Bergmann's Rule – what's in a name?

Despite the great interest it generates, the definition of Bergmann's Rule is vague and often contested. Debate focuses on whether the rule should be described in terms of pattern or process, what taxa it should apply to and what taxonomic level it should be associated with. Here I review the historical development of studies of Bergmann's Rule. I suggest that Bergmann thought that his rule should be strongest at the intra‐specific level, rather than between closely related species as is usually thought. I argue that the rule is a pattern that can be studied regardless of mechanism in any taxon and at any taxonomic level.     

The real cost of sequencing: higher than you think!

Advances in sequencing technology have led to a sharp decrease in the cost of ''data generation''. But is this sufficient to ensure cost-effective and efficient ''knowledge generation''?     

GENPLAT: an Automated Platform for Biomass Enzyme Discovery and Cocktail Optimization

The high cost of enzymes for biomass deconstruction is a major impediment to the economic conversion of lignocellulosic feedstocks to liquid transportation fuels such as ethanol. We have developed an integrated high throughput platform, called GENPLAT, for the discovery and development of novel enzymes and enzyme cocktails for the release of sugars from diverse pretreatment/biomass combinations. GENPLAT comprises four elements: individual pure enzymes, statistical design of experiments, robotic pipeting of biomass slurries and enzymes, and automated colorimeteric determination of released Glc and Xyl. Individual enzymes are produced by expression in Pichia pastoris or Trichoderma reesei, or by chromatographic purification from commercial cocktails or from extracts of novel microorganisms. Simplex lattice (fractional factorial) mixture models are designed using commercial Design of Experiment statistical software. Enzyme mixtures of high complexity are constructed using robotic pipeting into a 96-well format. The measurement of released Glc and Xyl is automated using enzyme-linked colorimetric assays. Optimized enzyme mixtures containing as many as 16 components have been tested on a variety of feedstock and pretreatment combinations.GENPLAT is adaptable to mixtures of pure enzymes, mixtures of commercial products (e.g., Accellerase 1000 and Novozyme 188), extracts of novel microbes, or combinations thereof. To make and test mixtures of ˜10 pure enzymes requires less than 100 μg of each protein and fewer than 100 total reactions, when operated at a final total loading of 15 mg protein/g glucan. We use enzymes from several sources. Enzymes can be purified from natural sources such as fungal cultures (e.g., Aspergillus niger, Cochliobolus carbonum, and Galerina marginata), or they can be made by expression of the encoding genes (obtained from the increasing number of microbial genome sequences) in hosts such as E. coli, Pichia pastoris, or a filamentous fungus such as T. reesei. Proteins can also be purified from commercial enzyme cocktails (e.g., Multifect Xylanase, Novozyme 188). An increasing number of pure enzymes, including glycosyl hydrolases, cell wall-active esterases, proteases, and lyases, are available from commercial sources, e.g., Megazyme, Inc. (www.megazyme.com), NZYTech (www.nzytech.com), and PROZOMIX (www.prozomix.com).Design-Expert software (Stat-Ease, Inc.) is used to create simplex-lattice designs and to analyze responses (in this case, Glc and Xyl release). Mixtures contain 4-20 components, which can vary in proportion between 0 and 100%. Assay points typically include the extreme vertices with a sufficient number of intervening points to generate a valid model. In the terminology of experimental design, most of our studies are "mixture" experiments, meaning that the sum of all components adds to a total fixed protein loading (expressed as mg/g glucan). The number of mixtures in the simplex-lattice depends on both the number of components in the mixture and the degree of polynomial (quadratic or cubic). For example, a 6-component experiment will entail 63 separate reactions with an augmented special cubic model, which can detect three-way interactions, whereas only 23 individual reactions are necessary with an augmented quadratic model. For mixtures containing more than eight components, a quadratic experimental design is more practical, and in our experience such models are usually statistically valid.All enzyme loadings are expressed as a percentage of the final total loading (which for our experiments is typically 15 mg protein/g glucan). For "core" enzymes, the lower percentage limit is set to 5%. This limit was derived from our experience in which yields of Glc and/or Xyl were very low if any core enzyme was present at 0%. Poor models result from too many samples showing very low Glc or Xyl yields. Setting a lower limit in turn determines an upper limit. That is, for a six-component experiment, if the lower limit for each single component is set to 5%, then the upper limit of each single component will be 75%. The lower limits of all other enzymes considered as "accessory" are set to 0%. "Core" and "accessory" are somewhat arbitrary designations and will differ depending on the substrate, but in our studies the core enzymes for release of Glc from corn stover comprise the following enzymes from T. reesei: CBH1 (also known as Cel7A), CBH2 (Cel6A), EG1(Cel7B), BG (β-glucosidase), EX3 (endo-β1,4-xylanase, GH10), and BX (β-xylosidase).     

