Swiss Institute Of Bioinformatics Research Articles

Sivelestat (Neutrophil Elastase Inhibitor) as an Anti-inflammatory and Anti-viral Agent: An In Silico Study.

Background Sivelestat is a potent and specific neutrophil elastase inhibitor. It is clinically used in treating lung injury and respiratory distress syndrome. This engaged us to undertake the present study in which sivelestat was studied as an anti-inflammatory and anti-viral agent. Methodology The docking study of sivelestat on matrix metalloproteinase-2 (MMP-2), matrix metalloproteinase-9 (MMP-9), chikungunya virus nonstructural protein-2 (CVnsP2) protease, and influenza A (H1N9) virus neuraminidase was assessed using the Chemistry at Harvard Macromolecular Mechanics (CHARMM) Dock (CDOCK) method. Furthermore, molecular physicochemical; bioactivity; absorption, distribution, metabolism, and excretion (ADME); toxicity; and Search Tool for Interacting Chemicals (STITCH) analyses were performed by using the Molinspiration (Molinspiration Cheminformatics, Slovensky Grob, Slovak Republic), SwissADME SwissADME (Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Switzerland), pkCSM (University of Melbourne, Melbourne, Australia), and STITCH-free online tools. Results The molecular physicochemical assessment of the ligand (sivelestat) showed no (zero) violation and agreed with the thumb rule of five, otherwise known as Lipinski's rule of five. ADME prediction of the ligand (sivelestat) is shown to possess a low gastrointestinal absorption (GIA) property. Similarly, toxicity analysis of the ligand (sivelestat) is predicted to have a hepatotoxicity effect. STITCH analysis reveals that the ligand (sivelestat) has exhibited interactions with the three human proteins. Conclusions The present molecular docking studies showed that the ligand (sivelestat) has successfully docked with all four enzymes of interest. Hence, the current finding has provided a good understanding of sivelestat as an effective suppressor activity against all four enzymes: MMP-2, MMP-9, CVnsP2 protease, and influenza neuraminidase.

Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk.

Atherosclerosis differs across major arteries. Although the biological basis is not fully understood, limited evidence of genetic differences has been documented. This study, therefore, was aimed to identify differentially expressed genes between clinically relevant major arteries and investigate their enrichment in endothelial dysfunction-related gene sets. A bioinformatic analysis of publicly available gene-level read counts for coronary, aortic, and tibial arteries was performed. Differential gene expression was conducted with DeSeq2 at a false discovery rate of 0.05. Differentially expressed genes were then subjected to over-representation analysis and active-subnetwork-oriented enrichment analysis, both at a false discovery rate of 0.005. Enriched terms common to both analyses were categorized for each contrast into immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related terms, and the top differentially expressed genes validated against Swiss Institute of Bioinformatics' Bgee database. There was mostly upregulation of differentially expressed genes for the coronary/tibial and aorta/tibial contrasts, but milder changes for the coronary/aorta contrast. Transcriptomic differences between coronary or aortic versus tibial samples largely involved immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related genes, suggesting potential to modulate endothelial dysfunction and atherosclerosis. These results imply atheroprone coronary and aortic environments compared with tibial artery tissue, which may explain observed relative inter-artery atherosclerosis risk.

Towards "Biodiversity PMC"

