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https://www.readbyqxmd.com/read/28211909/a-crispr-cpf1-system-for-efficient-genome-editing-and-transcriptional-repression-in-plants
#1
Xu Tang, Levi G Lowder, Tao Zhang, Aimee A Malzahn, Xuelian Zheng, Daniel F Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R Kirkland, Yong Zhang, Yiping Qi
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription...
February 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28209824/draft-genome-sequence-of-cellulosilyticum-sp-i15g10i2-a-novel-bacterium-isolated-from-a-coal-seam-gas-water-treatment-pond
#2
Joseph Adelskov, Bharat K C Patel
Cellulosilyticum sp. strain I15G10I2 was isolated from a coal seam gas water treatment pond at the Spring Gully water treatment facility, Roma, Queensland, Australia. Analysis of the genome of 4,489,861 bp and G+C content of 35.23% revealed that strain I15G10I2 shared limited similarity to members of the genus Cellulosilyticum, family Lachnospiraceae.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28197578/chemical-characterization-of-the-glycated-myofibrillar-proteins-from-grass-carp-ctenopharyngodon-idella-and-their-impacts-on-the-human-gut-microbiota-in-vitro-fermentation
#3
Kaining Han, Ye Yao, Shiyuan Dong, Sun Jin, Hang Xiao, Haohao Wu, Mingyong Zeng
In this study, the chemical characterization of glycoconjugates of myofibrillar proteins from grass carp conjugated with glucose via Maillard reaction for up to 24 h of dry-heating was investigated, and their impacts on the microbial community in vitro human fecal fermentation were firstly evaluated by high-throughput sequencing technologies. The glycation greatly increased the furosine levels in glycoconjugates, which reached the maximum level (2.87 ± 0.08 mg per 100 mg protein) for 9 h of heating, and resulted in the structural changes of myofibrillar proteins based on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared spectroscopy (FTIR) analysis...
February 15, 2017: Food & Function
https://www.readbyqxmd.com/read/28195358/parkinson-s-disease-and-parkinson-s-disease-medications-have-distinct-signatures-of-the-gut-microbiome
#4
Erin M Hill-Burns, Justine W Debelius, James T Morton, William T Wissemann, Matthew R Lewis, Zachary D Wallen, Shyamal D Peddada, Stewart A Factor, Eric Molho, Cyrus P Zabetian, Rob Knight, Haydeh Payami
BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE: The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. METHODS: A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool...
February 14, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28183172/dynamic-changes-of-yak-bos-grunniens-gut-microbiota-during-growth-revealed-by-pcr-dgge-and-metagenomics
#5
Yuanyang Nie, Zhiwei Zhou, Jiuqiang Guan, Baixue Xia, Xiaolin Luo, Yang Yang, Yu Fu, Qun Sun
Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Method: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon content of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analize the DGGE fingerprint...
January 26, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28177790/bacterial-community-composition-and-fermentation-in-the-rumen-of-xinjiang-brown-cattle-bos-taurus-tarim-red-deer-cervus-elaphus-yarkandensis-and-karakul-sheep-ovis-aries
#6
Wenxi Qian, Zhipeng Li, Weiping Ao, Guangyong Zhao, Guangyu Li, Jianping Wu
The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer and sheep and measured rumen fermentation products...
January 17, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28161182/differential-effects-of-monensin-and-a-blend-of-essential-oils-on-rumen-microbiota-composition-of-transition-dairy-cows
#7
M Schären, C Drong, K Kiri, S Riede, M Gardener, U Meyer, J Hummel, T Urich, G Breves, S Dänicke
In response to oral application, monensin alters the rumen microbiota, increasing ruminal propionate production and energy availability in the animal. Data from different studies indicate that the susceptibility of rumen bacteria to monensin is mainly cell-wall dependent but tracing its activity to specific microbial groups has been challenging. Several studies have shown a similar effect for essential oils but results are inconsistent. To investigate the influence of monensin and a blend of essential oils (BEO, containing thymol, guaiacol, eugenol, vanillin, salicylaldehyde, and limonene) on the rumen microbiome, rumen liquid samples were collected orally on d 56 postpartum from cows that had either received a monensin controlled-release capsule 3 wk antepartum, a diet containing a BEO from 3 wk antepartum onward, or a control diet (n = 12)...
February 1, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28146081/p-cresyl-sulfate
#8
REVIEW
Tessa Gryp, Raymond Vanholder, Mario Vaneechoutte, Griet Glorieux
If chronic kidney disease (CKD) is associated with an impairment of kidney function, several uremic solutes are retained. Some of these exert toxic effects, which are called uremic toxins. p-Cresyl sulfate (pCS) is a prototype protein-bound uremic toxin to which many biological and biochemical (toxic) effects have been attributed. In addition, increased levels of pCS have been associated with worsening outcomes in CKD patients. pCS finds its origin in the intestine where gut bacteria metabolize aromatic amino acids, such as tyrosine and phenylalanine, leading to phenolic end products, of which pCS is one of the components...
