Parallel Genetics of Gene Regulatory Sequences in Caenorhabditis elegans

Wie regulatorische Sequenzen die Genexpression steuern, ist von grundlegender Bedeutung für die Erklärung von Phänotypen in Gesundheit und Krankheit. Die Funktion regulatorischer Sequenzen muss letztlich in ihrer genomischen Umgebung und in entwicklungs- oder gewebespezifischen Zusammenhängen verstanden werden. Da dies eine technische Herausforderung ist, wurden bisher nur wenige regulatorische Elemente in vivo charakterisiert. Hier verwenden wir Induktion von Cas9 und multiplexed-sgRNAs, um hunderte von Mutationen in Enhancern/Promotoren und 3′ UTRs von 16 Genen in C. elegans zu erzeugen. Wir quantifizieren die Auswirkungen von Mutationen auf Genexpression und Physiologie durch gezielte RNA- und DNA-Sequenzierung. Bei der Anwendung unseres Ansatzes auf den 3′ UTR von lin-41, bei der wir hunderte von Mutanten erzeugen, stellen wir fest, dass die beiden benachbarten Bindungsstellen für die miRNA let-7 die lin-41-Expression größtenteils unabhängig voneinander regulieren können, mit Hinweisen auf eine mögliche kompensatorische Interaktion. Schließlich verbinden wir regulatorische Genotypen mit phänotypischen Merkmalen für mehrere Gene. Unser Ansatz ermöglicht die parallele Analyse von genregulatorischen Sequenzen direkt in Tieren.How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. The function of regulatory sequences must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3′ UTRs of 16 genes in C. elegans. We quantify the impact of mutations on expression and physiology by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3′ UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression largely independently of each other, with indications of a compensatory interaction. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of gene regulatory sequences directly in animals

Brainhack: a collaborative workshop for the open neuroscience community

International audienceBrainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science

Systems Biology of the Clock in Neurospora crassa

A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2) that encode a transcriptional activator (as well as a blue-light receptor) and an oscillator frequency (frq) that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE), based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid) biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2) control were resolved into four classes, circadian only (612 genes), light-responsive only (396), both circadian and light-responsive (328), and neither circadian nor light-responsive (987). In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes

Is Europe ready for integrated multi-trophic aquaculture? A survey on the perspectives of European farmers and scientists with IMTA experience

Integrated Multi-Trophic Aquaculture (IMTA) refers to the integrated farming of several species from different trophic levels in close proximity. In IMTA, one species is intended to complement another. The concept has long been in use in Asia and contributes significantly to the sustainability of aquaculture as it can potentially drive ecological efficiency, environmentally acceptability, product-diversity, profitability and benefit society. Although the concept has received increasing academic attention during the last two decades, it has not yet become a commercial reality in European mariculture. The reasons for this were explored, by interviewing farmers and scientists with previous experience on IMTA. The interviewing approach can be effective in identifying important omissions from the available literature and also possible exaggerations of positive results. For the purposes of this study, a qualitative survey was undertaken using a structured questionnaire with open-ended questions. As a result, the opinions of 34 farmers and scientists with substantial experience of IMTA from 12 European countries have been obtained. A broad spectrum of IMTA impediments has been identified. These have been separated into nine major categories; namely Biological, Conflicts, Environmental, Interest, Legislation, Market, Operational, R&D, and Vandalism. The importance of each category was found to vary among different locations and regions of Europe indicating the need for site-specific targeted approaches. Nevertheless, factors from several categories were raised in all countries/IMTA configurations which highlights that for IMTA to be further developed and adopted, the involvement of stakeholders and personnel from several disciplines is necessary (i.e. biologists, economists, engineers, farm managers, modellers, regulators, stakeholders and statisticians). This work identifies many of the challenges that European IMTA is likely to encounter, and proposes areas that are likely to benefit from focused research and development.PostprintPeer reviewe

ACC/AHA 2007 Guidelines on Perioperative Cardiovascular Evaluation and Care for Noncardiac Surgery: Executive Summary: A Report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Writing Committee to Revise the 2002 Guidelines on Perioperative Cardiovascular Evaluation for Noncardiac Surgery)

These guidelines represent an update to those published in 2002 and are intended for physicians and nonphysician caregivers who are involved in the preoperative, operative, and postoperative care of patients undergoing noncardiac surgery. They provide a framework for considering cardiac risk of noncardiac surgery in a variety of patient and surgical situations. The writing committee that prepared these guidelines strove to incorporate what is currently known about perioperative risk and how this knowledge can be used in the individual patient

ACC/AHA 2007 Guidelines on Perioperative Cardiovascular Evaluation and Care for Noncardiac Surgery: A Report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Writing Committee to Revise the 2002 Guidelines on Perioperative Cardiovascular Evaluation for Noncardiac Surgery)

"These guidelines are intended for physicians and nonphysician caregivers who are involved in the preoperative, operative, and postoperative care of patients undergoing noncardiac surgery. They provide a framework for considering cardiac risk of noncardiac surgery in a variety of patient and surgical situations. The writing committee that prepared these guidelines strove to incorporate what is currently known about perioperative risk and how this knowledge can be used in the individual patient. The tables and algorithms provide quick references for decision making. The overriding theme of this document is that intervention is rarely necessary to simply lower the risk of surgery unless such intervention is indicated irrespective of the preoperative context. The purpose of preoperative evaluation is not to give medical clearance but rather to perform an evaluation of the patient's current medical status; make recommendations concerning the evaluation, management, and risk of cardiac problems over the entire perioperative period; and provide a clinical risk profile that the patient, primary physician, and nonphysician caregivers, anesthesiologist, and surgeon can use in making treatment decisions that may influence short- and long-term cardiac outcomes. No test should be performed unless it is likely to influence patient treatment. The goal of the consultation is the optimal care of the patient.

Dataset: C. elegans Gene Regulatory Alleles and Reporter Bashing Studies

Manually curated gene regulatory non-coding alleles and reporter bashing studie

A Randomized Controlled Trial Comparing Video versus Text: Video Tutoring in High School Mathematics Assignments Using ASSISTments

The present Interactive Qualifying Project (IQP) performed at the Worcester Polytechnic Institute used the ASSISTments educational software platform to develop high school mathematics problems and tutoring as well as design and perform a randomized study to determine whether students learn better when they are exposed to video tutoring compared to receiving the same tutoring via static text. While most results were statistically insignificant, the trend exists that students who were struggling to understand a topic did benefit more from viewing the video tutoring. From this study we may suggest that video tutoring will benefit students who are struggling with a concept, and text tutoring is more efficient and beneficial to be used as a re-learning tool