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Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

World journal of Gastroenterology 2010年第33期16卷 4135-4144页

作者： Carlos W Nossa William E Oberdorf jφrn A Aas Bruce j Paster todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei Department of Medicine New York University School of Medicine Department of Molecular Genetics The Forsyth Institute Faculty of Dentistry University of Oslo Harvard School of Dental Medicine Lawrence Berkeley National Laboratory Center for Environmental Biotechnology New York University College of Dentistry Depar tment of Pa thology and Medicine New York University School of MedicineNew YorkNY 10016United States Department of Veterans Affairs New York Harbor Health SystemNewYorkNY 10010United States

AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut ***:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial *** primers evaluated were from the European rRNA *** assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length *** spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer *** sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 ***:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 *** 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on *** comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 *** 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species *** by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut ***

关键词： Foregut Microbiome 16S 454 sequencing Primer

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Analysis of Transcriptome Changes Induced by Ptr ToxA in Wheat Provides Insights into the Mechanisms of Plant Susceptibility

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Molecular Plant 2009年第5期2卷 1067-1083页

作者： Iovanna Pandelova Melania F. Betts Viola A. Manning Larry j. Wilhelm todd C. Mockler Lynda M. Ciuffetti Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing Oregon State University Corvallis OR 97331 USA

To obtain greater insight into the molecular events underlying plant disease susceptibility, we studied transcriptome changes induced by a host-selective toxin of Pyrenophora tritici-repentis, Ptr ToxA （ToxA）, on its host plant, wheat. Transcriptional profiling of ToxA-treated leaves of a ToxA-sensitive wheat cultivar was performed using the GeneChip Wheat Genome Array. An improved and up-to-date annotation of the wheat microarray was generated and a new tool for array data analysis （BRAT） was developed, and both are available for public use via a web-based interface. Our data indicate that massive transcriptional reprogramming occurs due to ToxA treatment, including cellular responses typically associated with defense. In addition, this study supports previous results indicating that ToxA-induced cell death is triggered by impairment of the photosynthetic machinery and accumulation of reactive oxygen species. Based on results of this study, we propose that ToxA acts as both an elicitor and a virulence factor.

关键词： Gene expression transcriptome analysis defense responses fungal pathogenesis plant-microbe interactions host-selective toxin.

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Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB

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mLife 2022年第2期1卷 114-130页

作者： Chun-Yang Li jason C.Crack Simone Newton-Payne Andrew R.j.Murphy Xiu-Lan Chen Benjamin j.Pinchbeck Shun Zhou Beth T.Williams Ming Peng Xiao-Hua Zhang Yin Chen Nick E.Le Brun jonathan D.todd Yu-Zhong Zhang Frontiers Science Center for Deep Ocean Multispheres and Earth System College of Marine Life SciencesOcean University of ChinaQingdaoChina State Key Laboratory of Microbial Technology Marine Biotechnology Research CenterShandong UniversityQingdaoChina Laboratory for Marine Biology and Biotechnology Pilot National Laboratory for Marine Science and TechnologyQingdaoShandongChina School of Chemistry Centre for Molecular and Structural BiochemistryUniversity of East AngliaNorwich Research ParkNorwichUK School of Biological Sciences University of East AngliaNorwichUK School of Life Sciences University of WarwickCoventryUK

Marine algae and bacteria produce approximately eight billion tonnes of the organosulfur molecule dimethylsulfoniopropionate(DMSP)in Earth's surface oceans *** is an antistress compound and,once released into the environment,a major nutrient,signaling molecule,and source of climate-active *** methionine transamination pathway for DMSP synthesis is used by most known DMSP-producing algae and *** S-directed S-adenosylmethionine(SAM)-dependent 4-methylthio-2-hydroxybutyrate(MTHB)S-methyltransferase,encoded by the dsyB/DSYB gene,is the key enzyme of this pathway,generating S-adenosylhomocysteine(SAH)and 4-dimethylsulfonio-2-hydroxybutyrate(DMSHB).DsyB/DSYB,present in most haptophyte and dinoflagellate algae with the highest known intracellular DMSP concentrations,is shown to be far more abundant and transcribed in marine environments than any other known S-methyltransferase gene in DMSP synthesis ***,we demonstrate in vitro activity of the bacterial DsyB enzyme from Nisaea denitrificans and provide its crystal structure in complex with SAM and SAH-MTHB,which together provide the first important mechanistic insights into a DMSP synthesis *** and mutational analyses imply that DsyB adopts a proximity and desolvation mechanism for the methyl transfer *** analysis suggests that this mechanism may be common to all bacterial DsyB enzymes and also,importantly,eukaryotic DSYB enzymes from e.g.,algae that are the major DMSP producers in Earth's surface oceans.

