Ten Simple Rules for Developing a Short Bioinformatics Training Course

This is an open-access article under the Creative Commonset.-- et al.This paper considers what makes a short course in bioinformatics successful. In today’s research environment, exposure to bioinformatics training is something that anyone embarking on life sciences research is likely to need at some point. Furthermore, as research technologies evolve, this need will continue to grow. In fact, as a consequence of the introduction of high-throughput technologies, there has already been an increase in demand for training relating to the use of computational resources and tools designed for high-throughput data storage, retrieval, and analysis. Biologists and computational scientists alike are seeking postgraduate learning opportunities in various bioinformatics topics that meet the needs and time restrictions of their schedules. Short, intensive bioinformatics courses (typically from a couple of days to a week in length, and covering a variety of topics) are available throughout the world, and more continue to be developed to meet the growing training needs.This work was partly supported by the Intramural Research Program of the NIH, NLM, NCBI, and by funds awarded to the EMBL-European Bioinformatics Institute by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific Programme EMBL-EBI.Peer reviewe

Steady state entanglement of two coupled qubits

The maximum entanglement between two coupled qubits in the steady state under two independent incoherent sources of excitation is reported. Asymmetric configurations where one qubit is excited while the other one dissipates the excitation are optimal for entanglement, reaching values three times larger than with thermal sources. The reason is the purification of the steady state mixture (that includes a Bell state) thanks to the saturation of the pumped qubit. Photon antibunching between the cross emission of the qubits can be used to experimentally evidence the large degrees of entanglement.Comment: 7 pages, 5 figure

Escalas de valoração de dor em pacientes críticos não comunicativos:revisão sistémica

RESUME

Discourse comprehension in L2: Making sense of what is not explicitly said

Using ERPs, we tested whether L2 speakers can integrate multiple sources of information (e.g., semantic, pragmatic information) during discourse comprehension. We presented native speakers and L2 speakers with three-sentence scenarios in which the final sentence was highly causally related, intermediately related, or causally unrelated to its context; its interpretation therefore required simple or complex inferences. Native speakers revealed a gradual N400-like effect, larger in the causally unrelated condition than in the highly related condition, and falling in-between in the intermediately related condition, replicating previous results. In the crucial intermediately related condition, L2 speakers behaved like native speakers, however, showing extra processing in a later time-window. Overall, the results show that, when reading, L2 speakers are able to process information from the local context and prior information (e.g., world knowledge) to build global coherence, suggesting that they process different sources of information to make inferences online during discourse comprehension, like native speakers.This work was supported by grants from the Spanish Government (PSI2011-23033, CONSOLIDER-INGENIO2010 CSD2007-00048, ECO2011-25295, and ECO2010-09555-E), from the Catalan Government (SGR 2009-1521) and from the Grup de Recerca en Neurociència Cognitiva (GRNC) - 2014SGR1210. It has also received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 613465

A gene signature derived from the loss of cdkn1a (P21) is associated with CMS4 colorectal cancer

The epithelial–mesenchymal transition (EMT) is associated with tumor aggressiveness and increased invasion, migration, metastasis, angiogenesis, and drug resistance. Although the HCT116 p21-/- cell line is well known for its EMT-associated phenotype, with high Vimentin and low E-cadherin protein levels, the gene signature of this rather intermediate EMT-like cell line has not been determined so far. In this work, we present a robust molecular and bioinformatics analysis, to reveal the associated gene expression profile and its correlation with different types of colorectal cancer tumors. We compared the quantitative signature obtained with the NanoString platform with the expression profiles of colorectal cancer (CRC) Consensus Molecular Subtypes (CMS) as identified, and validated the results in a large independent cohort of human tumor samples. The expression signature derived from the p21-/- cells showed consistent and reliable numbers of upregulated and downregulated genes, as evaluated with two machine learning methods against the four CRC subtypes (i.e., CMS1, 2, 3, and 4). High concordance was found between the upregulated gene signature of HCT116 p21-/- cells and the signature of the CMS4 mesenchymal subtype. At the same time, the upregulated gene signature of the native HCT116 cells was similar to that of CMS1. Using a multivariate Cox regression model to analyze the survival data in the CRC tumor cohort, we selected genes that have a predictive risk power (with a significant gene risk incidence score). A set of genes of the mesenchymal signature was proven to be significantly associated with poor survival, specifically in the CMS4 CRC human cohort. We suggest that the gene signature of HCT116 p21-/- cells could be a suitable metric for mechanistic studies regarding the CMS4 signature and its functional consequences in CRC. Moreover, this model could help to discover the molecular mechanisms of intermediate EMT, which is known to be associated with extraordinarily high stemness and drug resistance.R.S.-S. was supported by the Emerging Fields Initiative ‘Cell Cycle in Disease and Regeneration’ (CYDER) of the Friedrich Alexander University (Erlangen-Nürnberg, Germany). This article is partly based upon work from COST Action CA17118 TRANSCOLONCAN, supported by COST (European Cooperation in Science and Technology, www.cost.eu, last accessed 20 December 2021). The JDLR research group is supported by the Spanish Government, Instituto de Salud Carlos III (ISCiii, AES project PI18/00591) co-funded by FEDER/ERDF (European Regional Development Fund)

Vpliv naravnih protimikrobnih snovi na bakterijsko hidrofobnost, adhezijo in zeta potencial

