Academic literature on the topic 'Novel eye disease genes'
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Journal articles on the topic "Novel eye disease genes"
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Mihelec, Marija, Luke St Heaps, Maree Flaherty, Frank Billson, Christina Rudduck, Patrick P. L. Tam, John R. Grigg, Greg B. Peters, and Robyn V. Jamieson. "Chromosomal Rearrangements and Novel Genes in Disorders of Eye Development, Cataract and Glaucoma." Twin Research and Human Genetics 11, no. 4 (August 1, 2008): 412–21. http://dx.doi.org/10.1375/twin.11.4.412.
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AbstractDisorders of eye development such as microphthalmia and anophthalmia (small and absent eyes respectively), anterior segment dysgenesis where there may be pupillary and iris anomalies, and associated cataract and glaucoma, often lead to visual impairment or blindness. Currently treatment options are limited, as much is unknown about the molecular pathways that control normal eye development and induce the aberrant processes that lead to ocular defects. Mutation detection rates in most of the known genes are generally low, emphasizing the genetic heterogeneity of developmental ocular defects. Identification of the disease genes in these conditions improves the clinical information available for affected individuals and families, and provides new insights into the underlying biological processes for facilitation of better treatment options. Investigation of chromosomal rearrangements associated with an ocular phenotype has been especially powerful for disease gene identification. Molecular characterization of such rearrangements, which pinpoints the region by physically disrupting the causative gene or its regulatory sequences, allows for rapid elucidation of underlying genetic factors that contribute to the phenotype. Genes including PAX6, PITX2, FOXC1, MAF, TMEM114, SOX2, OTX2 and BMP4 have been identified in this way to be associated with developmental eye disorders. More recently, new methods in chromosomal analysis such as comparative genomic hybridization (CGH) microarray, have also enhanced our ability in disease gene identification.
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Harding and Moosajee. "The Molecular Basis of Human Anophthalmia and Microphthalmia." Journal of Developmental Biology 7, no. 3 (August 14, 2019): 16. http://dx.doi.org/10.3390/jdb7030016.
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Human eye development is coordinated through an extensive network of genetic signalling pathways. Disruption of key regulatory genes in the early stages of eye development can result in aborted eye formation, resulting in an absent eye (anophthalmia) or a small underdeveloped eye (microphthalmia) phenotype. Anophthalmia and microphthalmia (AM) are part of the same clinical spectrum and have high genetic heterogeneity, with >90 identified associated genes. By understanding the roles of these genes in development, including their temporal expression, the phenotypic variation associated with AM can be better understood, improving diagnosis and management. This review describes the genetic and structural basis of eye development, focusing on the function of key genes known to be associated with AM. In addition, we highlight some promising avenues of research involving multiomic approaches and disease modelling with induced pluripotent stem cell (iPSC) technology, which will aid in developing novel therapies.
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Sheng, Minjie, Haiying Cai, Ming Cheng, Jing Li, Jian Zhang, and Lihua Liu. "Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm." BioMed Research International 2021 (September 6, 2021): 1–10. http://dx.doi.org/10.1155/2021/2295412.
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Choroidal neovascularization (CNV) is a type of eye disease that can cause vision loss. In recent years, many studies have attempted to investigate the major pathological processes and molecular pathogenic mechanisms of CNV. Because many diseases are related to genes, the genes associated with CNV need to be identified. In this study, we proposed a network-based approach for identifying novel CNV-associated genes. To execute such method, we first employed a protein-protein interaction network reported in STRING. Then, we applied a network diffusion algorithm, Laplacian heat diffusion, on this network by selecting validated CNV-related genes as the seed nodes. As a result, some novel genes that had unknown but strong relationships with validated genes were identified. Furthermore, we used a screening procedure to extract the most essential genes. Eleven latent CNV-related genes were finally obtained. Extensive analyses were performed to confirm that these genes are novel CNV-related genes.
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Wang, Likun, Jinlu Zhang, Ningning Chen, Lei Wang, Fengsheng Zhang, Zhizhong Ma, Genlin Li, and Liping Yang. "Application of Whole Exome and Targeted Panel Sequencing in the Clinical Molecular Diagnosis of 319 Chinese Families with Inherited Retinal Dystrophy and Comparison Study." Genes 9, no. 7 (July 19, 2018): 360. http://dx.doi.org/10.3390/genes9070360.
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Inherited retinal dystrophies (IRDs) are a group of clinically and genetically heterogeneous diseases involving more than 280 genes and no less than 20 different clinical phenotypes. In this study, our aims were to identify the disease-causing gene variants of 319 Chinese patients with IRD, and compare the pros and cons of targeted panel sequencing and whole exome sequencing (WES). Patients were assigned for analysis with a hereditary eye disease enrichment panel (HEDEP) or WES examination based on time of recruitment. This HEDEP was able to capture 441 hereditary eye disease genes, which included 291 genes related to IRD. As RPGR ORF15 was difficult to capture, all samples were subjected to Sanger sequencing for this region. Among the 163 disease-causing variants identified in this study, 73 had been previously reported, and the other 90 were novel. Genes most commonly implicated in different inheritances of IRDs in this cohort were presented. HEDEP and WES achieved diagnostic yield with 41.2% and 33.0%, respectively. In addition, nine patients were found to carry pathogenic mutations in the RPGR ORF15 region with Sanger sequencing. Our study demonstrates that HEDEP can be used as a first-tier test for patients with IRDs.
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Lee, Bradford W., Virender B. Kumar, Pooja Biswas, Audrey C. Ko, Ramzi M. Alameddine, David B. Granet, Radha Ayyagari, Don O. Kikkawa, and Bobby S. Korn. "Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology." Open Ophthalmology Journal 12, no. 1 (April 16, 2018): 41–52. http://dx.doi.org/10.2174/1874364101812010041.
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Objective: This study utilized Next Generation Sequencing (NGS) to identify differentially expressed transcripts in orbital adipose tissue from patients with active Thyroid Eye Disease (TED) versus healthy controls. Method: This prospective, case-control study enrolled three patients with severe, active thyroid eye disease undergoing orbital decompression, and three healthy controls undergoing routine eyelid surgery with removal of orbital fat. RNA Sequencing (RNA-Seq) was performed on freshly obtained orbital adipose tissue from study patients to analyze the transcriptome. Bioinformatics analysis was performed to determine pathways and processes enriched for the differential expression profile. Quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) was performed to validate the differential expression of selected genes identified by RNA-Seq. Results: RNA-Seq identified 328 differentially expressed genes associated with active thyroid eye disease, many of which were responsible for mediating inflammation, cytokine signaling, adipogenesis, IGF-1 signaling, and glycosaminoglycan binding. The IL-5 and chemokine signaling pathways were highly enriched, and very-low-density-lipoprotein receptor activity and statin medications were implicated as having a potential role in TED. Conclusion: This study is the first to use RNA-Seq technology to elucidate differential gene expression associated with active, severe TED. This study suggests a transcriptional basis for the role of statins in modulating differentially expressed genes that mediate the pathogenesis of thyroid eye disease. Furthermore, the identification of genes with altered levels of expression in active, severe TED may inform the molecular pathways central to this clinical phenotype and guide the development of novel therapeutic agents.
