Adaptive Quantile Estimation and its Application in Analysis of Biological Signals

Quantiles and their estimations are the basis for solving numerous problems of statistics. The paper presents adaptive recursive estimation methods for this statistical parameter. Its specifical properties are investigated and the possibilities of applications in computer assisted analysis of biological signals are demonstrated even satisfying real time requirements.     

Estimation of multiple biomass growth rates and biomass concentration in a class of bioprocesses

In this paper, an approach to the estimation of multiple biomass growth rates and biomass concentration is proposed for a class of aerobic bioprocesses characterized by on-line measurements of dissolved oxygen and carbon dioxide concentrations, as well as off-line measurements of biomass concentration. The approach is based on adaptive observer theory and includes two steps. In the first step, an adaptive estimator of two out of three biomass growth rates is designed. In the second step, the third biomass growth rate and the biomass concentration are estimated, using two different adaptive estimators. One of them is based on on-line measurements of dissolved oxygen concentration and off-line measurement of biomass concentrations, while the other needs only on-line measurements of the carbon dioxide concentration. Simulations demonstrated good performance of the proposed estimators under continuous and batch-fed conditions.     

猪链球菌毒力因子和鉴定方法的研究进展

猪链球菌(Streptococcus suis)是一种重要的人畜共患病病原体,能够引起猪疫病,人类感染该菌可导致脑膜炎、败血症甚至死亡。鉴于其对养猪业的巨大经济影响和对公共卫生事业的威胁,关于猪链球菌的研究日益深入,即对其毒力相关蛋白和鉴定方法的研究进展做一综述。     

应用不同方法检测食品中大肠菌群结果的比较

评价检测食品中大肠菌群不同方法。比较国家标准、行业标准和显色培养基检测方法检测大肠菌群结果的差别。国家标准和行业标准检测结果基本一致,但有差异,应用显色培养基检测大肠菌群优于目前使用的国家标准和出口食品检验行业标准方法。检测食品中大肠菌群,显色培养基检测方法快速、灵敏、特异。     

自适应蚁群算法在DNA中的应用

主要讨论了自适应蚁群算法在DNA序列比对中的应用,主要的过程是：首先,我们设一个计分函数和一个得分策略,在任意给出一对DNA序列,建立一个序列比对矩阵．现由4只蚂蚁从左上角向右下角移动,并且最终到达右下角,那么这4只蚂蚁随意走出4条路径,根据4条路径得出4对等长的比对,再依照计分函数分别计算出4条路径的比对得分,再由1．3式进一步验证4条路径的平均得分值,取其中得分最高（即最优路径）路径;进行第二次信息素增量的调整,方法是根据蚂蚁所走过的方向和该方向上得分比例计算出来的,信息素的变化量利用矩阵来存储,那么下一次蚂蚁所选的路径就要根据以前在各条路径上的信息素浓度总和的大小选择移动方向,最终经过有限次迭代,蚂蚁就会找到一条最优路径,也就是一条与原来DNA最相似的DNA链．     

Gene Conversion Among Paralogs Results in Moderate False Detection of Positive Selection Using Likelihood Methods

Previous studies have shown that recombination between allelic sequences can cause likelihood-based methods for detecting positive selection to produce many false-positive results. In this article, we use simulations to study the impact of nonallelic gene conversion on the specificity of PAML to detect positive selection among gene duplicates. Our results show that, as expected, gene conversion leads to higher rates of false-positive results, although only moderately. These rates increase with the genetic distance between sequences, the length of converted tracts, and when no outgroup sequences are included in the analysis. We also find that branch-site models will incorrectly identify unconverted sequences as the targets of positive selection when their close paralogs are converted. Bayesian prediction of sites undergoing adaptive evolution implemented in PAML is affected by conversion, albeit in a less straightforward way. Our work suggests that particular attention should be devoted to the evolutionary analysis of recent duplicates that may have experienced gene conversion because they may provide false signals of positive selection. Fortunately, these results also imply that those cases most susceptible to false-positive results—i.e., high divergence between paralogs, long conversion tracts—are also the cases where detecting gene conversion is the easiest. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

分子生物学方法在食品微生物检测中的应用

近年来,食品安全受到广泛关注。及时、准确地检测出食品中的病原微生物是食品安全检测的重要内容,食品病原微生物的分子生物学检测技术因其特异性和灵敏性而备受瞩目。我们主要介绍了基因探针检测法、PCR检测法和基因芯片检测法的原理、开发及其在食品微生物检测中的应用。     