The Swiss Institute of Bioinformatics (SIB) Literature services (SIBiLS, Gobeill et al. 2020) provides powerful search capabilities to explore the life and health sciences literature by mirroring the United States National Institute of Health's National Library of Medicine (NIH/NLM) (MEDLINE) and National Center for Biotechnology Information (NCBI) PubMed Central® contents. In the course of the BiCIKL project, SIBiLS started indexing a larger set of biodiversity-related contents in the broad sense including environmental sciences and ecology, to build a new literature database called "Biodiversity PMC". In addition to MEDLINE and PubMed Central, SIBiLS is now providing a unique entry point to half a million taxonomic treatments extracted by Plazi, as well as to a growing set of full-text article XMLs from Pensoft, which were not included into the original PubMed Central. The services can be accessed via a new Graphic User Inteface and an OpenAPI. In addition to usual search operators (using the Apache Lucene syntax), the contents are normalized using a large collection of life sciences terminologies and ontologies. Each instance of a term (or its synonym) is normalized with a unique accession number to support a semantically richer search experience. Of particular interest for the biodiversity communities, SIBiLS contents are normalized using ENVO (Environmental Ontology). Further, taxonomic names are normalized using both the NCBI Taxonomy and the Open Tree of Life, which include names from the Catalogue of Life. The resulting data graph contains 12 billion normalized descriptors and supports access via keyword search, as well as via an original question answering interface, which can help provide new perspectives when navigating the life and health sciences. The data (Journal Publishing Tag Set, JATS, and BioC) are fully available under CC-BY 4.0 licences.

Novel 1,4-Dihydropyridine Derivatives as Potential Agents with Analgesic Activity IN Orofacial Trigeminal Pain Test: Experimental Preclinical Randomized Trial

Background. In the majority of cases, contemporary pharmacological correction mainly focuses on the most effective analgesia. Therefore, the search for and research into new analgesic drugs are a priority in modern pharmacology.Objective — to establish the level of analgesic activity in eight novel heterocyclic compounds of 1,4-dihydropyridine derivatives synthesized in a classic test of orofacial trigeminal pain in animal experiments.Methods. An experimental preclinical randomized trial of the analgesic activity in 1,4-dihydropyridine derivatives was carried out. The experiment was conducted on 100 white male outbred rats in the laboratory of the Fundamental and Clinical Pharmacology Department, St. Luke Lugansk State Medical University, Lugansk People’s Republic. Novel 1,4-dihydropyridine derivatives were preliminarily investigated in a virtual biological screening by means of Swiss Target Prediction tool (Swiss Institute of Bioinformatics, Switzerland). The laboratory animals were divided into a control group (rats were exposed to acute pain syndrome by injecting 0.1 ml of 5% formalin solution into the vibrissae area without pharmacological correction), a comparison group (rats which received metamizole sodium (OOO Farmstandard) at a dose of 7 mg/kg 1.5 hour prior to acute pain syndrome modeling in the vibrissae area), and eight experimental groups (1.5 hours before formalin administration, novel 1,4-dihydropyridine derivatives under study at a dose of 5 mg/ kg were intragastrically injected). 10, 15 and 20 minutes after simulating acute pain, the number of scratching movements of the forelegs around orofacial region per minute was counted. Statistical processing of the results involved methods of mathematical statistics for quantitative variability and was carried out using Statistica 12.5 (IBM, USA).Results. Animals treated with 1,4-dihydropyridine derivatives d02-133 and d02-172 under the experimental conditions showed a significant (13–21 times) decrease in scratching movements frequency by the 10th minute of observation in comparison with the control group. By 15th minute, the analgesic activity of the cyanothioacetamide derivatives increased 14 and 11 times as compared to these indicators of the reference group. After 20 minutes, the analgesic activity of these compounds in terms of inhibiting nociceptive impulses, as compared to the control group, was also high, as the number of scratching movements in the vibrissae area in animals of these experimental groups was 8–9 times lower than in control group. The orofacial trigeminal pain test detected the most exhibited analgesic activity in novel cyanothioacetamide derivatives d02-139, d02-133, and d02-172, which appeared to be higher than that of metamizole sodium.Conclusion. It was found that novel original derivatives of 1,4-dihydropyridine showed a high degree of analgesic activity.

Gene expression databases for physiologically based pharmacokinetic modeling of humans and animal species.