关键词： catalytic mechanism DMSP synthesis marine sulfur cycle S-methyltransferase

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Biogenic production of DMSP and its degradation to DMS—their roles in the global sulfur cycle

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Science China(Life Sciences) 2019年第10期62卷 1296-1319页

作者： Xiao-Hua Zhang ji Liu jingli Liu Guipeng Yang Chun-Xu Xue Andrew R. j. Curson jonathan D. todd MOE Key Laboratory of Marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China Laboratory for Marine Ecology and Environmental Science Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China College of Chemistry and Chemical Engineering Ocean University of ChinaQingdao 266071China School of Biological Sciences University of East AngliaNorwich NR4 7TJUK

Dimethyl sulfide(DMS) is the most abundant form of volatile sulfur in Earth’s oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate(DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been *** heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and *** phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.

关键词： marine microorganism dimethylsulfoniopropionate (DMSP) dimethyl sulfide (DMS) DMSP biosynthesis DMSP cleavage

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Uptake of Phosphorus from Modified P-Enriched Douglas Fir Biochar and Its Effects on Crop Growth and P Use Efficiency

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journal of Geoscience and Environment Protection 2022年第9期10卷 207-229页

作者： Beatrice Arwenyo jac j. Varco Andrew Dygert jaime Berry julianna Mills Dinesh Mohan Charles U. Pittman jr. todd Mlsna Department of Chemistry Mississippi State University Mississippi State USA Department of Chemistry Gulu University Gulu Uganda Department of Plant and Soil Science Mississippi State University Mississippi State USA School of Environmental Sciences Jawaharlal Nehru University New Delhi India

The potential use of biochar as a sustainable soil amendment has recently gained global recognition. The use of biochar as a soil additive is attributed to its ability to improve soil chemical, physical and biological properties. Studies have shown that biochar amendments can enhance soil nutrient retention and availability, pH, water holding capacity, microbial activity and sequester carbon. In this study using corn (Zea mays L.) as an experimental crop, the influence of P availability from modified P enriched Douglas fir biochar (PEB), triple super phosphate fertilizer (SPF), and modified Douglas fir biochar (MB) on plant growth and P Use Efficiency (PUE) were compared. The rate of P applied (0, 30, 60, 90 and 120 kg·ha-1) was calculated based on % P content of each soil additive. Except for MB treatments, P recovery, crop growth and P Use Efficiency increased with application rates. The maximum above ground dry matter yields corresponding to PEB, SPF and MB treatments were estimated at 3488 kg·ha-1, 2449 kg·ha-1 and 639 kg·ha-1, while their respective agronomic P use efficiency (AGE) rates were 32 kg·kg-1, 17 kg·kg-1, 0.5 kg·kg-1. Also, recovery of K, Mg, Ca, Zn, Fe, Cu, B and Mn improved in both PEB (p value 0.9) and SPF (p value 2 > 0.9) treatments. More studies at field scale are needed to demonstrate the practicability of using modified P enriched Douglas fir biochar for soil amendments.

