Relevant bibliographies by topics / Genomic screens

Academic literature on the topic 'Genomic screens'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Genomic screens"

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Gaillochet, Christophe, Ward Develtere, and Thomas B. Jacobs. "CRISPR screens in plants: approaches, guidelines, and future prospects." Plant Cell 33, no. 4 (April 1, 2021): 794–813. http://dx.doi.org/10.1093/plcell/koab099.

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Abstract Clustered regularly interspaced short palindromic repeat (CRISPR)-associated systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene functions in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.
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Rorth, P., K. Szabo, A. Bailey, T. Laverty, J. Rehm, G. M. Rubin, K. Weigmann, et al. "Systematic gain-of-function genetics in Drosophila." Development 125, no. 6 (March 15, 1998): 1049–57. http://dx.doi.org/10.1242/dev.125.6.1049.

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A modular misexpression system was used to carry out systematic gain-of-function genetic screens in Drosophila. The system is based on inducible expression of genes tagged by insertion of a P-element vector carrying a GAL4-regulated promoter oriented to transcribe flanking genomic sequences. To identify genes involved in eye and wing development, the 2300 independent lines were screened for dominant phenotypes. Among many novel genes, the screen identified known genes, including hedgehog and decapentaplegic, implicated in these processes. A genetic interaction screen for suppressors of a cell migration defect in a hypomorphic slow border cells mutant identified known genes with likely roles in tyrosine kinase signaling and control of actin cytoskeleton, among many novel genes. These studies demonstrate the ability of the modular misexpression system to identify developmentally important genes and suggest that it will be generally useful for genetic interaction screens.
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Sheel, Ankur, and Wen Xue. "Genomic Amplifications Cause False Positives in CRISPR Screens." Cancer Discovery 6, no. 8 (August 2016): 824–26. http://dx.doi.org/10.1158/2159-8290.cd-16-0665.

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Hart, Traver, Kevin R. Brown, Fabrice Sircoulomb, Robert Rottapel, and Jason Moffat. "Measuring error rates in genomic perturbation screens: gold standards for human functional genomics." Molecular Systems Biology 10, no. 7 (July 2014): 733. http://dx.doi.org/10.15252/msb.20145216.

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Salamon, Hugh, Midori Kato-Maeda, Peter M. Small, Jorg Drenkow, and Thomas R. Gingeras. "Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data." Genome Research 10, no. 12 (November 21, 2000): 2044–54. http://dx.doi.org/10.1101/gr.152900.

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Genomic diversity within and between populations is caused by single nucleotide mutations, changes in repetitive DNA systems, recombination mechanisms, and insertion and deletion events. The contribution of these sources to diversity, whether purely genetic or of phenotypic consequence, can only be investigated if we have the means to quantitate and characterize diversity in many samples. With the advent of complete sequence characterization of representative genomes of different species, the possibility of developing protocols to screen for genetic polymorphism across entire genomes is actively being pursued. The large numbers of measurements such approaches yield demand that we pay careful attention to the numerical analysis of data. In this paper we present a novel application of an Affymetrix GeneChip to perform genome-wide screens for deletion polymorphism. A high-density oligonucleotide array formatted for mRNA expression and targeted at a fully sequenced 4.4-million–base pair Mycobacterium tuberculosis standard strain genome was adapted to compare genomic DNA. Hybridization intensities to 111,000 probe pairs (perfect complement and mismatch complement) were measured for genomic DNA from a clinical strain and from a vaccine organism. Because individual probe-pair hybridization intensities exhibit limited sensitivity/specificity characteristics to detect deletions, data-analytical methodology to exploit measurements from multiple probes in tandem locations across the genome was developed. The TSTEP (Tandem Set Terminal Extreme Probability) algorithm designed specifically to analyze the tandem hybridization measurements data was applied and shown to discover genomic deletions with high sensitivity. The TSTEP algorithm provides a foundation for similar efforts to characterize deletions in many hybridization measures in similar-sized and larger genomes. Issues relating to the design of genome content screening experiments and the implications of these methods for studying population genomics and the evolution of genomes are discussed.
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Jilderda, Laura J., Lin Zhou, and Floris Foijer. "Understanding How Genetic Mutations Collaborate with Genomic Instability in Cancer." Cells 10, no. 2 (February 6, 2021): 342. http://dx.doi.org/10.3390/cells10020342.

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Chromosomal instability is the process of mis-segregation for ongoing chromosomes, which leads to cells with an abnormal number of chromosomes, also known as an aneuploid state. Induced aneuploidy is detrimental during development and in primary cells but aneuploidy is also a hallmark of cancer cells. It is therefore believed that premalignant cells need to overcome aneuploidy-imposed stresses to become tumorigenic. Over the past decade, some aneuploidy-tolerating pathways have been identified through small-scale screens, which suggest that aneuploidy tolerance pathways can potentially be therapeutically exploited. However, to better understand the processes that lead to aneuploidy tolerance in cancer cells, large-scale and unbiased genetic screens are needed, both in euploid and aneuploid cancer models. In this review, we describe some of the currently known aneuploidy-tolerating hits, how large-scale genome-wide screens can broaden our knowledge on aneuploidy specific cancer driver genes, and how we can exploit the outcomes of these screens to improve future cancer therapy.
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The Transatlantic Multiple Sclerosis Genetics Cooperative. "A meta-analysis of genomic screens in multiple sclerosis." Multiple Sclerosis 7, no. 1 (February 1, 2001): 3–11. http://dx.doi.org/10.1191/135245801669625359.