In drug research, developing a sound understanding of the key mechanistic drivers of pharmacokinetics (PK) for new molecular entities is essential for human PK and dose predictions. Here, characterizing the absorption, distribution, metabolism, and excretion (ADME) processes is crucial for a mechanistic understanding of the drug-target and drug-body interactions. Sufficient knowledge on ADME processes enables reliable interspecies and human PK estimations beyond allometric scaling. The physiologically based PK (PBPK) modeling framework allows the explicit consideration of organ-specific ADME processes. The sum of all passive and active ADME processes results in the observed plasma PK. Gene expression information can be used as surrogate for protein abundance and activity within PBPK models. The absolute and relative expression of ADME genes can differ between species and strains. This is affecting both, the PK and pharmacodynamics and is therefore posing a challenge for the extrapolation from preclinical findings to humans. We developed an automated workflow that generates whole-body gene expression databases for humans and other species relevant in drug development, animal health, nutritional sciences, and toxicology. Solely, bulk RNA-seq data curated and provided by the Swiss Institute of Bioinformatics from healthy, normal, and untreated primary tissue samples were considered as an unbiased reference of normal gene expression. The databases are interoperable with the Open Systems Pharmacology Suite (PK-Sim and MoBi) and enable seamless access to a central source of curated cross-species gene expression data. This will increase data transparency, increase reliability and reproducibility of PBPK model simulations, and accelerate mechanistic PBPK model development in the future.

Enabling Published Taxonomic Data to be used to Address the Biodiversity Crisis: Biodiversity Literature Repository and TreatmentBank

To understand the loss of species, a benchmark is needed, e.g. the status of biodiversity in 1992 when the Convention on Biological Diversity recognized biodiversity crisis to compare to its status in the successive year. Though we are far from knowning how many species there are on planet Earth, we keep track of their descriptions and number through the information kept in our libraries. Each species discovered is represented therein by at least one taxononic treatment. The library includes an estimated 500 million pages and is updated daily with an estimated 17–18,000 new species annually and over 100,000 treatments augmenting the knowledge of existing species. In reality, we do not know how many species exist. We know that the catalogue of life is incomplete and basic knowlege of known species is often lacking and not even updated regularly. On the other hand, the scientific standard to cite previous works and facts is at the same time an ideal prerequisit to build a knowledge graph in the era of digital knowledge. TreatmentBank (TB) and the Biodiversity Literature Repository (BLR), two European Research Infrastructures, provide a service to convert unstructured biodiversity data from scholarly publications into semantically enhanced, digital accessible knowledge (Fawcett et al. 2022) making it findable, accessible, interoperable, reusable (FAIR, Wilkinson et al. 2016) and providing long term access in collaboration with Zenodo. Data sources are either legacy publications or active journals using an XML workflow such as Zookeys or the Biodiversity Data Journal, published by the pioneer of taxonomically enhanced Taxpub XML publishing, Pensoft. As part of the Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL), bidirectional linking of taxonomic names with the Catalogue of Life, DNA-sequences with the International Nucleotide Sequence Database Collaboration (INSDC) and material citations with their respective natural history collection or their depositions in the Global Biodiversity Information Facility (GBIF) is targeted. As input to allow queries including text and data mining for traits and biotic interactions, the treatments are uploaded to the Swiss Institute of Bioinformatics (SIB) Library Service (SIBiLS) using TaxPub and schema based on Journal Article Tag Suite (JATS) widely used in life science publishing and PubMed Central, allowing the use of the advanced text and data mining tools in the life science community. Another research infrastructure that ensures an RDF representation and conversion into Linked Open Data (LOD) is OpenBiodiv allowing users to explore DAK as part of growing linked open biodiverstiy and related data. All the data fit for GBIF use is reused by GBIF representing close to 60% of all published data sets, which makes TreatmentBank and BLR, for example, a sole provider of data for approximately 90,000 species not recorded in GBIF by other publishers. The long-term strategy is to build up the momentum to be an infrastructure relevant for global biodiversity conservation and research. Long-term support will be achieved by negotiations with respective agencies and publishers, and through building up a global user community using the biodiversity digital acccessible knowledge.

