes present in specimens. In this study, DNA was extracted from 18 samples (vaginal, oral, fecal, yoghurt) and analyzed by real-time PCR and NGS...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27899923/community-metabolome-correlations-of-gut-microbiota-from-child-turcotte-pugh-of-a-and-b-patients
#3
Xiao Wei, Shan Jiang, Xiangna Zhao, Huan Li, Weishi Lin, Boxing Li, Jing Lu, Yansong Sun, Jing Yuan
The gut flora are widely involved in the cometabolism with the host and have evident effects on the metabolic phenotype of host. This study performed a metabolome analysis of the intestinal microbiota specific for liver cirrhosis. The study population included patients with Child-Turcotte-Pugh score of A (AP, n = 5) and B (BP, n = 5), and control subjects (NM, n = 3). Metagenomic DNA from fecal microbiota was extracted followed by metagenomic sequencing through Illumina MiSeq high throughput sequencing of 16S rRNA regions...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27889120/comparison-of-commercial-dna-extraction-kits-and-quantitative-pcr-systems-for-better-sensitivity-in-detecting-the-causative-agent-of-paratuberculosis-in-dairy-cow-fecal-samples
#4
D Fock-Chow-Tho, E Topp, E A Ibeagha-Awemu, N Bissonnette
Mycobacterium avium ssp. paratuberculosis (MAP) causes ruminant paratuberculosis (Johne's disease) worldwide. Oral-fecal contamination is the most important mode of transmission of paratuberculosis, so eradicating MAP-shedding animals could prevent disease propagation. Fecal culture, a well-known method for MAP diagnosis, requires costly specialized media and a long incubation time that sometimes ends in disappointing bacterial contamination. To facilitate the efforts of control programs, we evaluated the performance of direct fecal quantitative PCR (qPCR) assays for their sensitivity and robustness for MAP detection...
November 23, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/27888152/an-improved-methodology-to-overcome-key-issues-in-human-fecal-metagenomic-dna-extraction
#5
Jitendra Kumar, Manoj Kumar, Shashank Gupta, Vasim Ahmed, Manu Bhambi, Rajesh Pandey, Nar Singh Chauhan
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (> 23 kb) metagenomic DNA (260/280 ratio > 1...
November 22, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27882242/development-of-a-loop-mediated-isothermal-amplification-for-diagnosis-of-ascaris-lumbricoides-in-fecal-samples
#6
Esther A Shiraho, Agola L Eric, Ibrahim N Mwangi, Geoffrey M Maina, Joseph M Kinuthia, Martin W Mutuku, Robert M Mugambi, Jackson M Mwandi, Gerald M Mkoji
Ascaris lumbricoides is a nematode parasite that causes the common tropical infection ascariasis in humans. It is also considered among the neglected tropical diseases. Diagnosis relies mainly on microscopy-based methods which are laborious, are limited by low sensitivity, and require high expertise. We have developed a loop mediated isothermal amplification (LAMP) for diagnosis of ascariasis in fecal samples, based on the first internal transcribed (ITS-1) spacer region of the ribosomal DNA. We used Primer Explorer V4 software to design primers...
2016: Journal of Parasitology Research
https://www.readbyqxmd.com/read/27853122/prevalence-associated-risk-factors-and-phylogenetic-analysis-of-toxocara-vitulorum-infection-in-yaks-on-the-qinghai-tibetan-plateau-china
#7
Kun Li, Yanfang Lan, Houqiang Luo, Hui Zhang, Dongyu Liu, Lihong Zhang, Rui Gui, Lei Wang, Muhammad Shahzad, Suolang Sizhu, Jiakui Li, Yangzom Chamba
Toxocara vitulorum has been rarely reported in yaks at high altitudes and remote areas of Sichuan Province of Tibetan Plateau of China. The current study was designed to investigate the prevalence, associated risk factors, and phylogenetic characteristics of T. vitulorum in yak calves on the Qinghai Tibetan plateau. Fecal samples were collected from 891 yak calves and were examined for the presence of T. vitulorum eggs by the McMaster technique. A multivariable logistic regression model was employed to explore variables potentially associated with exposure to T...