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XU, AXIANG, and SHENGKUN SUN. "Genomic profiling screens small molecules of metastatic prostate carcinoma." Oncology Letters 10, no. 3 (July 8, 2015): 1402–8. http://dx.doi.org/10.3892/ol.2015.3472.

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Ashoti, Ator, Francesco Limone, Melissa van Kranenburg, Anna Alemany, Mirna Baak, Judith Vivié, Frederica Piccioni, et al. "Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen." PLOS ONE 17, no. 2 (February 17, 2022): e0263262. http://dx.doi.org/10.1371/journal.pone.0263262.

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Genome-wide screens that have viability as a readout have been instrumental to identify essential genes. The development of gene knockout screens with the use of CRISPR-Cas has provided a more sensitive method to identify these genes. Here, we performed an exhaustive genome-wide CRISPR/Cas9 phenotypic rescue screen to identify modulators of cytotoxicity induced by the pioneer transcription factor, DUX4. Misexpression of DUX4 due to a failure in epigenetic repressive mechanisms underlies facioscapulohumeral muscular dystrophy (FHSD), a complex muscle disorder that thus far remains untreatable. As the name implies, FSHD generally starts in the muscles of the face and shoulder girdle. Our CRISPR/Cas9 screen revealed no key effectors other than DUX4 itself that could modulate DUX4 cytotoxicity, suggesting that treatment efforts in FSHD should be directed towards direct modulation of DUX4 itself. Our screen did however reveal some rare and unexpected genomic events, that had an important impact on the interpretation of our data. Our findings may provide important considerations for planning future CRISPR/Cas9 phenotypic survival screens.
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Kaplow, Irene M., Rohit Singh, Adam Friedman, Chris Bakal, Norbert Perrimon, and Bonnie Berger. "RNAiCut: automated detection of significant genes from functional genomic screens." Nature Methods 6, no. 7 (July 2009): 476–77. http://dx.doi.org/10.1038/nmeth0709-476.

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Dissertations / Theses on the topic "Genomic screens"

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Wilson, Jennifer L. (Jennifer Lynn). "Network analyses for functional genomic screens in cancer." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104236.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 128-151).
Gene interference screens are a widely adopted and popular tool for uncovering gene function but imperfections in the technology limit the power of these investigations. There are many completed and on-going RNAi investigations across a multitude of biological systems because these experiments are scalable, cost-effective, and relatively easily adapted to multiple experimental environments. The most influential disadvantage is that many of the individual reagents are non-specific and interfere with genes other than the intended target. Efforts to improve limitations in RNAi have focused on statistical models and improving reagents, yet have not explored using biological context to select gene targets. This thesis uses network modeling and data integration to provide context for gene interference studies, and demonstrates the utility of this approach in two systems: Acute Lymphoblastic Leukemia (ALL) is a disease of undifferentiated B-cells that results from accumulation of genetic lesions, yet we have an incomplete understanding of all genes contributing to the disease and how they interact. To discover genetic mediators of this disease, we employ a genome-scale shRNA screen, and complement this data with differential mRNA expression and ChIP-seq data using network integration. The integrated model identifies processes not represented in any input set and predicts novel genes contributing to disease. We specifically validate the role of Wwpl as a tumor suppressor in ALL. Aberrant growth factor pathway activity drives cancer pathology and is the target of molecular cancer therapies. Specifically, the epidermal growth factor receptor (EFGR) pathway and its ligand, transforming growth factor alpha (TGF[alpha]) are clinically relevant to gastric cancer. We use an shRNA screen and Prize Collecting Steiner Forest (PCSF) algorithm to discover the pathway regulating TGF shedding. This pathway identifies common regulators of TGF[alpha] shedding and NF[chi]B regulation, yet targeting NF[chi]B and the EGFR pathway has thus far been unsuccessful in cancer therapies. Our network identifies IRAK1 as a viable path forward for modulating both TGF[alpha] and NF[chi]B in gastric cancer.
by Jennifer L. Wilson.
Ph. D.
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Burrows, Anna. "Genome-Wide Loss-of-Function Genetic Screens Identify Novel Senescence Genes and Putative Tumor Suppressors." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10191.

