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Genome scale screen

Jonathan M Stokes, Arnaud Gutierrez, Allison J Lopatkin, Ian W Andrews, Shawn French, Ivan Matic, Eric D Brown, James J Collins
Antibiotic screens typically rely on growth inhibition to characterize compound bioactivity-an approach that cannot be used to assess the bactericidal activity of antibiotics against bacteria in drug-tolerant states. To address this limitation, we developed a multiplexed assay that uses metabolism-sensitive staining to report on the killing of antibiotic-tolerant bacteria. This method can be used with diverse bacterial species and applied to genome-scale investigations to identify therapeutic targets against tolerant pathogens...
March 11, 2019: Nature Methods
Laura V Milko, Julianne M O'Daniel, Daniela M DeCristo, Stephanie B Crowley, Ann Katherine M Foreman, Kathleen E Wallace, Lonna F Mollison, Natasha T Strande, Zahra S Girnary, Lacey J Boshe, Arthur S Aylsworth, Muge Gucsavas-Calikoglu, Dianne M Frazier, Neeta L Vora, Myra I Roche, Bradford C Powell, Cynthia M Powell, Jonathan S Berg
OBJECTIVE: To assess the performance of a standardized, age-based metric for scoring clinical actionability to evaluate conditions for inclusion in newborn screening and compare it with the results from other contemporary methods. STUDY DESIGN: The North Carolina Newborn Exome Sequencing for Universal Screening study developed an age-based, semiquantitative metric to assess the clinical actionability of gene-disease pairs and classify them with respect to age of onset or timing of interventions...
March 6, 2019: Journal of Pediatrics
Omar T Hammouda, Frank Böttger, Joachim Wittbrodt, Thomas Thumberger
In the era of CRISPR gene editing and genetic screening, there is an increasing demand for quick and reliable nucleic acid extraction pipelines for rapid genotyping of large and diverse sample sets. Despite continuous improvements of current workflows, the handling-time and material costs per sample remain major limiting factors. Here we present a robust method for low-cost DIY-pipet tips addressing these needs; i.e. using a cellulose filter disc inserted into a regular pipet tip. These filter-in-tips allow for a rapid, stand-alone four-step genotyping workflow by simply binding the DNA contained in the primary lysate to the cellulose filter, washing it in water and eluting it directly into the buffer for the downstream application (e...
2019: PloS One
Panagiota Giardoglou, Dimitris Beis
Coronary artery disease (CAD) is the leading form of cardiovascular disease (CVD), which is the primary cause of mortality worldwide. It is a complex disease with genetic and environmental risk factor contributions. Reports in human and mammalian models elucidate age-associated changes in cardiac function. The diverse mechanisms involved in cardiac diseases remain at the center of the research interest to identify novel strategies for prevention and therapy. Zebrafish ( Danio rerio ) have emerged as a valuable vertebrate model to study cardiovascular development over the last few decades...
February 28, 2019: Biomedicines
Kelly E Regan-Fendt, Jielin Xu, Mallory DiVincenzo, Megan C Duggan, Reena Shakya, Ryejung Na, William E Carson, Philip R O Payne, Fuhai Li
Systems biology perspectives are crucial for understanding the pathophysiology of complex diseases, and therefore hold great promise for the discovery of novel treatment strategies. Drug combinations have been shown to improve durability and reduce resistance to available first-line therapies in a variety of cancers; however, traditional drug discovery approaches are prohibitively cost and labor-intensive to evaluate large-scale matrices of potential drug combinations. Computational methods are needed to efficiently model complex interactions of drug target pathways and identify mechanisms underlying drug combination synergy...
2019: NPJ Systems Biology and Applications
Tikvah K Hayes, Flora Luo, Ofir Cohen, Amy B Goodale, Yenarae Lee, Sasha Pantel, Mukta Bagul, Federica Piccioni, David E Root, Levi A Garraway, Matthew Meyerson, Cory M Johannessen
Combinatorial inhibition of MEK1/2 and CDK4/6 is currently undergoing clinical investigation in NRAS-mutant melanoma. To prospectively map the landscape of resistance to this investigational regimen, we utilized a series of gain- and loss-of-function forward genetic screens to identify modulators of resistance to clinical inhibitors of MEK1/2 and CDK4/6 alone and in combination. First, we identified NRAS-mutant melanoma cell lines that were dependent on NRAS for proliferation and sensitive to MEK1/2 and CDK4/6 combination treatment...