January 29, 2017: Toxins
https://www.readbyqxmd.com/read/28130771/effects-of-acarbose-on-the-gut-microbiota-of-prediabetic-patients-a-randomized-double-blind-controlled-crossover-trial
#9
Xiuying Zhang, Zhiwei Fang, Chunfang Zhang, Huihua Xia, Zhuye Jie, Xueyao Han, Yingli Chen, Linong Ji
INTRODUCTION: The α-glucosidase inhibitor acarbose is an efficacious medicine for the treatment and prevention of type 2 diabetes mellitus (T2DM). However, the response of gut microbiota to acarbose is important, as the microbiota may have a critical role in the development of metabolic diseases, and acarbose is metabolized exclusively within the gastrointestinal tract. We explored the changes in the proportion and diversity of gut microbiota before and after treatment with acarbose in patients with prediabetes...
January 27, 2017: Diabetes Therapy: Research, Treatment and Education of Diabetes and related Disorders
https://www.readbyqxmd.com/read/28097050/microbial-communities-mediating-algal-detritus-turnover-under-anaerobic-conditions
#10
Jessica M Morrison, Chelsea L Murphy, Kristina Baker, Richard M Zamor, Steve J Nikolai, Shawn Wilder, Mostafa S Elshahed, Noha H Youssef
BACKGROUND: Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored...
2017: PeerJ
https://www.readbyqxmd.com/read/28078750/metabolic-adaptation-of-colonic-microbiota-to-galactooligosaccharides-a-proof-of-concept-study
#11
M Mego, C Manichanh, A Accarino, D Campos, M Pozuelo, E Varela, J Vulevic, G Tzortzis, G Gibson, F Guarner, F Azpiroz
BACKGROUND: Prebiotics have been shown to reduce abdominal symptoms in patients with functional gut disorders, despite that they are fermented by colonic bacteria and may induce gas-related symptoms. AIM: To investigate changes in the metabolic activity of gut microbiota induced by a recognised prebiotic. METHODS: Healthy subjects (n = 20) were given a prebiotic (2.8 g/day HOST-G904, HOST Therabiomics, Jersey, Channel Islands) for 3 weeks...
March 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28072880/characterisation-of-early-life-fecal-microbiota-in-susceptible-and-healthy-pigs-to-post-weaning-diarrhoea
#12
Samir Dou, Pascale Gadonna-Widehem, Véronique Rome, Dounia Hamoudi, Larbi Rhazi, Lyes Lakhal, Thibaut Larcher, Narges Bahi-Jaber, Arturo Pinon-Quintana, Alain Guyonvarch, Isabelle L E Huërou-Luron, Latifa Abdennebi-Najar
Early-life microbial exposure is of particular importance to growth, immune system development and long-lasting health. Hence, early microbiota composition is a promising predictive biomarker for health and disease but still remains poorly characterized in regards to susceptibility to diarrhoea. In the present study, we aimed to assess if gut bacterial community diversity and composition during the suckling period were associated with differences in susceptibility of pigs to post-weaning diarrhoea. Twenty piglets from 5 sows (4 piglets / litter) were weaned in poor housing conditions to challenge their susceptibility to post-weaning diarrhoea...
2017: PloS One
https://www.readbyqxmd.com/read/28038683/the-gut-microbiota-in-conventional-and-serrated-precursors-of-colorectal-cancer
#13
Brandilyn A Peters, Christine Dominianni, Jean A Shapiro, Timothy R Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B Hayes, Jiyoung Ahn
BACKGROUND: Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut microbiota and colorectal cancer; however, its relationship to the different early precursors of colorectal cancer is understudied. We tested, for the first time, the relationship of the gut microbiota to specific colorectal polyp types. RESULTS: Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples...
December 30, 2016: Microbiome
https://www.readbyqxmd.com/read/28035686/interaction-between-atypical-antipsychotics-and-the-gut-microbiome-in-a-bipolar-disease-cohort
#14
Stephanie A Flowers, Simon J Evans, Kristen M Ward, Melvin G McInnis, Vicki L Ellingrod
OBJECTIVES: The atypical antipsychotic (AAP) class is often associated with metabolic disease, but the mechanistic underpinnings of this risk are not understood. Due to reports linking gut bacteria function to metabolic disease, we hypothesize that AAP-treatment in adults results in gut dysbiosis potentiating metabolic criteria. This report describes recent findings linking AAP-treatment with differences in gut microbiota communities in a human cohort with bipolar disorder (BD). METHODS: In a cross- sectional design, we obtained 16S ribosomal sequences from 117 BD patients (49 AAP-treated, 68 non-AAP treated)...