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Violanti, Sara Silvia, Ilaria Bononi, Carla Enrica Gallenga, Fernanda Martini, Mauro Tognon, and Paolo Perri. "New Insights into Molecular Oncogenesis and Therapy of Uveal Melanoma." Cancers 11, no. 5 (May 19, 2019): 694. http://dx.doi.org/10.3390/cancers11050694.
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Uveal melanoma (UM), which is the most common cancer of the eye, was investigated in recent years by many teams in the field of biomedical sciences and eye clinicians. New knowledge was acquired on molecular pathways found to be dysregulated during the multistep process of oncogenesis, whereas novel therapeutic approaches gave significant results in the clinical applications. Uveal melanoma-affected patients greatly benefited from recent advances of the research in this eye cancer. Tumour biology, genetics, epigenetics and immunology contributed significantly in elucidating the role of different genes and related pathways during uveal melanoma onset/progression and UM treatments. Indeed, these investigations allowed identification of new target genes and to develop new therapeutic strategies/compounds to cure this aggressive melanoma of the eye. Unfortunately, the advances reported in the treatment of cutaneous melanoma have not produced analogous benefits in metastatic uveal melanoma. Nowadays, no systemic adjuvant therapy has been shown to improve overall survival or reduce the risk of metastasis. However, the increasing knowledge of this disease, and the encouraging results seen in clinical trials, offer promise for future effective therapies. Herein, different pathways/genes involved in uveal melanoma onset/progression were taken into consideration, together with novel therapeutic approaches.
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Reis, Linda M., Huban Atilla, Peter Kannu, Adele Schneider, Samuel Thompson, Tanya Bardakjian, and Elena V. Semina. "Distinct Roles of Histone Lysine Demethylases and Methyltransferases in Developmental Eye Disease." Genes 14, no. 1 (January 14, 2023): 216. http://dx.doi.org/10.3390/genes14010216.
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Histone lysine methyltransferase and demethylase enzymes play a central role in chromatin organization and gene expression through the dynamic regulation of histone lysine methylation. Consistent with this, genes encoding for histone lysine methyltransferases (KMTs) and demethylases (KDMs) are involved in complex human syndromes, termed congenital regulopathies. In this report, we present several lines of evidence for the involvement of these genes in developmental ocular phenotypes, suggesting that individuals with structural eye defects, especially when accompanied by craniofacial, neurodevelopmental and growth abnormalities, should be examined for possible variants in these genes. We identified nine heterozygous damaging genetic variants in KMT2D (5) and four other histone lysine methyltransferases/demethylases (KMT2C, SETD1A/KMT2F, KDM6A and KDM5C) in unrelated families affected with developmental eye disease, such as Peters anomaly, sclerocornea, Axenfeld-Rieger spectrum, microphthalmia and coloboma. Two families were clinically diagnosed with Axenfeld-Rieger syndrome and two were diagnosed with Peters plus-like syndrome; others received no specific diagnosis prior to genetic testing. All nine alleles were novel and five of them occurred de novo; five variants resulted in premature truncation, three were missense changes and one was an in-frame deletion/insertion; and seven variants were categorized as pathogenic or likely pathogenic and two were variants of uncertain significance. This study expands the phenotypic spectra associated with KMT and KDM factors and highlights the importance of genetic testing for correct clinical diagnosis.
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Choy, K. W., C. C. Wang, A. Ogura, T. K. Lau, M. S. Rogers, K. Ikeo, T. Gojobori, D. S. C. Lam, and C. P. Pang. "Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes." Physiological Genomics 25, no. 1 (March 13, 2006): 9–15. http://dx.doi.org/10.1152/physiolgenomics.00121.2005.
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To complement cDNA libraries from the human eye at early gestation and to discover candidate genes associated with early ocular development, we used freshly dissected human eyeballs from week 9–14 of gestation to construct the early human fetal eye cDNA library. A total of 15,809 clones were isolated and sequenced from the unamplified and unnormalized library. We screened 11,246 good-quality ESTs, leading to the identification of 5,534 nonredundant clusters. Among them, 4,010 (72%) genes matched in the human protein database (Ensembl). The remaining 28% (1,524) corresponded to potentially novel or previously unidentified ESTs. We used BLASTX to compare our EST data with eight organisms and found common expression of a high portion of genes: Caenorhabditis briggsae (26%), Caenorhabditis elegans (27%), Anopheles gambiae (37%), Drosophila melanogaster (32%), Danio rerio (42%), Fugu rubripes (49%), Rattus norvegicusvalitus (52%), and Mus musculus (59%). Nevertheless, 48% (2,680 of 5,534) of the genes expressed in the early developing eye were not shared with current NEIBank human eye cDNA data. In addition, eight known retinal disease genes existed in our ESTs. Among them, six ( COL11A1, BBS5, PDE6B, OAT, VMD2, and PGK1) were conserved among the genomes of other organisms, indicating that our annotated EST set provides not only a valuable resource for gene discovery and functional genomic analysis but also for phylogenetic analysis. Our foremost early gestation human eye cDNA library could provide detailed comparisons across species to identify physiological functions of genes and to elucidate evolutionary mechanisms.
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Lin, Ting-Yi, Yun-Chia Chang, Yu-Jer Hsiao, Yueh Chien, Ying-Chun Jheng, Jing-Rong Wu, Lo-Jei Ching, et al. "Identification of Novel Genomic-Variant Patterns of OR56A5, OR52L1, and CTSD in Retinitis Pigmentosa Patients by Whole-Exome Sequencing." International Journal of Molecular Sciences 22, no. 11 (May 25, 2021): 5594. http://dx.doi.org/10.3390/ijms22115594.
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Inherited retinal dystrophies (IRDs) are rare but highly heterogeneous genetic disorders that affect individuals and families worldwide. However, given its wide variability, its analysis of the driver genes for over 50% of the cases remains unexplored. The present study aims to identify novel driver genes, disease-causing variants, and retinitis pigmentosa (RP)-associated pathways. Using family-based whole-exome sequencing (WES) to identify putative RP-causing rare variants, we identified a total of five potentially pathogenic variants located in genes OR56A5, OR52L1, CTSD, PRF1, KBTBD13, and ATP2B4. Of the variants present in all affected individuals, genes OR56A5, OR52L1, CTSD, KBTBD13, and ATP2B4 present as missense mutations, while PRF1 and CTSD present as frameshift variants. Sanger sequencing confirmed the presence of the novel pathogenic variant PRF1 (c.124_128del) that has not been reported previously. More causal-effect or evidence-based studies will be required to elucidate the precise roles of these SNPs in the RP pathogenesis. Taken together, our findings may allow us to explore the risk variants based on the sequencing data and upgrade the existing variant annotation database in Taiwan. It may help detect specific eye diseases such as retinitis pigmentosa in East Asia.
