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Metagenomic Shotgun Sequencing Provides Prevalence Data for Pathogens, and Source-Tracking Indices Useful in Public Health Risk Assessment of Environmental Waters

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Journal of Geoscience and Environment Protection 2020年第6期8卷 115-129页

作者： Brian Mercer Karim dawkins Lisa Meday Nwadiuto Esiobu Microbial Biotech Lab Sanson Building Florida Atlantic University Boca Raton USA Environmental Resource Management Department Water Quality Seminole Tribe of Florida Holywood USA

State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Samples from a freshwater receiving pond (ABI-1002) and two upstream storm water ditches (ABI-1003) and (ABI-1004) yielded alarmingly high Fecal coliform MF densities of 220, >2000 and >2000 CFU/100ml respectively. The indicator, Enterococcus bacteria exceeded allowable limits in all but the equipment control (ABI-1001). Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources of each ditch. High levels of Shigella sp. (0 (ABI-1001), 4945 (ABI-1002), 55,008 (ABI-1003), and 2221 (ABI-1004) genomic reads/100ml) correlated with virulence genes and antibiotic resistance genes found in fecal samples for ABI1003 and not ABI1004. Traditional culture methods (TCM) showed possible fecal contamination in two of the four samples, and no contamination in the others. MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. Our data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiomes shifts by field managers and policy makers.

关键词： Metagenomic Shotgun Sequencing Water Quality Risk Assessment Indicator Bacteria Environmental Microbiomes

Risk Factors Associated with Non-Compliance with Respiratory Protection Programs among Firefighters

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Occupational Diseases and Environmental Medicine 2020年第4期8卷 135-148页

作者： Brandon dawkins Giffe T. Johnson Raymond D. Harbison Center for Environmental and Occupational Risk Analysis and Management College of Public Health University of South Florida Tampa FL USA

Non-compliance with respiratory protection programs among firefighters may put them at increased risk of injury and illness from occupational exposures during fire extinguishing activities. This research aims to characterize respiratory protection practices among Florida firefighters. This information will allow better understanding of factors that are associated with non-compliance with respiratory protection guidelines. A survey questionnaire was used to characterize Florida fire departments in this cross-sectional study. Four hundred and seventy-seven surveys were administered to Florida firefighters both in person and electronically to collect information regarding firefighter knowledge and participation in their respective respiratory protection programs during the past twelve months. Survey questions were developed from the model set by the National Fire Protection Association (NFPA) which provides standards and regulations regarding firefighter protections. Summary statistics regarding firefighter department size, coverage area, and firefighter employment type were produced. Multinomial logistic regression analysis was performed to evaluate factors that impact respiratory protection programs. The 477 respondents were 91% male with a mean age of 39 years old (range 21 - 65 years). The majority of respondents, 76%, were non-smokers, 21% former smokers, and 3% current smokers. In regard to ethnicity, respondents were 77% Caucasian, 13% Hispanic, 3% African American, and 4% other. Most respondents were career firefighters, 97%, with less than ten years of experience, 44%, working in a fire department with at least 21 firefighters, 98%. Most respondents, 80%, had a written respiratory program in place. The most cited reason for not having implemented a written respiratory protection program was lack of knowledge related to the program. Multinomial logistic regression analysis of departments with response areas of at least 250,000 square miles produced a statistica

关键词： Fire Department Fit Testing National Fire Protection Association Respirator Respiratory Protection

HLA-B与TNF基因间区的单体型特异性的多态现象

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免疫学杂志 1993年第2期9卷 76-84页

作者：吴雄文张文杰 RL dawkins 赵修竹同济医科大学中澳友谊补体实验室武汉430030 澳大利亚伊丽莎白二世医学中心皇家佩恩医院临床免疫科

本文应用基因组探针探试了HLA-B与TNF基因间区有无多态现象,在代表着21个MHC祖传单体型(AH)的50个无关细胞株中检出了此区明显的多态性:用X探针(R17A)检出了3个等位基因型;用V探针(R9A)检出了4个等位基因型;用Y探针(R20A)检出了7个等位... 详细信息