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During every cell cycle and upon exogenous stress, tumor suppression programs are engaged to ensure genomic stability. In response to replicative aging and oncogenic stimuli, the p53 and Rb pathways are activated to prevent the proliferation of damaged cells. Several lines of evidence suggest that escape from senescence is a crucial early step in oncogenic progression. A major challenge in the cancer field is to combine genomic information regarding cancer-associated genetic changes with high-throughput functional studies, in order to confirm genetic requirements and pinpoint biological roles of these perturbed genes in oncogenesis. Furthermore, a complete genetic understanding of replicative senescence, and how it might be bypassed, is lacking. We describe here two genome scale loss-of-function genetic screens that interrogate these tumor suppressor programs. We utilized a unique sensitization approach to isolate senescence pathways and unmask compensatory mechanisms that may have been difficult to identify in previous studies. These genetic screens have generated comprehensive and validated datasets of putative senescence and p53 pathway genes. We present this dataset as a high-quality resource for further investigation into these biological pathways. We have uncovered several genes in distinct biological pathways which have not been demonstrated to have a functional role in senescence, and which may be putative tumor suppressors. We have identified BRD7 and BAF180, two SWI/SNF components, as critical regulators of p53. BRD7 and BAF180 are required for p53 activity and p21 expression during replicative and oncogene-induced senescence, and evidence suggests that they are inactivated in human cancer. In addition, we have uncovered a role for the deubiquitinating enzyme USP28 in the regulation of p53 accumulation during senescence, such that loss of USP28 results in bypass of the senescence program. We have also investigated several other novel senescence genes including SEMA6A, SEMA3b, and TMEM154. We have found that the expression of these genes is highly regulated during senescence by distinct means, including both p53-dependent and p53-independent mechanisms. These results demonstrate the efficacy of our sensitized screening approach, and also highlight the emerging view that the senescence program requires the combined action of multiple biological pathways for its execution.
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Pickering, H. "Identification of Chlamydia trachomatis immune targets through immunological and population-genomic screens and elucidation of potential roles in bacterial pathogenesis." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2017. http://researchonline.lshtm.ac.uk/3928322/.

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Ocular infection by Chlamydia trachomatis (Ct) results in trachoma, the leading infectious cause of blindness. Infection clears naturally, but repeated exposure in endemic areas and resulting inflammation promote tissue damage leading eventually to blinding sequelae. Antibiotic treatment as part of community-based intervention reduces prevalence of infection and disease but rarely eliminates the problem completely and progression to scarring and blindness does still occur. Sixty years of vaccine trials have produced variable results therefore new candidate antigens and better understanding of the underlying causes of infection and disease are required. Serum samples from trachoma-endemic communities in The Gambia were tested against the arrayed Ct proteome to identify antibody responses associated with protection from infection and from scarring disease. More focussed global antibody profiles were associated with partial immunity to infection. Several antibody targets were identified as individually associated with infection and disease outcome. Clinical Ct isolates collected from Guinea-Bissau were screened for evidence of natural selection to identify further immune targets and to validate those discovered through serological techniques. Evidence of positive selection was found for known Ct virulence factors, there was little evidence of balancing selection. Antibody targets associated with susceptibility to infection and scarring had evidence of purifying selection. One of the Ct antigens, CT442, identified as being an immune target and under natural selection was characterised further using cell-culture models. It was localised to the inclusion membrane through immunofluorescence microscopy, the primary point of contact with the host, and potentially interacted with pathways involved in intracellular vesicular trafficking based on interacting proteins identified through mass spectrometry. Ct infection is shown to stimulate a broad, polyclonal antibody response, individuals with more focussed responses are better protected from persistent infection and scarring progression. Purifying selection in antibody targets which associate with poor resolution of infection suggests two possible hypotheses for Ct evasion of immune responses. The decoy hypothesis, in which Ct actively promotes immune responses against irrelevant, decoy antigens to divert antibody responses away from protective antigens, and the blocking hypothesis, in which antibodies against certain Ct surface antigens block the binding of neutralising antibodies. Evidence of selection in CT442 show it is important but unlikely essential for Ct survival, the functions that are driving this evolution require further study.
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Allan, Kristina Jean. "Enhancing Oncolytic Virotherapy Using Functional Genomic Screening." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/37910.

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Li, Shuzhao. "A genomic screen for Zic1 target genes in neural development." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/li/LiS0806.pdf.

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Pedro, Rodrigues Joana Cristina. "Yeast genome-wide telomere screens and insights into cancer." Thesis, University of Newcastle upon Tyne, 2017. http://hdl.handle.net/10443/3898.

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Telomeres are the very ends of linear eukaryotic chromosomes and when too short or dysfunctional they can trigger senescence (ageing). If the cell can bypass senescence, it can lead to genetic instability or cancer. Telomere capping proteins such as the CST (Cdc13, Stn1 and Ten1) complex and Yku70 are essential for the telomeres not to be recognised as double strand breaks. In this thesis I have used published yeast genome-wide screens to identify genes that are relevant to cancer and telomere biology. Overall 14 out of 19 genetic interactions identified by genome-wide screens could be confirmed by small scale experiments. This work mainly focuses on the telomeric roles of VPS74 and the PAF1 complex. Here, I show that the Golgi gene VPS74, whose human orthologue, GOLPH3, is an oncogene, genetically interacts with telomere capping genes and DNA damage response genes. I demonstrate that Vps74 is important for cell fitness of yku70Δ cells and that the low fitness of Vps74 depleted cells is dependent on the presence of DNA damage checkpoint proteins. I have also systematically investigated the roles of PAF1 complex (Cdc73, Paf1, Ctr9, Leo1 and Rtf1, in yeast) components on telomere biology. The conserved PAF1 complex affects RNA abundance in eukaryotes. I demonstrate that individual PAF1 complex components perform different functions at telomeres. I show that loss of Cdc73 improves fitness of telomere defective yeast cells, while loss of other PAF1 components has the opposite effect. Moreover, I show that Paf1 and Ctr9 strongly reduce telomeric repeat-containing non-coding RNA (TERRA), while Cdc73, Leo1 and Rtf1 have little effect. Paf1 and Ctr9 function independently of Sir4 to regulate TERRA and this is because they stimulate TERRA decay, as well as decay of other RNAs. Additionally, I found that Paf1 and Ctr9 decrease TEN1 and STN1 mRNA levels. I suggest that the PAF1 complex plays a specialized role at telomeres, with Paf1 and Ctr9 maintaining telomere integrity and Cdc73 decreasing the fitness of telomere defective cells.
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Giedraitis, Vilmantas. "Candidate gene analyses and genome-wide screens in multiple sclerosis /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-408-9/.