关键词： Macronutrients Dry Matter Yield Micronutrients Application Rate

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颈椎术后并发第5颈椎神经根麻痹研究进展

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中华外科杂志 2013年第9期51卷 846-850页

作者：胡勇 todd j Albert 宁波市第六医院脊柱外科 315000 美国托马斯杰弗逊大学罗思曼骨科研究中心

第5颈椎（C5）神经根麻痹是一种颈椎减压术后比较常见但认知不足的潜在并发症，可见于颈椎前路或后路减压术后。尽管不同颈神经根均可累及，但最常见于C5神经根，因此临床常将其称为“术后C5神经根麻痹”。尽管有研究对术后C5神经根麻... 详细信息

第5颈椎（C5）神经根麻痹是一种颈椎减压术后比较常见但认知不足的潜在并发症，可见于颈椎前路或后路减压术后。尽管不同颈神经根均可累及，但最常见于C5神经根，因此临床常将其称为“术后C5神经根麻痹”。尽管有研究对术后C5神经根麻痹的可能原因进行了分析，但目前关于这些理论尚缺乏足够的临床和影像学资料证明其合理性。本文结合近年来国内外文献对颈椎术后C5神经根麻痹的发生率、发病机制、预防措施以及预后做一综合性分析。

关键词：颈神经根颈椎前路术后并发麻痹减压术后潜在并发症影像学资料发病机制

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Comparison of five video-assisted intubation devices by novice and expert laryngoscopists for use in the aeromedical evacuation environment

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Military Medical Research 2017年第2期4卷 61-69页

作者： Matthew C.Wallace SSgt Tyler Britton robbie Meek Sharon Walsh-Hart Col todd E.Carter Steven j.Lisco University of Cincinnati Medical Center Department of Anesthesiology

Background: The critically ill or injured patient undergoing military medical evacuation may require emergent intubation. Intubation may be life-saving, but it carries *** novice or infrequent laryngoscopist has a distinct disadvantage because experience is critical for the rapid and safe establishment of a secured airway. This challenge is compounded by the austere environment of the back of an aircraft under blackout conditions. This study determined which of five different video-assisted intubation devices(VAIDs) was best suited for in-flight use by U.S. Air Force Critical Care Air Transport Teams by comparing time to successful intubation between novice and expert laryngoscopists under three conditions, Normal Airway Lights on(NAL), Difficult Airway Lights on(DAL) and Difficult Airway Blackout(DAB), using manikins on a standard military transport stanchion and the floor with a minimal amount of setup time and extraneous light ***: A convenience sample size of 40 participants(24 novices and 16 experts) attempted intubation with each of the 5 different video laryngoscopic devices on high-fidelity airway manikins. Time to tracheal intubation and number of optimization maneuvers used were recorded. Kruskal-Wallis testing determined significant differences between the VAIDs in time to intubation for each particular scenario. Devices with significant differences underwent pair-wise comparison testing using rank-sum analysis to further clarify the difference. Device assembly times, startup times and the amount of light emitted were recorded. Perceived ease of use was surveyed. Results: Novices were fastest with the Pentax AWS in all difficult airway scenarios. Experts recorded the shortest median times consistently using 3 of the 5 devices. The AWS was superior overall in 4 of the 6 scenarios tested. Experts and novices subjectively judged the Glide Scope Ranger as easiest to use. The light emitted by all the devices was less than the USAF-issued hea

关键词： simulation difficult airway novice expert military video laryngoscopy light emission

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Pilot Studies on the Novel Hypothesis that TSPO (Peripheral Benzodiazepine Receptor) Is Involved in Benzodiazepine/“Z-Drug” Physical Dependence and/or Withdrawal

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Pharmacology & Pharmacy 2023年第3期14卷 72-83页

作者： Cheyenne Moffett Katherine j. Kost Austen Thompson joseph V. Pergolizzi jr. Tally M. Largent-Milnes robert B. Raffa todd Vanderah Department of Pharmacology and Comprehensive Pain and Addiction Center University of Arizona Tucson AZ USA NEMA Inc. Naples FL USA Neumentum Inc. Summit NJ USA Enalare Therapeutics Naples FL USA School of Pharmacy Temple University Philadelphia PA USA College of Pharmacy (Adjunct) University of Arizona Tucson AZ USA

Benzodiazepines and other benzodiazepine receptor agonists, such as the “Z” drugs, are widely prescribed medications mainly used for treating anxiety and seizures, and for inducing sedation. Unfortunately, despite their popularity, benzodiazepine prescribing often exceeds recommendations and the consequences can be severe. On September 23, 2020, the United States FDA announced a new requirement for a Boxed Warning for benzodiazepines prescribing. Along with this announcement, the FDA stated that relevant information regarding the initiation, continuation, and discontinuation of benzodiazepines is lacking. Here, we describe initial pilot studies intended to investigate the questions 1) can animal models be developed that demonstrate benzodiazepine physical dependence and/or withdrawal symptoms, and 2) determine whether translocator protein (TSPO) plays a role in benzodiazepine dependence and/or withdrawal processes. The former was demonstrated, methodological limitations prevented the latter.

