Encroaching genomics: adapting large-scale science to small academic laboratories

Einarson, Margret B., and Erica A. Golemis. Encroaching genomics: adapting large-scale science to small academic laboratories. Physiol Genomics 2: 85–92, 2000.—The process of conducting biological research is undergoing a profound metamorphosis due to the technological innovations and torrent of information resulting from the execution of multiple species genome projects. The further tasks of mapping polymorphisms and characterizing genome-wide protein-protein interaction (the characterization of the proteome) will continue to garner resources, talent, and public attention. Although some elements of these whole genome size projects can only be addressed by large research groups, consortia, or industry, the impact of these projects has already begun to transform the process of research in many small laboratories. Although the impact of this transformation is generally positive, laboratories engaged in types of research destined to be dominated by the efforts of a genomic consortium may be negatively impacted if they cannot rapidly adjust strategies in the face of new large-scale competition. The focus of this report is to outline a series of strategies that have been productively utilized by a number of small academic laboratories that have attempted to integrate such genomic resources into research plans with the goal of developing novel physiological insights.

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Synchronization of human retinal pigment epithelial-1 cells in mitosis

Journal of Cell Science ◽

10.1242/jcs.247940 ◽

2020 ◽

Vol 133 (18) ◽

pp. jcs247940

Author(s):

Stacey J. Scott ◽

Kethan S. Suvarna ◽

Pier Paolo D'Avino

Keyword(s):

Cell Lines ◽

Large Scale ◽

Retinal Pigment Epithelial ◽

Retinal Pigment ◽

Interaction Network ◽

Protein Protein Interaction ◽

Pigment Epithelial ◽

Adenocarcinoma Cells ◽

Sequential Treatments

ABSTRACTHuman retinal pigment epithelial-1 (RPE-1) cells are increasingly being used as a model to study mitosis because they represent a non-transformed alternative to cancer cell lines, such as HeLa cervical adenocarcinoma cells. However, the lack of an efficient method to synchronize RPE-1 cells in mitosis precludes their application for large-scale biochemical and proteomics assays. Here, we report a protocol to synchronize RPE-1 cells based on sequential treatments with the Cdk4 and Cdk6 inhibitor PD 0332991 (palbociclib) and the microtubule-depolymerizing drug nocodazole. With this method, the vast majority (80–90%) of RPE-1 cells arrested at prometaphase and exited mitosis synchronously after release from nocodazole. Moreover, the cells fully recovered and re-entered the cell cycle after the palbociclib–nocodazole block. Finally, we show that this protocol could be successfully employed for the characterization of the protein–protein interaction network of the kinetochore protein Ndc80 by immunoprecipitation coupled with mass spectrometry. This synchronization method significantly expands the versatility and applicability of RPE-1 cells to the study of cell division and might be applied to other cell lines that do not respond to treatments with DNA synthesis inhibitors.

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Synchronization of human retinal pigment ephitilial-1 (RPE-1) cells in mitosis

10.1101/2020.04.21.052803 ◽

2020 ◽

Author(s):

Stacey J. Scott ◽

Kethan Suvarna ◽

Pier Paolo D’Avino

Keyword(s):

Cell Lines ◽

Large Scale ◽

Retinal Pigment ◽

Interaction Network ◽

Protein Protein Interaction ◽

Adenocarcinoma Cells ◽

Sequential Treatments ◽

Dna Synthesis Inhibitors ◽

Protein Protein Interaction Network

ABSTRACTHuman retinal pigment ephitilial-1 (RPE-1) cells are increasingly being used as a model to study mitosis because they represent a non-transformed alternative to cancer cell lines, such as HeLa cervical adenocarcinoma cells. However, the lack of an efficient method to synchronize RPE-1 cells in mitosis precludes their application for large-scale biochemical and proteomics assays. Here we report a protocol to synchronize RPE-1 cells based on sequential treatments with the Cdk4/6 inhibitor PD 0332991 (palbociclib) and the microtubule depolymerizing drug nocodazole. With this method, the vast majority (80-90%) of RPE-1 cells arrested at prometaphase and exited mitosis synchronously after release from nocodazole. Furthermore, we show that this protocol could be successfully employed for the characterization of the protein-protein interaction network of the kinetochore protein Ndc80 by immunoprecipitation coupled with mass spectrometry. This synchronization method significantly expands the versatility and applicability of RPE-1 cells to the study of cell division and might be applied to other cell lines that do not respond to treatments with DNA synthesis inhibitors.

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New Frontiers inSchistosomaGenomics and Transcriptomics

Journal of Parasitology Research ◽

10.1155/2012/849132 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 9

Author(s):

Laila A. Nahum ◽

Marina M. Mourão ◽

Guilherme Oliveira

Keyword(s):

Large Scale ◽

Biological Research ◽

Mitochondrial Genomes ◽

Future Directions ◽

Important Species ◽

Blood Flukes ◽

Causative Agents ◽

Mitochondrial Sequences ◽

Modern Technologies

Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium,S. japonicum, andS. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of sixSchistosomaspecies have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization ofSchistosomagenomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.