October 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/27833384/fecal-microbiota-in-pouchitis-and-ulcerative-colitis
#8
Kai-Yu Li, Jian-Lin Wang, Jiang-Peng Wei, Sen-Yang Gao, Ying-Ying Zhang, Li-Tian Wang, Gang Liu
AIM: To investigate the changes in microbiota in feces of patients with ulcerative colitis (UC) and pouchitis using genomic technology. METHODS: Fecal samples were obtained from UC patients with or without an ileal pouch-anal anastomosis (IPAA) procedure, as well as healthy controls. The touchdown polymerase chain reaction technique was used to amplify the whole V3 region of the 16S rRNA gene, which was transcribed from DNA extracted from fecal samples. Denaturing gradient gel electrophoresis was used to separate the amplicons...
October 28, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27829577/chronic-early-life-stress-in-rat-pups-alters-basal-corticosterone-intestinal-permeability-and-fecal-microbiota-at-weaning-influence-of-sex
#9
Nabila Moussaoui, Jonathan P Jacobs, Muriel Larauche, Mandy Biraud, Mulugeta Million, Emeran Mayer, Yvette Taché
Background/Aims: Wistar rat dams exposed to limited nesting stress (LNS) from postnatal days (PND) 2 to 10 display erratic maternal behavior and their pups show delayed maturation of the hypothalamic-pituitary-adrenal axis and impaired epithelial barrier at PND10 and a visceral hypersensitivity at adulthood. Little is known about the impact of early life stress on the offspring before adulthood and the influence of sex. We investigated whether male and female rats previously exposed to LNS displays at weaning altered corticosterone, intestinal permeability and microbiota...
November 8, 2016: Journal of Neurogastroenterology and Motility
https://www.readbyqxmd.com/read/27812352/impact-of-different-fecal-processing-methods-on-assessments-of-bacterial-diversity-in-the-human-intestine
#10
Yu-Hsin Hsieh, Courtney M Peterson, Anne Raggio, Michael J Keenan, Roy J Martin, Eric Ravussin, Maria L Marco
The intestinal microbiota are integral to understanding the relationships between nutrition and health. Therefore, fecal sampling and processing protocols for metagenomic surveys should be sufficiently robust, accurate, and reliable to identify the microorganisms present. We investigated the use of different fecal preparation methods on the bacterial community structures identified in human stools. Complete stools were collected from six healthy individuals and processed according to the following methods: (i) randomly sampled fresh stool, (ii) fresh stool homogenized in a blender for 2 min, (iii) randomly sampled frozen stool, and (iv) frozen stool homogenized in a blender for 2 min, or (v) homogenized in a pneumatic mixer for either 10, 20, or 30 min...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27779903/monitoring-seven-potentially-pathogenic-escherichia-coli-serogroups-in-a-closed-herd-of-beef-cattle-from-weaning-to-finishing-phases
#11
Jennyka Hallewell, Tim Reuter, Kim Stanford, Ed Topp, Trevor W Alexander
The goal of this study was to monitor Shiga toxin-producing Escherichia coli (STEC) serogroups and virulence genes in cattle (n = 30) originating from a closed herd. Fecal samples were collected (1) at weaning, (2) upon arrival to a feedlot, (3) after 30 days on feed (DOF), and (4) after 135 DOF. DNA was extracted from feces for detection of virulence and serogroup genes by polymerase chain reaction (PCR) and immunomagnetic separation and pulsed-field gel electrophoresis (PFGE) were performed to collect and subtype STEC isolates...
October 25, 2016: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/27761718/gene-migration-for-re-emerging-amebiasis-in-iran-s-northwest-iraq-borders-a-microevolutionary-scale-for-reflecting-epidemiological-drift-of-entamoeba-histolytica-metapopulations
#12
Asad Mohammadzadeh, Adel Spotin, Mahmoud Mahami-Oskouei, Ali Haghighi, Nozhat Zebardast, Kobra Kohansal
In the microevolutionary scales of Entamoeba isolates, the gene migration shows how Entamoeba spp. has epidemiologically drifted among border countries. Five hundred fecal samples were taken from patients suffering gastrointestinal disorders, abdominal pain, and diarrhea at Saggez, northwest Iran located within the border Iraq country. Following parasitological techniques, DNA samples were extracted and amplified by polymerase chain reaction (PCR) of 18S rRNA region to identify Entamoeba infections. To distinguish the Entamoeba spp...
