Harming the non-conscious

Peter Singer has argued that nothing done to a fetus before it acquires consciousness can harm it. At the same time, he concedes that a child can be harmed by something done to it when it was a non-conscious fetus. But this implies that the non-conscious fetus can be harmed. The mistake lies in thinking that, since existence can be intrinsically bad for a being only if it is conscious, it can be harmed only if it is conscious. In fact, its being harmed only implies that it could have been conscious (and led a good life).     

The Elston-Stewart algorithm for continuous genotypes and environmental factors.

The Elston-Stewart algorithm for a normally distributed trait under a polygenic model is explained in detail and extended to allow for other continuous environmental variables. This formulation is especially useful for large pedigrees, as it avoids the need to invert matrices. Whereas it may not be feasible by this method to estimate all the various components of previously suggested models for polygenic inheritance, it can allow for a reasonably flexible pedigree correlational structure under which valid tests can be performed for fixed effects that may affect the phenotype.     

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models.

An efficient method was developed for making complete sets of oligonucleotides of defined length, covalently attached to the surface of a glass plate, by synthesizing them in situ. A device carrying all octapurine sequences was used to explore factors affecting molecular hybridization of the tethered oligonucleotides, to develop computer-aided methods for analyzing the data, and to test the feasibility of using the method for sequence analysis. Further development is needed before the method can be used routinely, but our work shows that it has a number of potential advantages over gel-based methods: it should be easy to automate; the quality of the sequence results can be evaluated statistically; it provides a powerful way of comparing related sequences and detecting mutation; it can be applied to both DNA and RNA; and specific motifs can be incorporated into all sequences of the array to focus analysis on sequences of biological interest.     

CNVDetector: locating copy number variations using array CGH data

CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling. AVAILABILITY: CNVDetector (for Windows platform) can be downloaded from http:www.csie.ntu.edu.tw/~kmchao/tools/CNVDetector/. The manual of CNVDetector is also available.     

Tropolone—a compound that can aid in differentiating between tyrosinase and peroxidase

In studies dealing with melanogenesis in mammalian tissues, ultrastructural localization of enzymes, identification of subcellular organelles, differentiation and lignification in plant tissues, it is important to have means to differentiate between tyrosinase and peroxidase activities. For a variety of reasons, established criteria used for this purpose are not always reliable. We suggest that tropolone can aid in differentiating between tyrosinase and peroxidase activities since: (a) it is a very effective inhibitor of tyrosinase; (b) in the presence of hydrogen peroxide it can serve as a substrate for peroxidase; (c) at concentrations that inhibit tyrosinase, it does not inhibit peroxidase activity; and (d) it inhibits tyrosinase activity even in the presence of hydrogen peroxide and peroxidase. In a system containing a mixture of tyrosinase and peroxidase, tropolone can differentiate reliably between peroxidase and monohydroxyphenolase or o-dihydroxyphenolase activities of tyrosinase. Moreover, tropolone can differentiate reliably between peroxidase and tyrosinase activities using slices or crude dialysed extracts of various plant tissues.     

On the Population Dynamics of the Malaria Vector

A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can established itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing.     

Cross-blot and cross-dot system: a high-performance system for the detection of antigen-antibody complexes on nitrocellulose

We present a reliable, simple, and quick system for screening antibody-antigen complexes on nitrocellulose. The apparatus necessary for this system is inexpensive and easy to use, and it can be adapted to blot or dot analysis without any modification. The number of antibody-antigen combinations that can be tested in one experiment ranges from 25 to 31 for blot analysis and from 345 to 600 for dot analysis. This system also offers numerous experimental advantages: it makes it possible to estimate with only one experiment the contribution of the different reaction stages to background noise and so allows unambiguous interpretation of the antibody-antigen reaction. Furthermore, this system can be used for any hybridization experiment on nitrocellulose.     