本文应用基因组探针探试了HLA-B与TNF基因间区有无多态现象,在代表着21个MHC祖传单体型(AH)的50个无关细胞株中检出了此区明显的多态性:用X探针(R17A)检出了3个等位基因型;用V探针(R9A)检出了4个等位基因型;用Y探针(R20A)检出了7个等位基因型。家系分析表明:Y、X及V等位基因与HLA单体型连锁。这些等位基因的一个显著特点是:相同的AH具有相同的Y、X、V等位基因型(即呈单体型性质)。在检出的15个不同的Y-X-V单体型中,有11个与特定的AH连锁(单体型特异性性质)。本项研究表明:包括HLA-B与TNF间区基因在内的整个MHC的AH是保守的。

关键词：人白细胞抗原肿瘤坏死因子基因型

A Systematic Review of Terrestrial Plant Invasion Mechanisms Mediated by Microbes and Restoration Implications

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American Journal of Plant Sciences 2022年第2期13卷 205-222页

作者： K. dawkins J. Mendonca O. Sutherland N. Esiobu Microbial Biotech Lab Florida Atlantic University Boca Raton USA

Terrestrial invasive plant species continue to wreak havoc on a global economic and ecological scale. With the advent of climate change and pending future catastrophes, the spread of resilient invasive plants will only increase exponentially. Here, the search continues for a better understanding of the below-ground microbially driven mechanisms involved in plant invasion where other above-ground mechanisms have been exhausted. Microbes govern the world around us and interact with every living and non-living facet of the world. To reinforce the important underpinnings of the role of microorganisms in plant invasion, a systematic review of recently published articles was undertaken. Using the ScienceDirect database, five (5) search queries were used to generate 1221 research articles. After a two-step reduction was made based on relevance of the articles, a final total of 59 articles were retrieved. An additional 18 relevant articles were also assessed through the PubMed database for analysis to account for other invasive plants. Thirty-seven (37) invasive species were investigated where soil physiochemical and microbial community structure changes were most prevalent (32% & 39% respectively) while enhanced mutualism, allelopathy and pathogen accumulation were reported less (16%, 10% & 3% respectively). In all invasive species assessed, the impact on plant invasion and inability of the native plants to compete was due to specific microbial associations of the invasive plant or disruption of the soil microbial community. This microbial community shift coincided with changes in physiochemical properties of the soil and the subsequent negative soil feedback for native plants. There is still an expanding potential for the use of biocontrol agents to aid restoration once the underpinnings of biotic resistance and enemy release are understood in a microbial and physiochemical context. The active and functional microbial community structure of the invasive plant rhizosphere

关键词： Invasive Plant Biotic Resistance Biocontrol Agents Enemy Release Restoration

Prevalence and Disinfection of Bacteria Associated with Various Types of Wristbands

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Advances in Infectious Diseases 2023年第2期13卷 193-209页

作者： Joseph Mendonca Belen Wertheimer Daynalee Dixon Bodhi Stone Karim dawkins Miranda Christian Nwadiuto Esiobu Microbial Biotechnology Laboratory Department of Biological Sciences Florida Atlantic University Boca Raton FL USA West Palm Beach TV (WPTV) West Palm Beach FL USA

