基因表达时间延迟调控关系识别软件ITdGR

基因表达调控网络的深入研究有利于分子药物靶标的发现以及推新药的研发,是未来生物医学研究的重要内容。针对基因表达调控的时间延迟问题,我们初步设计开发了一套基于基因表达谱数据识别基因表达时间延迟调控关系的软件ITdGR(Identification of Time-delayed Gene Regulations)。并已经成功地将该软件应用于酿酒酵母细胞周期的基因表达谱数据中,识别出的调控关系与已有的知识相符。该软件为基因调控网络重构以及基因表达动态研究提供了一个方便和快捷的工具。     

Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes)

Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.     

Skin self-examinations and visual identification of atypical nevi: Comparing individual and crowdsourcing approaches

PurposeSkin self-examination (SSE) is one method for identifying atypical nevi among members of the general public. Unfortunately, past research has shown that SSE has low sensitivity in detecting atypical nevi. The current study investigates whether crowdsourcing (collective effort) can improve SSE identification accuracy. Collective effort is potentially useful for improving people's visual identification of atypical nevi during SSE because, even when a single person has low reliability at a task, the pattern of the group can overcome the limitations of each individual.MethodsAdults (N = 500) were recruited from a shopping mall in the Midwest. Participants viewed educational pamphlets about SSE and then completed a mole identification task. For the task, participants were asked to circle mole images that appeared atypical. Forty nevi images were provided; nine of the images were of nevi that were later diagnosed as melanoma.ResultsConsistent with past research, individual effort exhibited modest sensitivity (.58) for identifying atypical nevi in the mole identification task. As predicted, collective effort overcame the limitations of individual effort. Specifically, a 19% collective effort identification threshold exhibited superior sensitivity (.90).ConclusionsThe results of the current study suggest that limitations of SSE can be countered by collective effort, a finding that supports the pursuit of interventions promoting early melanoma detection that contain crowdsourced visual identification components.     

The science of research: The principles underlying the discovery of cognitive and other biological mechanisms

Studies of cognitive function include a wide spectrum of disciplines, with very diverse theoretical and practical frameworks. For example, in Behavioral Neuroscience cognitive mechanisms are mostly inferred from loss of function (lesion) experiments while in Cognitive Neuroscience these mechanisms are commonly deduced from brain activation patterns. Although neuroscientists acknowledge the limitations of deriving conclusions using a limited scope of approaches, there are no systematically studied, objective and explicit criteria for what is required to test a given hypothesis of cognitive function. This problem plagues every discipline in science: scientific research lacks objective, systematic studies that validate the principles underlying even its most elemental practices. For example, scientists decide what experiments are best suited to test key ideas in their field, which hypotheses have sufficient supporting evidence and which require further investigation, which studies are important and which are not, based on intuitions derived from experience, implicit principles learned from mentors and colleagues, traditions in their fields, etc. Philosophers have made numerous attempts to articulate and frame the principles that guide research and innovation, but these speculative ideas have remained untested and have had a minimal impact on the work of scientists. Here, I propose the development of methods for systematically and objectively studying and improving the modus operandi of research and development. This effort (the science of scientific research or S2) will benefit all aspects of science, from education of young scientists to research, publishing and funding, since it will provide explicit and systematically tested frameworks for practices in science. To illustrate its goals, I will introduce a hypothesis (the Convergent Four) derived from experimental practices common in molecular and cellular biology. This S2 hypothesis proposes that there are at least four fundamentally distinct strategies that scientists can use to test the connection between two phenomena of interest (A and B), and that to establish a compelling connection between A and B it is crucial to develop independently confirmed lines of convergent evidence in each of these four categories. The four categories include negative alteration (decrease probability of A or p(A) and determine p(B)), positive alteration (increase p(A) and determine p(B)), non-intervention (examine whether A precedes B) and integration (develop ideas about how to get from A to B and integrate those ideas with other available information about A and B). I will discuss both strategies to test this hypothesis and its implications for studies of cognitive function.     