Characterization of Three cDNAs Obtained by Spliced Leader-PCR Screening of a Taenia solium cDNA Library

Cysticerci or metacestodes of Taenia solium cause cysticercosis, being the neurocysticercosis (NCC) the main pathology. The characterization of genes is essential for the knowledge of parasite biology, the understanding of the parasite-host relationship, and the identification of possible targets for diagnosis, treatment, and protection. The objective of this work was the molecular and bioinformatic characterization of three news cDNAs (TsTF10, TsAAP8, and TsrGAP8), obtained by spliced leader-PCR screening of a Taenia solium cDNA library. The sequences of the three cDNA were compared with the sequences in the nucleic acid and protein databases (GenBank, EMBL) and analyzed by bioinformatic programs (CDD-Search of the National Center for Biotechnology Information, Interpro of the European Bioinformatics Institute, Motif scan and Expert Protein Analysis System of the Proteomics Server from Swiss Institute of Bioinformatics). Considering the high identities with similar molecules of related helminths (Taenia asiatica, Echinococcus granulosus, Echinococcus multilocularis, and Hymenolepis diminuta) and the functional domains found, the TsTF10, TsAAP8, and TsrGAP8 genes of Taenia could act as a nuclear transcription factor gamma, a putative vacuolar ATPase membrane sector associated protein and a Rho GTPase activating protein, respectively. Although few B epitopes could be predicted in the sequences, it could be relevant to evaluate them as possible candidates for diagnosis and protection in cysticercosis. The characterization and analysis of these sequences and the prediction of their possible usefulness as antigens, vaccines, or therapeutic targets contribute to the designing and planning of future studies.

LUX-MS identifies interacting molecules on cell surfaces

Proteins on the surfaces of cells act as gateways between the cell and its surroundings. The interactions of these proteins with one another and with their ligands can be difficult to determine. A team led by Bernd Wollscheid of the Swiss Federal Institute of Technology (ETH), Zurich, and the Swiss Institute of Bioinformatics has developed a light-controlled method called LUX-MS that enables the researchers to identify proteins and ligands that are close to one another on cell surfaces ( Nat. Commun. 2021, DOI: 10.1038/s41467-021-27280-x ). LUX-MS works with a wider variety of ligands than previous methods do. The researchers couple ligands , such as antibodies, peptides, or small molecules, to thiorhodamine, which serves as a singlet oxygen generator when irradiated with light from a light-emitting diode. The singlet oxygen oxidizes certain amino acids, such as histidine, in nearby proteins. Proteins farther away are not oxidized. The researchers add a biotin

Managing the life cycle of a portfolio of open data resources at the SIB Swiss Institute of Bioinformatics.

Data resources are essential for the long-term preservation of scientific data and the reproducibility of science. The SIB Swiss Institute of Bioinformatics provides the life science community with a portfolio of openly accessible, high-quality databases and software platforms, which vary from expert-curated knowledgebases, such as UniProtKB/Swiss-Prot (part of the UniProt consortium) and STRING, to online platforms such as SWISS-MODEL and SwissDrugDesign. SIB’s mission is to ensure that these resources are available in the long term, as long as their return on investment and their scientific impact are high. To this end, SIB provides its resources, in addition to stable financial support, with a range of high-quality, innovative services that are, to our knowledge, unique in the field. Through this first-class management framework with central services, such as user-centric consulting activities, legal support, open-science guidance, knowledge sharing and training efforts, SIB supports the promotion of excellence in resource development and operation. This review presents the ecosystem of data resources at SIB; the process used for the identification, evaluation and development of resources; and the support activities that SIB provides. A set of indicators has been put in place to select the resources and establish quality standards, reflecting their multifaceted nature and complexity. Through this paper, the reader will discover how SIB’s leading tools and databases are fostered by the institute, leading them to be best-in-class resources able to tackle the burning matters that society faces from disease outbreaks and cancer to biodiversity and open science.