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Yang, Xue, Vafa Bayat, Nataliya DiDonato, Yang Zhao, Brian Zarnegar, Zurab Siprashvili, Vanessa Lopez-Pajares, et al. "Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis." Human Molecular Genetics 29, no. 4 (October 19, 2019): 541–53. http://dx.doi.org/10.1093/hmg/ddz251.
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Abstract Missense mutations in the RNA exosome component exosome component 2 (EXOSC2), also known as ribosomal RNA-processing protein 4 (RRP4), were recently identified in two unrelated families with a novel syndrome known as Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies (SHRF, #OMIM 617763). Little is known about the mechanism of the SHRF pathogenesis. Here we have studied the effect of mutations in EXOSC2/RRP4 in patient-derived lymphoblasts, clustered regularly interspaced short palindromic repeats (CRISPR)-generated mutant fetal keratinocytes and Drosophila. We determined that human EXOSC2 is an essential gene and that the pathogenic G198D mutation prevents binding to other RNA exosome components, resulting in protein and complex instability and altered expression and/or activities of critical genes, including those in the autophagy pathway. In parallel, we generated multiple CRISPR knockouts of the fly rrp4 gene. Using these flies, as well as rrp4 mutants with Piggy Bac (PBac) transposon insertion in the 3′UTR and RNAi flies, we determined that fly rrp4 was also essential, that fly rrp4 phenotypes could be rescued by wild-type human EXOSC2 but not the pathogenic form and that fly rrp4 is critical for eye development and maintenance, muscle ultrastructure and wing vein development. We found that overexpression of the transcription factor MITF was sufficient to rescue the small eye and adult lethal phenotypes caused by rrp4 inhibition. The autophagy genes ATG1 and ATG17, which are regulated by MITF, had similar effect. Pharmacological stimulation of autophagy with rapamycin also rescued the lethality caused by rrp4 inactivation. Our results implicate defective autophagy in SHRF pathogenesis and suggest therapeutic strategies.
Dissertations / Theses on the topic "Novel eye disease genes"
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Hardcastle, Alison Jane. "The isolation of novel genes expressed in the retina." Thesis, University of Newcastle Upon Tyne, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335124.
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Patel, Sapna P. "An in silico approach to identify novel genes preferentially expressed in the eye." Thesis, University of Edinburgh, 2004. http://hdl.handle.net/1842/25059.
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Specific or preferential expression of a gene in a particular tissue or organ is often indicative of its importance in function or development. It would be beneficial to discover novel genes with preferential expression to enhance understanding of the tissue or organ in question. In this thesis, an in silico method was employed to find novel genes preferentially expressed in the mouse eye. The chosen in silico method was digital differential display (DDD), which utilises the publicly available UniGene database as a resource. UniGene is composed of expressed sequence tag (EST) sequences that are clustered by homology, such that each cluster is considered to represent a gene. Crucially, ESTs in UniGene are traceable to their library of origin. This allows DDD to statistically compare, for each cluster, the proportional representation of ESTs in different user-defined pools of libraries. Using an eye pool and a non-eye pool of libraries, DDD was performed on the mouse, human and rat UniGene sets. The production amongst the DDD results of genes homologous between mouse and human, both those known to be eye relevant as well as those not recognised as having preferential expression, supports the validity of the genes produced. The DDD results used for further analysis comprised 292 mouse UniGene clusters that were more highly represented in the eye pool than in the non-eye pool. Of the 154 clusters that represented known genes, 48% were known to be eye relevant. Thirty-one of the 138 novel clusters were selected for expression studies. Ten of these were later recognised as known genes, with 5 having eye relevance. Fifteen of the 31 novel clusters were confirmed by RT-PCR to show preferential expression, with 4 appearing eye specific. Three of the 15 genes are known (Aip11, Crygf and Otx2) and another 9 putative genes show expression in various regions of the eye. These novel genes may well have a role in eye development or function and are candidates for mouse and human eye mutations.
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Závodszky, Eszter. "The role of novel neurodegenerative disease genes in autophagy regulation." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708679.
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Archacki, Stephen R. "MOLECULAR IDENTIFICATION OF NOVEL GENES ASSOCIATED WITH ATHEROSCLEROSIS." Cleveland State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=csu1310652996.
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Lefebvre, Valerie. "Identification of Novel Parkinson’s Disease Genes Involved in Parkin Mediated Mitophagy." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30222.
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Mitochondrial dysfunction has been implicated as one of the primary causes of Parkinson's disease (PD). The proteins PINK1, a serine-threonine kinase, and Parkin, an E3 ubiquitin ligase, are mutated in many genetic cases of PD. In healthy individuals, Parkin is recruited to damaged mitochondria and leads to autophagic degradation of mitochondria in a process termed mitophagy. Following depolarization of the mitochondrial membrane, PINK1 is stabilized on the outer mitochondrial membrane, and triggers Parkin translocation from the cytosol to mitochondria. Precisely how this phenomenon is regulated is still unclear. We employed RNA interference (RNAi) technology in a 384-well format to identify novel genes that are required for Parkin recruitment to mitochondria. We identified ATPase inhibitory factor 1 (IF1) as the strongest hit required for Parkin recruitment following treatment with the protonophore CCCP. We show that IF1 is upstream of PINK1 and Parkin, and required to sense mitochondrial damage by allowing the loss of membrane potential. In cells treated with CCCP, the absence of IF1 permits the ATP synthase to run freely in reverse, consuming ATP to maintain potential across the inner mitochondrial membrane, thus blocking PINK1 and Parkin activation. Interestingly, Rho0 cells, that lack mitochondrial DNA, have downregulated endogenous expression of IF1 in order to maintain mitochondrial function. Overexpression of IF1 in Rho0 cells results in the depletion of mitochondrial membrane potential and the initiation of mitophagy. These data demonstrate a unique role for IF1 in the regulation of mitochondrial quality control that has not been explored in the etiology of PD.
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Watson, Nicola Sophia Alexandra. "Identification of novel genes involved in Paget's disease by Differential Display PCR." Thesis, University of Aberdeen, 1999. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU535579.