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Sawcer, Stephen James. "A linkage genome screen in multiple sclerosis." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627121.

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Jarvis, Morgan L. "Development of a novel screen protocol for the identification of genes causing replication associated genomic instability in Schizosaccharomyces pombe." Thesis, Kingston, Ont. : [s.n.], 2008. http://hdl.handle.net/1974/1227.

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Deligiannaki, Myrto. "Identification of novel septate junction components through genome-wide glial screens." Diss., Ludwig-Maximilians-Universität München, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:19-183079.

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Epithelial barriers are central to the development of metazoans by compartmentalizing the body in distinct chemical milieus essential for the function of many organs. One such barrier is the blood-brain barrier, which isolates the nervous system from the body fluid to maintain its ionic homeostasis and ensure nerve pulse transmission. In Drosophila, the blood-brain barrier is formed late in embryogenesis by a thin epithelium of subperineurial glia that ensheath the nervous system. Similar to other epithelia, subperineurial glia seal the paracellular space by forming large multiprotein complexes at the lateral membrane, the septate junctions (SJs), which impede free diffusion and mediate barrier function. To identify novel genes required for blood-brain barrier formation, we followed a genome-wide in vivo RNAi approach. We initially screened almost the whole genome for genes required in glia for adult viability and impressively identified 3679 potential candidates. Subsequently, we tested these candidates for requirement in subperineurial glia for adult survival and identified 383 genes. At a last step, we directly asked if blood-brain barrier formation is compromised in the knock-down of the genes by performing the embryonic dye penetration assay in a selection of candidates and identified five genes that play a role during barrier development. Three of these genes, macroglobulin complement-related (mcr) and the previously uncharacterized pasiflora1 and pasiflora2 are further characterized in the context of this thesis. Here we show that all three proteins are novel components of the Drosophila SJ. Pasiflora1 and Pasiflora2 belong to a previously uncharacterized family of tetra-spanning membrane proteins, while Mcr was reported to be a secreted protein in S2 cells required for phagocytosis and clearance of specific pathogens. Through detailed phenotypic analysis we demonstrate that the mutants show leaky blood-brain and tracheal barriers, overelongated tracheal tubes and mislocalization of SJ proteins, phenotypes that are characteristic of SJ mutants. Consistent with the observed phenotypes, the genes are co-expressed in SJ-forming embryonic epithelia and glia and are required cell-autonomously to exert their function. In columnar epithelia, the proteins localize at the apicolateral membrane compartment, where they colocalize with other SJ proteins, and similar to known SJ components, their restricted localization depends on other complex members. Using fluorescence recovery after photobleaching experiments, we demonstrate for Pasiflora proteins that they are core SJ components, as they are required for complex formation and themselves show restricted mobility within the membrane of wild-type epithelial cells, but fast diffusion in cells with disrupted SJs. Taken together, our results show that Pasiflora1 and Pasiflora2 are novel integral SJ components and implicate a new family of tetraspan proteins in the development of cell junctions. In addition, we find a new unexpected role for Mcr as a transmembrane SJ protein, which raises questions about a potential intriguing link between epithelial barrier function, phagocytosis and innate immunity and has potential implications for the function of occluding junctions.
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Books on the topic "Genomic screens"

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Edmonds, Dawn Elaine. A genome-wide screen in Saccharomyces cerevisiae to identify novel genes that interact with telomerase. 2006.

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Book chapters on the topic "Genomic screens"

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Pucci, Michael J., John F. Barrett, and Thomas J. Dougherty. "Bacterial “Genes-to-Screens” in the Post-Genomic Era." In Pathogen Genomics, 83–96. Totowa, NJ: Humana Press, 2002. http://dx.doi.org/10.1007/978-1-59259-172-5_7.

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Adikari, Samantha, Elizabeth Hong-Geller, and Sofiya Micheva-Viteva. "Methods for Enrichment of Bacterial Persister Populations for Phenotypic Screens and Genomic Studies." In Methods in Molecular Biology, 71–82. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1621-5_5.

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McDonald, Sherin, Arunkumar Annan Sudarsan, Hanan Babeker, Kiranmayee Budharaju, and Maruti Uppalapati. "Generation of Protein Inhibitors for Validation of Cancer Drug Targets Identified in Functional Genomic Screens." In Methods in Molecular Biology, 307–31. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1740-3_17.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "RNA-Based Mechanisms of Gene Silencing." In Introduction to Epigenetics, 117–33. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_6.

