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Biophysical Reviews - Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for...     

Opportunities and strategies to further reduce animal use for Leptospira vaccine potency testing

Hamsters are routinely infected with virulent Leptospira for two purposes in the regulation of biologics: the performance of Codified potency tests and maintenance of challenge culture for the Codified potency tests. Options for reducing animal use in these processes were explored in a plenary lecture at the “International Workshop on Alternative Methods for Leptospira Vaccine Potency Testing: State of the Science and the Way Forward” held at the Center for Veterinary Biologics in September 2012. The use of validated in vitro potency assays such as those developed by the U.S. Department of Agriculture for Leptospira (L.) canicola, Leptospira grippotyphosa, Leptospira pomona, and Leptospira icterohaemorrhagiae rather than the Codified hamster vaccination–challenge assay was encouraged. Alternatives such as reduced animal numbers in the hamster vaccination–challenge testing were considered for problematic situations. Specifically, the merits of sharing challenge controls, reducing group sizes, and eliminating animals for concurrent challenge dose titration were assessed. Options for maintaining virulent, stable cultures without serial passage through hamsters or with decreased hamster use were also discussed. The maintenance of virulent Leptospira without the use of live animals is especially difficult since a reliable means to maintain virulence after multiple in vitro passages has not yet been identified.     

假说检验和科学方法

本文的意图是让研究者审视研究方法,并在研究设计中充分使用假说检验,并在选择模式物种时充分理解其自然史.我们的总前提是,按照"强推论"(指假定拒绝某一假说而不是支持某一偏爱假说)的逻辑,科学能够进展得更快、更可观、更有确定性.我们强调并提供了符合逻辑的一系列步骤,即确定科学问题或确定具有未知生物学意义的问题;列出所有可靠的、能解释所观察现象的假说,每个假说列出其可检验的、可证明其无根据的预测;然后是符合预测检验的实验或研究设计.我们也强调,模式物种对于解决科学的理论问题以及得出推论是很重要的.本文所展示的不是新思想,只是提醒研究者要注意遵循的基本研究途径.     

USDA regulatory guidelines and practices for veterinary Leptospira vaccine potency testing

Batch-release potency testing of leptospiral vaccines licensed by the United States Department of Agriculture (USDA) historically was conducted through animal vaccination-challenge models. The hamster vaccination-challenge assay was Codified in 1974 for bacterins containing Leptospira pomona, Leptospira icterohaemorrhagiae, and Leptospira canicola, and in 1975 for bacterins containing Leptospira grippotyphosa. In brief, 10 hamsters are vaccinated with a specified dilution of bacterin. After a holding period, the vaccinated hamsters, as well as nonvaccinated controls, are challenged with virulent Leptospira and observed for mortality. Eighty percent of vaccinated hamsters must survive in the face of a valid challenge. The high cost of the Codified tests, in terms of monetary expense and animal welfare, prompted the Center for Veterinary Biologics (CVB) to develop ELISA alternatives for them. Potency tests for other serogroups, such as Leptospira hardjo-bovis, that do not have Codified requirements for potency testing continue to be examined on a case-by-case basis.     

Antibiotic and Disinfectant Resistance in Tap Water Strains – Insight into the Resistance of Environmental Bacteria

Although antibiotic-resistant bacteria (ARB) have been isolated from tap water worldwide, the knowledge of their resistance patterns is still scarce. Both horizontal and vertical gene transfer has been suggested to contribute to the resistance spread among tap water bacteria. In this study, ARB were isolated from finished water collected at two independent water treatment plants (WTPs) and tap water collected at several point-of-use taps during summer and winter sampling campaigns. A total of 24 strains were identified to genus or species level and subjected to antibiotic and disinfectant susceptibility testing. The investigated tap water ARB belonged to phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. The majority of the isolates proved multidrug resistant and resistant to chemical disinfectant. Neither seasonal nor WTP-dependent variabilities in antibiotic or disinfectant resistance were found. Antibiotics most effective against the investigated isolates included imipenem, tetracyclines, erythromycin, and least effective – aztreonam, cefotaxime, amoxicillin, and ceftazidime. The most resistant strains originate from Afipia sp. and Methylobacterium sp. Comparing resistance patterns of isolated tap water ARB with literature reports concerning the same genera or species confirms intra-genus or even intra-specific variabilities of environmental bacteria. Neither species-specific nor acquired resistance can be excluded.     