Comparison of Methods for Detection of Erysipelothrix spp. and Their Distribution in Some Australasian Seafoods

For many years, Erysipelothrix rhusiopathiae has been known to be the causative agent of the occupationally related infection erysipeloid. A survey of the distribution of Erysipelothrix spp. in 19 Australasian seafoods was conducted, and methodologies for the detection of Erysipelothrix spp. were evaluated. Twenty-one Erysipelothrix spp. were isolated from 52 seafood parts. Primary isolation of Erysipelothrix spp. was most efficiently achieved with brain heart infusion broth enrichment followed by subculture onto a selective brain heart infusion agar containing kanamycin, neomycin, and vancomycin after 48 h of incubation. Selective tryptic soy broth, with 48 h of incubation, was the best culture method for the detection of Erysipelothrix spp. with PCR. PCR detection was 50% more sensitive than culture. E. rhusiopathiae was isolated from a variety of different fish, cephalopods, and crustaceans, including a Western rock lobster (Panulirus cygnus). There was no significant correlation between the origin of the seafoods tested and the distribution of E. rhusiopathiae. An organism indistinguishable from Erysipelothrix tonsillarum was isolated for the first time from an Australian oyster and a silver bream. Overall, Erysipelothrix spp. were widely distributed in Australasian seafoods, illustrating the potential for erysipeloid-like infections in fishermen.     

Methods for Analysis of Protein Glutathionylation and their Application to Photosynthetic Organisms

Protein S-glutathionylation, the reversible formation of a mixed-disulfide between glutathione and protein thiols, is involved in protection of protein cysteines from irreversible oxidation, but also in protein redox regulation. Recent studies have implicated S-glutathionylation as a cellular response to oxidative/nitrosative stress, likely playing an important role in signaling. Considering the potential importance of glutathionylation, a number of methods have been developed for identifying proteins undergoing glutathionylation. These methods, ranging from analysis of purified proteins in vitro to large-scale proteomic analyses in vivo, allowed identification of nearly 200 targets in mammals. By contrast, the number of known glutathionylated proteins is more limited in photosynthetic organisms, although they are severely exposed to oxidative stress. The aim of this review is to detail the methods available for identification and analysis of glutathionylated proteins in vivo and in vitro. The advantages and drawbacks of each technique will be discussed as well as their application to photosynthetic organisms. Furthermore, an overview of known glutathionylated proteins in photosynthetic organisms is provided and the physiological importance of this post-translational modification is discussed.     

实时荧光定量PCR及其在传染性疾病检测中的应用

实时荧光定量PCR技术被广泛应用于实验研究、临床检测中。与普通的PCR相比,实时荧光定量PCR技术具有特异性强、灵敏度高、重复性好、定量准确、速度快、全封闭反应等优点。我们综述了实时荧光定量PCR技术的原理、定量方法,及其在传染性疾病检测研究中的应用。     

产脂酵母产脂培养条件研究及脂肪检测方法初探

目的：研究产脂酵母产脂条件及脂肪提取方法。方法：探讨了单因素如：pH、碳源、氮源、葡萄糖浓度、金属微量元素等对其产脂能力的影响,并进行了正交试验;脂肪测定方法研究,用对比分析法,并对其中的方法加以改进,采用光谱扫描以确定酵母脂肪最大吸收波长。结果：试验范围所得酵母产脂最佳条件是：接种量3%,MnCl_2 0．05%、FesO_4 0．04%、(NH_4)_2SO_4 0．3%、葡萄糖2%、pH 6．5,培养5d,45ml的发酵液其油脂的吸光度(252nm)可达2．4082;酵母脂肪最大吸收波长为252nm,在此波长下测定,获得了快速、准确的结果。结论：所得产脂条件可为进一步的开发研究打下基础。研究出的酵母脂肪测定方法,是一种快速、简便的方法,可满足产脂酵母菌种筛选和产脂条件研究的需要。     