Biological Activity Investigation of Phytocomponents in Mangosteen (Garcinia mangostana L.): In Silico Study

Indonesia has abundant medicinal plants, which have been historically used by the population in treatingdiseases for generations. Traditional Indonesian medicine and the medicinal plants used could lead to thediscovery of novel drugs. The mangosteen or Garcinia mangostana L. is a well-known medicinal plantthat has been used to treat various diseases worldwide. The pharmacological activities and phytochemicalcomposition of the whole plant of mangosteen have been investigated and identified by scientists in recentdecades. Therefore, this study aims to generate the prediction of the biological activity of phytocompotentsin mangosteen. In this study, we extracted 18 phyocomponents of mangosteen from PubChem, an openchemistry database at the National Institutes of Health (NIH), USA. Then, we predicted the pharmacokineticproperties and druglike nature of the phytocomponents using the SwissADME web server, Swiss Instituteof Bioinformatics, Swiss. Furthermore, PASS (Prediction of Activity Spectra for Substances) web resourcehas been employed as a strong potential tool to predict the biological activity. In summary, we revealed thebiological activity of 18 phytocomponents of the mangosteen. However, further trials, such as in vitro andin vivo evaluation, are needed to prove the validity of these findings.

PROSPECTIVE BIOLOGICAL ACTIVE COMPOUNDS AMONG 7-SUBSTITUTED OF 3-BENZYL-8-PROPYLXANTHINES FOR TREATMENT OF METABOLIC SYNDROME PATHOLOGIES

Aim – the search for biologically active compounds with diuretic and hypoglycemic action among 7-substituted of 3-benzyl-8-propylxanthines, which can be used for the treatment of pathologies of “metabolic syndrome”. Materials and methods. 30 new chemical compounds among derivatives of 7-substituted of 3-benzyl-8-propylxanthines by PASS prediction filter were chosen for diuretic and hypoglycemic activity researches. Diuretic, hypoglycemic activity and for the most active compounds – the acute toxicity were studied in vivo. The molecular docking, which is based on EADock DSS mechanism of the modulation displayed the interaction between some of functional groups inside discovered xanthine ligands and known receptors and enzymes presented in Ligand-protein Database of Swiss Institute of Bioinformatics. Results. It has been shown that synthesized compounds displayed strong diuretic and medium hypoglycemic activities. The molecular docking modulation (SwissDock) of interaction of xanthine derivatives hits with proposed receptors and enzymes revealed prospective of using 7-substituted of 3-benzyl-8-propylxanthines as potential drugs for treatment of metabolic syndrome pathologies. Conclusion. The diuretic activity of the new 23 compounds of 7-substituted of 3-benzyl-8-propylxanthines and hypoglycemic activity of the new 7 derivatives of 7-substituted of 3-benzyl-8-propylxanthines was studied. Results of performed investigation illustrate that 7-substituted of 3-benzyl-8-propylxanthines demonstrate biological activity comparable to standard drugs. We also proposed probable molecular targets for the most active compounds by molecular docking method. It was shown that derivatives of 7-substituted of 3-benzyl-8-propylxanthines can be used for metabolic syndrome disorders prevention.

Comparative genomics reveals an outstanding sex chromosome diversity in cichlid fishes driven by genomic novelties and convergent evolution