Prospects for chemiluminescent and bioluminescent immunoassay and nucleic acid assays in food testing and the pharmaceutical industry

The sensitivity, speed and convenience of chemiluminescent (CL) and bioluminescent (BL) immunoassays and probe assays have led to a diverse range of applications for these technologies, mainly in the clinical laboratory. These methods are now being explored by the food and pharmaceutical industries. Demanding detection limits and the complexity of sample preparation for food and pharmaceutical analyses present daunting challenges for the analyst. Immunoassay and nucleic acid amplification technologies have been applied to food testing, but these have mostly favoured non-luminescent endpoints. Food assays with CL or BL endpoints are now emerging, e.g., Clostridium botulinum type A detection using a CL immunosorbent assay; Salmonella and Zygosaccharomyces detection using a combination of PCR and CL detection. The analytical challenges posed by the pharmaceutical industry include testing for contaminants in raw materials and drug products, and drug discovery. The sensitivity and rapid signal acquisition characteristics of CL and BL are advantageous for the high throughput, massively parallel testing of micro-sized samples demanded in drug discovery. Current progress and the prospects for CL and BL immunoassay and nucleic acid technologies in this and other pharmaceutical and food applications is reviewed. © 1998 John Wiley & Sons, Ltd.     

Heritability: uses and abuses

This paper begins with a brief summary of the history of the development of ideas in the field of quantitative genetics. Next there is discussion of the controversy surrounding the contention that IQ tests validly estimate some highly heritable general intelligence factor. The validity of the reasoning supporting this contention is questioned. The theory of correlation between relatives has been of vast importance in plant and animal breeding because it is possible to design and carry out experiments to estimate variance components in expressions for covariances between relatives. However, data on humans is observational and individuals are not randomly assigned to environments, so that estimation of heritability from such data is not on the same firm foundation as it is in plant and animal breeding contexts. This revised version was published online in August 2006 with corrections to the Cover Date.     

106 例宫颈炎患者支原体检测及抗生素敏感性分析

目的：对本地区宫颈炎患者解脲脲原体（Uu）和人型支原体（Mh）进行监测,分析抗生素敏感情况,为临床诊疗提供实验依 据。方法：无菌采集宫颈炎患者宫颈分泌物,用支原体培养、鉴定、药敏试剂盒进行培养和药敏试验。结果：支原体总检出率为 71.70 %。Uu 检出率为52.83 %,Uu 合并Mh 检出率16.04 %,Mh 检出率为2.83 %。56 例单纯Uu 株体外抗生素敏感性显示：对四 环素族多西环素100 %、美满霉素98.21 %高度敏感;对大环内酯类敏感性不一：克拉霉素96.43 %,阿奇霉素91.07 %,交沙霉素 76.79 %,红霉素67.86 %,罗红霉素32.14 %;对喹诺酮类如加替沙星83.93 %较敏感,而对左氧氟沙星,司帕沙星敏感性差;对克 林霉素和甲砜霉素不敏感;17 例Uu 合并Mh的抗生素敏感性为：美满霉素100 %,多西环素100 %,交沙霉素88.23 %,加替沙星 64.7 %,对左氧氟沙星、司帕沙星、红霉素、阿奇霉素、克拉霉素,罗红霉素、甲砜霉素、克林霉素均不敏感。3 株单纯Mh 例数少未 做统计。结论：宫颈炎患者中支原体检出率较高,其中单纯Uu 检出率较Uu、Mh 混合阳性率高,对四环素类、大环内酯类族中的多 数抗生素敏感,治疗选择余地大。Uu、Mh 混合敏感性抗生素种类少,应优先选择四环素类抗生素治疗。     

Company disclosure and consumer perceptions of the privacy implications of direct-to-consumer genetic testing

This study examines the way direct-to-consumer genetic testing (DTCGT) companies communicate privacy information and how consumers understand privacy implications of DTCGT. We first conducted an analysis of DTCGT websites to determine what information they provide regarding the treatment of consumer information and samples. 86 companies offered DTCGT services that could be purchased online from Canada. We then surveyed 415 consumers (180 had purchased, 235 considered but did not purchase DTCGT). While most websites had some privacy information, few provided sufficient information for consumers to make informed purchase decisions. Nearly half of participants reported reading the company’s privacy policy and many felt they received enough information about privacy implications, but their expectations were generally not consistent with company practices. The most common expectation was that the company would share results only with them and destroy their sample after testing. We discuss these issues regarding privacy expectations in the context of DTCGT.     

