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Analysis of a Tropical Warm Spring Microbiota Using 16S rRNA Metabarcoding

Advances in Microbiology 2020年第4期10卷 145-165页

作者： deborah Fasesan Karim Dawkins Roberto Ramirez Hadiza Rasheed-Jada Abiodun Onilude Oyekanmi Nash Nwadiuto Esiobu center for Genomics Research and Innovation National Biotechnology Development Agency Abuja Nigeria Department of Microbiology University of Ibadan Ibadan Nigeria Microbial Biotechnology Laboratory Florida Atlantic University Boca Raton USA

The Ikogosi Warm Spring is a unique ecological niche in Western Nigeria with an average temperature and pH of 38°c.a.d 5.8 respectively. It mixes with an adjacent cold spring (28°c & pH 7.6), about 100 meters from source, yielding a confluence body of water of 32°c.a.d pH 7.7. To explore the bacterial community structure of this uncommon environment and to scan for potentially useful bacteria, metagenomes extracted directly from five samples (source and mid-point of warm spring;source and midpoint of cold spring, and the confluence) were analyzed. Using the MiSeq Illumina next generation sequencing protocols, the V3-V4 region of the 16S rRNA gene pool was sequenced and analyzed by QIIME (Quantitative Insights into Microbial Ecology) and R software. At least 11% (47,446) of all the sequences were unknown to any of the databases employed. Bacterial diversity and abundance at the source of both springs were extremely low, accounting for less than 0.07% of the total sequence reads at the confluence, 100 m downstream. In contrast to the highly diversified mesophilic confluence community where 21 different phyla were identified, only 4 and 5 phyla were recovered from the source-point of the warm spring and cold spring respectively. The most prevalent phyla in all samples were members of the versatile Proteobacteria (35% - 50% relative abundance), and the hardy Firmicutes (33% - 40%). Operational taxonomic units (OTUs) obtained from all the samples averaged at 1414. Temperature and pH were equally significant predictors of genomic diversity and richness, with the warm and cold spring sources having less than 5 bacteria phyla. Exiguobacterium sp. (a potential plastic degrader) and other deep rooted bacteria were found in the warm spring while the cold spring outflow contained among others such as Rubrobacter sp. and chloroflexi sp. (which is close to the phylogenetic root of the domain Bacteria). Many taxonomically unresolved sequences could indicate the presence of potenti

关键词： Ikogosi Warm Springs Amplicon Metagenomics Next-Gen Sequencing QIIME Bacterial Diversity Source

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A Th2-score in the tumor microenvironment as a predictive biomarker of response to Bacillus calmette Guérin in patients with non-muscle invasive bladder carcinoma:A retrospective study

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Oncology Research 2023年第2期31卷 207-220页

作者： GUSTAVO MARTÍN VILLOLDO MARÍA TERESA POMBO MARIANA ARIS JOAQUÍN cHEMI PABLO MANDÓ SUPRIYA NAGARAJU JUAN cAMEAN ADRIÁN BURIONI deborah EGEA MORA AMAT JOSÉLEÓN MELLADO JOSÉMORDOH ALBERTO VILLARONGA MARÍA MARcELA BARRIO Urology Department Instituto Alexander FlemingCiudad Autónoma de Buenos Aires1426Argentina Immunohistochemistry Department Instituto Alexander FlemingCiudad Autónoma de Buenos Aires1426Argentina centro de Investigaciones Oncológicas Fundación Cáncer FUCACiudad Autónoma de Buenos Aires1426Argentina Urology Department MD Anderson Cancer CenterHoustonTX77030USA Pathology Department Instituto Alexander FlemingCiudad Autónoma de Buenos Aires1426Argentina

