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Bacterial Consortium in the Biodegradation of Polycyclic Aromatic Hydrocarbons-Phenanthrene

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Bacterial Consortium in the Biodegradation of Polycyclic Aro...

作者： john farmer 东北师范大学

学位级别：硕士

Many aromatic hydrocarbons are known to be toxic and carcinogenic to humans and their contamination of soils and water bodies is of great environmental concern. Hence microbial degradation of these hydrocarbons to less toxic compounds has become a vital tool in making the environment safe for humans as well as other life forms.In this study, industrial waste water samples were randomly collected from three different locations in Shuangyang local brewery. These samples were designated by the letters: HY, YY and WS. The waste water samples were used to isolate bacterium species using LB liquid medium. These bacterium cultures were transferred to a fresh media containing a concentration of Phenanthrene. The pH and Optical Density (OD) readings were measured and recorded on daily basis for a period of one week and this was the first transfer. This was done in other to ascertain the biodegradation capability of the bacterium strains in the Phenanthrene medium and the pH at which these strains degrade the pollutant- Phenanthrene. However, this process was repeated for another four consecutive weeks (five transfers). Meanwhile, from the fifth transfer the aliquot culture MSM-PHE medium was again transferred to a fresh liquid LB media and allowed to grow overnight. The bacterial cultures were again transferred to a solid MSM agar medium to obtain single colonies of bacterial strains. These cultures were transferred to a liquid MSM medium for 24 hrs and transferred again to the solid medium. This process was repeated for another three weeks to isolate pure clones. Pure clones were isolated with distinct colors and morphologies. The genetic DNA of these pure colonies was extracted, purified and two primers were used for the PCR analysis and the isolates were identified by blast analysis. These single isolates were later inoculated in a liquid MSM-PHE culture medium and their densities (biomass) were measured and recorded for a week. The isolates were also inoculated on

关键词： biodegradation Phenanthrene waste water pH Optical Density (OD) pure clones genetic DNA biosurfactant emulsion clear zones

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the singlecell level

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Molecular Plant 2021年第3期14卷 372-383页

作者： Andrew farmer Sandra Thibivilliers Kook Hui Ryu john Schiefelbein Marc Libault National Center for genome Resources Santa FeNM 87505USA Department of Agronomy and Horticulture Center for Plant Science InnovationUniversity of Nebraska-LincolnBeadle CenterLincolnNE 68503USA Department of Molecular Cellularand Developmental BiologyUniversity of MichiganAnn ArborMI 48109USA

Similar to other complex organisms,plants consist of diverse and specialized cell *** gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional *** a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis *** comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific ***,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell *** to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their *** reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin *** data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

关键词： single-cell RNA-seq single-nucleus ATAC-seq Arabidopsis root

Probiotic metabolites from Bacillus coagulans ganedenBC30^(TM) support maturation of antigen-presenting cells in vitro

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World Journal of gastroenterology 2012年第16期18卷 1875-1883页

作者： Kathleen F Benson Kimberlee A Redman Steve g Carter David Keller Sean farmer john R Endres gitte S Jensen NIS Labs 1437 EsplanadeKlamath FallsOR 97601United States ganeden Biotech 5915 Landerbrook DriveMayfield HeightsOH 44124United States AIBMR Life Sciences 4117 S MeridianPuyallupWA 98373United States

AIM:To study the effects of probiotic metabolites on maturation stage of antigen-presenting immune ***:ganeden Bacillus coagulans 30(gBC30) bacterial cultures in log phase were used to isolate the secreted metabolite(MET) fraction.A second fraction was made to generate a crude cell-wall-enriched fraction,by centrifugation and lysis,followed by washing.A preparation of MET was subjected to size exclusion centrifugation,generating three fractions:gen-presenting mononuclear *** maturation status of mononuclear phagocytes was evaluated by staining with monoclonal antibodies towards CD14,CD16,CD80 and CD86 and analyzed by flow ***:Treatment of PBMC with MET supported maturation of mononuclear phagocytes toward both macrophage and dendritic cell *** biological activity unique to the metabolites included a reduction of CD14+ CD16+ pro-inflammatory cells,and this property was associated with the high molecular weight metabolite *** were also seen for the dendritic cell maturation markers CD80 and *** CD14dim cells,an increase in both CD80 and CD86 expression was seen,in contrast to a selective increase in CD86 expression on CD14bright *** co-expression of CD80 and CD86 indicates effective antigen presentation to T cells and support of T helper cell *** selective expression of CD86 in the absence of CD80 points to a role in generating T regulatory ***:The data show that a primary mechanism of action of gBC30 metabolites involves support of more mature phenotypes of antigen-presenting cells,important for immunological decision-making.