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AbstractAlthough epigenetic states are typically associated with DNA-methylation and posttranslational histone modifications, RNAs often play an important role in their regulation. Specific examples have already been discussed in the context of dosage compensation (see book ► Chap. 10.1007/978-3-030-68670-3_4 of Wutz) and genomic imprinting (see book ► Chap. 10.1007/978-3-030-68670-3_5 of Grossniklaus). In this Chapter, we will take a closer look at a particular class of RNAs implicated in gene silencing. Although the focus will lie on RNA-based silencing mechanisms in plants, many of its components, such as RNase III-related DICERLIKE endonucleases or small RNA-binding ARGONAUTE proteins, are conserved in animals, plants, and fungi. On the one hand, small RNAs are involved in post-transcriptional silencing by targeting mRNAs for degradation or inhibiting their translation, a feature that has been exploited for large-scale genetic screens. On the other hand, they also play a central role in transcriptional gene silencing, for instance in the repression of transposable elements across a wide variety of organisms. In plants, this involves a complex system whereby small RNAs derived from transposons and repeats direct DNA-methylation and repressive histone modifications in a sequence-specific manner. Recent results link this so-called RNA-dependent DNA-methylation to paramutation, a classical epigenetic phenomenon where one allele directs a heritable epigenetic change in another.
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Chini, Andrea. "Application of Yeast-Two Hybrid Assay to Chemical Genomic Screens: A High-Throughput System to Identify Novel Molecules Modulating Plant Hormone Receptor Complexes." In Methods in Molecular Biology, 35–43. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-592-7_4.

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Javid, Babak, and Eric J. Rubin. "Whole Genome Screens in Macrophages." In Phagocyte-Pathogen Interactions, 537–43. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816650.ch35.

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Sanjana, Neville E. "Multiscale Genome Engineering: Genome-Wide Screens and Targeted Approaches." In Research and Perspectives in Neurosciences, 83–86. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-60192-2_8.

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Desler, Claus, Jon Ambæk Durhuus, and Lene Juel Rasmussen. "Genome-Wide Screens for Expressed Hypothetical Proteins." In Methods in Molecular Biology, 25–38. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-424-7_3.

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Liao, Xihao, Xin-Hui Xing, and Chong Zhang. "New Method for Genome-Scale Functional Genomic Study in Bacteria with Superior Performance: CRISPR Interference Screen." In Methods in Molecular Biology, 123–41. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1720-5_7.

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Yau, Edwin H., and Tariq M. Rana. "Next-Generation Sequencing of Genome-Wide CRISPR Screens." In Methods in Molecular Biology, 203–16. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7514-3_13.

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Conference papers on the topic "Genomic screens"

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Marcotte, Richard, Kevin Brown, Azin Sayad, Maliha Haider, Troy Ketela, Jason Moffat, and Benjamin G. Neel. "Abstract 5084: Functional genomic classification of breast cancer using pooled lentivirus shRNA screens." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-5084.

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Inoue, Akira, Bahar Salimian Rizi, Alessandro Carugo, Sahil Seth, Christopher Bristow, Giannicola Genovese, Andrea Viale, David G. Menter, Scott Kopetz, and Giulio F. Draetta. "Abstract 414: Identifying selective vulnerabilities in colorectal cancer molecular subtypes usingin vivofunctional genomic screens." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-414.

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Kim, Suntae, Patrick J. Grohar, Carleen Klumpp, Ashish Lal, Scott E. Martin, Lee J. Helman, and Natasha J. Caplen. "Abstract 520: Functional genomic screens identify microRNA regulators of the oncogenic fusion transcription factor EWS-FLI1." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-520.

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Stover, Elizabeth H., Maria B. Baco, Ofir Cohen, Yvonne Li, Elizabeth Christie, Mukta Bagul, Amy Goodale, et al. "Abstract AP14: POOLED GENOMIC SCREENS IDENTIFY ANTI-APOPTOTIC GENES AS MEDIATORS OF CHEMOTHERAPY RESISTANCE IN OVARIAN CANCER." In Abstracts: 12th Biennial Ovarian Cancer Research Symposium; September 13-15, 2018; Seattle, Washington. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1557-3265.ovcasymp18-ap14.

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Maxson, Julia, Jason Gotlib, Daniel Pollyea, Angela Fleischman, Christopher Eide, Daniel Bottomly, Beth Wilmot, et al. "Abstract 2282: Rapid identification of targetable CSF3R mutations that define neutrophilic leukemia by combining functional and genomic screens." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-2282.

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Casas, Matias. "Abstract 5135: Functional genomic shRNA screens reveal that the canonical Wnt pathway protects lung cancer cells from EGFR inhibition." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-5135.

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Garcia, Felix Sanchez, Patricia Villagrasa, Junji Matsui, Bo-Juen Chen, Dylan Kotliar, Veronica Castro, Jose M. Silva, and Dana Pe'er. "Abstract 3168: Helios identifies novel oncogenes in breast cancer by integrating genomic characterization of primary tumors and functional shRNA-screens." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-3168.

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Frank, An, Sujatha Kumar, Christina Ghirelli, Kim Hoenderdos, Tabasum Huseni, Lauren Thibault, Lydia Kifle, et al. "Abstract B66: An integrated immuno-oncology platform using high-throughput cell based assays, gene editing and genomic screens in immune cells." In Abstracts: AACR Special Conference on Tumor Immunology and Immunotherapy; October 20-23, 2016; Boston, MA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/2326-6074.tumimm16-b66.