106例宫颈炎患者支原体检测及抗生素敏感性分析

目的：对本地区宫颈炎患者解脲脲原体（Uu）和人型支原体（Mh）进行监测,分析抗生素敏感情况,为临床诊疗提供实验依据。方法：无菌采集宫颈炎患者宫颈分泌物,用支原体培养、鉴定、药敏试剂盒进行培养和药敏试验。结果：支原体总检出率为71.70%。Uu检出率为52.83%,Uu合并Mh检出率16.04%,Mh检出率为2.83%。56例单纯Uu株体外抗生素敏感性显示：对四环素族多西环素100%、美满霉素98.21%高度敏感;对大环内酯类敏感性不一：克拉霉素96.43%,阿奇霉素91.07%,交沙霉素76.79%,红霉素67.86%,罗红霉素32.14%;对喹诺酮类如加替沙星83.93%较敏感,而对左氧氟沙星,司帕沙星敏感性差;对克林霉素和甲砜霉素不敏感;17例Uu合并Mh的抗生素敏感性为：美满霉素100%,多西环素100%,交沙霉素88.23%,加替沙星64.7%,对左氧氟沙星、司帕沙星、红霉素、阿奇霉素、克拉霉素,罗红霉素、甲砜霉素、克林霉素均不敏感。3株单纯Mh例数少未做统计。结论：宫颈炎患者中支原体检出率较高,其中单纯Uu检出率较Uu、Mh混合阳性率高,对四环素类、大环内酯类族中的多数抗生素敏感,治疗选择余地大。Uu、Mh混合敏感性抗生素种类少,应优先选择四环素类抗生素治疗。     

Estimating ecotoxicological risk and impact using indigenous aquatic microbial communities

Emphasis has increased on accuracy in predicting the effect that anthropogenic stress has on natural ecosystems. Although toxicity tests low in environmental realism, such as standardized single species procedures, have been useful in providing a certain degree of protection to human health and the environment, the accuracy of such tests for predicting the effects of anthropogenic activities on complex ecosystems is questionable. The use of indigenous communities of microorganisms to assess the hazard of toxicants in aquatic ecosystems has many advantages. Theoretical and practical aspects of microbial community tests are discussed, particularly in related to widely cited problems in the use of multispecies test systems for predicting hazard. Further standardization of testing protocols using microbial colonization dynamics is advocated on the basis of previous studies, which have shown these parameters to be useful in assessing risk and impact of hazardous substances in aquatic ecosystems.     

Nonparametric Evaluation of ANOVA Designs by Local,Regional, and Global Contingency Testing

Nonparametric analysis of ANOVA designs is proposed to be done by simultaneous contingency testing of discretised response variables. Selected treatment-response patterns are evaluated by predictive configural frequency analysis (local contingency). Treatment response associations are defined by regional contingencies. Total treatment-response relation is defined by global contingency. All methods are illustrated numerically by biometrical examples.     

DNA sampling and banking in clinical genetics and genetic research

Health-related direct-to-consumer (DTC) genetic testing has been a controversial practice. Especially problematic is predictive testing for Alzheimer disease (AD), since the disease is incurable, prevention is inconclusive, and testing does not definitively predict an individual's future disease status. In this paper, I examine two contrasting cases of subjects who learn through genetic testing that they have an elevated risk of developing AD later in life. In these cases, the subject's emotional response to the result is related to how well prepared she was for the real-life personal implications of possible test results. Analysis leads to the conclusion that when groups of health-related genetic tests are offered as packages by DTC companies, informed consumer choice is rendered impossible. Moreover, I argue, this marketing approach contravenes US Federal Trade Commission policies for non-deceptive commercial communications. I conclude by suggesting ways to improve the prospects for informed consumer choice in DTC testing.     

Seeing and knowing in twenty-first century genetic medicine: the clinical pedigree as epistemological tool and hybrid risk technique

This paper explores the clinical pedigree as a risk technique within the context of the predictive genetic testing (PGT) clinic. We situate the PGT clinic as a site of genetic governance in that it is a site both for the production of knowledge about genetic risk and for intervening in the everyday lives of individuals and their families who learn to cultivate their relations with themselves and their biological relatives in relation to genetic risk knowledge. Drawing on literature of the pedigree as socially constructed and on notions of risk governance, we suggest that the pedigree operates as an epistemological tool and risk technique – that is, as a visual device that assists in organizing the social relations of knowledge production and aids in effecting shifts in patient subjectivity in ways that are consistent with neoliberal notions of active citizenship.     