Assessment of diagnostic tests when disease verification is subject to selection bias

In the assessment of the statistical properties of a diagnostic test, for example the sensitivity and specificity of the test, it is common to derive estimates from a sample limited to those cases for whom subsequent definitive disease verification is obtained. Omission of nonverified cases can seriously bias the estimates. In order to adjust the estimates it is necessary to make assumptions about the mechanism for selecting cases for verification. Methods for making the necessary adjustments can then be derived.     

哺乳动物细胞灌流培养工艺研究进展

当前生物制药领域,由于成本压力、市场需求急剧波动以及生物仿制药的竞争日益激烈,现有的生物制造技术受到诸多挑战,生物技术公司越来越倾向于开发灵活、高效的创新型生产制造工艺。灌流培养作为当前哺乳动物细胞培养的重要工艺之一,不仅可以通过不断移出副产物和添加营养物来提供有利于细胞的稳定环境,以解决蛋白质量不稳定或者表达量偏低等问题,还可以通过提高单位体积产率来优化产能利用率并提高生产效率。通过系统介绍灌流培养用于哺乳动物细胞培养的研究进展,为其进一步开发与应用提供参考。     

Detection of the microbial activity of aerobic heterotrophic, anoxic heterotrophic and aerobic autotrophic activated sludge organisms with an electrochemical sensor

The microbial activity of aerobic heterotrophic, anoxic heterotrophic and aerobic autotrophic microorganisms in biological wastewater treatment was determined by means of an electrochemical bioactivity sensor. The development of the sensor resulted in a system which can determine the microbial activities that are relevant for effective wastewater treatment. The signals of the sensor system are proportional to the substrate degradation and it can show inhibiting effects on the biomass. The most important advantages of the system are: it is independent of O₂ consumption, the three most important types of metabolic activities in wastewater technology can be measured with one sensor, furthermore the measurement is suitable for automation and it is on-line. The result is a potential for the optimization of processes based on microbial activity.     

The brain as a source of selection on the social niche: examples from the psychophysics of mate choice in túngara frogs

The main premise of this article is that various cognitive functions involved in signal analysis, memory, and decision making, all modulated by the animal's internal milieu, can generate selection for the forms of signals used in social interactions. Thus, just as an animal's view of its world, its Umwelt, determines how it interacts with its ecological niche, it can influence the evolution of its social niche. Thus, the brain is not only a landscape on which selection can act, but also it is a powerful source of selection on the animal's social niche.     

Adioophilin在动脉粥样硬化中的作用机制

adipophilin是脂滴周围相关蛋白,能促进脂质蓄积和细胞内脂滴的形成,在泡沫细胞的形成中起到重要作用,是动脉粥样硬化脂质蓄积的一个标记物。但目前对其脂质蓄积机制的研究不是十分明确。本文对adipophilin在调节脂质蓄积过程中的机制做一综述,以期为动脉粥样硬化治疗提供新的理论依据和药物靶点,推动动脉粥样硬化治疗方法的发展。     

The probability of correctly resolving a split as an experimental design criterion in phylogenetics

We illustrate how recently developed large sequence-length approximations to probabilities of correct phylogenetic reconstruction for maximum likelihood estimation can be used to evaluate experimental design strategies. The specific criterion of interest is the probability of correctly resolving an a priori defined split of interest in a phylogenetic tree. Design strategies considered include increased taxon sampling and increasing sequence length. Our analyses of specific examples strongly suggest that it is better to sample taxa that connect as close as possible to the split of interest. Assuming this can be done, these examples suggest it is better to sample additional taxa than to add a comparable number of sites for the existing taxa. If the rates of evolution in the added taxa are slow, it is better to choose taxa connecting to a long edge, but if rates are comparable to a sister lineage, it is not necessarily the best strategy to sample taxa connected to a long edge. We also examined deleting taxa while increasing the number of sites. Although deleting a small number of taxa distant from the split of interest can be beneficial, deleting too many or making poor choices as to what should be deleted can lead to smaller probabilities of correct reconstruction than for the original sequence data.     