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Munoz, Diana, Frank P. Stegmeier, and Michael Schlabach. "Abstract B21: CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions." In Abstracts: AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; January 4-7, 2017; San Diego, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-8514.synthleth-b21.

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Meyers, Robin M., Andrew J. Aguirre, Barbara A. Weir, Francisca Vazquez, Cheng-Zhong Zhang, Uri Ben-David, April Cook, et al. "Abstract B39: Genomic copy number alterations introduce a gene-independent viability bias in CRISPR-Cas9 knock-out screens of cancer cell lines." In Abstracts: AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1557-3265.pmccavuln16-b39.

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Reports on the topic "Genomic screens"

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Perrimon, Norbert. Parallel Genomic and Chemical Screens to Identify Both Therapeutic Targets and Inhibitors of These Targets in the Treatment of Neurofibromatosis. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada465264.

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Sadot, Einat, Christopher Staiger, and Zvi Kam Weizmann. functional genomic screen for new plant cytoskeletal proteins and the determination of their role in actin mediated functions and guard cells regulation. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7587725.bard.

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The original objectives of the approved proposal were: 1. To construct a YFP fused Arabidopsis cDNA library in a mammalian expression vector. 2. To infect the library into a host fibroblast cell line and to screen for new cytoskeletal associated proteins using an automated microscope. 3. Isolate the new genes. 4. Characterize their role in plants. The project was approved as a feasibility study to allow proof of concept that would entail building the YFP library and picking up a couple of positive clones using the fluorescent screen. We report here on the construction of the YFP library, the development of the automatic microscope, the establishment of the screen and the isolation of positive clones that are plant cDNAs encoding cytoskeleton associated proteins. The rational underling a screen of plant library in fibroblasts is based on the high conservation of the cytoskeleton building blocks, actin and tubulin, between the two kingdoms (80-90% homology at the level of amino acids sequence). In addition, several publications demonstrated the recognition of mammalian cytoskeleton by plant cytoskeletal binding proteins and vice versa. The major achievements described here are: 1. The development of an automated microscope equipped with fast laser auto-focusing for high magnification and a software controlling 6 dimensions; X, Y position, auto focus, time, color, and the distribution and density of the fields acquired. This system is essential for the high throughput screen. 2. The construction of an extremely competent YFP library efficiently cloned (tens of thousands of clones collected, no empty vectors detected) with all inserts oriented 5't03'. These parameters render it well representative of the whole transcriptome and efficient in "in-frame" fusion to YFP. 3. The strategy developed for the screen allowing the isolation of individual positive cDNA clones following three rounds of microscopic scans. The major conclusion accomplished from the work described here is that the concept of using mammalian host cells for fishing new plant cytoskeletal proteins is feasible and that screening system developed is complete for addressing one of the major bottlenecks of the plant cytoskeleton field: the need for high throughput identification of functionally active cytoskeletal proteins. The new identified plant cytoskeletal proteins isolated in the pilot screen and additional new proteins which will be isolated in a comprehensive screen will shed light on cytoskeletal mediated processes playing a major role in cellular activities such as cell division, morphogenesis, and functioning such as chloroplast positioning, pollen tube and root hair elongation and the movement of guard cells. Therefore, in the long run the screen described here has clear agricultural implications.
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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.

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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.
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Avni, Adi, and Kirankumar S. Mysore. Functional Genomics Approach to Identify Signaling Components Involved in Defense Responses Induced by the Ethylene Inducing Xyalanase Elicitor. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7697100.bard.

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Plant-microbe interactions involve a large number of global regulatory systems, which are essential for plants to protect themselves against pathogen attack. An ethylene-inducing xylanase (EIX) of Trichoderma viride is a potent elicitor of plant defense responses, like hypersensitive response (HR), in specific cultivars of tobacco (Nicotiana tabacum) and tomato (Lycopersicon esculentum). The central goal of this proposal was to investigate the molecular mechanisms that allow plants to specifically activate defense responses after EIX treatment. We proposed to identify cellular signaling components involved in the induction of HR by the EIX elicitor. The molecular genetic analysis of the signal transduction pathway that modulates hypersensitive responses is an important step in understanding the induction of plant defense responses. The genes that mediate LeEIX2-EIX dependent activation of resistance mechanisms remain to be identified. We used two approaches to identify the cellular signaling components that induce HR mediated by the EIX elicitor. In the first approach, we performed a yeast two-hybrid screening using LeEix2 as bait to identify plant proteins that interact with it. In the second approach, we used virus-induced gene silencing (VIGS) for a high-throughput screen to identify genes that are required for the induction of LeEIX2-EIX mediated HR. VIGS will also be used for functional characterization of genes that will be identified during the yeast two-hybrid screen. This investigation will shed light on cellular processes and signaling components involved in induction of general plant defense against pathogens and will provide the basis for future biotechnological approaches to improve plant resistance to pathogens. Several genes were indentified by the two approaches. We used the VIGS and yeast two hybrid approaches to confirm that activity of the genes initially identified by different procedure. Two genes inhibit the induction of HR by the fungal elicitor in the different systems; Tobacco-Harpin binding protein 1 and cyclopropyl isomerase.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.

