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用生物信息学和系统基因组学作为解决热带树木进化中复杂问题的工具

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用生物信息学和系统基因组学作为解决热带树木进化中复杂问题的工...

作者： Armijos Carrion Angelo damian 广西大学

学位级别：硕士

叶绿体序列由于其高度保守的性质,已被广泛用作系统发育研究的有用工具。使用二代测序方法(NgS)可以容易地从植物中获得完整的叶绿体基因组,为物种划分和系统学提供了宝贵的数据。此外,这些基因组已经广泛用于农业、进化和生态研究、食... 详细信息

叶绿体序列由于其高度保守的性质,已被广泛用作系统发育研究的有用工具。使用二代测序方法(NgS)可以容易地从植物中获得完整的叶绿体基因组,为物种划分和系统学提供了宝贵的数据。此外,这些基因组已经广泛用于农业、进化和生态研究、食品检测等,并且目前它们是遗传序列数据库中保存最多的真核基因组,例如日本DNA数据库(国家遗传学研究所)、EMBL(欧洲生物信息学研究所)和基因银行(国家生物技术信息中心)。考虑到无论是通过NgS法还是在线平台获取这些遗传资源的高度可行性,如今许多高通量测序方法可用来揭示不同生物基因组的详细特征,从而进一步探索适用不同进化研究的的生物信息学流程。然而,许多用以重建质体序列的测序方法和生物信息学方法的快速发展,可能导致在选择最有效的方法和设置的混乱。对完整质体基因组进行大规模测序的趋势,凸显对标准化和有充分记录的生物信息学工作流的需求。对允许精确基因组序列再现性的高效工作流程的要求尤其明显。此外,大多数已发表的研究仍然没有提供必要的细节来复制他们的生物信息学分析,并且经常仅仅列出所使用的软件工具的名称和版本号。另一方面,随着NgS技术提供的基因组资源的快速增加,高效和标准化的元数据管理方法对于生物数据的后处理阶段变得越来越重要。特别是在使用环状叶绿体基因组数据的基于细胞器的研究中,主要结构区域的随机组合(顺序和方向)是对无论大小分类单元形成用于系统发育重建的“现成对齐”数据集的能力的主要限制。此外,在目前的实际操作中,在基因组中可帮助用来对比其他编码区的最多变的区域常被删掉。尽管如此,目前还没有一款软件可以通过对主要的质体区域的检测、组织和定位达到这种程度,这使得固化过程既耗时又容易出错。为了解决这两个主要问题,本论文将集中在四个主要章节:第一章介绍叶绿体基因组测序、组装、注释、比对、系统进化树推断中最常用的方法和工作流程,以及对软件选择和精确设置高度敏感的过程。在NgS驱动的基因组研究中,生物信息学工作流程的标准化和可重复性举足轻重。这是由以前几个植物系统发育学研究以及影响下游分析进而影响最终结果的软件工具获得的经验。第二章描述利用最新系统发育策略对孔药楠(Sinoporahongkongensis)叶绿体基因组重新组装的实际应用,主要由分子实验、生物信息学工作流程以及质体基因组测序和表征的结果三个部分组成。其中,组装和注释这个质体基因组的生物信息学步骤做详细描述。在组装和注释这个基因组后,将其与樟科和其他科的代表性物种进行比较。在此,我们比对18个物种的所有叶绿体DNA(cp DNA)区域然后进行一个简单的系统进化树推理,作为整个工作流完整性的概念证明。第三章介绍一个方便快捷且容易使用的软件---ECu ADOR。这个软件基于Perl脚本算法,专门用于自动检测和重组从任何来源(NgS,桑格测序或组装输出)获得的质体序列。ECu ADOR使用滑动窗口方法检测原始序列中的长重复序列,然后识别反向重复序列(IRs)(即使在人为或测序错误的情况下),并自动将序列重排为广泛使用的LSC-IRb-SSC-IRa顺序。这有助于快速的后续编辑步骤,例如基因组比对、可变区检测、单核苷酸多态性(SNP)检测和系统发育分析。ECu ADOR对被子植物不同科的161个质体测试成功。ECu ADOR首先为每个数据集鉴别并重新排序中心区域(LSC-IRb-SSC-IRa),然后为叶绿体序列进行新注释。该过程耗时不到20分钟,最大内存需求为150 MB,准确率超过99%。ECu ADOR是唯一一个从头开始的一步识别和重新排序工具,方便来自NgS数据的核外基因组的后续处理分析。这个程序可在https://***/Biodiv genomic/ECu ADOR/下载。第四章为本研究最重要的结果的总结,强调主要目的、新颖性、发现和未来方向。此研究试图涵盖当今现代系统发育学所面临问题的广阔领域,并总结由于分子和基因组数据的出现,系统发育学领域正在经历的一些最紧迫的挑战。我们强调自动化数据挖掘方法仍然不完整且会随着时间的推移而变化,而这些方法可能会产生错误的数据和结果。这种错误可能会降低系统发育的准确性,并且在缺乏专业知识的情况下无法被发现。