Intravesical Bacillus calmette Guerin(BcG)is the gold standard therapy for intermediate/high-risk nonmuscle invasive bladder cancer(NMIBc).However,the response rate is~60%,and 50%of non-responders will progress to muscle-invasive *** induces massive local infiltration of inflammatory cells(Th1)and ultimately cytotoxic tumor *** searched for predictive biomarker of BcG response by analyzing tumor-infiltrating lymphocyte(TIL)polarization in the tumor microenvironment(TME)in pre-treatment ***-treatment biopsies from patients with NMIBc who received adequate intravesical instillation of BcG(n=32)were evaluated retrospectively by *** polarization was assessed by quantifying the T-Bet+(Th1)and GATA-3+(Th2)lymphocyte ratio(G/T),and the density and degranulation of EPX+*** addition,PD-1/PD-L1 staining was *** results correlated with BcG *** most non-responders,Th1/Th2 markers were compared in pre-and post-BcG *** was 65.6%in the study *** responders had a higher G/T ratio and a greater number of degranulated EPX+*** combined into a Th2-score showed a significant assoc.a.ion with higher scores in responders(p=0.027).A Th2-score cut-off value>48.1 allowed discrimination of responders with 91%sensitivity but lower ***-free survival was significantly assoc.a.ed with the Th2-score(p=0.007).In post-BcG biopsies from recurring patients,TILs increased Th2-polarization,probably reflecting BcG failure to induce a pro-inflammatory status and,thus,a lack of ***-L1/PD-1 expression was not assoc.a.ed with the response to *** results support the hypothesis that a preexisting Th2-polarized TME predicts a better response to BcG,assuming a reversion to Th1 polarization and antitumor activity.

关键词： Non-muscle invasive bladder cancer BcG predictive biomarkers Lymphocyte polarization

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c.a.acterization of Fam20c expression in odontogenesis and osteogenesis using transgenic mice

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International Journal of Oral Science 2015年第2期7卷 89-94页

作者： Er-Xia Du Xiao-Fang Wang Wu-chen Yang deborah Kaback Siu-Pok Yee chun-Lin Qin Anne George Jian-Jun Hao Division of Orthodontics Department of Craniofacial SciencesSchool of Dental MedicineUniversity of Connecticut Department of Biomedical Sciences Texas A&M Health Science CenterBaylor College of Dentistry Department of Genetics and Developmental Biology University of Connecticut Health Center Department of Oral Biology University of Illinois

Our previous studies have demonstrated that Fam20 c promotes differentiation and mineralization of odontoblasts,ameloblasts,osteoblasts and osteocytes during tooth and bone *** of the Fam20 c gene inhibits bone and tooth growth by increasing fibroblast growth factor 23 in serum and causing hypophosphatemia in conditional knockout ***,control and regulation of the expression of Fam20 c.a.e still *** this study,we generated a transgenic reporter model which expresses green fluorescence protein（GFP） driven by the Fam20 c *** was used to insert a 16 kb fragment of the mouse Fam20 c gene（containing the 15 kb promoter and 1.1 kb of exon 1） intoa pBluescript SK vector with the topaz variant of GFP and a bovine growth hormone polyadenylation *** expression was subsequently evaluated by histomorphometry on cryosections from E14 to adult *** was evident in the bone and teeth as early as *** GFP signal was maintained stably in odontoblasts and osteoblasts until 4 weeks after *** expression of GFP was significantly reduced in teeth,alveolar bone and muscle by 8 weeks of *** also observed colocalization of the GFP signal with the Fam20 c.a.tibody in postnatal 1- and 7-day-old *** generation of Fam20c-GFP transgenic mice will provide a unique model for studying Fam20 c gene expression and the biological function of this gene during odontogenesis and osteogenesis.

关键词： transgenic promoter pBluescript osteogenesis teeth transgene reporter Fluorescence insert alveolar

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Amino acid quality indices of the leaves of clerodendrum volubile

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Journal of c.a.tal Life Medicine 2016年第4期4卷 320-323页

作者： Ochuko Lucky Erukainure Folashade Oluwayemisi Owolabi Temiloluwa Adebola Adesioye deborah Olabisi Akinyele Grace Ijeoma Okonrokwo Department of Food Technology Federal Institute of Industrial ResearchLagosNigeria Technology Transfer Division Federal Institute of Industrial ResearchOshodiNigeria

Objective:To evaluate the amino acid profile and quality indices of clerodendrum volubile(***)***:Dried leaves of *** were blended,defatted and subjected to amino acid analysis using the technicon sequential multi-sample amino acid *** amino acid quality indices which covers for chemical score,essential amino acid index,nutritional index,true digestibility,protein digestibility corrected amino acid score,and digestible indispensable amino acid score were evaluated using standard ***:Amino acid analysis revealed glutamic.a.id to have the highest concentration,with cysteine having the *** acid had the highest chemical score,this was followed by glycine,histidine and arginine,*** least scores were observed in serine and *** acid had the highest value for true digestibility and protein digestibility corrected amino acid score,with the least observed in *** indispensable amino acid score evaluation showed histidine to have the highest value for infants(birth to 6 months),threonine for children(6 months to 3 years),while isoleucine was observed to have the highest value for older children,adolescents and *** essential amino acid index value was less than 4,while nutritional index value was less than ***:These results indicated the leaves of *** as a potential source of amino acids in the human diet as portrayed by its amino acids profile and qualities.