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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Ostersetzer-Biran, Oren, and Alice Barkan. Nuclear Encoded RNA Splicing Factors in Plant Mitochondria. United States Department of Agriculture, February 2009. http://dx.doi.org/10.32747/2009.7592111.bard.

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Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for a small number of genes required in organellar genome expression and respiration. Yet, the vast majority of the organellar proteins are encoded by nuclear genes, thus necessitating complex mechanisms to coordinate the expression and accumulation of proteins encoded by the two remote genomes. Many organellar genes are interrupted by intervening sequences (introns), which are removed from the primary presequences via splicing. According to conserved features of their sequences these introns are all classified as “group-II”. Their splicing is necessary for organellar activity and is dependent upon nuclear-encoded RNA-binding cofactors. However, to-date, only a tiny fraction of the proteins expected to be involved in these activities have been identified. Accordingly, this project aimed to identify nuclear-encoded proteins required for mitochondrial RNA splicing in plants, and to analyze their specific roles in the splicing of group-II intron RNAs. In non-plant systems, group-II intron splicing is mediated by proteins encoded within the introns themselves, known as maturases, which act specifically in the splicing of the introns in which they are encoded. Only one mitochondrial intron in plants has retained its maturaseORF (matR), but its roles in organellar intron splicing are unknown. Clues to other proteins required for organellar intron splicing are scarce, but these are likely encoded in the nucleus as there are no other obvious candidates among the remaining ORFs within the mtDNA. Through genetic screens in maize, the Barkan lab identified numerous nuclear genes that are required for the splicing of many of the introns within the plastid genome. Several of these genes are related to one another (i.e. crs1, caf1, caf2, and cfm2) in that they share a previously uncharacterized domain of archaeal origin, the CRM domain. The Arabidopsis genome contains 16 CRM-related genes, which contain between one and four repeats of the domain. Several of these are predicted to the mitochondria and are thus postulated to act in the splicing of group-II introns in the organelle(s) to which they are localized. In addition, plant genomes also harbor several genes that are closely related to group-II intron-encoded maturases (nMats), which exist in the nucleus as 'self-standing' ORFs, out of the context of their cognate "host" group-II introns and are predicted to reside within the mitochondria. The similarity with known group-II intron splicing factors identified in other systems and their predicted localization to mitochondria in plants suggest that nuclear-encoded CRM and nMat related proteins may function in the splicing of mitochondrial-encoded introns. In this proposal we proposed to (i) establish the intracellular locations of several CRM and nMat proteins; (ii) to test whether mutations in their genes impairs the splicing of mitochondrial introns; and to (iii) determine whether these proteins are bound to the mitochondrial introns in vivo.
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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Glazer, Itamar, Alice Churchill, Galina Gindin, and Michael Samish. Genomic and Organismal Studies to Elucidate the Mechanisms of Infectivity of Entomopathogenic Fungi to Ticks. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7593382.bard.

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The overall goal of this research was to elucidate the factors affecting early development of Metarhizium spp. (previously named M. anisopliae) on ticks or tick cuticle extracts and the molecular basis of these early infection processes. The original objectives were: 1. Characterize the pre-penetration events (adhesion, germination and appressorium formation) of spores of M. anisopliae strains with high or low virulence during tick infection. 2. Create GFP-expressing strains of M. anisopliae tick pathogens having high and low virulence to compare their progress of infection by microscopy. 3. Use microarray analyses, primarily with existing M. anisopliae EST sequences in GenBank, to identify and characterize fungal genes whose expression is regulated in response to host cuticle extracts. Objective 3 was later modified (as approved by BARD) to use RNAseq to characterize the early stages of fungal gene expression during infection of intact host cuticles. This new method provides a massively larger and more informative dataset and allows us to take advantage of a) recently published genomes of Metarhizium robertsii and M. acridum for RNAseq data analysis, and b) newly developed and highly efficient cDNA sequencing technologies that are relatively low cost and, therefore, allow deep sequencing of multiple transcriptome samples. We examined pre-penetration and penetration events that differentiate high and low virulence strains of Metarhizium spp., focusing on spore adhesion, germination, appressorium formation, and penetration of tick integuments. Initiation of fungal infection was compared on susceptible and resistant tick species at different tick developmental stages. In vitro studies comparing the effects of protein and fatty acid profiles from tick cuticle extracts demonstrated that resistant tick cuticles contain higher concentrations of specific lipids that inhibit fungal development than do susceptible tick cuticles, suggesting one mechanism of Ixodidae resistance to fungal entomopathogens (Objective 1). We used molecular markers to determine that the three M. anisopliae strains from Israel that we studied actually were three distinct species. M. brunneum is highly virulent against the tick Rhipicephalus annulatus, M. pingshaense and M. robertsii are intermediate in virulence, and M. majus is of low virulence. We transformed all four Metarhizium species to express GFP and used them in pathogenicity assays against diverse tick species. Key findings were that a) resistant ticks inhibit Metarhizium infection prior to hemocoel invasion by reducing fungal viability on the cuticle surface (Objective 2), as was supported by the in vitro studies of Objective 1, and b) Metarhizium kills susceptible ticks after cuticle penetration but prior to hemocoel colonization. Transcriptome studies of the most virulent species, M. brunneum, are in progress and include analyses of ungerminated conidia and conidia germination and development on a low nutrient medium or on susceptible R. annulatus exoskeleton (Objective 3). We anticipate these studies will contribute to identifying fungal genetic factors that increase virulence and speed of kill and may help reveal tick chemistries that could be included in biocontrol formulations to increase efficacy. Methodologies developed to screen tick cuticle extracts for ability to support conidia germination and development may help in the selection of wild fungi with increased virulence against resistant ticks. The overall knowledge gained should contribute not only to the improvement of tick control but also to the control of other blood-sucking arthropods and related plant pests. Use of bio-based agents for controlling arthropods will contribute to a healthier, more sustainable environment and serve a growing number of organic food farmers.
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Perl-Treves, Rafael, M. Kyle, and Esra Galun. Development and Application of a Molecular Genetic Map for Melon (Cucumis melo). United States Department of Agriculture, October 1993. http://dx.doi.org/10.32747/1993.7568094.bard.