December 30, 2016: Pharmacotherapy
https://www.readbyqxmd.com/read/28018327/correlation-of-gut-microbiota-composition-with-resistance-to-experimental-autoimmune-encephalomyelitis-in-rats
#15
Suzana Stanisavljević, Jovanka Lukić, Svetlana Soković, Sanja Mihajlovic, Marija Mostarica Stojković, Djordje Miljković, Natasa Golić
Multiple sclerosis is a chronic inflammatory disease of the central nervous system (CNS). It is widely accepted that autoimmune response against the antigens of the CNS is the essential pathogenic force in the disease. It has recently become increasingly appreciated that activated encephalitogenic cells tend to migrate toward gut associated lymphoid tissues (GALTs) and that interrupted balance between regulatory and inflammatory immunity within the GALT might have decisive role in the initiation and propagation of the CNS autoimmunity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27992409/in-vivo-high-throughput-profiling-of-crispr-cpf1-activity
#16
Hui K Kim, Myungjae Song, Jinu Lee, A Vipin Menon, Soobin Jung, Young-Mook Kang, Jae W Choi, Euijeon Woo, Hyun C Koh, Jin-Wu Nam, Hyongbum Kim
CRISPR from Prevotella and Francisella 1 (Cpf1) is an effector endonuclease of the class 2 CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) gene editing system. We developed a method for evaluating Cpf1 activity, based on target sequence composition in mammalian cells, in a high-throughput manner. A library of >11,000 target sequence and guide RNA pairs was delivered into human cells using lentiviral vectors. Subsequent delivery of Cpf1 into this cell library induced insertions and deletions (indels) at the integrated synthetic target sequences, which allowed en masse evaluation of Cpf1 activity by using deep sequencing...
December 19, 2016: Nature Methods
https://www.readbyqxmd.com/read/27940538/distribution-and-differential-survival-of-traditional-and-alternative-indicators-of-fecal-pollution-at-freshwater-beaches
#17
Danielle D Cloutier, Sandra L McLellan
: Alternative indicators have been developed that can be used to identify host sources of fecal pollution, yet little is known about how their distribution and fate compare to traditional indicators. Escherichia coli and enterococci were widely distributed at the six beaches studied and were detected in almost 95% of water samples (n = 422) and 100% of sand samples (n = 400). Berm sand contained the largest amount of E. coli (P < 0.01), whereas levels of enterococci were highest in the backshore (P < 0...
February 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27923606/blautia-massiliensis-sp-nov-isolated-from-a-fresh-human-fecal-sample-and-emended-description-of-the-genus-blautia
#18
Guillaume A Durand, Thao Pham, Sokhna Ndongo, Sory Ibrahima Traore, Grégory Dubourg, Jean-Christophe Lagier, Caroline Michelle, Nicholas Armstrong, Pierre-Edouard Fournier, Didier Raoult, Matthieu Million
The strain GD9(T) is the type strain of the newly proposed species Blautia massiliensis sp. nov., belonging to the family Lachnospiraceae. It was isolated from a fresh stool sample collected from a healthy human using the culturomics strategy. Cells are Gram-negative rods, oxygen intolerant, non-motile and non-spore forming. The 16S rRNA gene sequencing showed that strain GD9(T) was closely related to Blautia luti, with a 97.8% sequence similarity. Major fatty acids were C14:0 (19.8%) and C16:0 (53.2%). Strain GD9(T) exhibits a genome of 3,717,339 bp that contains 3,346 protein-coding genes and 81 RNAs genes including 63 tRNAs...
December 5, 2016: Anaerobe
https://www.readbyqxmd.com/read/27903830/early-life-sugar-consumption-affects-the-rat-microbiome-independently-of-obesity
#19
Emily E Noble, Ted M Hsu, Roshonda B Jones, Anthony A Fodor, Michael I Goran, Scott E Kanoski
BACKGROUND: The gut microbiome has been implicated in various metabolic and neurocognitive disorders and is heavily influenced by dietary factors, but there is a paucity of research on the effects of added sugars on the gut microbiome. OBJECTIVE: With the use of a rodent model, our goal was to determine how added-sugar consumption during the juvenile and adolescent phase of development affects the gut microbiome. METHODS: Forty-two juvenile male Sprague-Dawley rats [postnatal day (PND) 26; 50-70 g] were given access to 1 of 3 different 11%-carbohydrate solutions designed to model a range of monosaccharide ratios commonly consumed in sugar-sweetened beverages: 1) 35% fructose:65% glucose, 2) 50% fructose:50% glucose, 3) 65% fructose:35% glucose, and 4) control (no sugar)...
January 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/27903747/improved-glucose-homeostasis-in-obese-mice-treated-with-resveratrol-is-associated-with-alterations-in-the-gut-microbiome
#20
Miranda M Sung, Ty T Kim, Emmanuel Denou, Carrie-Lynn M Soltys, Shereen M Hamza, Nikole J Byrne, Grant Masson, Heekuk Park, David S Wishart, Karen L Madsen, Jonathan D Schertzer, Jason R B Dyck
Oral administration of resveratrol is able to improve glucose homeostasis in obese individuals. Herein we show that resveratrol ingestion produces taxonomic and predicted functional changes in the gut microbiome of obese mice. In particular, changes in the gut microbiome were characterized by a decreased relative abundance of Turicibacteraceae, Moryella, Lachnospiraceae, and Akkermansia and increased relative abundance of Bacteroides and Parabacteroides Moreover, fecal transfer from healthy resveratrol-fed donor mice is sufficient to improve glucose homeostasis in obese mice, suggesting that the resveratrol-mediated changes in the gut microbiome may play an important role in the mechanism of action of resveratrol...
November 30, 2016: Diabetes
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