一种利用通用图像处理软件提高黑白生物特征图质量的方法

生物分类学工作者发表分类学文章常常需要制作和处理黑白生物特征图.本文利用通用图像处理软件Photoshop和Ilhustrator的不同功能特点,结合扫描仪、数位板等电脑外设,总结了一套专门适用生物分类特征草图覆墨的操作方法.方法包括草图输入、绘制墨线路径、覆墨、绘制阴影、排版输出等步骤.     

生物墨线绘图的方法与技巧

介绍生物墨线绘图基本方法与技巧,包括缩放的方法与技巧、绘图工具的选择和应用以及在草图的绘制和上墨过程中的方法技巧。     

研发动态

生物领域专家研究科学创新方法;我国首次完成益生乳酸菌全基因组序列测定;中国科学家分离出控制水稻产量的单基因;合成基因组学公司和基因组技术亚洲中心完成油椰子基因组首张草图;科学家绘出鸭嘴兽基因组草图;研究者绘出棕榈树大部分基因组草图。     

《本草图经》橄榄的本草考证

通过古代本草典籍及现代文献，对《本草图经》中记载的药物橄榄从植物形态、产地、功效等3个方面进行考证。结果表明，《本草图经》记载的橄榄以及附图“泉州橄榄”，其基原物种为橄榄科植物橄榄[Canarium album (Lour.) Rauesch.]；《本草图经》中记载的波斯橄榄，其基原物种为橄榄科植物方榄(Canarium bengalense Roxb.)；而《植物名实图考》中的橄榄，其基原物种是杜英科植物山杜英[Elaeocarpus sylvestris (Lour.) Poir.]。从而基本厘清《本草图经》的橄榄品种，以及橄榄的一些混淆品种，为橄榄的实验研究及开发应用提供基础保障。     

读《本草图经》序，仰苏颂本草撰述思想

苏颂撰述的《本草图经》是一部独具文献价值和撰述思想的本草经典。尽管《本草图经》的撰述缘起朝廷倡议和组织,药图及其经文素材来源于全国各级地方政府和广大医药劳动人民工作,但是由苏颂“俾专撰述”的《本草图经》集中体现了他的本草撰述学术思想。研究苏颂的本草撰述学术思想,对深入发掘《本草图经》所蕴涵的宝贵文献信息、传承我国源远流长的丰富的本草医药科学和本草生活文化,具有积极的历史和现实意义。     

《本草图经》兴化军防己的本草考证

对《本草图经》中兴化军防己的附图及文字记载进行本草考证,探究其原植物品种。通过古今文献考证和植物学比较研究,从植物形态、药材性状、产地分布及性味功用等方面进行分析,认为《本草图经》中的兴化军防己应为今之防己科植物木防己[Cocculus orbiculatus (L.) DC.],为防己类中药的古今品种沿革及基原考证提供参考。     

关于乌贼墨的化学组成

有关乌贼墨治疗子宫等出血性疾病的临床报告发表后,许多单位来信、来访要求较详细地介绍一下乌贼墨的研究情况,以便更好地利用这一新药源。为了满足这一需要,本文将对乌贼墨的组成和乌贼黑色素的化学结构作一简要介绍。 国内外有关乌贼墨的研究很少。药用方面,国外未见报道,我国也刚开始不久,许多问题还有待今后深入研究。     

墨天牛属昆虫COⅠ基因比较及系统学初步研究

【目的】对11种墨天牛线粒体DNA细胞色素氧化酶C亚基Ⅰ基因(COⅠ)进行比较并对墨天牛属系统发育关系进行初步探讨。【方法】本文测定分析了11种墨天牛线粒体DNA细胞色素氧化酶C亚基Ⅰ基因(COⅠ),并采用简约法和贝叶斯推论法构建了墨天牛属的分子进化树。【结果】序列比对分析得到470 bp大小的COⅠ基因片段,其中可变异位点169个(36.0%),保守位点301个(64.0%),转换/颠换的平均值(R值)为1.03,说明此段序列适合于分子进化树。利用不同系统发育重建方法得到的进化树具有相似的拓扑结构,同时结合形态学分类特征对墨天牛属昆虫的分子系统进化关系进行探讨。结果显示分子结果与形态分类结果相似。【结论】利用COⅠ基因构建的墨天牛属系统发育树是探讨墨天牛分类的有效方法。     

高黎贡山地区民族植物学的研究Ⅰ.勒墨人

应用民族植物学的方法,对生活在云南西部高黎贡山东坡的勒墨人进行了调查。主要研究结果如下勒墨人对野生植物及环境有较大的依赖性;从 事刀耕火种轮歇栽培,并种植漆树(Toxicodendron vernicifiuum)和桤木(Alnus nepalensis)以促进轮歇地的休闲管理;栽培和管理漆树、收割生漆交换或出售,是勒墨人轮歇农业的一大特色;他们采集利用60余种野生食用植物和100余种药用植物,云黄连(Coptis teeta)和贝母(Fritillaria cirrhosa)等重要药材用于同外界进行物资交换;在对自然界的崇拜过程中,勒墨人对当地生物多样性的保护起到了积极的作用。     

鸡基因组研究新进展

鸡基因组测序草图的完成标志着禽类功能基因组时代的到来。鸡不仅是全世界广泛饲养且有重要经济价值的禽类,而且是极具生命科学研究价值的模式动物。因此,鸡基因组测序草图的完成将对遗传育种和生物学研究有重要的影响。本文综述了近年来鸡基因组研究的最新进展,主要内容包括鸡基因组的有关数据、物理图谱、遗传连锁图谱、比较基因组学、序列表达标签、生物信息学等方面所取得的成绩,同时对鸡基因组研究结果的应用前景进行了展望。     

Liquid-phase dispersion in an airlift reactor with a net draft tube

Liquid-phase dispersion in an airlift reactor with a net draft tube was considered. Four net tubes with different ratios of draft tube to reactor diameters and superficial air velocities ranged from zero to 6.05 cm/s were investigated. The sparger was a porous plate. The parameter of the dispersion effect, axial dispersion coefficient, was characterized by measuring the residence time distribution in the liquid phase with single-pulse tracer input. The values of the dispersion coefficient of the proposed airlift reactor were much higher than those of the bubble column under the same operating conditions.     