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This project has generated a systematic survey of DNA polymorphism in Cucumis melo. An RFLP and RAPD survey of the major cultivar groups and botanical varieties of this species has been conducted, with the purpose of assessing the degree of molecular variation and phylogenetic relationships within the melon germplasm and, at the same time, develop sets of markets suitable for mapping the melon genome. Additional activities regarding variation in the melon germplasm in fruit traits and regeneration ability have been initiated as well. The necessary populations required for the development of a molecular map of the C. melo genome have been prepared. An F2 that segregated for 4 viral resistances, powdery mildew resitance and sex type has been derived from a PI 414723 x Topmark cross, and a RILs population has been prepared from it. We have confirmed the resistances in the population and have analyzed the genetic relationships between these resistances. Progress toward the construction of a molecular map of C. melo and the development of markers linked to those traits is described. We have so far screened the first few tens of markers in the F2 population, and many additional ones were screened in DNA bulks prepared from such population.
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Cytryn, Eddie, Mark R. Liles, and Omer Frenkel. Mining multidrug-resistant desert soil bacteria for biocontrol activity and biologically-active compounds. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598174.bard.

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Control of agro-associated pathogens is becoming increasingly difficult due to increased resistance and mounting restrictions on chemical pesticides and antibiotics. Likewise, in veterinary and human environments, there is increasing resistance of pathogens to currently available antibiotics requiring discovery of novel antibiotic compounds. These drawbacks necessitate discovery and application of microorganisms that can be used as biocontrol agents (BCAs) and the isolation of novel biologically-active compounds. This highly-synergistic one year project implemented an innovative pipeline aimed at detecting BCAs and associated biologically-active compounds, which included: (A) isolation of multidrug-resistant desert soil bacteria and root-associated bacteria from medicinal plants; (B) invitro screening of bacterial isolates against known plant, animal and human pathogens; (C) nextgeneration sequencing of isolates that displayed antagonistic activity against at least one of the model pathogens and (D) in-planta screening of promising BCAs in a model bean-Sclerotiumrolfsii system. The BCA genome data were examined for presence of: i) secondary metabolite encoding genes potentially linked to the anti-pathogenic activity of the isolates; and ii) rhizosphere competence-associated genes, associated with the capacity of microorganisms to successfully inhabit plant roots, and a prerequisite for the success of a soil amended BCA. Altogether, 56 phylogenetically-diverse isolates with bioactivity against bacterial, oomycete and fungal plant pathogens were identified. These strains were sent to Auburn University where bioassays against a panel of animal and human pathogens (including multi-drug resistant pathogenic strains such as A. baumannii 3806) were conducted. Nineteen isolates that showed substantial antagonistic activity against at least one of the screened pathogens were sequenced, assembled and subjected to bioinformatics analyses aimed at identifying secondary metabolite-encoding and rhizosphere competence-associated genes. The genome size of the bacteria ranged from 3.77 to 9.85 Mbp. All of the genomes were characterized by a plethora of secondary metabolite encoding genes including non-ribosomal peptide synthase, polyketidesynthases, lantipeptides, bacteriocins, terpenes and siderophores. While some of these genes were highly similar to documented genes, many were unique and therefore may encode for novel antagonistic compounds. Comparative genomic analysis of root-associated isolates with similar strains not isolated from root environments revealed genes encoding for several rhizospherecompetence- associated traits including urea utilization, chitin degradation, plant cell polymerdegradation, biofilm formation, mechanisms for iron, phosphorus and sulfur acquisition and antibiotic resistance. Our labs are currently writing a continuation of this feasibility study that proposes a unique pipeline for the detection of BCAs and biopesticides that can be used against phytopathogens. It will combine i) metabolomic screening of strains from our collection that contain unique secondary metabolite-encoding genes, in order to isolate novel antimicrobial compounds; ii) model plant-based experiments to assess the antagonistic capacities of selected BCAs toward selected phytopathogens; and iii) an innovative next-generation-sequencing based method to monitor the relative abundance and distribution of selected BCAs in field experiments in order to assess their persistence in natural agro-environments. We believe that this integrated approach will enable development of novel strains and compounds that can be used in large-scale operations.
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