Simplifier: a web tool to eliminate redundant NGS contigs

Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms.

Availability

Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.     

Bear deterrence with scare devices,a non-lethal tool in the use-of-force continuum

Wild animals eating agricultural products and coming close to people's residences are primary causes of human–wildlife conflict worldwide. When carnivores eat anthropogenic foods and cause human safety concerns, it often results in the removal of the animals and public demand for reduced wildlife populations. The use of remote methods, such as scare devices, to deter carnivores has been touted in the literature; however, efficacy evidence remains thin. I test the efficacy of a widely available motion-activated solar alarm lamp to deter grizzly bears (Ursus arctos) from farms in Montana, USA. When scare devices were activated, there was a 46% reduction in the odds bears would access an attractant. For every additional scare device, there was an additional 44% reduction in the odds of a bear getting the food. Additionally, scare devices caused bears to be more vigilant and increase movement behavior. More bears in a group led to loss of deterrence efficacy, and there was no evidence for habituation to the aversive stimuli. This deterrence method was most effective in August and for fungicide-treated wheat. Out of 21 farms, scare devices stopped bears from returning to 11 sites. Overall, scare devices can be a cheap and easy first step to preventing, or resolving, some grizzly bear issues in the use-of-force continuum, which hierarchically organizes conflict responses from non-lethal to more severe.     

El Tor型霍乱弧菌及其细胞壁缺陷型分子遗传学背景的研究

El Tor 型霍乱弧菌(以下简称 El Tor 弧菌)可以在人工培养条件下长期存活。当微环境改变时可形成细胞壁有不同程度缺陷的菌株如抗噬菌体突变株或 L 型菌株。我们以 DNA 酶切图谱和 El Tor 弧菌溶血素、神经氨酸酶基因探针杂交图谱为参数对 El Tor 弧菌的野生型及其细胞壁缺陷型变异株在遗传背景上进行了比较分析研究。结果提示细胞壁缺陷型菌株与其野生型在DNA 水平上高度同源。此外,文中还介绍了一种从 L 型菌株中制备 DNA 的方法。     

光周期对布氏田鼠和长爪沙鼠体重和能量代谢的影响

本文测定了光周期对雄性布氏田鼠和长爪沙鼠的体重、基础代谢率和能量代谢的影响。动物从长光照(16L∶8D , LD) 转入短光照(8L∶16D , SD) 条件下驯化6 周(田鼠) 和7 周(沙鼠) 。结果显示: (1) 无论在LD还是SD 条件下, 两种动物的体重都趋于增加, 但反应程度不同也具有种间差异性。两种动物的体重对光周期的反应有时段性, 约14 d 前两种动物的体重增加迅速, 而后增加缓慢, 3 周左右趋于稳定。短光照条件下布氏田鼠和长爪沙鼠的体重分别增长了37 %和11 % , 均低于长光照组(分别为47 %和25 %) , 说明短光照条件下布氏田鼠和长爪沙鼠的体重增长较长光照缓慢; (2) 光照对两种动物的摄入能、消化能和可代谢能均没有显著影响,摄入能与体重的增长无关; (3) 光照对两种动物的基础代谢率无显著影响。这些结果表明: 布氏田鼠和长爪沙鼠在自然环境中, 可能以光周期作为一种信号, 当环境温度降低、食物质量变劣时, 采取降低体重以减少绝对能量需求的策略而适应环境。     

广东新会维管植物区系的研究

新会市位于广东省中南部 ,地理位置为北纬 2 2°0 5′4 3″～ 2 2°4 8′2 4″,东经 1 1 2°4 7′0 3″～ 1 1 3°1 5′2 4″,南濒南海 .该地区共有维管植物 1 6 98种 ,隶属于 2 0 9科 81 6属 ,其中蕨类植物 32科 5 4属 82种 ,种子植物 1 78科 76 2属1 6 1 6种 .区系地理学研究表明 :蕨类植物地理成分以热带亚热带分布属居多 ,达 2 6属 ,占蕨类总属数的 4 8.1 3% ,而且是以单种属或少种属占优势 .种子植物地理成分以泛热带、热带亚洲分布占绝对优势 ,全部热带成分已达78.0 9% ;其特征科主要有 :山矾科、冬青科、壳斗科、桑科、金缕梅科、山茶科、樟科、萝摩科、大戟科、蝶形花科、野牡丹科、茜草科等 ;中国特有属杉木属、穗花杉属、石笔木属、四药门花属、马蹄参属、天星藤属、大血藤属、刚毛药花属、台闽苣苔属、酸竹属及广东特有属绣球茜草属、异枝竹属等 .与邻近的香港、惠东古田、鼎湖山和黑石顶的植物区系比较其相似性很高 ,体现出南亚热带地区植物区系成分的过渡性及热带区系的渗透性     