基因临床研究与应用的伦理探讨

??????? 基因临床研究与应用的伦理问题主要是基因技术对接受者自身与其子代的安全性及对整个人类基因库的影响,和基因信息的合理管理。在基因临床研究与应用中,除遵循生命伦理的基本原则外,还应遵循互惠性、相关性、一致性、公民性、普世性等特殊的伦理原则。我国应加强对基因临床研究与应用现况、临床医师基因伦理认知以及医学院校生命伦理教学状况的实证研究,为基因技术在我国医疗卫生领域的发展提供决策依据。     

Comparative evaluation of standard dilution method and commercial kit for frozen plate antifungal susceptibility testing of yeasts using 200 clinical isolates

A comparative evaluation of standard microdilution methods and a commercial kit for frozen plate antifungal susceptibility testing of yeasts was performed using amphotericin B, flucytosine, fluconazole, miconazole, and itraconazole on 200 yeast isolates. The isolates included 100 strains of Candida albicans, eight of C. tropicalis, twelve of C. parapsilosis, eight of C. glabrata, five of Cryptococcus neoformans, thirteen of Trichosporon asahii, and 54 other strains of seven other species of ascomycotic yeasts. Microdilution testing was performed according to the standard method for antifungal susceptibility testing published by the Japanese Society for Medical Mycology (JSMM), which are a modification of the method developed by the National Committee for Clinical Laboratory Standards (NCCLS) M27-P. The commercial kit was prepared according to the manufacturer's instructions. The degree of agreement within +/-1 dilution for 200 clinical isolates against five antifungal agents was excellent with values for amphotericin B, flucytosine, fluconazole, miconazole, and itraconazole of 100%, 99.0%, 97.5%, 97.0%, and 97.0%, respectively. Overall, the frozen plate antifungal susceptibility testing kit provided convenient and reproducible results comparable to those obtained with the JSMM standard method.     

Ordered multiple comparisons with the best and their applications to dose-response studies

This article considers the problem of comparing several treatments (dose levels, interventions, etc.) with the best, where the best treatment is unknown and the treatments are ordered in some sense. Order relations among treatments often occur quite naturally in practice. They may be ordered according to increasing risks, such as tolerability or safety problems with increasing dose levels in a dose-response study, for example. We tackle the problem of constructing a lower confidence bound for the smallest index of all treatments being at most marginally less effective than the (best) treatment having the largest effect. Such a bound ensures at confidence level 1 -alpha that all treatments with lower indices are relevantly less effective than the best competitor. We derive a multiple testing strategy that results in sharp confidence bounds. The proposed lower confidence bound is compared with those derived from other testing strategies. We further derive closed-form expressions for power and sample size calculations. Finally, we investigate several real data sets to illustrate various applications of our methods.     

Microelectrode array (MEA) platform as a sensitive tool to detect and evaluate Ostreopsis cf. ovata toxicity

In the last decade, the occurrence of harmful dinoflagellate blooms of the genus Ostreopsis has increased both in frequency and in geographic distribution with adverse impacts on public health and the economy. Ostreopsis species are producers of palytoxin-like toxins (putative palytoxin and ovatoxins) which are among the most potent natural non-protein compounds known to date, exhibiting extreme toxicity in mammals, including humans. Most existing toxicological data are derived from in vivo mouse assay and are related to acute effects of pure palytoxin, without considering that the toxicity mechanism of dinoflagellates can be dependent on the varying composition of complex biotoxins mixture and on the presence of cellular components.In this study, in vitro neuronal networks coupled to microelectrode array (MEA)-based system are proposed, for the first time, as sensitive biosensors for the evaluation of marine alga toxicity on mammalian cells. Toxic effect was investigated by testing three different treatments of laboratory cultured Ostreopsis cf. ovata cells: filtered and re-suspended algal cells; filtered, re-suspended and sonicated algal cells; conditioned growth medium devoid of algal cells. The great sensitivity of this system revealed the mixture of PTLX-complex analogues naturally released in the growth medium and the different potency of the three treatments to inhibit the neuronal network spontaneous electrical activity. Moreover, by means of the multiparametric analysis of neuronal network activity, the approach revealed a different toxicity mechanism of the cellular component compared to the algal conditioned growth medium, highlighting the potential active role of the first treatment.