关键词： Benzodiazepine TSPO Rats In Vivo Tests Western-Blot Analysis

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Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

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Synthetic and Systems Biotechnology 2022年第2期7卷 738-749页

作者： Francesca V.Gambacorta Ellen R.Wagner Tyler B.jacobson Mary Tremaine Laura K.Muehlbauer Mick A.McGee justin j.Baerwald Russell L.Wrobel john F.Wolters Mike Place joshua j.Dietrich Dan Xie jose Serate Shabda Gajbhiye Lisa Liu Maikayeng Vang-Smith joshua j.Coon Yaoping Zhang Audrey P.Gasch Daniel Amador-Noguez Chris todd Hittinger Trey K.Sato Brian F.Pfleger DOE Great Lakes Bioenergy Research Center University of Wisconsin-MadisonMadisonWIUSA Department of Chemical and Biological Engineering University of Wisconsin-MadisonMadisonWIUSA Laboratory of Genetics Center for Genomic Science InnovationUniversity of Wisconsin-MadisonMadisonWIUSA Department of Bacteriology University of Wisconsin-MadisonMadisonWIUSA Department of Chemistry University of Wisconsin-MadisonMadisonWIUSA Wisconsin Energy Institute J.F.Crow Institute for the Study of EvolutionUniversity of Wisconsin-MadisonMadisonWIUSA Department of Biomolecular Chemistry University of Wisconsin-MadisonMadisonWIUSA

Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces ***,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing *** equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase *** then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered *** localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic ***-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway *** genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase *** then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron *** resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.

关键词： Saccharomyces cerevisiae Isobutanol Functional genomics analysis Pathway localization Fe incorporation

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A global review of the ecological significance of symbiotic associations between birds and fungi

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Fungal Diversity 2019年第5期98卷 161-194页

作者： todd F.Elliott Michelle A.jusino james M.Trappe Heino Lepp Guy-Anthony Ballard jeremy j.Bruhl Karl Vernes Ecosystem Management School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW 2351Australia Department of Plant Pathology University of FloridaGainesvilleFL 32611USA Department of Forest Ecosystems and Society Oregon State UniversityCorvallisOR 97331USA Forestry Sciences Laboratory Pacific Northwest Research StationU.S.Forest ServiceCorvallisOR 97331USA Honorary Scientific Associate Australian National Botanic GardensCanberraACTAustralia School of Environmental and Rural Sciences University of New EnglandArmidaleNSW 2351Australia Vertebrate Pest Research Unit Biosecurity NSWNSW Department of Primary IndustriesUniversity of New EnglandPO Box U86Armidale 2351NSWAustralia Botany School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW 2351Australia

Symbiotic associations between mammals and fungi have been well documented and are widely regarded as vital to ecosystem functions around the *** between birds and fungi are also ecologically vital but have been far less thoroughly *** manuscript is the first to review a wide range of symbiotic associations between birds and *** compile the largest list to date of bird species reported to eat fungi(54 bird species in 27 families)and follow up with a discussion of these symbioses and suggestions for how future studies can determine the prevalence of associations between birds and *** review the importance of fungi for cavity-excavating birds and show that at least 30 bird species in three families form varying levels of associations with fungi for cavity *** also review the use of fungal rhizomorphs in nest construction and show that 176 bird species in 37 families use fungal material in their *** of these interactions have wide-reaching ecosystem implications,particularly in regard to fungal dispersal and biogeography,plant health,ecosystem function,bird nutrition/fitness and bird behaviour.

关键词： Mycorrhizae Fungal dispersal Ornithomycological associations Bird nutrition Mycophagy Rhizomorphs Cavity-nesting Tree hollows

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