Event Abstract Back to Event Comparative genomics reveals an outstanding sex chromosome diversity in cichlid fishes driven by genomic novelties and convergent evolution Athimed El Taher1, Michael Matschiner2, 3, Fabrizia Ronco1, Walter Salzburger1 and Astrid Böhne1, 4* 1 University of Basel, Zoological Institute, Switzerland 2 Paleontological Institute and Museum, Faculty of Mathematics and Natural Sciences, University of Zurich, Switzerland 3 Centre for Ecological and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway 4 Zoological Research Museum Alexander Koenig (LG), Center for Molecular Biodiversity Research (ZMB), Germany Sexual reproduction is ancient and almost universal in the eukaryotic kingdom. However, the mechanisms that actually determine male or female sex are highly divers encompassing a variety of extrinsic and intrinsic drivers. Intrinsic factors, commonly referred to as genetic sex determination, comprise systems as simple as a single base pair difference between the sexes to highly differentiated sex chromosomes. Why sex-determining systems change frequently in some taxa, whereas the same sex chromosome pair persists over long evolutionary time in others, remains an open question. With ~3000 species, cichlid fishes are one of the largest vertebrate families and an extraordinary example of adaptive radiations. If different sex-determining mechanisms contribute to the species richness of this fish lineage is largely unknown. The oldest and most diverse African cichlid assemblage is the one of Lake Tanganyika, which consists of 250 endemic species. Using whole genome sequencing, comparative genomics and expression data, we investigate the genetic basis of sex determination and the evolution of sex chromosomes in this radiation. We identified at least 28 sex chromosome transitions in cichlids with a transition rate of 0.19 per million years. To the best of our knowledge this is the highest transition rate so far described. We show that closely related species can have different sex chromosomal systems indicative of recent turnover events. On the other hand, it also seems that particular chromosomes evolved convergently as sex chromosomes in distantly related cichlid lineages. Chromosomal fusions likely played a role in cichlid sex chromosome evolution. Cichlids perfectly exemplify the diversity as well as the constraints of sex chromosome evolution and can reveal the forces driving the evolution of sex-determining systems. Acknowledgements Calculations were performed at sciCORE (http://scicore.unibas.ch/) scientific computing center at University of Basel, with support by the SIB - Swiss Institute of Bioinformatics. Keywords: Cichlid, sex chromosome, adaptive radiation, speciation, Lake Tanganyika cichlid fishes, Comparative genomics, Transcriptomics Conference: XVI European Congress of Ichthyology, Lausanne, Switzerland, 2 Sep - 6 Sep, 2019. Presentation Type: Oral Topic: EVOLUTIONARY GENOMICS OF FISHES Citation: El Taher A, Matschiner M, Ronco F, Salzburger W and Böhne A (2019). Comparative genomics reveals an outstanding sex chromosome diversity in cichlid fishes driven by genomic novelties and convergent evolution. Front. Mar. Sci. Conference Abstract: XVI European Congress of Ichthyology. doi: 10.3389/conf.fmars.2019.07.00040 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Jun 2019; Published Online: 14 Aug 2019. * Correspondence: Dr. Astrid Böhne, University of Basel, Zoological Institute, Basel, CH-4001, Switzerland, a.boehne@leibniz-zfmk.de Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Athimed El Taher Michael Matschiner Fabrizia Ronco Walter Salzburger Astrid Böhne Google Athimed El Taher Michael Matschiner Fabrizia Ronco Walter Salzburger Astrid Böhne Google Scholar Athimed El Taher Michael Matschiner Fabrizia Ronco Walter Salzburger Astrid Böhne PubMed Athimed El Taher Michael Matschiner Fabrizia Ronco Walter Salzburger Astrid Böhne Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Biochemistry laboratory reports: Filling in the introduction and discussion.

Laboratory reports written in the style of a standard scientific article are commonly used to assess student learning in biochemistry laboratory courses. While most students can complete the Materials and Methods or Results sections successfully, many have difficulty with the Introduction and Discussion. They fail to place their data in a larger experimental context or to compare their results to those previously published. To address this issue in a laboratory course focusing on l-lactate dehydrogenase, a new exercise was introduced that was designed 1) to provide more background information about l-lactate dehydrogenase; 2) to give students additional experience in using PubMed and Web of Science to locate specific papers about l-lactate dehydrogenase; 3) to introduce the major bioinformatics databases at the National Center for Biological Information, ExPASy (Swiss Institute of Bioinformatics), BRENDA (Braunschweig Enzyme Database), and the Protein Data Bank; 4) to allow students to recover detailed information about l-lactate dehydrogenases; and 5) to provide practice in reading a research article that is similar to what they do in the lab. The students completed a data sheet summarizing these activities and then prepared three laboratory reports. The lab reports improved over the course of the semester and were qualitatively better than in past years. The materials developed for this laboratory course can be adapted to similar projects that use another protein as a model system. They could also be modified for use in Course-based Undergraduate Research Experiences or research projects for undergraduate or graduate students. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):619-622, 2018.

