Issues Faced in a Remote Instrumentation Laboratory

An Online Lab is a multi-university shared laboratory environment, where students can exercise their knowledge as they would do in a physical lab. The idea is to have maximum resource utilization and collaboration between universities by sharing of ideas. This kind of remote laboratory negates the economic issues to set up a laboratory and allows every student to have an experience of real laboratory. As part of Ministry of Human Resource Development (MHRD) Robotics Lab project a study on state of art of remote labs was conducted. This paper discusses some key issues in the design and operation of such remote labs. The lab should be remotely usable by a large student body, with varied levels of sophistication, all the way from elementary learners, to PhD students doing research. In addition, the high design load implies that the architecture should be highly parallel, and structurally reliable

Enabling remote design and troubleshooting experiments using the ilab shared architecture

12th Biennial International Conference on Engineering, Construction, and Operations in Challenging Environments; and Fourth NASA/ARO/ASCE Workshop on Granular Materials in Lunar and Martian Exploration Honolulu, Hawaii, United States March 14-17, 2010The MIT iLab Project is dedicated to the goal of increasing laboratory experimentation opportunities for engineering students worldwide. Since its inception in 1998, the project has furthered this goal through the development of individual remote laboratories, or iLabs, as well as a distributed software infrastructure designed to streamline the implementation and sharing of remote laboratories. iLabs are designed to complement traditional, hands-on laboratories by providing practical educational experiences where they would not otherwise be available. Such remote labs, developed and hosted by MIT and other institutions within the iLab Consortium, have been successfully used by instructors at schools across the educational spectrum and around the world. While certainly valuable, many of the original experiments available through the iLab platform provide a limited experience in that they are observational in nature. They only provide students the ability to study the behavior of a pre-defined system under test. Such labs have proven to be valuable additions to engineering curricula, but do not have the flexibility that is inherent in a traditional laboratory experience. To address this, the MIT iLab Project has begun focusing on the development of iLabs that provide students with the ability to design or troubleshoot experimental systems. Through two particular remote labs, focusing on electronic control system analysis and basic electronics test and measurement respectively, the project is designing remote labs that provide a more flexible learning experience for students and are more attractive to instructors in a broad set of disciplines.National Science Foundation (U.S.) (award 0702735)Singapore-MIT Alliance for Research and Technology CenterMicrosoft CorporationCarnegie Corporation of New YorkMaricopa County Community College District. Maricopa Advanced Technology Education Cente

Collaborative development of remote electronics laboratories in the ELVIS ilab

Remote laboratories represent a significant value to engineering curricula in a variety of cases. Whether it is a complement to a hands-on experience or a substitute when a traditional lab is not feasible, remote laboratories can be a valuable educational resource. Since 1998, the MIT iLab Project has worked to increase the quality and availability of remote laboratories. Using the iLab Shared Architecture, developers of new labs can leverage a set of generic support functions and then share those labs easily and with minimal administrative cost. More recently, the iLab Project, in partnership with Obafemi Awolowo University in Nigeria, Makerere University in Uganda and the University of Dar-es-Salaam in Tanzania and in coordination with the Maricopa Advanced Technology Education Center (MATEC), has focused on building iLabs around the National Instruments Educational Laboratory Virtual Instrumentation Suite (ELVIS) platform. The ELVIS is a low-cost, small-footprint unit that contains most of the common test instruments found in a typical electrical engineering lab. By coupling the ELVIS with iLabs, a variety of remote electronics laboratories can be built and shared around the world. Using this common hardware/software platform, participants in the iLab Project at different levels of the educational spectrum have developed experiments that meet their individual curricular needs and are able to host them for use by other peer institutions. Not only does this increase the variety of ELVISbased iLabs, but it also spurs the creation of teams that can then build other, more diverse iLabs and substantively participate in project-wide collaborative development efforts. Through such coordinated efforts, iLabs can provide rich practical experiences for studentsMaricopa County Community College District. Maricopa Advanced Technology Education CenterCarnegie Corporation of New YorkMicrosoft CorporationNational Science Foundation (U.S.) (award 0702735)Singapore-MIT Alliance for Research and Technology Cente

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.

Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for validated systematic integration of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By using IDEAS as our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of more than 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.National Institute of Diabetes and Digestive and Kidney Diseases (grant number R24DK106766-01A1), the National Human Genome Research Institute (grant number U54HG006998

Power and limitations of electrophoretic separations in proteomics strategies

Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

DNA sequence motifs and epigenetic modifications contribute to specific binding by a transcription factor, but the extent to which each feature determines occupancy in vivo is poorly understood. We addressed this question in erythroid cells by identifying DNA segments occupied by GATA1 and measuring the level of trimethylation of histone H3 lysine 27 (H3K27me3) and monomethylation of H3 lysine 4 (H3K4me1) along a 66 Mb region of mouse chromosome 7. While 91% of the GATA1-occupied segments contain the consensus binding-site motif WGATAR, only ∼0.7% of DNA segments with such a motif are occupied. Using a discriminative motif enumeration method, we identified additional motifs predictive of occupancy given the presence of WGATAR. The specific motif variant AGATAA and occurrence of multiple WGATAR motifs are both strong discriminators. Combining motifs to pair a WGATAR motif with a binding site motif for GATA1, EKLF or SP1 improves discriminative power. Epigenetic modifications are also strong determinants, with the factor-bound segments highly enriched for H3K4me1 and depleted of H3K27me3. Combining primary sequence and epigenetic determinants captures 52% of the GATA1-occupied DNA segments and substantially increases the specificity, to one out of seven segments with the required motif combination and epigenetic signals being bound

Evolutionary and biomedical insights from the rhesus macaque genome

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases

Identification and Replication of Loci Involved in Camptothecin-Induced Cytotoxicity Using CEPH Pedigrees

To date, the Centre d'Etude Polymorphism Humain (CEPH) cell line model has only been used as a pharmacogenomic tool to evaluate which genes are responsible for the disparity in response to a single drug. The purpose of this study was demonstrate the model's ability to establish a specific pattern of quantitative trait loci (QTL) related to a shared mechanism for multiple structurally related drugs, the camptothecins, which are Topoisomerase 1 inhibitors. A simultaneous screen of six camptothecin analogues for in vitro sensitivity in the CEPH cell lines resulted in cytotoxicity profiles and orders of potency which were in agreement with the literature. For all camptothecins studied, heritability estimates for cytotoxic response averaged 23.1±2.6%. Nonparametric linkage analysis was used to identify a relationship between genetic markers and response to the camptothecins. Ten QTLs on chromosomes 1, 3, 5, 6, 11, 12, 16 and 20 were identified as shared by all six camptothecin analogues. In a separate validation experiment, nine of the ten QTLs were replicated at the significant and suggestive levels using three additional camptothecin analogues. To further refine this list of QTLs, another validation study was undertaken and seven of the nine QTLs were independently replicated for all nine camptothecin analogues. This is the first study using the CEPH cell lines that demonstrates that a specific pattern of QTLs could be established for a class of drugs which share a mechanism of action. Moreover, it is the first study to report replication of linkage results for drug-induced cytotoxicity using this model. The QTLs, which have been identified as shared by all camptothecins and replicated across multiple datasets, are of considerable interest; they harbor genes related to the shared mechanism of action for the camptothecins, which are responsible for variation in response