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Kishore R, Arnaboldi V, J. Chen W, W. Sternberg P. Expanding automated gene summaries for Caenorhabditis and parasitic nematode species in WormBase. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001267. [PMID: 39087205 PMCID: PMC11289675 DOI: 10.17912/micropub.biology.001267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
Abstract
WormBase and the Alliance of Genome Resources provide several types of gene data including annotations to ontology terms and controlled vocabularies. These are used to automatically generate text summaries to give users a cogent view of gene function. However, automated summaries are not available for genes that lack curated annotations. To increase the genome coverage of the summaries in WormBase, we developed a new software module that generates additional gene summaries for C. elegans and new gene summaries for nine other nematode species: four Caenorhabditis species ( C. brenneri, C. briggsae, C. japonica, C. remanei ), P. pacificus , and four parasitic species ( B. malayi, O. volvulus, S. ratti and T. muris ).
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Affiliation(s)
- Ranjana Kishore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States
| | - Wen J. Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States
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Mingjie Y, Yair A, Tali G. The RIDD activity of C. elegans IRE1 modifies neuroendocrine signaling in anticipation of environment stress to ensure survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552841. [PMID: 37609168 PMCID: PMC10441387 DOI: 10.1101/2023.08.10.552841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Xbp1 splicing and regulated IRE1-dependent RNA decay (RIDD) are two RNase activities of the ER stress sensor IRE1. While Xbp1 splicing has important roles in stress responses and animal physiology, the physiological role(s) of RIDD remain enigmatic. Genetic evidence in C. elegans connects XBP1-independent IRE1 activity to organismal stress adaptation, but whether this is via RIDD, and what are the targets is yet unknown. We show that cytosolic kinase/RNase domain of C. elegans IRE1 is indeed capable of RIDD in human cells, and that sensory neurons use RIDD to signal environmental stress, by degrading mRNA of TGFβ-like growth factor DAF-7. daf-7 was degraded in human cells by both human and worm IRE1 RNAse activity with same efficiency and specificity as Blos1, confirming daf-7 as RIDD substrate. Surprisingly, daf-7 degradation in vivo was triggered by concentrations of ER stressor tunicamycin too low for xbp-1 splicing. Decrease in DAF-7 normally signals food limitation and harsh environment, triggering adaptive changes to promote population survival. Because C. elegans is a bacteriovore, and tunicamycin, like other common ER stressors, is an antibiotic secreted by Streptomyces spp., we asked whether daf-7 degradation by RIDD could signal pending food deprivation. Indeed, pre-emptive tunicamycin exposure increased survival of C. elegans populations under food limiting/high temperature stress, and this protection was abrogated by overexpression of DAF-7. Thus, C. elegans uses stress-inducing metabolites in its environment as danger signals, and employs IRE1's RIDD activity to modulate the neuroendocrine signaling for survival of upcoming environmental challenge.
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Affiliation(s)
- Ying Mingjie
- Department of Biology, Drexel University, Philadelphia, PA
- Department of Pathology and Lab Medicine, The Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA, USA
| | - Argon Yair
- Department of Pathology and Lab Medicine, The Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA, USA
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Salim C, Kan AK, Batsaikhan E, Patterson EC, Jee C. Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. Sci Rep 2022; 12:1804. [PMID: 35110557 PMCID: PMC8810865 DOI: 10.1038/s41598-022-05256-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
Despite the catastrophic consequences of alcohol abuse, alcohol use disorders (AUD) and comorbidities continue to strain the healthcare system, largely due to the effects of alcohol-seeking behavior. An improved understanding of the molecular basis of alcohol seeking will lead to enriched treatments for these disorders. Compulsive alcohol seeking is characterized by an imbalance between the superior drive to consume alcohol and the disruption or erosion in control of alcohol use. To model the development of compulsive engagement in alcohol seeking, we simultaneously exploited two distinct and conflicting Caenorhabditis elegans behavioral programs, ethanol preference and avoidance of aversive stimulus. We demonstrate that the C. elegans model recapitulated the pivotal features of compulsive alcohol seeking in mammals, specifically repeated attempts, endurance, and finally aversion-resistant alcohol seeking. We found that neuropeptide signaling via SEB-3, a CRF receptor-like GPCR, facilitates the development of ethanol preference and compels animals to seek ethanol compulsively. Furthermore, our functional genomic approach and behavioral elucidation suggest that the SEB-3 regulates another neuropeptidergic signaling, the neurokinin receptor orthologue TKR-1, to facilitate compulsive ethanol-seeking behavior.