Method for Novel Anti-Cancer Drug Development using Tumor Explants of Surgical Specimens

The current therapies for malignant glioma have only palliative effect. For therapeutic development, one hurdle is the discrepancy of efficacy determined by current drug efficacy tests and the efficacy on patients. Thus, novel and reliable methods for evaluating drug efficacy are warranted in pre-clinical phase. In vitro culture of tumor tissues, including cell lines, has substantial phenotypic, genetic, and epigenetic alterations of cancer cells caused by artificial environment of cell culture, which may not reflect the biology of original tumors in situ. Xenograft models with the immunodeficient mice also have limitations, i.e., the lack of immune system and interspecies genetic and epigenetic discrepancies in microenvironment. Here, we demonstrate a novel method using the surgical specimens of malignant glioma as undissociated tumor blocks to evaluate treatment effects. To validate this method, data with the current first-line chemotherapeutic agent, temozolomide (TMZ), are described. We used the freshly-removed surgical specimen of malignant glioma for our experiments. We performed intratumoral injection of TMZ or other drug candidates, followed by incubation and analysis on surgical specimens. Here, we sought to establish a tumor tissue explant method as a platform to determine the efficacy of novel anti-cancer therapies so that we may be able to overcome, at least, some of the current limitations and fill the existing gap between the current experimental data and the efficacy on an actual patient''s tumor. This method may have the potential to accelerate identifying novel chemotherapeutic agents for solid cancer treatment.     

南京方山朴树种群结构与分布格局研究

采用相邻格子样方法对南京方山国家地质公园朴树种群结构和分布格局进行了研究。结果表明：（1）各样地朴树种群的年龄结构基本相似,Ⅰ、Ⅱ级幼苗普遍较少,幼苗贮备严重不足。种群个体分布多集中在Ⅲ级,Ⅳ级以上种群个体分布渐趋减少。（2）从静态生命表可以看出,由于Ⅰ、Ⅱ级幼苗、幼树数量偏少,导致种群Ⅰ、Ⅱ龄级的死亡率为负值,而Ⅶ、Ⅷ龄级的死亡率最大。部分龄级存在着不同程度的个体缺失,存活曲线呈明显下凹和断点波折,种群整体呈衰退趋势。（3）利用负二项参数（K）、扩散系数（C）、扩散型指数（I_δ）、Cassie指标（C_a）、丛生指数（I）、平均拥挤度指数（m^*）和聚块性指标（m^*/m）等参数对种群的空间格局进行了研究,表明朴树种群的空间分布格局为集群分布,但不同样地种群的集聚程度存在一定差异。     

响应面法优化松茸发酵产多糖的培养条件

运用响应面法对松茸产多糖的发酵培养条件进行优化研究。首先根据C、N源实验结果,利用Plackett-Bur-man设计,对影响多糖产量的相关因素进行评估,筛选出具有显著效应的3个因素:玉米粉、豆粕和KH2PO4。在此基础上,利用最陡爬坡试验逼近以上3个因素的最大响应区域,采用Box-Behnken设计法对各因素的水平组合进行优化,获得松茸产多糖优化发酵的培养条件:玉米粉质量分数4.54%,豆粕质量分数4.96%,KH2PO4质量分数0.15%,MgSO4.7H2O质量分数0.05%,VB1质量分数0.001%,初始pH5.5,摇床转速180 r/min,发酵时间10 d。在此优化培养条件下松茸总多糖产量可达5.97 g/L。     

Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes

The evolution of the central nervous system (CNS) is one of the most striking changes during the transition from invertebrates to vertebrates. As a major source of genetic novelties, gene duplication might play an important role in the functional innovation of vertebrate CNS. In this study, we focused on a group of CNS-biased genes that duplicated during early vertebrate evolution. We investigated the tempo-spatial expression patterns of 33 duplicate gene families and their orthologs during the embryonic development of the vertebrate Xenopus laevis and the cephalochordate Brachiostoma belcheri. Almost all the identified duplicate genes are differentially expressed in the CNS in Xenopus embryos, and more than 50% and 30% duplicate genes are expressed in the telencephalon and mid-hindbrain boundary, respectively, which are mostly considered as two innovations in the vertebrate CNS. Interestingly, more than 50% of the amphioxus orthologs do not show apparent expression in the CNS in amphioxus embryos as detected by in situ hybridization, indicating that some of the vertebrate CNS-biased duplicate genes might arise from non-CNS genes in invertebrates. Our data accentuate the functional contribution of gene duplication in the CNS evolution of vertebrate and uncover an invertebrate non-CNS history for some vertebrate CNS-biased duplicate genes.     

大桑菊合剂的提取工艺研究

目的:大桑菊合剂为医院制剂,由桑叶、菊花、薄荷、连翘、鱼腥草等中药经乙醇提取制成,为完善大桑菊合剂的制备工艺,对该制剂的制备工艺进行初步的研究。方法:①实验设计:以加水量、提取时间、提取次数和醇沉浓度为考察因素,各因素均取3水平,采用正交试验L(934)优选制备工艺。②含量测定方法:以大桑菊饮合剂中总黄酮的含量为指标,以芦丁为标准品,利用紫外分光光度计于503nm下测定吸光值,计算样品中总黄酮的含量,以此作为筛选大桑菊合剂最佳制备工艺的重要指标。结果:最佳制备工艺为不浸泡,加8倍水,提取3次,每次1小时。结论:经正交设计优化的大桑菊合剂的中药制备工艺合理、可行。