February 28, 2019: Cancer Research
Pierre Bodénès, Hsiang-Yu Wang, Tsung-Hua Lee, Hung-Yu Chen, Chun-Yen Wang
This review presents a critical assessment of emerging microfluidic technologies for the application on biological productions of biofuels and other chemicals from microalgae. Comparisons of cell culture designs for the screening of microalgae strains and growth conditions are provided with three categories: mechanical traps, droplets, or microchambers. Emerging technologies for the in situ characterization of microalgae features and metabolites are also presented and evaluated. Biomass and secondary metabolite productivities obtained at microscale are compared with the values obtained at bulk scale to assess the feasibility of optimizing large-scale operations using microfluidic platforms...
2019: Biotechnology for Biofuels
Satya Swathi Nadakuduti, Colby G Starker, Dae Kwan Ko, Thilani B Jayakody, C Robin Buell, Daniel F Voytas, David S Douches
Genome-editing is being implemented in increasing number of plant species using engineered sequence specific nucleases (SSNs) such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR/Cas9), Transcription activator like effector nucleases (TALENs), and more recently CRISPR/Cas12a. As the tissue culture and regeneration procedures to generate gene-edited events are time consuming, large-scale screening methodologies that rapidly facilitate validation of genome-editing reagents are critical...
2019: Frontiers in Plant Science
Adan Codina, Paul A Renauer, Guangchuan Wang, Ryan D Chow, Jonathan J Park, Hanghui Ye, Kerou Zhang, Matthew B Dong, Brandon Gassaway, Lupeng Ye, Youssef Errami, Li Shen, Alan Chang, Dhanpat Jain, Roy S Herbst, Marcus Bosenberg, Jesse Rinehart, Rong Fan, Sidi Chen
The genetic makeup of cancer cells directs oncogenesis and influences the tumor microenvironment. In this study, we massively profiled genes that functionally drive tumorigenesis using genome-scale in vivo CRISPR screens in hosts with different levels of immunocompetence. As a convergent hit from these screens, Prkar1a mutant cells are able to robustly outgrow as tumors in fully immunocompetent hosts. Functional interrogation showed that Prkar1a loss greatly altered the transcriptome and proteome involved in inflammatory and immune responses as well as extracellular protein production...
February 11, 2019: Cell Systems
Eduard Ocaña-Pallarès, Sebastián R Najle, Claudio Scazzocchio, Iñaki Ruiz-Trillo
Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles)...
February 21, 2019: PLoS Genetics
Marcela Franco, Ashwini Jeggari, Sylvain Peuget, Franziska Böttger, Galina Selivanova, Andrey Alexeyenko
Despite the widening range of high-throughput platforms and exponential growth of generated data volume, the validation of biomarkers discovered from large-scale data remains a challenging field. In order to tackle cancer heterogeneity and comply with the data dimensionality, a number of network and pathway approaches were invented but rarely systematically applied to this task. We propose a new method, called NEAmarker, for finding sensitive and robust biomarkers at the pathway level. scores from network enrichment analysis transform the original space of altered genes into a lower-dimensional space of pathways...
February 20, 2019: Scientific Reports
Troy P Hubbard, Jonathan D D'Gama, Gabriel Billings, Brigid M Davis, Matthew K Waldor
Transposon insertion sequencing (TIS) is a widely used technique for conducting genome-scale forward genetic screens in bacteria. However, few methods enable comparison of TIS data across multiple replicates of a screen or across independent screens, including screens performed in different organisms. Here, we introduce a post hoc analytic framework, comparative TIS (CompTIS), which utilizes unsupervised learning to enable meta-analysis of multiple TIS data sets. CompTIS first implements screen-level principal-component analysis (PCA) and clustering to identify variation between the TIS screens...
February 20, 2019: MSphere
Xilong Liang, Xue Hou, Jianying Li, Yiqiang Han, Yuxian Zhang, Naijie Feng, Jidao Du, Wenhui Zhang, Dianfeng Zheng, Shumei Fang
BACKGROUND: Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean...