Cultivation of genetically modified organisms: resource needs for monitoring adverse effects on biodiversity

Genetically modified organisms (GMO) in non-European countries are introduced into the agro-environment on large scale with little knowledge of adverse effects on biodiversity. In the European Union (EU) possible effects of GMOs on biodiversity have to be accurately and precisely monitored. Monitoring biodiversity with a high precision is expensive and may only be achieved in close cooperation between GMO monitoring and general biodiversity monitoring. The EuMon project sampled metadata on biodiversity monitoring in Europe. Basing on the metadata, we estimated resource needs for biodiversity monitoring as needed for detecting potential adverse effects of GMOs on biodiversity. On average the analyzed schemes with a potential to detect at least a 5% change of biodiversity monitor 242.6 ± 105.4 sites at 322.6 ± 172.1 person days employing 63 ± 23 persons per year. The time invested in monitoring, given as person days, however, differed greatly between schemes and species groups, so that real manpower might be considerably higher.     

A new gel tube method for the direct detection, identification and susceptibility testing of bacteria in clinical samples

We recently developed a simple new method which is designed to separate and concentrate bacteria from a sample by centrifugation in a gel system. Bacterial enzyme activity is then detected inside the gel without further manipulation using a colorimetric or fluorogenic substrate. The method provides a rapid, direct means of detecting bacteria in clinical samples, dispensing with the 24-h period normally required to isolate colonies on agar. Various applications of the method are described below, e.g. screening of negative urine samples, identification of Escherichia coli in urine samples, identification of Staphylococcus aureus in blood culture broths and detection of oxacillin-resistant S. aureus in blood culture broths. The advantages of the gel system and other applications are discussed.     

Molecular identification of five Indian sciaenids (pisces: perciformes,sciaenidae) using RAPD markers

The randomly amplified polymorphic DNA (RAPD) markers were used to detect interspecific genetic variability and genetic relatedness among five Indian sciaenids namely Otolithes cuvieri, Johnieops sina, Johnieops macrorhynus, Johnieops vogleri and Protonibea diacanthus for the first time. Eight RAPD primers (OPA01, OPA06, OPA07, OPA18, OPP12, OPP14, OPP16 and OPP11) generated 40 species specific diagnostic bands. The highest genetic divergence was detected between J. macrorhynus and P. diacanthus (0.586) where as the lowest one was observed between J. sina and J. vogleri (0.274). Handling editor: C. Strumbauer     

应用DNA指纹图谱技术鉴定整肠生菌株BL63516的研究

目的建立应用DNA指纹图谱技术鉴定微生态制剂——整肠生菌株BL63516的方法,提高菌种鉴别水平。方法应用RAPD（随机扩增多态性）方法,采用50条随机引物对7株地衣芽胞杆菌进行基因组DNA指纹图谱分析,选择多态性好、重复性好、稳定性强的随机引物,对BL63516与其他地衣芽胞杆菌进行区分。结果发现选用引物$87或$88分别对7株地衣芽胞杆菌进行基因组DNA指纹图谱分析,BL63516菌株扩增的DNA片段的大小、数量均与其他地衣芽胞杆菌有明显差异。结论此方法具有可重复性,方便、快速和准确的优势,可用于微生态制剂整肠生菌株的鉴别。     

Exploring the functional significance of forest diversity: A new long-term experiment with temperate tree species (BIOTREE)