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In order to identify novel genes which were expressed in Paget's disease, the Differential Display PCR technique was used to compare gene expression in samples of Pagetic and normal bone, and in human bone long term marrow cultures. Several genes appeared to be differentially expressed in Pagetic bone in comparison to controls, however the display patterns were difficult to interpret and consistent differences were not observed. Pagetic marrow cultures were studied and were found to be abnormal in that osteoclast-like cell formation was 20-fold higher in Pagetic marrow than in age-matched controls. This study also examined Pagetic marrow samples aspirated from both affected and unaffected sites, and it was found that large numbers of oseteoclast-like cells formed in Pagetic cultures regardless of the site of marrow aspiration, suggesting that there may be an abnormality in osteoclast precursors in Paget's disease. Differential display of these marrow samples revealed consistent differences in gene expression between Pagetic and normal marrow, and of four differentially expressed mRNAs which were cloned and sequenced, one was selected for further study owing to its significant homology to murine Centrosomin A, a gene thought to be involved in cell cycle division and microtubule formation. The centrosomin-like DD clone was confirmed to be significantly over-expressed in Pagetic marrow by semi-quantiative PCR, and using 232bp DD product as a probe, a ZAP Express osteoclastoma cDNA library was screened by hybridisation to identify cross-hybridising clones. Thirty four positive clones were identified, and two of these clones, CLC 1 and CLC 2, were isolated and sequenced. Database searches identified CLC 2 (4kb) as being a partial clone of human eukaryotic translation initiation factor-3 (eIF-3) - p180 subunit. Further characterisation of both CLC-1 and 2 may provide important information on their functions, both within the cell and their possible role in Paget's disease.
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Kriegsman, Barry. "Elucidating the Roles of Novel Genes in MHC-I Presentation." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1018.
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The major histocompatibility complex class I (MHC-I) antigen presentation pathway is necessary for the immune system to be able to detect, control, and eliminate cancers. MHC-I binds oligopeptides derived from cellular proteins and presents them on the cell surface to CD8+ T cells. Consequently, the CD8+ T cells can monitor whether any cells are making abnormal proteins and, if so, can destroy those cells. Because MHC-I presentation is not essential for cell viability, immune selection pressure often leads to cancers that are MHC-I low as they can better evade CD8+ T cell recognition. It is, therefore, important to fully understand the mechanisms of MHC-I presentation as this will identify new ways to target and exploit the pathway for cancer therapeutics. Although several components of the MHC-I pathway have already been characterized, some knowledge gaps remain. Unbiased forward genetic screens from our lab identified some novel gene candidates, such as IRF2, which positively regulate MHC-I presentation. In this dissertation, I will reveal which antigen presentation pathway genes are transcriptionally controlled by IRF2 and contribute to the MHC-I presentation deficiency observed in cells lacking IRF2 and I will also show that IRF2 negatively regulates PD-L1 expression. By influencing both MHC-I antigen presentation and PD-L1 expression in this manner, cancers lacking IRF2 (of which there are many) are both harder to see and more difficult to eliminate.
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Hsieh, Shie-Liang. "Characterisation of novel genes and mapping of polymorphic markers in the human major histocompatibility complex." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.315942.
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Fernandes, Caroline. "Genome-wide screen for novel regulators of Parkinson's disease genes in «Drosophila melanogaster»." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103725.
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Introduction: Compromised mitochondrial integrity leads to neuronal cell death in Parkinson's disease and other neurodegenerative diseases. Cells have several quality control mechanisms in place to counteract dysfunction and preserve a healthy mitochondrial network. Recent studies have implicated the autosomal recessive Parkinson's disease genes, Parkin and Pink1, in a common pathway regulating mitochondrial quality control. Together, Parkin and Pink1 promote isolation and selective degradation of damaged mitochondria, but the mechanisms governing this process are unclear. Methods: The goal of our study was to use a genetically sensitized Drosophila model of Parkinson's disease to identify novel regulators of the Pink1/Parkin pathway. We screened deficiencies spanning the second and third chromosome for dominant enhancers and suppressors of the Pink1/parkin wing posture phenotype, which derives from mitochondrial defects in these mutants. Results: From this screen we identified several cytological regions that strongly interact with Parkin and/or Pink1. Of these, four were further dissected revealing five interacting genes. Among them, opa1 and drp1 have been previously implicated in the Pink1/Parkin pathway. The other three genes, p60, β4galNacTA, and debra, represent novel regulators of Parkin and Pink1 function. Conclusion/implications: The unbiased identification of previously known Pink1/Parkin interactors demonstrates the validity of this approach. Moreover, the discovery of novel genes involved in the Pink1/Parkin pathway will allow better understanding of the mechanisms governing mitochondrial quality control and will aid in the development of therapeutic treatments.Introduction : L'altération de la fonction mitochondriale entraîne la dégénérescence de certains neurones chez les personnes atteintes de maladies neurodégénératives dont la maladie de Parkinson. Les cellules saines sont dotées d'un système de contrôle leur permettant de faire face et de réparer les dysfonctionnements des mitochondries et ainsi de préserver leur intégrité. Des études récentes ont révélé l'implication de deux gènes à l'origine de syndromes parkinsoniens autosomiques récessifs, Pink1 et Parkin, dans une voie de signalisation commune contrôlant le maintien de la fonction mitochondriale. Pink1 et Parkin interviennent ensemble dans l'isolation et la dégradation des mitochondries défectueuses. Cependant, à l'heure actuelle, les mécanismes moléculaires contrôlant ce processus restent à élucider. Méthodes : Le but de notre étude a été d'identifier de nouveaux régulateurs de la voie de signalisation Pink1/Parkin par crible génétique dans un modèle drosophile de la maladie de Parkinson. Pour cela, nous avons criblé une collection de lignées de drosophiles déficientes sur les chromosomes deux et trois pour leur capacité à modifier (augmenter ou diminuer) le phénotype de posture de l'aile caractéristique de la mutation de Pink1/Parkin. Résultats: Nous avons identifié plusieurs régions cytologiques qui interagissent fortement avec Parkin et/ou Pink1. Quatre de ces régions ont été disséquées de façon à révéler cinq gènes. Parmi eux, opa1 et drp1 avaient déjà été impliques dans la voie de signalisation Pink1/Parkin. Les trois autres gènes p60, β4galNacTA et debra représentent de nouveaux régulateurs de la fonction de Pink1 et Parkin. Conclusion/implications : D'une part, l'identification non biaisée de gènes déjà connus comme interagissant avec Pink1/Parkin démontre la validité de cette approche. D'autre part, la découverte de nouveaux gènes candidats de la voie Pink1/Parkin pour le maintien de l'intégrité mitochondriale permettra de mieux comprendre les mécanismes moléculaires contrôlant ce processus et aidera à l'élaboration de traitements.
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Puli, Oorvashi Roy G. "Defective proventriculus (Dve), a Novel Role in Dorsal-Ventral Patterning of the Drosophila Eye." University of Dayton / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1406732166.