October 20, 2016: Parasitology Research
https://www.readbyqxmd.com/read/27704526/integrating-feeding-behavior-ecological-data-and-dna-barcoding-to-identify-developmental-differences-in-invertebrate-foraging-strategies-in-wild-white-faced-capuchins-cebus-capucinus
#13
Elizabeth K Mallott, Paul A Garber, Ripan S Malhi
OBJECTIVES: Invertebrate foraging strategies in nonhuman primates often require complex extractive foraging or prey detection techniques. As these skills take time to master, juveniles may have reduced foraging efficiency or concentrate their foraging efforts on easier to acquire prey than adults. MATERIALS AND METHODS: We use DNA barcoding, behavioral observations, and ecological data to assess age-based differences in invertebrate prey foraging strategies in a group of white-faced capuchins (Cebus capucinus) in northeastern Costa Rica...
October 5, 2016: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/27687850/helicobacter-pylori-dna-isolation-in-the-stool-an-essential-pre-requisite-for-bacterial-noninvasive-molecular-analysis
#14
Floriana Giorgio, Enzo Ierardi, Claudia Sorrentino, Mariabeatrice Principi, Michele Barone, Giuseppe Losurdo, Andrea Iannone, Antonio Giangaspero, Rosa Monno, Alfredo Di Leo
PURPOSE: Real-time polymerase chain reaction (RT-PCR) is a widely used technique for bacterial and viral infection diagnosis. Herein, we report our preliminary experience in retrieving H. pylori genetic sequences in stools and analyzing genotypic clarithromycin resistance by RT-PCR (noninvasive), with the aim of comparing this procedure with that performed on biopsy samples (invasive). MATERIALS AND METHODS: After 'in vitro' demonstration of H. pylori DNA detection from pure and stool-mixed bacteria, 52 consecutive patients at the first diagnosis of infection were investigated...
December 2016: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/27680171/potential-cross-contamination-of-similar-giardia-duodenalis-assemblage-in-children-and-pet-dogs-in-southern-brazil-as-determined-by-pcr-rflp
#15
Rosiléia Marinho de Quadros, Paulo Henrique Exterchoter Weiss, Sandra Marcia Tietz Marques, Luiz Claudio Miletti
Giardia duodenalis is an enteric parasite that has distinct genetic groups. Human infections are mainly caused by assemblages A and B, although sporadic infections by assemblages C and D have also been reported. Animals can be infected by a wide range of assemblages (A to H). The aim of this study is to identify the assemblages and sub-assemblages of G. duodenalis with zoonotic features in fecal samples of school-aged children, and in dogs that coexist in the same households in Lages, Santa Catarina, Brazil...
2016: Revista do Instituto de Medicina Tropical de São Paulo
https://www.readbyqxmd.com/read/27631013/microflora-disturbance-during-progression-of-glucose-intolerance-and-effect-of-sitagliptin-an-animal-study
#16
Xinfeng Yan, Bo Feng, Peicheng Li, Zhaosheng Tang, Lin Wang
Background. Emerging evidences have shown a close interplay between obesity, diabetes, and intestinal flora disturbance. Dipeptidyl peptidase-4 inhibitor, exemplified by sitagliptin, is highly efficacious in treating type 2 diabetes (T2DM), yet little is known if sitagliptin exerts beneficial effects on microbiota associated with obesity and T2DM. We evaluated changes of gut microbiota following the induction of obesity and T2DM in a streptozotocin treated high fat/high carbohydrate fed (HF/HC-STZ) rat model and explored the effect of sitagliptin on gut microbiota for HF/HC-STZ rats...