Effects of biodiversity on ecosystem functioning have been mainly studied in experiments that artificially create gradients in grassland plant diversity. Woody species were largely excluded from these early experiments, despite the ecological and socioeconomic importance of forest ecosystems. We discuss conceptual aspects of mechanistically driven research on the biodiversity–ecosystem functioning relationship in forests, including the comparison of scientific approaches like ‘observational studies’, ‘removal experiments’, and ‘synthetic-assemblage experiments’. We give a short overview on the differences between herbaceous and forest ecosystems, focusing on canopy characteristics, and the possibilities for individual versus population-based investigations.We present detailed information about the first large-scale, multisite and long-term biodiversity–ecosystem functioning experiment with tree species of temperate forests (BIOTREE – BIOdiversity and ecosystem processes in experimental TREE stands). At three sites of differing geology and local climate, we planted 200,000 saplings on a total area of 70 ha. At two sites, diversity gradients were established by varying the number of tree species (BIOTREE-SPECIES). At a third site, only functional diversity at a constant level of tree species richness was manipulated by selecting mixtures that differ in the functional trait values of the corresponding species (BIOTREE-FD). Additional experimental treatments at the subplot level include silvicultural management options, the addition of subdominant species, and the reduction of genetic diversity. Response variables focus on productivity, biogeochemical cycles and carbon sequestration, and resource use complementarity.We explore the use of different measures of functional diversity for a posteriori classifications of functional richness and their use in the analysis of our tree diversity experiment. The experiment is thought to provide a long-term research platform for a variety of scientific questions related to forest biodiversity and ecosystem processes.     

Polychaete assemblages of a sub-arctic Newfoundland fjord: habitat, distribution, and identification

This study explores the association of 24 polychaete species with sandy and muddy habitats located in a sub-arctic fjord, and across Atlantic Canada including Labrador, Newfoundland, and the Gulf of St. Lawrence. Key characters used to facilitate species identification are also summarized. Within Bonne Bay, distinctive polychaete assemblages were associated with specific sediment types and polychaete species richness and density were significant both predictors of corresponding total (infaunal) density and species richness. Polychaetes were denser and more diverse in sandy sediments, partly because sandy locales were associated with the outer portion of the bay, and therefore were closer to the more productive and diverse Gulf of St. Lawrence. In general, species that occupied both sediment types were more widely distributed within Bonne Bay and across the region. The biogeography of most species also suggests that the Bonne Bay fauna is transitional between Labrador and Acadian biogeographic provinces.     

Evaluation of the RAPID ID 32A system for the identification of Bacteroides fragilis and related organisms

S.A. JENKINS, D.B. DRUCKER, M.G.L. KEANEY AND L.A. GANGULI. 1991. This study evaluated the ability of a rapid identification system for anaerobic bacteria. ATB 32A, now renamed RAPID ID 32A (API-bioMérieux UK Ltd., Basingstoke), to identify accurately 74 strains of the 'B. fragilis group'. ATB 32A identified correctly 78.4% of strains to species level, without supplemental tests. The percentage of strains identified to species level rose to 94.6% when a supplementary test (advised by bioMérieux) for catalase production was used to differentiate between Bacteroides ovatus and Bacteroides uniformis. RAPID ID 32A is a rapid, accurate method for the identification of members of the 'B. fragilis group' isolated within a routine clinical laboratory.     

Reverse dot blot hybridization: A useful method for the direct identification of lactic acid bacteria in fermented food

Abstract A rapid method for a reliable and simultaneous identification of different lactic acid bacteria in fermented food has been developed. Various 16S and 23S rRNA-targeted, species-specific oligonucleotides were applied as capture probes in a non-radioactive reverse dot blot hybridization. A simple and fast DNA extraction method in combination with in vitro amplification of rRNA gene fragments enables the direct detection of typical starter organisms without any preceding enrichment or cultivation steps. Various lactic acid bacteria occurring in cheese, yogurt, sausages, sauerkraut and sourdough could be identified at the species level within 1 day.     

Evaluation of the RAPID ID 32A system for the identification of Bacteroides fragilis and related organisms

This study evaluated the ability of a rapid identification system for anaerobic bacteria, ATB 32A, now renamed RAPID ID 32A (API-bioMérieux UK Ltd., Basingstoke), to identify accurately 74 strains of the 'B. fragilis group'. ATB 32A identified correctly 78.4% of strains to species level, without supplemental tests. The percentage of strains identified to species level rose to 94.6% when a supplementary test (advised by bioMérieux) for catalase production was used to differentiate between Bacteroides ovatus and Bacteroides uniformis. RAPID ID 32A is a rapid, accurate method for the identification of members of the 'B. fragilis group' isolated within a routine clinical laboratory.     

