抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

/pdf/bioinformatics-enrichment-tools-paths-toward-the-2yo1xl3r2j.pdf

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Feature selection techniques have become an apparent need in many bioinformatics applications. In addition to the large pool of techniques that have already been developed in the machine learning and data mining fields, specific applications in bioinformatics have led to a wealth of newly proposed techniques.

In this article, we make the interested reader aware of the possibilities of feature selection, providing a basic taxonomy of feature selection techniques, and discussing their use, variety and potential in a number of both common as well as upcoming bioinformatics applications.

Contact: yvan.saeys@psb.ugent.be

Supplementary information: http://bioinformatics.psb.ugent.be/supplementary_data/yvsae/fsreview

A review of feature selection techniques in bioinformatics

Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database In particular, a variety of tools that perform GO enrichment analysis are currently available Most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set A few tools also exist that support analyzing ranked lists The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (eg by level of expression or of differential expression) GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list Building on a complete theoretical characterization of the underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations This enables rigorous statistical analysis of thousand of genes and thousands of GO terms in order of seconds The output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched GO terms GOrilla is an efficient GO analysis tool with unique features that make a useful addition to the existing repertoire of GO enrichment tools GOrilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation GOrilla is publicly available at: http://cbl-gorillacstechnionacil

https://link.springer.com/content/pdf/10.1186%2F1471-2105-10-48.pdf

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

Contribution to the jumping spider fauna (Araneae, Salticidae) of the Greek Dodecanese island of Rhodes, with a description of Pseudophrys rhodiensis and six new records. During a recent survey of jumping spiders on the Greek Dodecanese island of Rhodes, a total of 24 species from 21 genera were recorded. One species, Pseudeuophrys rhodiensis Schafer sp. nov., is here described as new. Six further species of jumping spiders are newly recorded for the island; three of which (Aelurillus concolor, Evarcha insularis comb. nov. and Salticus noordami) are new for the entire Dodecanese. In addition, a number of taxonomic problems regarding the jumping spider fauna of Rhodes are briefly discussed.

https://bioone.org/journals/Arachnologische-Mitteilungen-Arachnology-Letters/volume-55/issue-1/aramit5512/Ein-Beitrag-zur-Springspinnenfauna-Araneae-Salticidae-der-griechischen-Dodekanes-Insel/10.30963/aramit5512.pdf

Ein Beitrag zur Springspinnenfauna (Araneae, Salticidae) der griechischen Dodekanes-Insel Rhodos mit der Neubeschreibung von Pseudeuophrys rhodiensis und sechs weiteren Erstnachweisen

The identification of proteins in proteomics experiments is usually based on mass information derived from tandem mass spectrometry data. To improve the performance of the identification algorithms, additional information available in the fragment peak intensity patterns has been shown to be useful. In this study, we consider the effect of iTRAQ labeling on the fragment peak intensity patterns of singly charged peptides from MALDI tandem MS data. The presence of an iTRAQ-modified basic group on the N-terminus leads to a more pronounced set of b-ion peaks and distinct changes in the abundance of specific peptide types. We performed a simple intensity prediction by using a decision-tree machine learning approach and were able to show that the relative ion abundance in a spectrum can be correctly predicted and distinguished from closely related sequences. This information will be useful for the development of improved method-specific intensity-based protein identification algorithms.

Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

Eric Duffey's spider collection in the Manchester Museum, accumulated over more than 40 years, contains more than 300 samples from a diverse range of biotopes in most southern European countries. Most of this material was previously unsorted. It has now been sorted and identified to species level. It contains more than 2500 specimens of more than 500 species in 240 genera and 42 families. The collection details of all of these samples are listed here, and a number of selected specimens are illustrated.

/pdf/south-european-spiders-from-the-duffey-collection-in-the-lz8th959eg.pdf

South European spiders from the Duffey collection in the Manchester Museum (Arachnida: Araneae)

Optimization of experimental conditions is critical in ensuring robust experimental reproducibility. Through detailed metabolomic analysis we found that cell culture conditions significantly impacted on glutaminase (GLS1) sensitivity resulting in variable sensitivity and irreproducibility in data. Baseline metabolite profiling highlighted that untreated cells underwent significant changes in metabolic status. Both the extracellular levels of glutamine and lactate and the intracellular levels of multiple metabolites changed drastically during the assay. We show that these changes compromise the robustness of the assay and make it difficult to reproduce. We then devised 9metabolically rationalized standard9 assay conditions, in which glutaminase-1 inhibition reduced glutamine metabolism differently in both cell lines assayed, and decreased the proliferation of one of them. The adoption of optimized conditions such as the ones described here should lead to an improvement in reproducibility and help eliminate false negatives as well as false positives in these assays.

https://www.biorxiv.org/content/biorxiv/early/2017/08/28/167148.full.pdf

Rational cell culture optimization enhances experimental reproducibility in cancer cells.

In recent years, the use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput pro- filing of the metabolic composition of biological samples. However, the large amount of data obtained is often diffi- cult to analyse. This paper focuses on a particular problem, that of detecting and potentially removing derivative peaks of a substance of interest. A mixture model for clustering peaks based on chromatographic peak shape correlation is presented, and comparison of this model to the behaviour of a leading mass spectrometry analysis tool is presented. Based on the results, the mixture model is shown to have better overall performance characteristics.

/pdf/mixture-model-clustering-for-peak-filtering-in-metabolomics-3z3cw0hpzb.pdf

Rainer Breitling

Papers

Ein Beitrag zur Springspinnenfauna (Araneae, Salticidae) der griechischen Dodekanes-Insel Rhodos mit der Neubeschreibung von Pseudeuophrys rhodiensis und sechs weiteren Erstnachweisen

Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

South European spiders from the Duffey collection in the Manchester Museum (Arachnida: Araneae)

Rational cell culture optimization enhances experimental reproducibility in cancer cells.

Mixture model clustering for peak filtering in metabolomics