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Affiliation(s)
- Chinnu Salim
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Ann Ke Kan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Enkhzul Batsaikhan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - E Clare Patterson
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Changhoon Jee
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA.
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Abstract
Since 1992, FlyBase has provided a freely available online database of information about the model organism Drosophila melanogaster. Data in FlyBase is curated manually from research papers as well as computationally from a variety of relevant sources, to serve as an information hub that enables and accelerates research discovery. This chapter aims to give users new to the database an overview of the layout and types of data available, as well as introducing some tools with which to access the data. More experienced users will find useful information about recent improvements and descriptions to enable more efficient navigation of the database.
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Affiliation(s)
| | - Aoife Larkin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN, USA
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Yu S, Zheng C, Chu JSC. Identification of Essential Genes in Caenorhabditis elegans with Lethal Mutations Maintained by Genetic Balancers. Methods Mol Biol 2022; 2377:345-362. [PMID: 34709626 DOI: 10.1007/978-1-0716-1720-5_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic balancer systems, which allow effective capture and maintenance of lethal mutations stably, play an important role in identifying essential genes. Whole-genome sequencing (WGS) followed by bioinformatics analysis, combined with genetic mapping data analysis, allows for an efficient and economical means of identifying genomic mutations in essential genes. Using this approach, we successfully identified 104 essential genes on ChrI, ChrIII, and ChrV in C. elegans. In this report, we described a protocol that sequences the genome of prebalanced Caenorhabditis elegans (C. elegans) strains to carry lethal mutations and identifies candidate causal mutations and candidate essential genes using a robust bioinformatics procedure.
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Affiliation(s)
- Shicheng Yu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Bioland Laboratory, Guangzhou, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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Smith JJ, Xiao Y, Parsan N, Medwig-Kinney TN, Martinez MAQ, Moore FEQ, Palmisano NJ, Kohrman AQ, Chandhok Delos Reyes M, Adikes RC, Liu S, Bracht SA, Zhang W, Wen K, Kratsios P, Matus DQ. The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo. PLoS Genet 2022; 18:e1009981. [PMID: 34982771 PMCID: PMC8759636 DOI: 10.1371/journal.pgen.1009981] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/14/2022] [Accepted: 12/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and chromatin regulating factors that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0 cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasive fos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis. Cellular invasion is required for animal development and homeostasis. Inappropriate activation of invasion however can result in cancer metastasis. Invasion programs are orchestrated by complex gene regulatory networks (GRN) that function in a coordinated fashion to turn on and off pro-invasive genes. While the core of GRNs are DNA binding transcription factors, they require aid from chromatin remodelers to access the genome. To identify the suite of pro-invasive chromatin remodelers, we paired high resolution imaging with RNA interference to individually knockdown 269 chromatin factors, identifying the evolutionarily conserved SWItching defective/Sucrose Non-Fermenting (SWI/SNF) ATP-dependent chromatin remodeling complex as a new regulator of Caenorhabditis elegans anchor cell (AC) invasion. Using a combination of CRISPR/Cas9 genome engineering and targeted protein degradation we demonstrate that the core SWI/SNF complex functions in a dose-dependent manner to control invasion. Further, we determine that the accessory SWI/SNF complexes, BAF and PBAF, contribute to invasion via distinctive mechanisms: BAF is required to prevent inappropriate proliferation while PBAF promotes AC attachment and remodeling of the basement membrane. Together, our data provide insights into how the SWI/SNF complex, which is mutated in many human cancers, can function in a dose-dependent fashion to regulate switching from invasive to proliferative fates.