Use of the gyrB gene for the identification of Pandoraea species

The recently described genus Pandoraea consists of five named species and four unnamed genomospecies, several of which have been identified in clinical specimens including respiratory secretions from persons with cystic fibrosis. We investigated whether it is possible to distinguish species of the genus Pandoraea by means of restriction fragment length polymorphism (RFLP) analysis and direct sequencing of the gyrB gene. Sixty-seven Pandoraea isolates were included. Species-specific RFLP patterns were obtained following digestion of the PCR-amplified gyrB gene with MspI. Specificity of RFLP groupings was confirmed by direct sequencing of several representative isolates. Our results indicate that RFLP analysis and sequencing of the gyrB gene are useful for the identification of Pandoraea species. We also found that further taxonomic studies within the beta-Proteobacteria using the gyrB gene would benefit from the development of additional primers allowing more efficient amplification of the gyrB gene. Our data also indicate that the taxonomic status of Pandoraea genomospecies 2 should be reinvestigated.     

A gender-specific discriminator in Sprague-Dawley rat urine: the deployment of a metabolic profiling strategy for biomarker discovery and identification

The use of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) as complementary analytical techniques for open metabolic profiling is illustrated in the context of defining urinary biochemical discriminators between male and female Sprague-Dawley rats. Subsequent to the discovery of a female-specific urinary discriminator by LC-MS, further LC, MS, and NMR methods have been applied in a coordinated effort to identify this urinary component. Thereafter, the biological relevance and context of the identified component, in this case a steroid metabolite, has been achieved. This approach will be deployed in future studies of disease, drug efficacy, and toxicity to discover and identify biologically relevant markers.     

DNA指纹图谱在乳酸菌分类鉴定中的应用

目的 探讨DNA指纹图谱在乳酸菌分类鉴定中的应用。方法 选用S23随机引物,对乳酸菌基因组DNA进行RAPD随机扩增,获得能够区分不同菌株的DNA指纹图谱,依据图谱DNA条带的多态性,对10株乳酸菌菌株进行分类与鉴定。结果 实验室保藏菌株LAP2、LAT、LAM、LAC和LAO之间的基因组DNA相似性达80%,亲缘关系最为相近,而LAB菌株与所有菌株的亲缘关系最远。结论 DNA指纹图谱技术与常规方法结合使用,将使乳酸菌的分类、鉴定更为准确、便捷。     

Cytological identification of the chromosomes involved in Nishimura's rice translocation lines

During the past three decades, Nishimura's reciprocal translocation lines of rice have been used in rice cytogenetics to locate genes on chromosomes, to number extra chromosomes of trisomic series and to associate individual linkage groups with specific chromosomes. In this report, we present our identification of the chromosomes involved in 11 of Nishimura's translocation lines using both meiotic pachytene and mitotic prometaphase chromosome analysis. In addition, the numbering of the 12 linkage groups suggested by Nagao and Takahashi, and modified later by many workers, has been revised to agree with the numbering of the identified chromosomes.     

Digital repository of associations between environmental variables: A new resource to facilitate knowledge synthesis

Responsible care and management of Earth's resources requires scientific support, but the pool of underused research is growing rapidly. Environmental science research studies describe associations between variables (e.g. statistical relationships between stressors and responses). We propose open-access and online sharing of such associations. This concept differs from various efforts around the world to promote sharing of primary research data, but holds similar goals of improved use of existing knowledge. The initiative is made possible by recent developments in information technology and evolving online culture (e.g. crowdsourcing and citizen science). We have begun to connect existing projects that catalog and store associations, thereby moving toward a single virtual repository. Researchers and decision makers may share and re-use associations for myriad purposes, including: increasing efficiency and timeliness of systematic reviews, environmental assessments and meta-analyses, identifying knowledge gaps and research opportunities, providing evolved metrics of research impact, and demonstrating connections between research and environmental improvement.