The potential role of personal items in the transmission of pathogens is poorly understood. In this study, we cultured bacteria of public health importance found on wristbands, determined whether there is a correlation between wristband material and prevalence, and tested three household disinfectants for efficacy in reducing bacteria on wristbands made of plastic, rubber, metal, and cloth, using standard microbiological assays. Total cultivable bacteria, Staphylococci, Enterobacteria (Escherichia coli), and Pseudomonas on 20 smartwatch wristbands were cultured from randomly recruited subjects. Nearly all wristbands (95%) were contaminated, with the highest average numbers of 3.46E+4 cfu/cm2 and 1.52E+4 cfu/cm2 on rubber and plastic bands respectively. Metallic gold and silver wristbands had zero to 18 cfu/cm2. While the high prevalence of Staphylococcus spp (85% of wristbands)—skin microbiota;was not unexpected, the occurrence of Pseudomonas spp (30%), and enteric bacteria (60%), even at relatively low numbers is of public health significance. Bacterial load on individual subjects varied remarkably with males and females harboring average total bacteria of 4.045 and 3.42 log10cfu/cm2 of wristband, respectively. The most important predictor of wristband bacteria load was the texture of wristband material and activity (hygiene) of the subject at sampling time. Potential pathogens—Staphylococcus aureus (8143 cfu/cm2) and Pseudomonas spp. (1126 cfu/cm2) were most abundant on cloth and rubber wristbands, respectively, while the presence of the E. coli group was associated with animal handling activity by a veterinarian. Lysol Disinfectant Spray and 70% Ethanol were highly effective regardless of wristband material with >99.99% kill rate and a log cfu/cm2 reduction of 3 - 4.0 and 3 - 4.5 respectively within 30 seconds. Apple Cider Vinegar (ACV) was not as potent. Only 2 - 3.5 log cfu/

关键词： Apple Cider Vinegar Disinfectants Escherichia coli Lysol Pseudomonas aeruginosa Public Health Staphylococcus aureus Wristbands

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周而复始

科技英语学习 2009年第4期 20-22页

作者： Richard dawkins 左连凯

最近，我在南非克鲁格尔国家公园看见一条沿道路形成的湿线，歪歪扭扭但可以明显看出某种复杂却有周期的图案。我的向导也是动物学专家，告诉我那是发情期公象留下的尿迹。公象到了这种非常时期（也许是南半球动物区系类似大象的动物在... 详细信息

最近，我在南非克鲁格尔国家公园看见一条沿道路形成的湿线，歪歪扭扭但可以明显看出某种复杂却有周期的图案。我的向导也是动物学专家，告诉我那是发情期公象留下的尿迹。公象到了这种非常时期（也许是南半球动物区系类似大象的动物在“远足”的时候），会不同程度地持续尿遗失禁，显然是为了留下味迹。这条沿路两边摆动的尿迹波形曲线可能是长长的阴茎随大象四足踩着笨重的脚步周而复始却不规律地移动而摇摆形成的（事实上阴茎不是地道的牛顿摆；假若如此，这条曲线应是正弦波）。

关键词：周而复动物学国家公园克鲁格曲线大象

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自私的基因

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

2019年

作者： (英)理查德·道金斯(Richard dawkins)

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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 and 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 and 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

中国湖北汉族随机正常人群HLA扩展单体型的检测

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科学通报 1992年第21期37卷 2001-2003页

作者：陈芳琦吴锋郭淮莲余中清 R.L.dawkins 赵修竹同济医科大学中澳友谊补体实验室同济医科大学附属同济医院神经内科武汉430030 同济医科大学附属协和医院武汉430030 澳大利亚皇家佩斯医院临床免疫室

已发现在多个人种中HLA-Ⅲ(complotype,补体型即由补体C2,Bf,C4A,C4B基因组成的单体型)与HLA-Ⅰ、Ⅱ类基因间存在连锁不平衡现象。Alper等将补体型及与其连锁不平衡的HLA-B、DR座位等位基因组成的单体型称HLA扩展单体型(HLA extended ha... 详细信息

已发现在多个人种中HLA-Ⅲ(complotype,补体型即由补体C2,Bf,C4A,C4B基因组成的单体型)与HLA-Ⅰ、Ⅱ类基因间存在连锁不平衡现象。Alper等将补体型及与其连锁不平衡的HLA-B、DR座位等位基因组成的单体型称HLA扩展单体型(HLA extended haplotype,HLA-EH),而补体型及与其不存在连锁不平衡的HLA-B、DR座位等位基因组成的单体型称HLA非扩展单体型(HLA nonextended haplotype)。

关键词： HLA 补体型扩展单体型