两种教学方法在护理专业人体形态学教学中的应用及比较

目的:探讨A和B两神教学方法在护理专业人体形态学教学中的应用及比较.方法:通过应用A和B两种教学法,对全日制护理学专科2010-2班和护理学专科2011-2班的人体形态学期末考试平均成绩和及格率进行比较和分析.结果:采用A教学法的护理学专科2011-2班的最高分为88分,最低分为42,平均成绩为75.45分,标准差为10.34.采用B教学法的护理学专科2010-2班的最高分为84分,最低分为36,平均成绩为64.34分,标准差为11.65.对护理学专科2011-2班和2010-2班的平均成绩进行F检验,F=1.12＜1.50,故P＞0.10,方差齐,敌可用方差相等情形的两样本t检验,t=5.36＞2.66,故P＜0.01,两组平均成绩之间差异有统计学意义;采用A教学法的护理学专科2011-2班的及格率为81.54％,采用B教学法的护理学专科2010-2班的及格率为65.15％.对于以上两个班及格率进行卡方检验,x=4.49＞3.84,故P＜0.05,两组及格率之间差异有统计学意义.以上结果说明采用A教学法的护理学专科2011-2班的平均成绩和及格率明显高于采用B教学法的护理学专科2010-2班.结论:在人体形态学教学中,A教学法跟B教学法比具有明显的优势,同时A教学法自身也有不足之处.     

16份石榴RAPD扩增产物的两种电泳方法检测及其序列特征

本实验以16个石榴品种为实验材料,筛选出10个重复性及多态性均较好的引物进行RAPD分析。分别采用琼脂糖凝胶以及聚丙烯酰胺凝胶(PAGE)电泳检测方法对PCR扩增结果进行检测并对其结果进行比较,结果显示,两种电泳方式均能得到较为清晰的扩增条带,且两种电泳方式获得的条带总数及多态性条带数均有所不同,琼脂糖凝胶电泳方法共检测出76条带,其中有43条为多态性谱带,多态性比率为56.4%;而在PAGE电泳方法共检测出123条谱带,多态性谱带数为87条,多态性比率为70.95%。PAGE电泳方法检测出的条带数约为琼脂糖凝胶电泳方法检测出条带数的1.5倍。基于两种电泳方法所得RAPD标记的多态性位点,利用NYSYS软件计算遗传相似系数,并构建遗传关系聚类图,分析结果显示,石榴遗传多样性丰富,两种电泳方法所得聚类结果大致相同,可以利用RAPD分子标记及两种电泳检测方法对不同数量的石榴进行分子水平的品种鉴定和遗传多样性的分析。同时通过对来自几个引物随机挑选的17个片段进行克隆,测序结果显示17个片段都是对应引物的RAPD扩增产物,其中有3条是编码蛋白的基因片段,表明了RAPD不仅扩增基因组上的非编码蛋白序列,同时也可以扩增编码蛋白的基因片段,这为更好地认识RAPD技术的实质以及促进石榴产业的发展提供了理论依据。     

Development and Application of Different Methods for the Detection of Toxoplasma gondii in Water

Two methods, centrifugation and flocculation, were evaluated to determine their efficiencies of recovery of Toxoplasma gondii oocysts from contaminated water samples. Demineralized and tap water replicates were inoculated with high numbers of sporulated or unsporulated T. gondii oocysts (1 × 10⁵ and 1 × 10⁴ oocysts). The strain, age, and concentration of the seeded oocysts were recorded. Oocysts were recovered either by centrifugation of the contaminated samples at various g values or by flocculation with two coagulants, Fe₂(SO₄)₃ and Al₂(SO₄)₃. The recovery rates were determined with the final pellets by phase-contrast microscopy. Sporulated oocysts were recovered more effectively by flocculation with Al₂(SO₄)₃ (96.5% ± 21.7%) than by flocculation with Fe₂(SO₄)₃ (93.1% ± 8.1%) or by centrifugation at 2,073 × g (82.5% ± 6.8%). For the unsporulated oocysts, flocculation with Fe₂(SO₄)₃ was more successful (100.3% ± 26.9%) than flocculation with Al₂(SO₄)₃ (90.4% ± 19.1%) or centrifugation at 2,565 × g (97.2% ± 12.5%). The infectivity of the sporulated oocysts recovered by centrifugation was confirmed by seroconversion of all inoculated mice 77 days postinfection. These data suggest that sporulated Toxoplasma oocysts purified by methods commonly used for waterborne pathogens retain their infectivity after mechanical treatment and are able to induce infections in mammals. This is the first step in developing a systematic approach for the detection of Toxoplasma oocysts in water.     