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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Genes ◽

10.3390/genes10070536 ◽

2019 ◽

Vol 10 (7) ◽

pp. 536 ◽

Cited By ~ 2

Author(s):

Xiaobo Zhao ◽

Liming Gan ◽

Caixia Yan ◽

Chunjuan Li ◽

Quanxi Sun ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

Sequencing Data ◽

Regulatory Processes ◽

Genome Wide ◽

Non Coding Rnas ◽

Identification And Characterization ◽

Lower Expression ◽

Weighted Correlation

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

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A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening

10.26434/chemrxiv.12682316 ◽

2020 ◽

Author(s):

Christoph Gorgulla ◽

Krishna PadmanabhaDas ◽

Kendra E. Leigh ◽

Marco Cespugli ◽

Patrick D. Fischer ◽

...

Keyword(s):

Virtual Screening ◽

In Silico ◽

Active Sites ◽

Large Scale ◽

Protein Protein Interaction ◽

The Face ◽

Computing Platforms ◽

Screening Platform ◽

Novel Coronavirus ◽

Further Development

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.

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THE STATE'S RESPONSIBILITY IN THE WELFARE OF PEOPLE AND ECONOMIC RECOVERY IN THE FACE OF COVID-19 FROM THE PERSPECTIVE OF LAW AND HUMAN RIGHTS

Nurani Jurnal Kajian Syari ah dan Masyarakat ◽

10.19109/nurani.v21i2.8940 ◽

1970 ◽

Vol 21 (2) ◽

pp. 187-198

Author(s):

Serlika Aprita ◽

Lilies Anisah

Keyword(s):

Human Rights ◽

Best Practices ◽

Government Regulation ◽

Large Scale ◽

Problem Solver ◽

The World ◽

The Face ◽

The Government ◽

Almost All ◽

The Impact

The Covid-19 pandemic was taking place in almost all countries around the world. Along with the increasingly vigorous government strategy in tackling the spread of the corona virus that was still endemic until now, the government had started to enforce the Large-Scale Social Restrictions (PSBB) with the signing of Government Regulation (PP) No. 21 of 2020 about PSBB which was considered able to accelerate countermeasures while preventing the spread of corona that was increasingly widespread in Indonesia. The research method used was normative prescriptive. The government put forward the principle of the state as a problem solver. The government minimized the use of region errors as legitimacy to decentralization. The government should facilitated regional best practices in handling the pandemic. Thus, the pandemic can be handled more effectively. The consideration, the region had special needs which were not always accommodated in national policies. The government policy should be able to encourage the birth of regional innovations in handling the pandemic as a form of fulfilling human rights in the field of health. Innovation was useful in getting around the limitations and differences in the context of each region. In principle, decentralization required positive incentives, not penalties. Therefore, incentive-based central policies were more awaited in handling and minimizing the impact of the pandemic.

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Encircling the regions of the pharmacogenomic landscape that determine drug response

10.1101/383588 ◽

2018 ◽

Cited By ~ 2

Author(s):

Adrià Fernández-Torras ◽

Miquel Duran-Frigola ◽

Patrick Aloy

Keyword(s):

Large Scale ◽

Drug Response ◽

Drug Sensitivity ◽

Drug Repositioning ◽

Gene Sets ◽

Diffusion Analysis ◽

Genome Wide ◽

Molecular Determinants ◽

Gene Modules

AbstractBackgroundThe integration of large-scale drug sensitivity screens and genome-wide experiments is changing the field of pharmacogenomics, revealing molecular determinants of drug response without the need for previous knowledge about drug action. In particular, transcriptional signatures of drug sensitivity may guide drug repositioning, prioritize drug combinations and point to new therapeutic biomarkers. However, the inherent complexity of transcriptional signatures, with thousands of differentially expressed genes, makes them hard to interpret, thus giving poor mechanistic insights and hampering translation to clinics.MethodsTo simplify drug signatures, we have developed a network-based methodology to identify functionally coherent gene modules. Our strategy starts with the calculation of drug-gene correlations and is followed by a pathway-oriented filtering and a network-diffusion analysis across the interactome.ResultsWe apply our approach to 189 drugs tested in 671 cancer cell lines and observe a connection between gene expression levels of the modules and mechanisms of action of the drugs. Further, we characterize multiple aspects of the modules, including their functional categories, tissue-specificity and prevalence in clinics. Finally, we prove the predictive capability of the modules and demonstrate how they can be used as gene sets in conventional enrichment analyses.ConclusionsNetwork biology strategies like module detection are able to digest the outcome of large-scale pharmacogenomic initiatives, thereby contributing to their interpretability and improving the characterization of the drugs screened.