关键词：生物信息学自动化工作流系统发育学二代测序质体完整叶绿体基因组

MicroRNA profile in neosquamous esophageal mucosa following ablation of Barrett's esophagus

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World Journal of gastroenterology 2017年第30期23卷 5508-5518页

作者： Loveena Sreedharan george C Mayne David I Watson Timothy Bright Reginald V Lord Alfiya Ansar Tingting Wang Jakob Kist David StJ Astill damian J Hussey Department of Surgery Flinders Medical Centre Flinders University St Vincent’s Centre for Applied Medical Research Department of Anatomical Pathology Flinders Medical Centre

AIM To investigate the micro RNA expression profile in esophageal neosquamous epithelium from patients who had undergone ablation of Barrett's *** High throughput screening using Taq Man~ Array Human Micro RNA quantitative PCR was used to determine expression levels of 754 micro RNAs in distal esophageal mucosa(1 cm above the gastro-esophageal junction) from 16 patients who had undergone ablation of non-dysplastic Barrett's esophagus using argon plasma coagulation vs pretreatment mucosa, posttreatment proximal normal non-treated esophageal mucosa, and esophageal mucosal biopsies from 10 controls without Barrett's esophagus. Biopsies of squamous mucosa were also taken from 5 cm above the pre-ablation squamo-columnar junction. Predicted m RNA target pathway analysis was used to investigate the functional involvement of differentially expressed micro *** Forty-four micro RNAs were differentially expressed between control squamous mucosa vs post-ablation neosquamous mucosa. Nineteen micro RNAs were differentially expressed between post-ablation neosquamous and post-ablation squamous mucosa obtained from the more proximal non-treated esophageal segment. Twelve microRNAs were differentially expressed in both neosquamous vs matched proximal squamous mucosa and neosquamous vs squamous mucosa from healthy patients. Nine micro RNAs(mi R-424-5p, mi R-127-3p, mi R-98-5p, mi R-187-3p, mi R-495-3p, mi R-34c-5p, mi R-223-5p, mi R-539-5p, mi R-376a-3p, mi R-409-3p) were expressed at higher levels in post-ablation neosquamous mucosa than in matched proximal squamous and healthy squamous mucosa. These micro RNAs were also more highly expressed in Barrett's esophagus mucosa than matched proximal squamous and squamous mucosa from controls. Target prediction and pathway analysis suggests that these micro RNAs may be involved in the regulation of cell survival signalling pathways. Three micro RNAs(mi R-187-3p, mi R-135b-5p and mi R-31-5p) were expressed at higher

关键词： Neosquamous Barretts 食管脱离

The descriptive epidemiology of sitting in Chilean adults: Results from the National Health Survey 2009-2010

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Journal of Sport and Health Science 2019年第1期8卷 32-38页

作者： Nicolas Aguilar-Farias Pia Martino-Fuentealba ANDrea Cortinez-O'Ryan damian Chandia-Poblete Carlos A.Celis-Morales Paz Bahamondes Jaime Leppe Zamora Wendy J.Brown Department of Physical Education Sports and Recreation Universidad de La Frontera BHF glasgow Cardiovascular Research Centre Institute of Cardiovascular and Medical Science University of Glasgow School of Physiotherapy Universidad del Desarrollo School of Human Movement and Nutrition Sciences The University of Queensland