2016: Journal of Diabetes Research
https://www.readbyqxmd.com/read/27605567/maternal-interleukin-genotypes-are-associated-with-nicu-outcomes-among-low-birth-weight-infants
#17
Kelley L Baumgartel, Maureen W Groer, Susan M Cohen, Dianxu Ren, Diane L Spatz, Yvette P Conley
BACKGROUND: Maternal interleukin (IL) single nucleotide polymorphisms (SNPs) are associated with obstetrical outcomes. Conversely, infant SNPs are associated with subsequent neonatal intensive care unit (NICU) outcomes. Little is known about relationships between maternal SNPs and neonatal outcomes. PURPOSE: To examine the relationships between maternal IL genotypes and neonatal outcomes. METHODS: An ancillary study was conducted among mothers (N = 63) who delivered very low-birth-weight infants (N = 74)...
September 6, 2016: Biological Research for Nursing
https://www.readbyqxmd.com/read/27592213/liver-steatosis-induced-by-small-bowel-resection-is-prevented-by-oral-vancomycin
#18
Lauren K Barron, Christopher P Gayer, Anne Roberts, Jamie M Golden, Bola G Aladegbami, Jun Guo, Christopher R Erwin, Brad W Warner
BACKGROUND: Intestinal failure-associated liver disease causes significant mortality in patients with short bowel syndrome. Steatosis, a major component of intestinal failure-associated liver disease has been shown to persist even after weaning from parenteral nutrition. We sought to determine whether steatosis occurs in our murine model of short bowel syndrome and whether steatosis was affected by manipulation of the intestinal microbiome. METHODS: Male C57BL6 mice underwent 50% small bowel resection and orogastric gavage with vancomycin or vehicle for 10 weeks...
December 2016: Surgery
https://www.readbyqxmd.com/read/27580853/ecological-scenario-and-trypanosoma%C3%A2-cruzi-dtu-characterization-of-a-fatal-acute-chagas-disease-case-transmitted-orally-esp%C3%A3-rito-santo-state-brazil
#19
Maria Augusta Dario, Marina Silva Rodrigues, Juliana Helena da Silva Barros, Samanta Cristina das Chagas Xavier, Paulo Sérgio D'Andrea, André Luiz Rodrigues Roque, Ana Maria Jansen
BACKGROUND: Trypanosoma cruzi infection via oral route results in outbreaks or cases of acute Chagas disease (ACD) in different Brazilian regions and poses a novel epidemiological scenario. In the Espírito Santo state (southeastern Brazil), a fatal case of a patient with ACD led us to investigate the enzootic scenario to avoid the development of new cases. At the studied locality, Triatoma vitticeps exhibited high T. cruzi infection rates and frequently invaded residences. METHODS: Sylvatic and domestic mammals in the Rio da Prata locality, where the ACD case occurred, and in four surrounding areas (Baia Nova, Buenos Aires, Santa Rita and Todos os Santos) were examined and underwent parasitological and serological tests...
2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27536103/safety-profile-of-solid-lipid-nanoparticles-loaded-with-rosmarinic-acid-for-oral-use-in-vitro-and-animal-approaches
#20
Ana Raquel Madureira, Sara Nunes, Débora A Campos, João C Fernandes, Cláudia Marques, Monica Zuzarte, Beatriz Gullón, Luís M Rodríguez-Alcalá, Conceição Calhau, Bruno Sarmento, Ana Maria Gomes, Maria Manuela Pintado, Flávio Reis
Rosmarinic acid (RA) possesses several protective bioactivities that have attracted increasing interest by nutraceutical/pharmaceutical industries. Considering the reduced bioavailability after oral use, effective (and safe) delivery systems are crucial to protect RA from gastrointestinal degradation. This study aims to characterize the safety profile of solid lipid nanoparticles produced with Witepsol and Carnauba waxes and loaded with RA, using in vitro and in vivo approaches, focused on genotoxicity and cytotoxicity assays, redox status markers, hematological and biochemical profile, liver and kidney function, gut bacterial microbiota, and fecal fatty acids composition...
2016: International Journal of Nanomedicine
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