关键词： Amino acids clerodendrum volubile Leafy vegetable Malnutrition

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Tree succession across a seasonally dry tropical forest and forest-savanna ecotone in northern Minas Gerais,Brazil

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Journal of Plant Ecology 2017年第5期10卷 859-868页

作者： Polyanne A.coelho Paola Ferreira Santos Eduardo de Paiva Paula deborah M.G.Apgaua Bruno Gini Madeira Gisele cristina de Oliveira Menino Yule Roberta Ferreira Nunes Rubens M.Santos David Y.P.Tng Department of Forest Sciences Federal University of LavrasC.P.3037CEP 37200-000LavrasMinas GeraisBrazil Department of General Biology State University of Montes ClarosC.P.126CEP 39401-089Montes ClarosMinas GeraisBrazil Instituto Federal Goiano C.P.66CEP 75901-970Rio VerdeGoiâniaBrazil centre for Tropical Environmental and Sustainability Sciences College of Marine and Environmental SciencesJames Cook University14-88 McGregor RdSmithfield QLD 4878CairnsQueenslandAustralia

Aims Understanding succession in tropical forest is an important aspect of vegetation science,but to date,successional processes in sea-sonally dry tropical forests(SDtFs)have received much less atten-tion than evergreen humid tropical *** aim to fill this knowledge *** We investigated vegetation succession in SDtF areas consisting of three different successional stages(early,intermediate,late),and a SDtF-savanna ecotone in the municipal district of Juramento,north of Minas Gerais State,*** twelve 400 m2 plots in each area,we compared vegetation parameters and structural variables(absolute density and basal area)and examined the floristic composition of the tree component to find gradients of *** Findings We found evidence of species turnover along a successional gradi-ent,with the intermediate stage showing the highest species rich-ness and *** was accompanied with a significant increase in the number of tree individuals and basal area from the early to intermediate successional ***,the intermediate and late SDtF successional stages were more similar in structure and *** ecotone was the most species rich and was similar to the intermediate SDtF and early successional stage in species richness and floristic composition *** results will have implications for guiding SDtF management and recovery programs.

关键词： c.a.inga floristic Similarity ecotone forest succession resilience.

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风险

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作者： (澳)狄波拉·勒普顿(deborah Lupton)

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Water Quality and Ecotoxicity Assessment in Surface Waters from cubatao River and Surroundings,Sao Paulo,Brazil

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Journal of Water Resource and Protection 2017年第12期9卷 1510-1525页

作者： Vanessa Silva Granadeiro Garc.a.Eduardo Toshio Domingues Matsushita Letíc.a.cristina Alves Mesquita deborah Ines Teixeira Favaro Sueli Ivone Borrely Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SPCentro de Tecnologia das RadiacoesCidade UniversitáriaSao PauloBrazil Instituto de Fisica da Universidade de Sao Paulo IF/USPButantaSao PauloBrazil Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SPLaboratório de Análises por Ativacao NeutronicaCidade UniversitáriaSao PauloBrazil

The monitoring of water bodies means the attempt of protecting vulnerable groups of organisms inhabiting streams and rivers. Industrial and domestic disc.a.ges may worsen the water quality and affect biological balance, structure and the functioning of the ecosystem. cubat?o city, is one of the largest industrial centers in Brazil and in Latin America, where the constant disc.a.ge of effluents into cubat?o River and its tributaries caused a degradation scenario in the hydrographic basin of the region. The objective of this study was to evaluate the acute and chronic effects of surface water from cubat?o River and two of its tributaries (Perequê and Pil?es) by ecotoxicological assays. In addition, physical chemical parameters were analyzed. ceriodaphnia dubia and Vibrio fischeri were exposed-organisms during the studied period. The study was conducted between 2010 and 2011 in four campaigns and nine sites along the basin of cubat?o River. The ecotoxicity was measured by Vibrio fischeri bioluminescence, Ec50 values ranging from 31.25% to 71.61%. In contrast, based on a bioequivalence t-test statistical analysis, the results obtained with ceriodaphnia dubia revealed no toxicity in the sampling sites. A critical analysis of raw data of luminescence was carried out showing higher values during the 2nd campaign. From the numbers obtained for physical-chemical parameters P5 was far the worst due to chlorides, hardness and conductivity. From the Pearson correlation analysis carried out with toxicity to V. fischeri and the physical chemical parameters, the dissolved oxygen in water resulted in a moderate positive correlation. Sediment contamination was also demonstrated in the region.