Full textBooks on the topic "Novel eye disease genes"
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Joram, Piatigorsky, Shinohara Toshimichi, Zelenka Peggy S, National Eye Institute, and University of California, Los Angeles., eds. Molecular biology of the eye: Genes, vision, and ocular disease : proceedings of a National Eye Institute-UCLA symposium held at Santa Fe, New Mexico, February 6-12, 1988. New York: Liss, 1988.
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Mansoor, Quratulain. Novel Approach for Autonomous Detection of Glaucoma Eye Disease Using Deep Learning. Independently Published, 2019.
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Mayes, Caryl Ann. A screen for novel genes involved in drosphila compound eye development and the cloning and characterisation of rasputin, a homologue of G3BP. 2000.
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Mayes, Caryl Ann. A screen for novel genes involved in drosophila compound eye development and the cloning and characterisation of rasputin, a homologue of G3BP. 2000.
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Banerjee, Amitava, and Kaleab Asrress. Risk factors for cardiovascular disease. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0086.
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The most prevalent cardiovascular diseases (CVDs) are atherosclerotic, affecting all arterial territories. Epidemiologic studies such as the Framingham and INTERHEART studies have firmly established the commonest or ‘traditional’ risk factors for CVD; namely, smoking, hypertension, diabetes mellitus, hypercholesterolaemia, and a family history of CVD. The ‘risk-factors approach’ to CVD looks at these factors, individually and in combination, in the causation of disease. The complex causation pathways involve interplay of individual factors, whether genetic or environmental. More recently, there has been increasing interest in ‘epigenetics’ or the way in which the environment interacts with genes in the process underlying CVD. This chapter presents an analysis of the traditional and novel risk factors for CVD.
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Brown, Matthew. Genetics of spondyloarthropathies. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0041.
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Spondyloarthropathies are a diverse group of conditions, of which ankylosing spondylitis is the prototypic disease, with shared clinical features, genetic risk factors, and histopathological characteristics. These conditions are highly familial and heritable. Several genes have been associated with spondyloarthropathies, with genes in the IL-23 signalling pathway being shared by the major types of spondyloarthritis. These discoveries have already led to the development and successful clinical introduction of novel treatments for psoriasis and psoriatic arthritis, and major advances in our understanding of the pathogenesis of the conditions. Many more genes remain to be identified which are involved in these common conditions; identifying these genes is likely to be highly informative as to their causes.
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Brown, Matthew. Genetics of spondyloarthropathies. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199642489.003.0041_update_003.
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Spondyloarthropathies are a diverse group of conditions, of which ankylosing spondylitis is the prototypic disease, with shared clinical features, genetic risk factors, and histopathological characteristics. These conditions are highly familial and heritable. Several genes have been associated with spondyloarthropathies, with genes in the IL-23 signalling pathway being shared by the major types of spondyloarthritis. These discoveries have already led to the development and successful clinical introduction of novel treatments for psoriasis and psoriatic arthritis, and major advances in our understanding of the pathogenesis of the conditions. Many more genes remain to be identified which are involved in these common conditions; identifying these genes is likely to be highly informative as to their causes.
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Lewis, Myles, and Tim Vyse. Genetics of connective tissue diseases. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0042.
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The advent of genome-wide association studies (GWAS) has been an exciting breakthrough in our understanding of the genetic aetiology of autoimmune diseases. Substantial overlap has been found in susceptibility genes across multiple diseases, from connective tissue diseases and rheumatoid arthritis (RA) to inflammatory bowel disease, coeliac disease, and psoriasis. Major technological advances now permit genotyping of millions of single nucleotide polymorphisms (SNPs). Group analysis of SNPs by haplotypes, aided by completion of the Hapmap project, has improved our ability to pinpoint causal genetic variants. International collaboration to pool large-scale cohorts of patients has enabled GWAS in systemic lupus erythematosus (SLE), systemic sclerosis and Behçet's disease, with studies in progress for ANCA-associated vasculitis. These 'hypothesis-free' studies have revealed many novel disease-associated genes. In both SLE and systemic sclerosis, identified genes map to known pathways including antigen presentation (MHC, TNFSF4), autoreactivity of B and T lymphocytes (BLK, BANK1), type I interferon production (STAT4, IRF5) and the NFκB pathway (TNIP1). In SLE alone, additional genes appear to be involved in dysregulated apoptotic cell clearance (ITGAM, TREX1, C1q, C4) and recognition of immune complexes (FCGR2A, FCGR3B). Future developments include whole-genome sequencing to identify rare variants, and efforts to understand functional consequences of susceptibility genes. Putative environmental triggers for connective tissue diseases include infectious agents, especially Epstein-Barr virus; cigarette smoking; occupational exposure to toxins including silica; and low vitamin D, due to its immunomodulatory effects. Despite numerous studies looking at toxin exposure and connective tissue diseases, conclusive evidence is lacking, due to either rarity of exposure or rarity of disease.
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Pezzini, Alessandro. Genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198722366.003.0011.
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Ischaemic stroke is a heterogeneous multifactorial disorder. Although epidemiological data from twin and family studies provide substantial evidence for a genetic basis for stroke, the contribution of genetic factors identified so far is small. Large progress has been made in single-gene disorders associated with ischaemic stroke, particularly at young age. By contrast, little is known about the genes associated with multifactorial stroke. The reported genome-wide association studies of ischaemic stroke have shown that no single common genetic variant imparts major risk, but data on early-onset disease are scarce in this regard. Larger studies with samples numbering in the thousands are ongoing to identify common variants with smaller effects on risk. This approach, in addition with new analytic techniques, will likely contribute to the identification of additional genes, novel pathways, and eventually novel therapeutic approaches to cerebrovascular disorders in the near future. The aims of this review are to summarize data on clinical, genetic, and epidemiologic aspects of monogenic conditions associated with juvenile ischaemic stroke, to discuss recent findings and methodological limitations regarding the genetics of sporadic ischaemic stroke in this age category, and to provide a brief overview of the potential future approaches to stroke genetics.
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Barton, Anne. Basics of genetics. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0037.
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Genetic factors are important in predisposing to nearly all of the conditions managed by rheumatologists; indeed, musculoskeletal diseases, like other complex diseases, are thought to be caused by environmental triggers in genetically susceptible individuals. Studying genetic susceptibility factors is more straightforward than environmental factors because, first, genetic changes are stable and do not vary throughout life; second, genetic changes exist before disease onset and so could be causative rather than occurring as a result of disease; and, third, genetic variation is easy to measure reliably using modern technologies. By comparison, environmental exposures can occur many years before disease onset, may vary during life, and are hard to accurately capture and measure. Enormous progress has been made in recent years in identifying susceptibility genes. This knowledge may allow better targeting of available therapies, the development of novel therapies, and an improved understanding of what determines disease severity in individual patients. In this chapter, the basic concepts in genetics are explained.