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Affiliation(s)
- Jayson J. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nithin Parsan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Taylor N. Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Michael A. Q. Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Frances E. Q. Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nicholas J. Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Abraham Q. Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mana Chandhok Delos Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Rebecca C. Adikes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Biology Department, Siena College, Loudonville, New York, United States of America
| | - Simeiyun Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sydney A. Bracht
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Cell Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kailong Wen
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - Paschalis Kratsios
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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7
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Hunter WB, Wintermantel WM. Optimizing Efficient RNAi-Mediated Control of Hemipteran Pests (Psyllids, Leafhoppers, Whitefly): Modified Pyrimidines in dsRNA Triggers. PLANTS 2021; 10:plants10091782. [PMID: 34579315 PMCID: PMC8472347 DOI: 10.3390/plants10091782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
The advantages from exogenously applied RNAi biopesticides have yet to be realized in through commercialization due to inconsistent activity of the dsRNA trigger, and the activity level of RNAi suppression. This has prompted research on improving delivery methods for applying exogenous dsRNA into plants and insects for the management of pests and pathogens. Another aspect to improve RNAi activity is the incorporation of modified 2′-F pyrimidine nucleotides into the dsRNA trigger. Modified dsRNA incorporating 32–55% of the 2′-F- nucleotides produced improved RNAi activity that increased insect mortality by 12–35% greater than non-modified dsRNA triggers of the same sequence. These results were repeatable across multiple Hemiptera: the Asian citrus psyllid (Diaphorina citri, Liviidae); whitefly (Bemisia tabaci, Aleyroididae); and the glassy-winged sharpshooter (Homalodisca vitripennis, Cicadellidae). Studies using siRNA with modified 2′-F- pyrimidines in mammalian cells show they improved resistance to degradation from nucleases, plus result in greater RNAi activity, due to increase concentrations and improved binding affinity to the mRNA target. Successful RNAi biopesticides of the future will be able to increase RNAi repeatability in the field, by incorporating modifications of the dsRNA, such as 2′-F- pyrimidines, that will improve delivery after applied to fruit trees or crop plants, with increased activity after ingestion by insects. Costs of RNA modification have decreased significantly over the past few years such that biopesticides can now compete on pricing with commercial chemical products.
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Affiliation(s)
- Wayne Brian Hunter
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Subtropical Insects Res., Fort Pierce, FL 34945, USA
- Correspondence:
| | - William M. Wintermantel
- U.S. Department of Agriculture, Agriculture Research Service, Crop Improvement and Protection Research, Salinas, CA 93905, USA;
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Dahlberg CL, Grove CA, Hulsey-Vincent H, Ismail S. Student Annotations of Published Data as a Collaboration between an Online Laboratory Course and the C. elegans Database, WormBase. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:jmbe-22-21. [PMID: 33884078 PMCID: PMC8012049 DOI: 10.1128/jmbe.v22i1.2331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/08/2020] [Indexed: 06/12/2023]
Abstract
Course-based undergraduate research experiences (CUREs) provide the same benefits as individual, mentored faculty research while expanding the availability of research opportunities. One important aspect of CUREs is students' engagement in collaboration. The shift to online learning during the COVID-19 pandemic created an immediate need for meaningful, collaborative experiences in CUREs. We developed a partnership with the Caenorhabditis elegans (C. elegans) database, WormBase, in which students submitted annotations of published manuscripts to the website. Due to the stress on students during this time of crisis, qualitative data were collected in lieu of quantitative pre- and postanalyses. Most students reported on cognitive processes that represent mid-level Bloom's categories. By partnering with WormBase, students gained insight into the scientific community and contributed as community members. We describe possible modifications for future courses, potential expansion of the WormBase collaboration, and future directions for quantitative analysis.
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Affiliation(s)
| | - Christian A. Grove
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | - Samiya Ismail
- Biology Department, Western Washington University, Bellingham, WA 98225
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Shpilka T, Du Y, Yang Q, Melber A, Uma Naresh N, Lavelle J, Kim S, Liu P, Weidberg H, Li R, Yu J, Zhu LJ, Strittmatter L, Haynes CM. UPR mt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans. Nat Commun 2021; 12:479. [PMID: 33473112 PMCID: PMC7817664 DOI: 10.1038/s41467-020-20784-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
As organisms develop, individual cells generate mitochondria to fulfill physiological requirements. However, it remains unknown how mitochondrial network expansion is scaled to cell growth. The mitochondrial unfolded protein response (UPRmt) is a signaling pathway mediated by the transcription factor ATFS-1 which harbors a mitochondrial targeting sequence (MTS). Here, using the model organism Caenorhabditis elegans we demonstrate that ATFS-1 mediates an adaptable mitochondrial network expansion program that is active throughout normal development. Mitochondrial network expansion requires the relatively inefficient MTS in ATFS-1, which allows the transcription factor to be responsive to parameters that impact protein import capacity of the mitochondrial network. Increasing the strength of the ATFS-1 MTS impairs UPRmt activity by increasing accumulation within mitochondria. Manipulations of TORC1 activity increase or decrease ATFS-1 activity in a manner that correlates with protein synthesis. Lastly, expression of mitochondrial-targeted GFP is sufficient to expand the muscle cell mitochondrial network in an ATFS-1-dependent manner. We propose that mitochondrial network expansion during development is an emergent property of the synthesis of highly expressed mitochondrial proteins that exclude ATFS-1 from mitochondrial import, causing UPRmt activation. The mitochondrial network expands to accommodate cell growth, but how scaling occurs is unclear. Here, the authors show in C. elegans that ATFS-1 mitochondrial import is reduced when mitochondrial proteins are highly expressed, activating the unfolded protein response and causing expansion.