Interactions between bacterial cells and contact materials play an important role in food safety and technology. As bacterial strains become ever more resistant to antibiotics, the aim of this study was to analyse adhesion of selected foodborne bacterial strains on polystyrene surface and to evaluate the effects of natural antimicrobials on bacterial cell hydrophobicity, adhesion, and zeta potential as strategies of adhesion prevention. The results showed strain-specific adhesion rate on polystyrene. The lowest and the highest adhesion were found for two B. cereus lines. Natural antimicrobials ferulic and rosmarinic acid substantially decreased adhesion, whereas the effect of epigallocatechin gallate was neglectful. Similar results were found for the zeta potential, indicating that natural antimicrobials reduce bacterial adhesion. Targeting bacterial adhesion using natural extracts we can eliminate potential infection at an early stage. Future experimental studies should focus on situations that are as close to industrial conditions as possible.Interakcije med bakterijskimi celicami in površinami delovnih materialov imajo pomembno vlogo v živilski tehnologiji pri zagotavljanju varnih živil. Poznano je, da različni bakterijski sevi postajajo bolj in bolj odporni proti antibiotikom in drugim biocidom. Zato je bil namen naših raziskav analizirati adhezijo izbranih patogenih bakterij, ki se prenašajo z živili. Proučevali smo njihov oprijem na polistirensko površino in ovrednotili vpliv naravnih protimikrobnih snovi na bakterijsko hidrofobnost, adhezijo in zeta potencial, v smislu možnih strategij za preprečevanje adhezije. Rezultati so pokazali, da je adhezija sevno specifična lastnost, saj je bila najmanjša in največja stopnja adhezije določena za različna seva bakterij vrste Bacillus cereus. Naravni protimikrobni snovi, ferulična in rožmarinska kislina, sta zmanjšali stopnjo adhezije na polistiren, medtem ko je bil vpliv epigalokatehin galata zanemarljiv. Podobne rezultate smo dobili pri zeta potencialu, kar nakazuje na možnosti delovanja naravnih snovi kot protiadhezivnih komponent. Uporaba naravnih protimikrobnih snovi lahko prepreči oziroma zmanjša stopnjo adhezije bakterijskih celic in s tem eliminira možnosti kontaminacij ali okužb v začetni fazi. Nadaljnje eksperimentalno delo bo potrebno za ovrednotenje razmer, ki so čim bolj podobne industrijskemu okolju

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections

Colossal dielectric constants in transition-metal oxides

Many transition-metal oxides show very large ("colossal") magnitudes of the dielectric constant and thus have immense potential for applications in modern microelectronics and for the development of new capacitance-based energy-storage devices. In the present work, we thoroughly discuss the mechanisms that can lead to colossal values of the dielectric constant, especially emphasising effects generated by external and internal interfaces, including electronic phase separation. In addition, we provide a detailed overview and discussion of the dielectric properties of CaCu3Ti4O12 and related systems, which is today's most investigated material with colossal dielectric constant. Also a variety of further transition-metal oxides with large dielectric constants are treated in detail, among them the system La2-xSrxNiO4 where electronic phase separation may play a role in the generation of a colossal dielectric constant.Comment: 31 pages, 18 figures, submitted to Eur. Phys. J. for publication in the Special Topics volume "Cooperative Phenomena in Solids: Metal-Insulator Transitions and Ordering of Microscopic Degrees of Freedom

iAnn: an event sharing platform for the life sciences

Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. Availability: http://iann.pro/iannviewer Contact: [email protected]

Crosslinking by ZapD drives the assembly of short, discontinuous FtsZ filaments into ring-like structures in solution

In most bacteria, division depends on a cytoskeletal structure, the FtsZ ring, that functions as a scaffold to recruit additional proteins, with which it forms the machinery responsible for division, the divisome. The detailed architecture of the ring, in particular the mechanisms of assembly, stabilization, and disassembly, are still largely unknown. Here, we highlight the role of FtsZ-associated proteins (Zaps) that stabilize the FtsZ ring by crosslinking the filaments. Among Zap proteins, ZapD binds the C-terminal domain of FtsZ, which serves as a hub for its regulation. We demonstrate that ZapD crosslinks FtsZ filaments into ring-like structures formed by a discontinuous arrangement of short filaments. Using cryo-electron tomography combined with biochemical analysis, we reveal the three-dimensional organization of the ring-like structures and shed light on the mechanism of FtsZ filament crosslinking by ZapD. Together, our data provide a model of how FtsZ-associated proteins can stabilize FtsZ filaments into discontinuous ring-like structures reminiscent of that existing in the bacterial cell.This project has been supported by the Max Planck-Bristol Centre for Minimal Biology (A.M.-S.) and the Deutsche Forschungsgemeinschaft (P. S.). J.S. and M. Jasnin are supported by the French Agence Nationale de la Recherche (ANR) and the Deutsche Forschungsgemeinschaft (DFG) call ANR-DFG 2020 NLE for the project no. JA-3038/2-1 (to M. Jasnin). J.-H.K. is funded by the Germany’s Excellence Strategy – EXC-2094 – 390783311. This work was also supported by the Spanish Government through Grant PID2019-104544GB-I00/AEI/10.13039/501100011033 (M.Jimenez, C.A. and G.R.). M.S.-S. was supported by European Social Fund through Grant PTA2020-018219-I/AEI/10.13039/501100011033. J.R.L.-O and M S.-S. acknowledge support from the Molecular Interactions Facility at the CIB Margarita Salas-CSIC. A.M.-S and J.-H.K. are part of IMPRS-LS, J.-H.K. is also a CeNS Center for NanoScience associate.Peer reviewe