Book chapters on the topic "Novel eye disease genes"
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Onouchi, Yoshihiro. "Identification of Novel Kawasaki Disease Susceptibility Genes by Genome-Wide Association Studies." In Kawasaki Disease, 23–29. Tokyo: Springer Japan, 2016. http://dx.doi.org/10.1007/978-4-431-56039-5_4.
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Remaley, Alan T., U. Kurt Schumacher, H. Bryan Brewer, and Jeffrey M. Hoeg. "Isolation of Novel Genes Regulated by Dietary Cholesterol by a Pcr-Based Subtraction Library." In Cardiovascular Disease 2, 327–32. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-1959-1_41.
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Zanzoni, Andreas. "A Computational Network Biology Approach to Uncover Novel Genes Related to Alzheimer’s Disease." In Systems Biology of Alzheimer's Disease, 435–46. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-2627-5_26.
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Yuan, Fang, Ruichun Wang, Mingxiang Guan, and Guorong He. "A Novel Computational Method for Predicting Disease Genes Based on Functional Similarity." In Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 42–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-14932-0_6.
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Fang, Yuan, and Hui Wang. "DCGene: A Novel Predicting Approach of the Disease Related Genes on Functional Annotation." In Emerging Intelligent Computing Technology and Applications, 956–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04070-2_101.
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Papas, T. S., D. K. Watson, N. Sacchi, S. J. O’Brien, and R. Ascione. "The Mammalian ETS Genes: Two Unique Chromosomal Locations in Cat, Mice and Man and Novel Translocated Position in Human Leukemias." In Minimal Residual Disease in Acute Leukemia 1986, 23–42. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4273-8_3.
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St. George-Hyslop, P. H. "Genetic Evidence for a Novel Familial Alzheimer’s Disease Locus on Chromosome 14: Analysis of Candidate Genes." In Etiopathogenesis, 3–18. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4684-9203-3_1.
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Garanto, Alejandro. "Delivery of Antisense Oligonucleotides to the Mouse Retina." In Methods in Molecular Biology, 321–32. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2010-6_22.
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AbstractThe eye is the organ in charge of vision and, given its properties, has become an excellent organ to test genetic therapies, including antisense oligonucleotide (AON) technology. In fact, the first AON receiving FDA and EMA approval was meant to treat an eye condition. Currently, dozens of clinical trials are being conducted for a variety of subtypes of inherited retinal disease. Although most of them are based on gene augmentation therapies, a phase 3 and two phase 1/2 clinical trials using AONs are ongoing. Since the retina is a layered structure of nondividing cells, obtaining human retinal tissue and expanding it in the lab is not possible, unless induced pluripotent stem cell technology is used. Mouse models have helped to elucidate the function of many genes, and the retinal structure is quite similar to that of humans. Thus, drug delivery to the mouse eye can provide valuable information for further optimization of therapies. In this chapter, the protocol for intravitreal injections of AONs is described in detail.
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Port, Fillip, and Michael Boutros. "Tissue-Specific CRISPR-Cas9 Screening in Drosophila." In Methods in Molecular Biology, 157–76. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2541-5_7.
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AbstractOver the last century research in Drosophila has resulted in many fundamental contributions to our understanding of the biology of multicellular organisms. Many of these breakthroughs have been based on the identification of novel gene functions in large-scale genetic screens. However, conventional forward-genetic screens have been limited by the random nature of mutagenesis and difficulties in mapping causal mutations, while reverse-genetic RNAi screens suffer from incomplete knockdown of gene expression. Recently developed large-scale CRISPR-Cas9 libraries promise to address these limitations by allowing the induction of targeted mutations in genes with spatial and temporal control. Here, we provide a guide for tissue-specific CRISPR screening in Drosophila, including the characterization of Gal4 UAS-Cas9 lines, selection of sgRNA libraries, and various quality control measures. We also discuss confounding factors that can give rise to false-positive and false-negative results in such experiments and suggest strategies on how to detect and avoid them. Conditional CRISPR screening represents an exciting new approach for functional genomics in vivo and is set to further expand our knowledge of the molecular underpinning of development, homeostasis, and disease.
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Das, Priyanka, Rajeev N. Bahuguna, Rohit Joshi, Sneh Lata Singla-Pareek, and Ashwani Pareek. "In search of mutants for gene discovery and functional genomics for multiple stress tolerance in rice." In Mutation breeding, genetic diversity and crop adaptation to climate change, 444–50. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0045.
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Abstract Mutation breeding is a commanding tool, which has been adapted to generate altered genetic material to study functional genomics, including understanding the molecular basis of stress tolerance. Hitherto, several rice lines have been generated through mutagenesis and the mutated genes responsible for the 'gain of function' in terms of plant architecture, stress tolerance, disease resistance and grain quality have been characterized. Oryza sativa L. cv. IR64 is a high-yielding rice cultivar but sensitive to abiotic stresses such as acute temperatures, salinity and drought. In this study, a population of rice IR64 mutants was generated using gamma irradiation. The population was then subjected to a preliminary phenotypic screening under abiotic stresses such as heat and salinity at the seedling stage. On the basis of root length, shoot length, fresh weight, dry weight and chlorophyll measurements, we identified eight 'gain-of-function' mutant lines and used them for further biochemical and molecular characterization. Phenotyping results demonstrated that the identified mutant plants have gained the potential to thrive under heat and salinity conditions. This information would be of wide scientific interest and helpful for developing novel cultivars able to maintain yield in saline, hot and dry areas.
Conference papers on the topic "Novel eye disease genes"
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Hashemi, Mahshad, and Eghbal Mansoori. "Identifying novel disease genes based on protein complexes and biological features." In 2021 11th International Conference on Computer Engineering and Knowledge (ICCKE). IEEE, 2021. http://dx.doi.org/10.1109/iccke54056.2021.9721466.
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Perera, Shehan, Kaveesha Hewage, Chamara Gunarathne, Rajitha Navarathna, Damayanthi Herath, and Roshan G. Ragel. "Detection of Novel Biomarker Genes of Alzheimer’s Disease Using Gene Expression Data." In 2020 Moratuwa Engineering Research Conference (MERCon). IEEE, 2020. http://dx.doi.org/10.1109/mercon50084.2020.9185336.
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Tang, Xiwei, Bihai Zhao, and Xiao Qiu. "A Novel Algorithm for Prioritizing Disease Candidate Genes from the Weighted PPI Network." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8982984.
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Shen, Xianjun, Yang Yi, Yan Wang, Xiaohui Chen, Jincai Yang, and Tingting He. "A novel approach to breast cancer-related disease genes discovered through variation of density modularity." In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2014. http://dx.doi.org/10.1109/bibm.2014.6999277.
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Yalamanchili, Hari Krishna, Hyun-Hwan Jeong, and Zhandong Liu. "Decoding TDP-43 Dependent Cryptic Splicing in Amyotrophic Lateral Sclerosis and Identifying Novel Disease-causing Genes." In BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3233547.3233698.