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The Role of Responsive Leadership in Meeting Customers' Needs during Crises

International Journal of Customer Relationship Marketing and Management ◽

10.4018/ijcrmm.289207 ◽

2022 ◽

Vol 13 (1) ◽

pp. 0-0

Keyword(s):

Large Scale ◽

Education Institution ◽

Face To Face ◽

Leadership Attributes ◽

Leadership Support ◽

The Face ◽

Quantitative Results ◽

The Impact

This case study conducted to investigate the impact of a responsive leadership approach in meeting customers' needs in a higher education institution in the UAE during the COVID-19 pandemic. For this purpose, a mixed-method model has been used. The data has been collected from a convenient sample working and studying at Al Qasimia University Language Center, in fall 2020. This result indicates that the provided responsive leadership support during COVID-19 was effective and helped in motivating learners and customers to keep learning and making progress greater than what was shown before COVID-19, during the face-to-face teaching and physical assessment. Although the qualitative and quantitative results in this case study revealed a significant impact of responsive leadership approach on customers’ progress, there is still a need to conduct other researches to develop and validate a responsive leadership inventory to facilitate measuring of responsive leadership attributes in a large scale sample and/or population.

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Impact of sustained TGFβ receptor inhibition on chromatin accessibility and gene expression in cultured human endometrial MSC

10.1101/2020.05.01.073346 ◽

2020 ◽

Author(s):

Raffaella Lucciola ◽

Pavle Vrljicak ◽

Caitlin Filby ◽

Saeedeh Darzi ◽

Shanti Gurung ◽

...

Keyword(s):

Gene Expression ◽

Retinoic Acid ◽

Gene Networks ◽

Large Scale ◽

Transforming Growth Factor ◽

Retinoic Acid Receptor ◽

Human Endometrium ◽

Acid Receptor ◽

Genome Wide ◽

The Impact

AbstractEndometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human endometrium. Clinical application of eMSC for therapeutic purposes is hampered by spontaneous differentiation and cellular senescence upon large-scale expansion in vitro. A83-01, a selective transforming growth factor-β receptor (TGFβ-R) inhibitor, promotes pharmacological expansion of eMSC in culture by blocking differentiation and senescence, but the underlying mechanisms are incompletely understood. In this study, we combined RNA-seq and ATAC-seq to study the impact of sustained TGFβ-R inhibition on gene expression and chromatin architecture of eMSC. Treatment of primary eMSC with A83-01 for 5 weeks resulted in differential expression of 1,463 genes. Gene ontology analysis showed enrichment of genes implicated in cell growth whereas extracellular matrix genes and genes involved in cell fate commitment were downregulated. ATAC-seq analysis demonstrated that sustained TGFβ-R inhibition results in opening and closure of 3,555 and 2,412 chromatin loci, respectively. Motif analysis revealed marked enrichment of retinoic acid receptor (RAR) binding sites, which was paralleled by the induction of RARB, encoding retinoic acid receptor beta (RARβ). Selective RARβ inhibition attenuated proliferation and clonogenicity of A83-01 treated eMSC. Taken together, our study provides new insights into the gene networks and genome-wide chromatin changes that underpin maintenance of an undifferentiated phenotype of eMSC in prolonged culture.Significance statementCycling human endometrium is a rich source of adult stem/progenitor cells that could be exploited for clinical purposes. Small molecules, such as A83-01, that modulate cell identity may open new avenues to maintain the functional properties of eMSC upon expansion in culture. By integrating complementary genome-wide profiling techniques, we mapped the dynamic changes in chromatin landscape and gene expression in response to prolonged A83-01 treatment of eMSC. Our findings provide new insights into the mechanisms of action of TGFβ-R inhibition that may lead to the development of more targeted pharmacological approaches for MSC expansion.

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DISTRIBUTION OF IMPACT INDUCED PRESSURES AT THE FACE OF UNIFORMLY SLOPED SEA DIKES: PRELIMINARY 2D EXPERIMENTAL RESULTS

Coastal Engineering Proceedings ◽

10.9753/icce.v33.structures.74 ◽

2012 ◽

Vol 1 (33) ◽

pp. 74 ◽

Cited By ~ 1

Author(s):

Dimitris Stagonas ◽

Gerald Muller ◽

Karunya Ramachandran ◽

Stefan Schimmels ◽

Alec Dane

Keyword(s):

Large Scale ◽

Tactile Sensor ◽

Breaking Waves ◽

Horizontal Distribution ◽

Breaking Wave ◽

The Face ◽

The University ◽

The Impact ◽

Sea Dikes ◽

Sea Dike

Although existing knowledge on the vertical distribution of impact pressures on sea-dikes is well established only very little is known with respect to their horizontal distribution. A collaboration developed between the University of Southampton, Uk and FZK, Hannover looks in more detail at the distribution of pressures induced by waves breaking on the face of a sea-dike. For this, 2D large scale experiments with waves breaking on a 1:3 sea dike were conducted but instead of pressure transducers a tactile pressure sensor was used to map the impact pressures. Such sensors were initially used with breaking waves in the University of Southampton and their use for large scale experiments was attempted here for the first time. In the current paper the calibration and application of the tactile sensor for experiments involving up to 1m high and 8sec long waves are initially described. Preliminary results illustrating the simultaneous distribution of impact induced pressures over an area of 426.7x487.7mm are then presented. Based on these pressure maps the vertical and horizontal location of maximum breaking wave induced pressures is also deduced.

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