Eukaryotic Molecular Biology Databases: An Overview

A biological database is a big, structured body of continuous information, generally connected with computerized software intended to update, query, and recover information elements deposited within the framework. A straightforward database could be a single folder comprising several data, each carrying the same number of data. Such famous databases are GenBank from the National Center for Biotechnology Information, SwissProt from the Swiss Institute of Bioinformatics and PIR from the Protein Information Resource. Biological databases are bibliotheques of life science data, gathered from science studies, published literature, high-performance experimental technology, and computational analysis. Here we brefly described some recently published molecular databases.

Contrast enhancement for cDNA microarray image based on fourth-order moment

Microarray technology, which can monitor the expression levels of thousands of genes simultaneously, has been widely used in biological experiment. Image processing, as one key step in microarray technology, plays an essential role in microarray analysis. Meanwhile, biological applications require a higher accuracy in each image processing step. However, the low contrast levels of image make it difficult to obtain better processing precision. This paper proposes a fully automatic contrast enhancement (CE) method based on fourth-order moment. Also, a background estimation method is presented to obtain a better microarray image processing result. Comparative results on contrast enhance and gridding revealed that the proposed CE algorithm performs better compared to the adaptive histogram equalization method. Numerous experiments on the Swiss Institute of Bioinformatics (SIB), Joe DeRisi individual (DeRisi), Gene Expression Omnibus (GEO), and Stanford Microarray Database (SMD) data sets also indicate that the proposed CE exerts a tremendous effect on gridding, but has nothing to do with segmentation.

A shape-independent algorithm for fully-automated gridding of cDNA microarray images

In this paper, a fully-automated microarray gridding algorithm is presented. This algorithm contains the block finding in an image by using variable length Blackman window, image contrast enhancement based on the Otsu thresholding approach, and identification of image objects including spots and artifacts through the 8-connected labeling method. Furthermore, a shape-independent algorithm based on the area of pixels in each object is proposed for noise elimination. The final gridding is performed using a new method based on the constructed spot matrix and a refinement procedure is exploited to minimize all probable grid-line errors. The performance of the proposed algorithm is evaluated by five public datasets including the Swiss Institute of Bioinformatics (SIB), Joe DeRisi's individual tiff files (DeRisi), University of California, San Francisco (UCSF), Gene Expression Omnibus (GEO), and Stanford Microarray Database (SMD). The obtained results reveal that the proposed algorithm reaches a higher level of accuracy and stability against some restrictions in microarray images such as noise, artifacts, and irregularities regarding the shapes of spots in comparison with other state-of-the-art methods.

Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins

Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC).Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC.This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.

UniProt Protein Knowledgebase.

The Universal Protein Resource (UniProt) is a freely available comprehensive resource for protein sequence and annotation data. UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). Across the three institutes more than 100 people are involved through different tasks such as expert curation, software development, and support.This chapter introduces the functionality and data provided by UniProt. It describes example use cases for which you might come to UniProt and the methods to help you achieve your goals.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Multimodal literacies and academic publishing: The eTalks

Academic publications and pedagogy have been deeply reconfigured by the emergence of a new kind of knowledge produced by multimodal literacies (text, image and sound together). Academic publishing needs a digital multimedia editing platform, that can be carefully edited and quoted in details, in the same way that printed sources are. Consequently, the Swiss Institute of Bioinformatics (Vital-IT, Lausanne, CH) is developing such a platform with the The eTalks application is implemented via an easy-to-use editor interface, designed for the use of researchers themselves, to create and edit original eTalks. This permits the linking together of images, sounds and textual materials with hyperlinks, enriching it with relevant information. The final release of eTalks allows complete 'citability' of its contents: each and every portion of the researchers' talks can be precisely referred to and thus cited with a specific identifier, just like any traditional, paper-based academic publication but with all the potential for plural literacies. It is openly accessible and the code is open source, including guidelines to install the eTalks. It is notably developed in collaboration with the Erasmus+ project #dariahTeach. The DRM (Digital Right Management) is a key issue in such an open access editing platform.