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Affiliation(s)
- Tomer Shpilka
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - YunGuang Du
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Andrew Melber
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nandhitha Uma Naresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Joshua Lavelle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sookyung Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Hilla Weidberg
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lara Strittmatter
- Electron Microscopy Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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11
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Hahnel SR, Dilks CM, Heisler I, Andersen EC, Kulke D. Caenorhabditis elegans in anthelmintic research - Old model, new perspectives. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:237-248. [PMID: 33249235 PMCID: PMC7704361 DOI: 10.1016/j.ijpddr.2020.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022]
Abstract
For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
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Affiliation(s)
| | - Clayton M Dilks
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | | - Erik C Andersen
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
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Petitot AS, Dereeper A, Da Silva C, Guy J, Fernandez D. Analyses of the Root-Knot Nematode ( Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants. Pathogens 2020; 9:pathogens9080644. [PMID: 32784493 PMCID: PMC7460394 DOI: 10.3390/pathogens9080644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/26/2022] Open
Abstract
The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection were previously characterized but no information is available about the molecular dialogue established with a resistant plant. We compared the M. graminicola transcriptomes of stage-two juveniles (J2s) before and during infection of susceptible or resistant rice. Among 36,121 M. graminicola genes surveyed, 367 were differentially expressed during infection of resistant or susceptible plants. Genes encoding cell wall-degrading enzymes, peptidases and neuropeptides were expressed for a longer time in resistant plants compared to susceptible plants. Conversely, genes related to nematode development were not activated in the resistant host. The majority of M. graminicola effector genes had similar expression patterns, whatever the host genotype. However, two venom allergen-like protein (VAP)-encoding genes were specifically induced in resistant plants and Mg-VAP1 silencing in J2s reduced their ability to colonize roots. This study highlighted that M. graminicola adapts its gene expression to the host susceptibility. Further investigation is required to assess the role of Mg-VAPs in the rice-nematode interaction.
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Affiliation(s)
- Anne-Sophie Petitot
- IRD, Cirad, Univ Montpellier, IPME, 911 Avenue Agropolis, BP 64501, CEDEX 5, 34394 Montpellier, France; (A.D.); (D.F.)
- Correspondence:
| | - Alexis Dereeper
- IRD, Cirad, Univ Montpellier, IPME, 911 Avenue Agropolis, BP 64501, CEDEX 5, 34394 Montpellier, France; (A.D.); (D.F.)
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (C.D.S.); (J.G.)
| | - Julie Guy
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (C.D.S.); (J.G.)
| | - Diana Fernandez
- IRD, Cirad, Univ Montpellier, IPME, 911 Avenue Agropolis, BP 64501, CEDEX 5, 34394 Montpellier, France; (A.D.); (D.F.)
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13
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Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME. The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res 2020; 48:D731-D742. [PMID: 31713623 PMCID: PMC7145519 DOI: 10.1093/nar/gkz1041] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboratory rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies. At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD's data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.