Making light work of enzyme catalysis: protochlorophyllide oxidoreductase

In the chlorophyll biosynthetic pathway, the enzyme protochlorophyllide oxidoreductase (POR) catalyses a key light-driven reaction that triggers a profound transformation in plant development. Because POR is activated by light, it can provide information on the way in which light energy can be harnessed to power enzyme reactions and it presents us with a unique opportunity to study catalysis at low temperatures and on ultrafast timescales that are not accessible for most analyses of enzyme function. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important generic model for studying enzyme catalysis and reaction dynamics.     

HHS guidance on synthetic DNA is the right step

Synthetic biology has advanced to the point where some pathogens can be manufactured from scratch. This technical leap has beneficent implications for medical research and vaccine design, but it also raises concerns that the technology could be used to produce a deadly pathogen for nefarious use. Addressing these concerns, the Department of Health and Human Services (HHS) released their Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA on October 13, 2010. They took the right approach: The oversight framework for gene synthesis companies included in this guidance is adaptable to new technical developments and changing risks, it can be implemented immediately, it can be readily adopted by other countries, and it will cost little. Though there have been some calls to increase the regulatory controls on synthetic biology, these should be resisted. For now, at least, the oversight is appropriate to the risks.     

保持培养细胞原位、原形的超薄切片制备法

本文介绍先用环氧树脂Epon812包埋剂制成丘状膜,再在膜上培养细胞,直接将膜与细胞一起包埋,制备超薄切片。此种方法不仅能克服以往培养细胞需要离心成团,容易造成细胞破碎、变形的缺点;还能避免琼脂预包埋法悬浮细胞造成的抗原封闭;并能得到为数较多的连续超薄切片。它操作简便,较好地保持了培养细胞生长的原来位置及原有形状,为培养细胞进行免疫电镜的操作和提高制备培养细胞超薄切片的数量和质量提供了一种有效的途径。     

豆天蛾的人工饲养

豆天蛾是一种大型的农业害虫,在我国西部和北部地区广泛分布,江苏连云港地区有着独特的食虫文化－－烧豆丹系列菜肴,模拟豆天蛾的生活习性进行人工饲养,不仅能保证大豆产量,变害为宝,而且还取得了良好的经济效益,是一项有价值的生物资源可持续利用的新技术。     

Environmental forcing, invasion and control of ecological and epidemiological systems

Destabilising a biological system through periodic or stochastic forcing can lead to significant changes in system behaviour. Forcing can bring about coexistence when previously there was exclusion; it can excite massive system response through resonance, it can offset the negative effect of apparent competition and it can change the conditions under which the system can be invaded. Our main focus is on the invasion properties of continuous time models under periodic forcing. We show that invasion is highly sensitive to the strength, period, phase, shape and configuration of the forcing components. This complexity can be of great advantage if some of the forcing components are anthropogenic in origin. They can be turned into instruments of control to achieve specific objectives in ecology and disease management, for example. Culling, vaccination and resource regulation are considered. A general analysis is presented, based on the leading Lyapunov exponent criterion for invasion. For unstructured invaders, a formula for this exponent can typically be written down from the model equations. Whether forcing hinders or encourages invasion depends on two factors: the covariances between invader parameters and resident populations and the shifts in average resident population levels brought about by the forcing. The invasion dynamics of a structured invader are much more complicated but an analytic solution can be obtained in quadratic approximation for moderate forcing strength. The general theory is illustrated by a range of models drawn from ecology and epidemiology. The relationship between periodic and stochastic forcing is also considered.     

AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads

ABSTRACT: BACKGROUND: With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses. FINDINGS: We present a tool called AdapterRemoval which is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5' and 3' ends of the reads. This is a flexible method that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data. CONCLUSIONS: AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in terms of sensitivity and specificity. AdapterRemoval has already been used in various large projects and it is possible to extend it further to accommodate application-specific biases in the data.