关键词： c.dubia cubatao River Ecotoxicity Assays V.fischeri Water Quality

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Impacts of Forest Harvest on Active carbon and Microbial Properties of a Volcanic.a.h cap Soil in Northern Idaho

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Open Journal of Soil Science 2015年第1期5卷 11-19页

作者： deborah S. Page-Dumroese Matt D. Busse Steven T. Overby Brian D. Gardner Joanne M. Tirocke USDA Forest Service Rocky Mountain Research Station Moscow USA USDA Forest Service Pacific Southwest Research Station Davis USA USDA Forest Service Rocky Mountain Research Station Flagstaff USA USDA Natural Resource conservation Service Moscow USA

Soil quality assessments are essential for determining impacts on belowground microbial community structure and function. We evaluated the suitability of active carbon (c), a rapid field test, as an indicator of soil biological quality in five paired forest stands (clear cut harvested 40 years prior and unharvested) growing on volcanic.a.h-cap soils in northern Idaho. Active c was compared with several traditional measures of soil microbial properties (microbial biomass, respiration, fungal hyphal biomass, bacterial number and biomass and PLFA community structure). Despite the significant differences in forest vegetation between paired stands, no differences in active c.a.d only a few significant differences in microbial properties were detected. Total bacteria (microscope counts) and PLFA signatures (gram positive bacteria, gram negative bacteria, actinomycetes) were significantly higher in the managed stands. Our results indicate that either mineral soil biological properties in managed stands were relatively unaffected at the time of harvest or some biological recovery occurred 40 years later. Additionally, volcanic.a.h-cap soils in moist ecosystems could be highly resilient to the impacts of harvest operations and therefore few significant biological c.a.ges could be detected.

关键词： Soil Quality Forest Soil Soil Monitoring Soil Organic Matter

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城市与城市文化

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作者： (澳)德波拉·史蒂文森(deborah Stevenson)

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Regulation of D-galacturonate metabolism in <i>caulobacter crescentus</i>by HumR, a LacI-family transcriptional repressor

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Advances in Bioscience and Biotechnology 2013年第10期4卷 63-74页

作者： Aaesha I. Sheikh deborah caswell cynthia Dick Spencer Gang Justin Jarrell Ankita Kohli Amanda Lieu Jared Lumpe Meghan Garrett Jennifer Parker c.a.g Stephens Biology Department Santa Clara University 500 El Camino Real Santa Clara USA

The oligotrophic freshwater bacterium caulobacter crescentus encodes a cluster of genes (cc_1487 to cc_1495) shown here to be necessary for metabolism of D-galacturonate, the primary constituent of pectin, a major plant polymer. Sequence analysis suggests that these genes encode a version of the bacterial hexuronate isomerase pathway. A conserved 14 bp sequence motif is assoc.a.ed with promoter regions of three operons within this cluster, and is conserved in homologous gene clusters in related alpha-Proteobacteria. Embedded in the hexuronate gene cluster is a gene (cc_1489) encoding a member of the LacI family of bacterial transcription factors. This gene product, designated here as HumR (hexuronate metabolism regulator), represses expression of the uxaA and uxac operon promoters by binding to the conserved operator sequence. Repression is relieved in the presence of galacturonate or, to a lesser extent, by glucuronate. Other genes potentially involved in pectin degradation and hexuronate transport are also under the control of HumR. Adoption of a LacI-type repressor to control hexuronate metabolism parallels the regulation of xylose, glucose, and maltose utilization in c. crescentus, but is distinct from the use of GntR-type repressors to control pectin and hexuronate utilization in gamma-Proteobacteria such as Escherichia coli.

关键词： caulobacter Galacturonate LacI

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