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Affiliation(s)
- Jennifer R Smith
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- To whom correspondence should be addressed. Tel: +1 414 955 8871; Fax: +1 414 955 6595;
| | - G Thomas Hayman
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Santoshi L R Ellanki
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Genomic Sciences and Precision Medicine Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary E Shimoyama
- Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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14
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Cho J, Gao S, Stein L, Sternberg PW. Vennter - An interactive analysis tool for WormBase interaction data using Venn diagrams. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000258. [PMID: 32550480 PMCID: PMC7251783 DOI: 10.17912/micropub.biology.000258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 11/18/2022]
Affiliation(s)
- Jaehyoung Cho
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sibyl Gao
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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15
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Schriml LM, Mitraka E, Munro J, Tauber B, Schor M, Nickle L, Felix V, Jeng L, Bearer C, Lichenstein R, Bisordi K, Campion N, Hyman B, Kurland D, Oates CP, Kibbey S, Sreekumar P, Le C, Giglio M, Greene C. Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic Acids Res 2020; 47:D955-D962. [PMID: 30407550 PMCID: PMC6323977 DOI: 10.1093/nar/gky1032] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/22/2018] [Indexed: 12/22/2022] Open
Abstract
The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-inferred mechanistic disease classifications, thus providing novel perspectives on related diseases. Expansion of disease terms, alternative anatomy, cell type and genetic disease classifications and workflow automation highlight the updates for the DO since 2015. The enhanced breadth and depth of the DO’s knowledgebase has expanded the DO’s utility for exploring the multi-etiology of human disease, thus improving the capture and communication of health-related data across biomedical databases, bioinformatics tools, genomic and cancer resources and demonstrated by a 6.6× growth in DO’s user community since 2015. The DO’s continual integration of human disease knowledge, evidenced by the more than 200 SVN/GitHub releases/revisions, since previously reported in our DO 2015 NAR paper, includes the addition of 2650 new disease terms, a 30% increase of textual definitions, and an expanding suite of disease classification hierarchies constructed through defined logical axioms.
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Affiliation(s)
- Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | - James Munro
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Becky Tauber
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Mike Schor
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Lance Nickle
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Victor Felix
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Linda Jeng
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Bearer
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Nicole Campion
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brooke Hyman
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Kurland
- New York University Langone Medical Center, Department of Neurosurgery, New York, NY, USA
| | - Connor Patrick Oates
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Siobhan Kibbey
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Chris Le
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Giglio
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | - Carol Greene
- University of Maryland School of Medicine, Baltimore, MD, USA
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16
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Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5532788. [PMID: 31328773 PMCID: PMC6643302 DOI: 10.1093/database/baz077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/12/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022]
Abstract
Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.
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Affiliation(s)
- Shawna Spoor
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | | | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Anthony Bretaudeau
- INRA, UMR IGEPP, BIPAA/GenOuest, INRIA/Irisa - Campus de Beaulieu, Rennes Cedex, France
| | - Helena Rasche
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Computational Biology Core, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - F Alex Feltus
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
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17
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Medwig-Kinney TN, Smith JJ, Palmisano NJ, Tank S, Zhang W, Matus DQ. A developmental gene regulatory network for C. elegans anchor cell invasion. Development 2020; 147:dev185850. [PMID: 31806663 PMCID: PMC6983719 DOI: 10.1242/dev.185850] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Cellular invasion is a key part of development, immunity and disease. Using an in vivo model of Caenorhabditis elegans anchor cell invasion, we characterize the gene regulatory network that promotes cell invasion. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conserved transcription factors, fos-1 (Fos), egl-43 (EVI1/MEL), hlh-2 (E/Daughterless) and nhr-67 (NR2E1/TLX), that mediate anchor cell specification and/or invasive behavior. Connections between these transcription factors and the underlying cell biology that they regulate are poorly understood. Here, using genome editing and RNA interference, we examine transcription factor interactions before and after anchor cell specification. Initially, these transcription factors function independently of one another to regulate LIN-12 (Notch) activity. Following anchor cell specification, egl-43, hlh-2 and nhr-67 function largely parallel to fos-1 in a type I coherent feed-forward loop with positive feedback to promote invasion. Together, these results demonstrate that the same transcription factors can function in cell fate specification and differentiated cell behavior, and that a gene regulatory network can be rapidly assembled to reinforce a post-mitotic, pro-invasive state.