关键词： Mononuclear phagocytes Dendritic cell maturation Co-stimulatory molecules Antigen-presentation Probiotics Metabolites

双参数混合正则化方法及在电导率反演成像中的应用

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地球物理学报 2011年第8期54卷 2154-2159页

作者：王文娟 Chris farmer john Ockendon 冯宝宾曹俊兴谭永基复旦大学数学科学学院上海200433 成都理工大学数学地质四川省高校重点实验室成都610059 牛津大学应用数学计算中心成都理工大学油气藏地质及开发工程国家重点实验室地球探测与信息技术教育部重点实验室成都610059

通过引入带有二阶正则算子的正则化项,建立了一种双参数混合正则化方法.为确定最佳正则化参数,这里主要应用L-曲线法、偏差原理和广义交叉校验准则的优化组合来确定.首先对理论模型进行了数值模拟,通过与截断奇异值分解法、共轭梯度法... 详细信息

通过引入带有二阶正则算子的正则化项,建立了一种双参数混合正则化方法.为确定最佳正则化参数,这里主要应用L-曲线法、偏差原理和广义交叉校验准则的优化组合来确定.首先对理论模型进行了数值模拟,通过与截断奇异值分解法、共轭梯度法及标准Tikhonov正则化法的结果比较,表明该方法不仅精度高,而且对于数据的随机扰动具有稳定性.然后将此方法应用于对电导率反演成像的计算中,得到的电导率反演成像精确细致可靠,也符合实际情况.这表明该方法求解地球物理反问题时,在增强反演的稳定性及减少多解性的同时,还能进一步提高反演计算速度.

关键词：病态方程电导率成像地球物理反演双参数混合正则化

Development of a facility for analysis of natural ^(32)Si

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Chinese Journal Of geochemistry 2006年第B8期25卷 199-200页

作者： Angus B. MacKenzie David C.W. Sanderson Joseph Melone john g. farmer Christoph Schnabel Helfrid Rossiter Scottish Universities Environmental Research Centre East Kilbride G75 0QF Scotland UK School of geosciences University of Edinburgh Edinburgh EH9 3JJ Scotland UK

Is environmental antimony a potential health problem?

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Chinese Journal Of geochemistry 2006年第B8期25卷 68-69页

作者： john g. farmer Joanna M. Cloy Margaret C. graham Angus B. MacKenzie gordon T. Cook School of geosciences University of Edinburgh Edinburgh Scotland UK Scottish Universities Environmental Research Centre East Kilbride Scotland UK

Multiple endocrine neoplasia 2B: Differential increase in enteric nerve subgroups in muscle and mucosa

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World Journal of gastrointestinal Pathophysiology 2017年第3期8卷 142-149页

作者： john M Hutson Pam J farmer Cristal J Peck Chung W Chow Bridget R Southwell Surgical Research/gastrointestinal Motility Laboratory Murdoch Children’s Research Institute Departments of Urology and Anatomical Pathology The Royal Children’s HospitalParkville Victoria Department of Paediatrics University of Melbourne

Multiple endocrine neoplasia 2B(MEN2B) is a rare syndrome caused by an activating mutation of the RET gene, leading to enteric gangliomatosis. This child presented with constipation at 1-mo old, was diagnosed with MEN2 B by rectal biopsy at 4 mo, had thyroidectomy at 9 mo and a colectomy at 4 years. We studied the extent of neuronal and nerve fibre proliferation and which classes of enteric nerves are affected by examining the colon with multiple neuronal antibodies. Resected transverse colon was fixed, frozen, sectioned and processed for fluorescence immunohistochemistry labelling with antibodies against TUJ1, Hu, ChAT, NOS, VIP, SP and CgRP and cKit. Control transverse colon was from the normal margin of Hirschsprung(HSCR) colon(4-year-old) and a child with familial adenomatous polyposis(FAP, 12 year). Myenteric ganglia were increased in size to as wide as the circular muscle. There was a large increase in nerve cells and nerve fibres. ChAT-, NOS-, VIP-and SP-immunoreactive nerve fibres all increased in the myenteric ganglia. NOS-IR nerves preferentially increased in the muscle, while VIP and SP increased in submucosal ganglia and mucosal nerve fibres. The density of ICC was normal. RET overactivation in MEN2B lead to a large increase in intrinsic nerve fibres in the myenteric and submucosal ganglia, with a relative increase in NOS-IR nerve fibres in the circular muscle and VIP and SP in the submucosal ganglia and mucosa. The changes were associated with severe constipation resulting in colectomy at 4 years.