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Ashraf, Faisal Bin, Rasif Ajwad, and M. A. Mottalib. "A novel gene-tree based approach to infer relations among disease-genes across different cancer types." In 2019 International Conference on Electrical, Computer and Communication Engineering (ECCE). IEEE, 2019. http://dx.doi.org/10.1109/ecace.2019.8678921.
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SCHULZ, SIMONE, ARMIN HUBER, PHILIPP SANDER, and REINHARD PAULSEN. "ISOLATION OF NOVEL EYE-SPECIFICALLY EXPRESSED GENES BY DIFFERENTIAL HYBRIDIZATION OF A RETINAL cDNA LIBRARY OF CALLIPHORA VICINA." In Proceedings of the International School of Biophysics. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799975_0009.
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Cambraia, Amanda, Mario Campos Junior, Fernanda Gubert, Juliana Ferreira Vasques, Marli Pernes da Silva Loureiro, Claudio Heitor Gress, José Mauro Bráz de Lima, Rosalia Mendez Otero, and Verônica Marques Zembrzuski. "A novel mutation in the RRM2 domain of TDP-43 in a Brazilian sporadic ALS patient." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.486.
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Introduction: Amyotrophic Lateral Sclerosis (ALS) is an adult-onset progressive and fatal neurodegenerative disease that selectively affects upper and lower motor neurons. Death occurs within 3 to 5 years of onset, usually from respiratory complications. Most cases of ALS are sporadic (SALS), but familial forms of the disease (FALS) represent approximately 10% of the cases. More than 30 genes have been associated with ALS and mutations in these genes account for more than a half of all familial cases and about 10% of sporadic cases. One of the most prevalent genes is TARDBP, responsible for approximately 4-6% of FALS and nearly 1-2% of SALS cases. The aim of this study was to perform the screening of known ALS genes, to increase the knowledge of the mutations that circulate in the population from Rio de Janeiro. Methods: The screening of mutations was performed through the Illumina Next Generation Sequencing (NGS) platform with the use of a sequencing panel that contained the TARDBP, SOD1, FUS, VAPB, SMN1 and SMN2 genes. Results: A novel missense mutation (p.Phe194Leu) in exon 5 of the TARDBP gene was found in a sporadic male patient who died at the age of 58 (2018). The mutation, a TTT/CTT substitution, was not detected in any mutation databases and in the literature. In silico analysis of this variant with different algorithms were performed and the results pointed to a probably damaging impact and that the mutation is disease causing. Conclusion: Through the study of the ALS genes by the NGS, we were able to identify a novel TARDBP mutation in a non-familial ALS patient. In addition, this study also increases the number of known TARDBP mutations in ALS patients and our knowledge of the mutations that affect the patients from of population from Rio de Janeiro.
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Sudakov, A. I., E. P. Kulikov, S. A. Mertsalov, A. A. Nikiforov, and V. A. Grigorenko. "GENETIC POLYMORPHISM AND COLORECTAL CANCER." In NOVEL TECHNOLOGIES IN MEDICINE, BIOLOGY, PHARMACOLOGY AND ECOLOGY. Institute of information technology, 2022. http://dx.doi.org/10.47501/978-5-6044060-2-1.105-109.
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The article analyzes the relationship of polymorphism of a number of genes with some features of colorectal cancer, such as the aggressiveness of its course and development of the disease, the effectiveness of preoperative chemoradiotherapy. The data obtained can be used to deter-mine individual tactics for treating patients.
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Jackson, Peter K. "Abstract SY14-02: From disease genetics to diagnostics to functional biology: High-throughput proteomics and protein interaction network building guides discovery of novel disease genes in ciliopathies, cystic disease, and cancer." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-sy14-02.
Full textReports on the topic "Novel eye disease genes"
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Sessa, Guido, and Gregory Martin. Role of GRAS Transcription Factors in Tomato Disease Resistance and Basal Defense. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696520.bard.
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The research problem: Bacterial spot and bacterial speck diseases of tomato are causedby strains of Xanthomonas campestris pv. vesicatoria (Xcv) and Pseudomonas syringae pv.tomato (Pst), respectively. These bacteria colonize aerial parts of the plant and causesignificant losses in tomato production worldwide. Protection against Xcv and Pst bycultural practices or chemical control has been unsuccessful and there are only limitedsources of genetic resistance to these pathogens. In previous research supported in part byBARD IS-3237-01, we extensively characterized changes in tomato gene expression uponthe onset of spot and speck disease resistance. A remarkable finding of these studies wasthe inducibility in tomato leaves by both Xcv and Pst strains of genes encodingtranscriptional activator of the GRAS family, which has not been previously linked todisease resistance. Goals: Central goals of this research were to investigate the role of GRAS genes in tomatoinnate immunity and to assess their potential use for disease control.Specific objectives were to: 1. Identify GRAS genes that are induced in tomato during thedefense response and analyze their role in disease resistance by loss-of-function experiments.2. Overexpress GRAS genes in tomato and characterize plants for possible broad-spectrumresistance. 3. Identify genes whose transcription is regulated by GRAS family. Our main achievements during this research program are in three major areas:1. Identification of tomato GRAS family members induced in defense responses andanalysis of their role in disease resistance. Genes encoding tomato GRAS family memberswere retrieved from databases and analyzed for their inducibility by Pst avirulent bacteria.Real-time RT-PCR analysis revealed that six SlGRAS transcripts are induced during theonset of disease resistance to Pst. Further expression analysis of two selected GRAS genesshowed that they accumulate in tomato plants in response to different avirulent bacteria orto the fungal elicitor EIX. In addition, eight SlGRAS genes, including the Pst-induciblefamily members, were induced by mechanical stress in part in a jasmonic acid-dependentmanner. Remarkably, SlGRAS6 gene was found to be required for tomato resistance to Pstin virus-induced gene silencing (VIGS) experiments.2. Molecular analysis of pathogen-induced GRAS transcriptional activators. In aheterologous yeast system, Pst-inducible GRAS genes were shown to have the ability toactivate transcription in agreement with their putative function of transcription factors. Inaddition, deletion analysis demonstrated that short sequences at the amino-terminus ofSlGRAS2, SlGRAS4 and SlGRAS6 are sufficient for transcriptional activation. Finally,defense-related SlGRAS proteins were found to localize to the cell nucleus. 3. Disease resistance and expression profiles of transgenic plants overexpressing SlGRASgenes. Transgenic plants overexpressing SlGRAS3 or SlGRAS6 were generated. Diseasesusceptibility tests revealed that these plants are not more resistant to Pst than wild-typeplants. Gene expression profiles of the overexpressing plants identified putative direct orindirect target genes regulated by SlGRAS3 and SlGRAS6. Scientific and agricultural significance: Our research activities established a novel linkbetween the GRAS family of transcription factors, plant disease resistance and mechanicalstress response. SlGRAS6 was found to be required for disease resistance to Pstsuggesting that this and possibly other GRAS family members are involved in thetranscriptional reprogramming that takes place during the onset of disease resistance.Their nuclear localization and transcriptional activation ability support their proposed roleas transcription factors or co-activators. However, the potential of utilizing GRAS familymembers for the improvement of plant disease resistance in agriculture has yet to bedemonstrated.