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Affiliation(s)
- Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Jayson J Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Sujata Tank
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
- Science and Technology Research Program, Smithtown High School East, St. James, NY 11780-1833, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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18
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Snoek BL, Sterken MG, Hartanto M, van Zuilichem AJ, Kammenga JE, de Ridder D, Nijveen H. WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. Database (Oxford) 2020; 2020:baz149. [PMID: 31960906 PMCID: PMC6971878 DOI: 10.1093/database/baz149] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 12/19/2022]
Abstract
Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Margi Hartanto
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Albert-Jan van Zuilichem
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
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19
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Coenye T, Kjellerup B, Stoodley P, Bjarnsholt T. The future of biofilm research - Report on the '2019 Biofilm Bash'. Biofilm 2019; 2:100012. [PMID: 33447799 PMCID: PMC7798458 DOI: 10.1016/j.bioflm.2019.100012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022] Open
Abstract
In May 2019, 29 scientists with expertise in various subdisciplines of biofilm research got together in Leavenworth (WA, USA) at an event designated as the ‘2019 Biofilm Bash’. The goal of this informal two-day meeting was first to identify gaps in our knowledge, and then to come up with ways how the biofilm community can fill these gaps. The meeting was organized around six questions that covered the most important items brought forward by the organizers and participants. The outcome of these discussions is summarized in the present paper. We are aware that these views represent a small subset of our field, and that inevitably we will have inadvertently overlooked important developing research areas and ideas. We are nevertheless hopeful that this report will stimulate discussions and help create new ways of how we can advance our field.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.,ESCMID Study Group on Biofilms, Basel, Switzerland
| | - Birthe Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University, Columbus, OH, USA.,National Biofilms Innovation Centre (NBIC), UK.,National Centre for Advanced Tribology at Southampton, University of Southampton, Southampton, UK
| | - Thomas Bjarnsholt
- ESCMID Study Group on Biofilms, Basel, Switzerland.,Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark.,Department of Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
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20
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Abstract
Using neXtProt release 2019-01-11, we manually curated a list of 1837 functionally uncharacterized human proteins. Using OrthoList 2, we found that 270 of them have homologues in Caenorhabditis elegans, including 60 with a one-to-one orthology relationship. According to annotations extracted from WormBase, the vast majority of these 60 worm genes have RNAi experimental data or mutant alleles, but manual inspection shows that only 15% have phenotypes that could be interpreted in terms of a specific function. One third of the worm orthologs have protein-protein interaction data, and two of these interactions are conserved in humans. The combination of phenotypic, protein-protein interaction, and gene expression data provides functional hypotheses for 8 uncharacterized human proteins. Experimental validation in human or orthologs is necessary before they can be considered for annotation.
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Affiliation(s)
- Paula Duek
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva, CMU , Michel-Servet 1 , 1211 Geneva 4 , Switzerland
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21
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Wang J, Mao D, Fazal F, Kim SY, Yamamoto S, Bellen H, Liu Z. Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. CURRENT PROTOCOLS IN BIOINFORMATICS 2019; 67:e85. [PMID: 31524990 PMCID: PMC6750039 DOI: 10.1002/cpbi.85] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
One of the greatest challenges in the bioinformatic analysis of human sequencing data is identifying which variants are pathogenic. Numerous databases and tools have been generated to address this difficulty. However, these many useful data and tools are broadly dispersed, requiring users to search for their variants of interest through human genetic databases, variant function prediction tools, and model organism databases. To solve this problem, we collected data and observed workflows of human geneticists, clinicians, and model organism researchers to carefully select and display valuable information that facilitates the evaluation of whether a variant is likely to be pathogenic. This program, Model organism Aggregated Resources for Rare Variant ExpLoration (MARRVEL) v1.2, allows users to collect relevant data from 27 public sources for further efficient bioinformatic analysis of the pathogenicity of human variants. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Dongxue Mao
- Department of Pediatrics-Neurology, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Fatima Fazal
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, Texas
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Department of Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Program in Developmental Biology, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Hugo Bellen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, Texas
| | - Zhandong Liu
- Department of Pediatrics, Jan and Dan Duncan Neurological Research Institute at Texas, Children's Hospital, Houston, Texas
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, Texas
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22
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Abstract
WormBase is an open-access model-organism database that provides current and accurate genetic information of C. elegans and related nematodes. Users can search WormBase by several fields, including a gene or human disease. A special feature of the database is the inclusion of micropublications, peer-reviewed data that may go unpublished in traditional venues.
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Affiliation(s)
| | - Daryl D Hurd
- a St. John Fisher College , Rochester , New York , USA
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