February 18, 2019: BMC Plant Biology
José I Rojas Echenique, Sergey Kryazhimskiy, Alex N Nguyen Ba, Michael M Desai
Screens for epistatic interactions have long been used to characterize functional relationships corresponding to protein complexes, metabolic pathways, and other functional modules. Although epistasis between adaptive mutations is also common in laboratory evolution experiments, the functional basis for these interactions is less well characterized. Here, we quantify the extent to which gene function (as determined by a genome-wide screen for epistasis among deletion mutants) influences the rate and genetic basis of compensatory adaptation in a set of 37 gene deletion mutants nested within 16 functional modules...
February 15, 2019: PLoS Genetics
Martha I Natukunda, Kyle A Parmley, Jessica D Hohenstein, Teshale Assefa, Jiaoping Zhang, Gustavo C MacIntosh, Asheesh K Singh
Cultivation of aphid-resistant soybean varieties can reduce yield losses caused by soybean aphids. However, discovery of aphid biotypes that are virulent on resistant soybean greatly threatens sustained utilization of host plant resistance to control soybean aphids. The objective of this study was to identify and genetically characterize aphid resistant soybean accessions in a diverse collection of 308 plant introductions in maturity groups (MG) I and II. In large-scale screening experiments conducted in the greenhouse, we identified 12 soybean accessions (10 aphid-resistant and 2 moderately resistant), including nine previously not reported for resistance against soybean aphids...
February 15, 2019: Journal of Economic Entomology
Boxuan Li, Ke Pu, Xinan Wu
Hepatocellular carcinoma (HCC) is a highly malignant tumor found in the bile duct epithelial cells, and the second most common tumor of the liver. However, the pivotal roles of most molecules of tumorigenesis in HCC are still unclear. Hence, it is essential to detect the tumorigenic mechanism and develop novel prognostic biomarkers for clinical application. The data of HCC mRNA-seq and clinical information from The Cancer Genome Atlas (TCGA) database were analyzed by weighted gene co-expression network analysis (WGCNA)...
February 11, 2019: Journal of Cellular Biochemistry
Aitor Blanco-Míguez, Guillermo Blanco, Alberto Gutierrez-Jácome, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
Advances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico screening of proteomes and metaproteomes is key to uncover bioactivities of translational, clinical and biotechnological interest, and to help assign functions to certain proteins, such as those predicted as hypothetical...
February 7, 2019: Journal of Biomedical Informatics
Roland Weis
Clone screening procedures for Pichia pastoris expression strain comparison rely on the availability of a cultivation environment that ensures equal growth and production capabilities for all assessed transformants. As clonal variation in such experiments is caused by diverging numbers and possibly also genomic locations of integrated (linearized) expression constructs, the productivity assessment of a larger number of strains is mandatory for selecting a set of strains for follow-up bioreactor cultivations in order to define the best-producing clone...
2019: Methods in Molecular Biology
Bo Zhou, Steve S Ho, Stephanie U Greer, Xiaowei Zhu, John M Bell, Joseph G Arthur, Noah Spies, Xianglong Zhang, Seunggyu Byeon, Reenal Pattni, Noa Ben-Efraim, Michael S Haney, Rajini R Haraksingh, Giltae Song, Hanlee P Ji, Dimitri Perrin, Wing H Wong, Alexej Abyzov, Alexander E Urban
K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and indels (both corrected for CN in aneuploid regions), loss of heterozygosity, megabase-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs), including small and large-scale complex SVs and nonreference retrotransposon insertions...
February 8, 2019: Genome Research
Yukio Koizumi, Jun Fukushima, Yayoi Kobayashi, Ayumi Kadowaki, Miyuki Natsui, Tomokazu Yamaguchi, Yumiko Imai, Toshihiro Sugiyama, Keiji Kuba
Malformin A1 (MA1) is a fungus-produced cyclic pentapeptide. MA1 exhibits teratogenicity to plants, fibrinolysis-enhancing activity, and cytotoxicity to mammalian cells. To clarify the cytotoxic mechanism of MA1, we screened for the genes involved in the cytotoxicity of MA1 in monocytoid U937 cells by using CRISPR/Cas9-based genome-wide knockout library. Screening was performed by positive selection for the cells resistant to MA1 treatment, and sgRNAs integrated into MA1-resistant cells were analyzed with high-throughput sequencing...
February 8, 2019: Chembiochem: a European Journal of Chemical Biology
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