Background: Although evidence on the health effects of sedentary behavior(SB) has grown systematically in recent years, few developing countries have reported population levels of SB, especially in South America. Our objective was to describe time spent sitting in a representative sample from Chile categorized by age, gender, educational level, and body mass index(BMI).Methods: A national health survey was conducted in Chile in a nationally representative sample(n = 5411) in 2009-2010. Sitting time(ST) was measured with the global Physical Activity Questionnaire Version ***: Data were from 5031 participants(43.26±0.41 years, mean±SE; 40.3% male). Overall, there were no gender differences in mean ST(men: 158.10±5.80 min/day, women 143.45±4.77 min/day; p = 0.05). ST was lower in those who lived in rural areas compared with urban areas(99.4 min/day vs. 160.0 min/day; p = 0.001). ST increased significantly with increasing BMI, but only in men(p = 0.009), and was positively related to years of education in both men and women(p gs were different from those reported in other countries and contexts, reinforcing the need for international surveillance and monitoring over time to inform policy makers. Differences in ST across different groups emphasize the need to develop tailored messages and interventions for reducing ST in different population subgroups.

关键词： Ageing Health behavior Health inequalities Lying Preventive medicine Reclining Screen time Surveillance

Modeling of the Absorption of the Electromagnetic Wave Energy in the Human Head Induced by Cell Phone

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Journal of Applied Mathematics and Physics 2014年第12期2卷 1079-1084页

作者： damian goik Marcin Sieniek Piotr gurgul Maciej Paszyński Department of Computer Science AGH University of Science and Technology Kraków Poland

In this paper, we present the Projection Based Interpolation (PBI) technique for construction of continuous approximation of MRI scan data of the human head. We utilize the result of the PBI algorithm to perform three-dimensional (3D) Finite Element Method (FEM) simulations of the heating of the human head induced by cell phone. In particular, we utilize the Pennes equation to describe the bioheat transfer with the right hand side representing the heat generated by cell phone. We utilize our own non-stationary time dependent multi-thread parallel direct solver for the solution of this computational problem. From our numerical results it follows that 15 minutes (1000 seconds) exposure to the cell phone radiation implies up to 2 degrees Celsius increase of the temperature of the brain in the range close to the cell phone.

关键词： Finite Element Method Projection Based Interpolation Pennes Equation Heating of the Human Head

A kinetic model for horizontal transfer and bacterial antibiotic resistance

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International Journal of Biomathematics 2017年第4期10卷 131-151页

作者： damian A. Knopoff Juan M. Sanchez Sanso Centro de Investigacion y Estudios de Matemdtica CONICET -- FaMAF Universidad Nacional de Cordoba Medina AUende s/n Cordoba 5000 Argentina Department of general Surgery Hospital Misericordia Nuevo Siglo Cordoba 5000 Argentina

This paper presents a mathematical model for bacterial growth, mutations, horizontal transfer and development of antibiotic resistance. The model is based on the so-called kinetic theory for active particles that is able to capture the main complexity features of the system. Bacterial and immune cells are viewed as active particles whose microscopic state is described by a scalar variable. Particles interact among them and the temporal evolution of the system is described by a generalized distribution function over the microscopic state. The model is derived and tested in a couple of case studies in order to confirm its ability to describe one of the most fundamental problems of modern medicine, namely bacterial resistance to antibiotics.

关键词： Kinetic theory active particles antibiotic resistance horizontal gene transfer

A brief history of the Rheic Ocean

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geoscience Frontiers 2012年第2期3卷 125-135页

作者： R.damian Nance gabriel gutirrez-Alonso J.Duncan Keppie Ulf Linnemann J.Brendan Murphy Cecilio Quesada Rob A.Strachan Nigel H.Woodcock Department of geological Sciences 316 Clippinger Laboratories Ohio University Departamento de geología Universidad de Salamanca 33708 Salamanca Departamento de geología Regional Instituto de geología Universidad Nacional Autónoma de Mxico Senckenberg Naturhistorische Sammlungen Dresden Museum fur Mineralogie und geologie Konigsbrucker Landstra βe 159D-01109 DresdenGermany Department of Earth Sciences St.Francis Xavier University Instituto geolóogico y Minero de Espaa Ríos Rosas 2328003 MadridSpain School of Earth & Environmental Sciences University of Portsmouth Department of Earth Sciences University of Cambridge Downing StreetCambridge CB2 3EQUK