实验兔出血症病毒检测方法的建立与免疫效果调查

目的检测全省六个实验兔场的兔子所携带的兔出血症病毒（RHDV）情况,调查实验兔RHDV抗体水平,评价不同疫苗的免疫效果,比较HAI与ELISA两种方法的符合率。方法采用HAI、ELISA方法对1168份实验兔RHDV抗体进行了检测,并与RT-PCR方法的检测结果进行对比分析。结果我省实验兔免疫情况较好,不同饲养场的实验兔免疫合格率虽有不同,但未发生疫情。通过比较发现ELISA法检测的抗体合格率明显高于HAI法。结论LISA、HAI和RT-PCR方法均适合实验兔RHDV的检测。     

Adaptive, pre-adaptive and non-adaptive components of radiations in ancient lakes: a review

Ancient lakes are ideal model systems for evolutionary studies, as they hold hundreds of endemic species. The vast majority of these still occur in the cradle of their origin. We distinguish three different modes of speciation (allo-, para- and sympatric) which have occurred in these habitats. Although radiations from ancient lakes are generally assumed to be adaptive, we cannot fully support this point of view, because non-adaptive radiations also appear to be common, for example through chromosomal changes, hybridization or sexual selection. Even in supposedly adaptive cladogenesis, e.g. as concerns the presumed trophic adaptations of cichlid (Pisces) mouth and tooth shapes, both adaptive and non-adaptive components are acting. Distribution patterns of non-marine ostracods (Crustacea) within and outside of ancient lakes indicate that sexual reproduction might be an additional requirement for successful radiations in ancient lakes, at least in certain groups. This can best be understood by invoking ecology-based hypotheses on the evolutionary superiority of sexual reproduction such as Fisher–Muller accelerated evolution and the Tangled Bank.     

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.     

A Comparative Test of Adaptive Explanations for Hypsodonty in Ungulates and Rodents

Hypsodonty has long been recognized as an adaptation for grazing: grazing is suggested to increase tooth wear due to endogenous (e.g., fiber, silica) and/or exogenous (e.g., dust, grit) properties of ingested food. However, it is unknown whether tooth crown height is correlated with the mastication of high fiber or silica in grasses, the ingestion of external abrasives, or both. Furthermore, comparative studies of hypsodonty have not explicitly taken into account phylogenetic biases due to shared ancestry in tooth morphology and/or feeding behavior. This study highlights the relationship between molar crown height and feeding habits in African ungulates and South American rodents when phylogenetic effects are controlled. Among ungulates, high hypsodonty indices are significantly associated with specific plant and foraging height preferences, while habitat and climate show no correlation with tooth crown height. For rodents, grass-eating species are significantly more hypsodont than frugivorous or folivorous species, and arboreal rodents are less hypsodont than terrestrial species. These results as well as those of a posteriori analyses controlling for aspects of the behavioral ecology (e.g., grass-eating, substrate preference) of the sample species confirm the role of both diet and grit in shaping the evolution of cheek tooth crown height in herbivorous mammals.     

实验用小型猪呼吸道支原体检测及方法比较

目的通过常用的三种不同方法对支原体的检测,了解实验用小型猪支原体感染情况,为今后实验用小型猪支原体检测方法国家标准的制定提供参考。方法采用培养法、PCR和ELISA方法分别对20头小型猪的气管、肺和血清进行检测。结果三种检测方法中,PCR方法支原体阳性检出率为15%,ELISA方法为20%,而培养法结果均为阴性。结论目前在普通级小型猪中存在支原体的感染。检测方法中PCR和ELISA方法较培养法更省时,敏感性更高。     

Identification and Classification of bcl Genes and Proteins of Bacillus cereus Group Organisms and Their Application in Bacillus anthracis Detection and Fingerprinting