关键词： Enteric nervous system RET Neuroganglioma MEN2B

DNA Barcoding of Insects and Its Direct Application for Plant Protection

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Open Journal of Applied Sciences 2024年第3期14卷 676-686页

作者： Peter Quandahor Iddrisu Yahaya Francis Kusi Issah Sugri Julius Yirzagla Abdul Karim Alhassan Jerry A. Nboyine george Y. Mahama godwin Opoku Mohammed Mujitaba Dawuda Asieku Yahaya Theophilus Kwabla Tengey Rofela Combey john Abraham CSIR-Savanna Agricultural Research Institute Tamale Ghana Faculty of Agriculture Food and Consumer Science University for Development Studies Tamale Ghan Department of Conservational Biology and Entomology School of Biological Sciences University of Cape Coast Ghana

The introduction of invasive insect pests across national borders has become a major concern in crop production. Accordingly, national plant protection organizations are challenge to reinforce their monitoring strategies, which are hampered by the weight and size of inspection equipment, as well as the taxonomic extensiveness of interrupted species. Moreover, some insect pests that impede farmer productivity and profitability are difficult for researchers to address on time due to a lack of appropriate plant protection measures. farmers’ reliance on synthetic pesticides and biocontrol agents has resulted in major economic and environmental ramifications. DNA barcoding is a novel technology that has the potential to improve Integrated Pest Management decision-making, which is dependent on the ability to correctly identify pest and beneficial organisms. This is due to some natural traits such as phenology or pesticide susceptibility browbeaten by IPM strategies to avert pest establishment. Specifically, Deoxyribonucleic acid (DNA) sequence information was applied effectively for the identification of some micro-organisms. This technology, DNA barcoding, allows for the identification of insect species by using short, standardized gene sequences. DNA barcoding is basically based on repeatable and accessible technique that allows for the mechanisation or automation of species discrimination. This technique bridges the taxonomic bio-security gap and meets the International Plant Protection Convention diagnostic standards for insect identification. This review therefore discusses DNA barcoding as a technique for insect pests’ identification and its potential application for crop protection.

关键词： DNA Barcoding Integrated Pest Management Taxonomy Biosecurity Crop Protection

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生物处理去除汽油残留物

世界环境 1992年第2期 27-29页

作者： Kevin g. Robinson KimyoungKim WilliamS.farmer john T. Novak 严博君 an assistant professor in civil engineering at the University of Tennessee-Knoxville. M. S. graduates in civil engineering at Virginia Polytechnic Institute and State University. a professor of civil engineering and associate director of the Center for Environmental and Hazardous Materials Studies at VPI & Su.

在过去几年里,地下水污染因其对饮用水源潜在的影响已成为人们关注的一个焦点。美国50%以上的人口把地下水作为饮用水源,地下水的抽取总量在今后预计将会增长。地下水中人为化学物的存在代表了一个严重的公共健康问题。美国环保局已认... 详细信息

在过去几年里,地下水污染因其对饮用水源潜在的影响已成为人们关注的一个焦点。美国50%以上的人口把地下水作为饮用水源,地下水的抽取总量在今后预计将会增长。地下水中人为化学物的存在代表了一个严重的公共健康问题。美国环保局已认定65类化学化合物为危险物质,100多种有机化合物为主要污染物。在40个州的饮用水井中已发现至少有33种有毒有机化学品,这个数字估计会随采集的样品数量而不断增加。

关键词：生物处理地下水污染生物降解有机化学品样品数量公共健康问题危险物质有机物降解活性污泥起始浓度