The Rheic Ocean was one of the most important oceans of the Paleozoic Era. It lay between Laurentia and gondwana from the Early Ordovician and closed to produce the vast Ouachita- Alleghanian-Variscan orogen during the assembly of Pangea. Rifting began in the Cambrian as a continua- tion of Neoproterozoic orogenic activity and the ocean opened in the Early Ordovician with the separation of several Neoproterozoic arc terranes from the continental margin of northern gondwana along the line of a former suture. The rapid rate of ocean opening suggests it was driven by slab pull in the outboard Iapetus Ocean. The ocean reached its greatest width with the closure of Iapetus and the accretion of the peri- gondwanan arc terranes to Laurentia in the Silurian. Ocean closure began in the Devonian and continued through the Mississippian as gondwana sutured to Laurussia to form Pangea. The ocean consequently plays a dominant role in the Appalachian-Ouachita orogeny of North America, in the basement geology of southern Europe, and in the Paleozoic sedimentary, structural and tectonothermal record from Middle America to the Middle East. Its closure brought the Paleozoic Era to an end.

关键词： Rheic Ocean Variscan-Alleghanian-Ouachita orogen Pangea North America Europe

β-glucan Fiber from Spent Brewer’s Yeast Reduces Early Atherosclerosis greater Than Psyllium in Hypercholesterolemic Syrian golden Hamsters

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Food and Nutrition Sciences 2013年第5期4卷 566-571页

作者： Thomas A. Wilson damian A. Barbato Robert J. Nicolosi Department of Clinical Laboratory and Nutritional Sciences Center for Health and Disease Research University of Massachusetts Lowell Lowell USA Department of Clinical Laboratory and Nutritional Sciences Center for Health and Disease Research University of Massachusetts Lowell Lowell USA.

β-glucans, mostly from oats, have been shown to reduce blood concentrations of total and LDL-cholesterol in animals and humans. After processing, spent brewer’s yeast, a by-product of the fermentation process, contains 85% - 90% β-glucans. The purpose of this study was to evaluate the effect of yeast-derived β-glucan fiber on plasma lipids and early atherosclerosis development in hamsters consuming a semi-purified hypercholesterolemic diet (HCD). Animals were fed either the HCD or the HCD containing psyllium or β-glucan fiber from yeast for 12 weeks. Both the psyllium and β-glucan fiber from yeast showed significant decreases in plasma total cholesterol, non-HDL-C, triacylglycerol, and aortic fatty streak area when compared to the HCD. Also, the β-glucan fiber from yeast had significantly less aortic fatty streak area compared to the psyllium diet. Findings from this study show that while both β-glucan fiber from yeast and psyllium produced similar reductions in plasma lipid and lipoprotein concentrations, the β-glucan fiber from yeast prevented the development early atherosclerosis better than psyllium in the hamsters.

关键词： β-glucan Fiber Plasma Cholesterol Aortic Fatty Streak Psyllium Hamsters

Laser system design for table-top X-ray light source

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High Power Laser Science and Engineering 2018年第1期6卷 76-97页

作者： Anne-Laure Calendron Joachim Meier Michael Hemmer Luis E.Zapata Fabian Reichert Huseyin Cankaya damian N.Schimpf Yi Hua guoqing Chang Aram Kalaydzhyan Arya Fallahi Nicholas H.Matlis Franz X.Kartner Center for Free-Electron Laser Science Deutsches Elektronen Synchrotron Centre for Ultrafast Imaging University of Hamburg Department of Physics University of Hamburg Department of Electrical Engineering&Computer Science&Research Laboratory of Electronics MIT

We present possible conceptual designs of a laser system for driving table-top free-electron lasers based on terahertz acceleration. After discussing the achievable performances of laser amplifiers with Yb:YAg at cryogenic and room temperature and Yb:YLF at cryogenic temperature, we present amplification modules with available results and concepts of amplifier chains based on these laser media. Their performances are discussed in light of the specifications for the tasks within the table-top light source. Technical and engineering challenges, such as cooling, control, synchronization and diagnostics, are outlined. Three concepts for the laser layout feeding the accelerator are eventually derived and presented.

关键词： concept free-electron laser lasers optics

How Should We Treat Patients Too Sick to Have any Surgery?

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How Should We Treat Patients Too Sick to Have any Surgery?