菟丝子及其一种伪品的鉴别

通过原植物鉴定、药材性状和粉末显微观察,理化反应及紫外光谱扫描比较,对菟丝子(Cuscuta chinensis)及其一种伪品进行鉴别。结果表明,菟丝子及其伪品在原植物的叶、花和果实、药材质地和气味,种皮栅状组织细胞的构成及其特点、热水浸煮时发生的现象、黄酮反应结果以及紫外光谱扫描显示的最大吸收波长位置,均存在明显差异。菟丝子的伪品系十字花科植物芥菜(原变种)(Brassica juncea var.juncea)的干燥成熟种子,上述实验结果为鉴别菟丝子及其伪品提供了依据。     

磷脂酰甘油分子种与杨树抗寒性关系的研究

用高效液相色谱（ＨＰＬＣ）方法分析了杨树叶磷脂酰甘油（ＰＧ）的分子种组成,用酶解和气相色谱（ＧＣ）方法分析了ＰＧ脂肪酸定位,比较了抗寒性不同的杨树叶片ＰＧ分子种。结果表明,杨树叶片ＰＧ主要含有以下的分子种脂肪酸组成（ｓｎ－１和ｓｎ－２）：１８：１８：２（１８：２／１８：３）,１８：３／１６：１（３ｔ）;１８：３／１６：０;１８：２／１６：１（３ｔ）;１６：０／１８：２,１８：２／１６：０;１８：１     

富勒烯的生物活性研究进展

90年代初以来,富勒烯类化合物的生物活性逐渐引起人们的注意,初步研究表明在抗艾滋病毒、酶活性抑制、切割DNA、光动力学治疗等方面具有独特的功效.此类化合物在生化、医学、药物学等领域有良好的应用前景.     

青海海北地区高山蒿草草甸植物群落的结构特征及其分布格局

对高山草甸主要植物群落结构特征及其分布格局的研究结果表明,矮嵩草草甸植物群落的丰富度最大,隶属１８科,４３属４５种,呈多优势种植物群落;小嵩草草甸居中,隶属１１科,３０属３５种,小嵩草（Ｋｏｂｒｅｓｉａｐｙｇｍａｅａ）为优势种;藏嵩草沼泽化草甸最小,隶属９科,２１属２３种,藏嵩草（Ｋ．ｔｉｂｅｔｉｃａ）为优势种。其中,有９个种群为３个群落中的共有种,分别占矮嵩草草甸、小嵩草草甸和藏嵩草沼泽化草甸总种数的２０．００％、２５．７１％和３９．１３％。它们在水分资源位上的生态位宽度较大。３个植物群落类型的种－面积关系呈对数曲线分布,群落的最小样方面积为０．２５ｍ２或０．５ｍ２较适宜。种－多度分布呈对数正态分布,其分布模型的表达式如下：Ｓ（Ｒ）＝Ｓ０ｅ－（ａ２Ｒ     

Heating of tissues by microwaves: A model analysis

We consider the thermal response times for heating of tissue subject to nonionizing (microwave or infrared) radiation. The analysis is based on a dimensionless form of the bioheat equation. The thermal response is governed by two time constants: one(τ₁) pertains to heat convection by blood flow, and is of the order of 20–30 min for physiologically normal perfusion rates; the second (τ₂) characterizes heat conduction and varies as the square of a distance that characterizes the spatial extent of the heating. Two idealized cases are examined. The first is a tissue block with an insulated surface, subject to irradiation with an exponentially decreasing specific absorption rate, which models a large surface area of tissue exposed to microwaves. The second is a hemispherical region of tissue exposed at a spatially uniform specific absorption rate, which models localized exposure. In both cases, the steady-state temperature increase can be written as the product of the incident power density and an effective time constant τ_eff, which is defined for each geometry as an appropriate function of τ₁ and τ₂. In appropriate limits of the ratio of these time constants, the local temperature rise is dominated by conductive or convective heat transport. Predictions of the block model agree well with recent data for the thresholds for perception of warmth or pain from exposure to microwave energy. Using these concepts, we developed a thermal averaging time that might be used in standards for human exposure to microwave radiation, to limit the temperature rise in tissue from radiation by pulsed sources. We compare the ANSI exposure standards for microwaves and infrared laser radiation with respect to the maximal increase in tissue temperature that would be allowed at the maximal permissible exposures. A historical appendix presents the origin of the 6-min averaging time used in the microwave standard. Bioelectromagnetics 19:420–428, 1998. © 1998 Wiley-Liss, Inc.