Escape by inking and secreting: marine molluscs avoid predators through a rich array of chemicals and mechanisms

Inking by marine molluscs such as sea hares, cuttlefish, squid, and octopuses is a striking behavior that is ideal for neuroecological explorations. While inking is generally thought to be used in active defense against predators, experimental evidence for this view is either scant or lacks mechanistic explanations. Does ink act through the visual or chemical modality? If inking is a chemical defense, how does it function and how does it affect the chemosensory systems of predators? Does it facilitate escape not only by acting directly on predators but also by being an alarm signal for conspecifics? This review examines these issues, within a broader context of passive and active chemical defensive secretions. It focuses on recent work on mechanisms of defense by inking in sea hares (Aplysia) and extends what we have learned about sea hares to other molluscs including the cephalopods.     

Lead Us Not into Tanktation: A Simulation Modelling Approach to Gain Insights into Incentives for Sporting Teams to Tank

Annual draft systems are the principal method used by teams in major sporting leagues to recruit amateur players. These draft systems frequently take one of three forms: a lottery style draft, a weighted draft, or a reverse-order draft. Reverse-order drafts can create incentives for teams to deliberately under-perform, or tank, due to the perceived gain from obtaining quality players at higher draft picks. This paper uses a dynamic simulation model that captures the key components of a win-maximising sporting league, including the amateur player draft, draft choice error, player productivity, and between-team competition, to explore how competitive balance and incentives to under-perform vary according to league characteristics. We find reverse-order drafts can lead to some teams cycling between success and failure and to other teams being stuck in mid-ranking positions for extended periods of time. We also find that an incentive for teams to tank exists, but that this incentive decreases (i) as uncertainty in the ability to determine quality players in the draft increases, (ii) as the number of teams in the league reduces, (iii) as team size decreases, and (iv) as the number of teams adopting a tanking strategy increases. Simulation models can be used to explore complex stochastic dynamic systems such as sports leagues, where managers face difficult decisions regarding the structure of their league and the desire to maintain competitive balance.     

Simultaneous alignment of short reads against multiple genomes

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.     

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks

Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable.     

Identification of a haemolysin-like peptide with antibacterial activity using the draft genome sequence of Staphylococcus epidermidis strain A487

Our interest in Staphylococcus epidermidis strain A487 was prompted by the unusual nature of its inhibitory activity in screening tests against methicillin-resistant Staphylococcus aureus isolates. The inhibitory activity was detected in deferred antagonism tests only if the agar plate was preheated for at least 35 min at ≥ 55 °C before inoculation of the indicator bacteria, this phenomenon indicating possible involvement of a heat-labile immunity agent or protease. The inhibitor was purified to homogeneity by ammonium sulphate precipitation, followed by cation-exchange and reversed-phase chromatography. Tandem MS revealed a novel peptide of molecular weight 2588.4 Da. The draft genome sequence of strain A487 was determined using 454 GS FLX technology, allowing the identification of the structural gene (hlp) encoding the mature peptide MQFITDLIKKAVDFFKGLFGNK. The deduced amino acid sequence of peptide 487 exhibited 70.8% similarity to that of a putative haemolysin from Staphylococcus cohnii. Analysis of the genome of strain A487 showed several additional inhibitor-encoding genes, including hld, the determinant for staphylococcal δ-lysin. This work indicates that potentially useful inhibitors could be overlooked in agar-based inhibitor screening programmes lacking a heat pretreatment step and also highlights the utility of draft genome sequence examination in antibacterial agent discovery.     

O2 transfer to pseudoplastic fermentation broths in air-lift reactors with different inner designs

The effect of two different draft tube designs on annulus air-lift reactor (AALR) performance was studied using the pseudoplastic fluid such as sodium carboxymethyl cellulose (CMC) and Streptomyces lincolnesis cultures. The results revealed that with fluids exhibiting strong pseudoplasticity, the AALR with a solid draft tube showed better capacity in O2 transfer than that of the reactor with a window draft tube. This was due to the fact that the pseudoplastic fluid in the former had higher circulating liquid velocity and thus lower apparent viscosity. An empirical equation of KLa based on the results for CMC was proposed by dimensional analysis and the least square method. The equation could also be used to estimate the O2 transfer capacity in large columns. © Rapid Science Ltd. 1998     

Draft proposals for nomenclature principles in floristic phytosociology

In 15 basic articles the author summarises draft nomenclatural principles in floristic phytosociology (theBraun$#x2014;Blanquet school). The draft is to be considered as an attempt to introduce into plant sociology such rules as respect the object and method of establishing sociological units, based on typisation¹. The conception of a unit, given by the diagnosis, is considered to be the most important criterion for the choice of a correct name.