The Bacillus cereus group includes three closely related species, B. anthracis, B. cereus, and B. thuringiensis, which form a highly homogeneous subdivision of the genus Bacillus. One of these species, B. anthracis, has been identified as one of the most probable bacterial biowarfare agents. Here, we evaluate the sequence and length polymorphisms of the Bacillus collagen-like protein bcl genes as a basis for B. anthracis detection and fingerprinting. Five genes, designated bclA to bclE, are present in B. anthracis strains. Examination of bclABCDE sequences identified polymorphisms in bclB alleles of the B. cereus group organisms. These sequence polymorphisms allowed specific detection of B. anthracis strains by PCR using both genomic DNA and purified Bacillus spores in reactions. By exploiting the length variation of the bcl alleles it was demonstrated that the combined bclABCDE PCR products generate markedly different fingerprints for the B. anthracis Ames and Sterne strains. Moreover, we predict that bclABCDE length polymorphism creates unique signatures for B. anthracis strains, which facilitates identification of strains with specificity and confidence. Thus, we present a new diagnostic concept for B. anthracis detection and fingerprinting, which can be used alone or in combination with previously established typing platforms.The Bacillus cereus group includes three closely related species, B. anthracis, B. cereus, and B. thuringiensis, as well as the more distantly related species B. mycoides and B. weihenstephanensis. These gram-positive, spore-forming bacteria form a highly homogeneous subdivision of the genus Bacillus, which also contains several other organisms belonging to the B. subtilis group. The importance and public awareness of B. cereus group organisms are associated with their distinct phenotypes and pathological effects. B. anthracis is the causative agent of anthrax, a disease that affects humans and animals worldwide and has also been developed as a biological warfare agent (17, 25). B. cereus is an opportunistic human pathogen which is responsible mainly for gastrointestinal illnesses resulting from food contamination (9), whereas B. thuringiensis is an insect pathogen whose toxin is a biological pesticide widely used in global agriculture (38). The systematics of the members of the B. cereus group poses significant challenges due to very high level of chromosomal synteny and protein identity (33). Intense efforts have focused on overcoming these challenges, and there has been a particular focus on developing methods for specific detection of B. anthracis and for differentiating among strains of these closely related organisms.Biodefense and forensic needs prompted large-scale sequencing of multiple bacillus genomes in a search for polymorphic sites for use in typing procedures (33). One type of polymorphism involves variation in the number of repeating nucleotide units that are referred to as variable-number tandem repeats (VNTRs). The resulting variation in the length and mass of the PCR products of these units can be demonstrated by gel and capillary electrophoresis (20), mass spectrometry (29), or microchannel fluidics (30). To date, several different VNTRs have been identified and tested. For example, Keim et al. studied the genetic relationship among a large collection of B. anthracis isolates based on the VNTRs found in the vrr genes (19, 20). Using a similar approach, Valjevac et al. used VNTRs of Bcms loci as markers to assess the phylogeny of members of the B. cereus group (46). Finally, length variation of the collagen-like (CL) region of the bclA gene was employed to differentiate among B. anthracis strains (6, 42).The CL sequences, which are composed of Gly-Xaa-Yaa (i.e., a glycine followed by two additional residues; GXY) repeats, have been identified in silico in more than 100 prokaryotic proteins (34). Recent studies demonstrated that some bacterial CL proteins (CLPs), such as streptococcal protein Scl and BclA, can form the collagen triple helix (4, 14, 48). Bacterial CLPs are typically surface exposed and are found in microorganisms pathogenic to humans and animals. BclA (Bacillus CLP of B. anthracis) is a major spore surface protein (41) and is found in all members of the B. cereus group (6; this study). A second CLP, designated BclB (47), was identified as a component of the B. anthracis exosporium; however, its distribution and structural properties have not been well characterized. Likewise, two closely related proteins, ExsH and ExsJ, contain GXY CL repeats and are presumably located in the exosporium of Bacillus strains (45).In this work we investigated in silico the occurrence and distribution of the bcl genes, presumably encoding CLPs, in all members of the B. cereus group. A new classification of the resulting Bcl protein variants is proposed based on the domain composition and folding of these proteins. As many as 10 bcl genes were found in a single B. cereus strain. Five genes were consistently observed in B. anthracis strains and designated bclA to bclE. We further analyzed sequence polymorphisms among these bcl genes and assessed use of them for B. anthracis detection and strain fingerprinting. Representative members of the B. cereus group and less closely related control bacilli were used to demonstrate specific bclB gene-based detection of B. anthracis spores. Finally, a combination of experiments and mathematical modeling was used to demonstrate how combined use of the bclABCDE sequence polymorphisms can be a powerful tool for strain fingerprinting in biodefense and forensic applications.