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Zhao, Bingyu, Saul Burdman, Ronald Walcott, and Gregory E. Welbaum. Control of Bacterial Fruit Blotch of Cucurbits Using the Maize Non-Host Disease Resistance Gene Rxo1. United States Department of Agriculture, September 2013. http://dx.doi.org/10.32747/2013.7699843.bard.
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The specific objectives of this BARD proposal were: (1) To determine whether Rxol can recognize AacavrRxo1 to trigger BFB disease resistance in stable transgenic watermelon plants. (2) To determine the distribution of Aac-avrRxo1 in a global population of Aae and to characterize the biological function of Aac-avrRxo1. (3) To characterize other TIS effectors of Aae and to identify plant R gene(s) that can recognize conserved TIS effectors of this pathogen. Background to the topic: Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovorax avenae subsp. citrulli (Aae), is a devastating disease that affects watermelon (Citrullus lanatus) and melon (Cucumis melo) production worldwide, including both Israel and USA. Two major groups of Aae strains have been classified based on their virulence on host plants, genetics and biochemical properties. Thus far, no effective resistance genes have been identified from cucurbit germplasm. In this project, we assessed the applicability of a non-host disease resistance gene, Rxol, to control BFB in watermelon. We also tried to identify Aae type III secreted (TIS) effectors that can be used as molecular probes to identify novel disease resistance genes in both cucurbits and Nieotianatabaeum. Major conclusions, solutions, achievements: We generated five independent transgenic watermelon (cv. Sugar Babay) plants expressing the Rxol gene. The transgenic plants were evaluated with Aae strains AAC001 and M6 under growth chamber conditions. All transgenic plants were found to be susceptible to both Aae strains. It is possible that watermelon is missing other signaling components that are required for Rxol-mediated disease resistance. In order to screen for novel BFB resistance genes, we inoculated two Aae strains on 60 Nieotiana species. Our disease assay revealed Nicotiana tabaeum is completely resistant to Aae, while its wild relative N. benthamiana is susceptible to Aae. We further demonstrated that Nieotiana benthamiana can be used as a surrogate host for studying the mechanisms of pathogenesis of Aae. We cloned 11 TIS effector genes including the avrRxolhomologues from the genomes of 22 Aae strains collected worldwide. Sequencing analysis revealed that functional avrRxol is conserved in group" but not group I Aae strains. Three effector genes- Aave_1548, Aave_2166 and Aave_2708- possessed the ability to trigger an HR response in N. tabacum when they were transiently expressed by Agrobaeterium. We conclude that N. tabacum carries at least three different non-host resistance genes that can specifically recognize AaeTIS effectors to trigger non-host resistance. Screening 522 cucurbits genotypes with two Aae strains led us to identify two germplasm (P1536473 and P1273650) that are partially resistant to Aae. Interestingly, transient expression of the TIS effector, Aave_1548, in the two germplasms also triggered HR-Iike cell death, which suggests the two lines may carry disease resistance genes that can recognize Aave_1548. Importantly, we also demonstrated that this effector contributes to the virulence of the bacterium in susceptible plants. Therefore, R genes that recognize effector Aave1548 have great potential for breeding for BFB resistance. To better understand the genome diversity of Aae strains, we generated a draft genome sequence of the Israeli Aae strain, M6 (Group I) using Iliumina technology. Comparative analysis of whole genomes of AAC001, and M6 allowed us to identify several effectors genes that differentiate groups I and II. Implications, both scientific and agricultural: The diversity of TIS effectors in group I and II strains of Aae suggests that a subset of effectors could contribute to the host range of group I and II Aae strains. Analysis of these key effectors in a larger Aae population may allow us to predict which cucurbit hosts may be at risk to BFB. Additionally, isolation of tobacco and cucurbit Rgenes that can recognize Aae type III effectors may offer new genetic resources for controlling BFB.
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Reisch, Bruce, Avichai Perl, Julie Kikkert, Ruth Ben-Arie, and Rachel Gollop. Use of Anti-Fungal Gene Synergisms for Improved Foliar and Fruit Disease Tolerance in Transgenic Grapes. United States Department of Agriculture, August 2002. http://dx.doi.org/10.32747/2002.7575292.bard.
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Original objectives . 1. Test anti-fungal gene products for activity against Uncinula necator, Aspergillus niger, Rhizopus stolonifer and Botrytis cinerea. 2. For Agrobacterium transformation, design appropriate vectors with gene combinations. 3. Use biolistic bombardment and Agrobacterium for transformation of important cultivars. 4. Characterize gene expression in transformants, as well as level of powdery mildew and Botrytis resistance in foliage of transformed plants. Background The production of new grape cultivars by conventional breeding is a complex and time-consuming process. Transferring individual traits via single genes into elite cultivars was proposed as a viable strategy, especially for vegetatively propagated crops such as grapevines. The availability of effective genetic transformation procedures, the existence of genes able to reduce pathogen stress, and improved in vitro culture methods for grapes, were combined to serve the objective of this proposal. Effective deployment of resistance genes would reduce production costs and increase crop quality, and several such genes and combinations were used in this project. Progress The efficacy of two-way combinations of Trichoderma endochitinase (CHIT42), synthetic peptide ESF12 and resveratrol upon the control of growth of Botrytis cinerea and Penicillium digitatum were evaluated in vitro. All pairwise interactions were additive but not synergistic. Per objective 2, suitable vectors with important gene combinations for Agrobacterium transformation were designed. In addition, multiple gene co-transformation by particle bombardment was also tested successfully. In New York, transformation work focused on cultivars Chardonnay and Merlot, while the technology in Israel was extended to 41B, R. 110, Prime, Italia, Gamay, Chardonnay and Velika. Transgenic plant production is summarized in the appendix. Among plants developed in Israel, endochitinase expression was assayed via the MuchT assay using material just 1-5 days after co-cultivation. Plants of cv. Sugraone carrying the gene coding for ESF12, a short anti-fungal lytic peptide under the control of the double 358 promoter, were produced. Leaf extracts of two plants showed inhibition zones that developed within 48 h indicating the inhibitory effect of the leaf extracts on the six species of bacteria. X fastidiosa, the causal organism of Pierce's disease, was very sensitive to leaf extracts from ESF12 transformed plants. Further work is needed to verify the agricultural utility of ESF12 transformants. In New York, some transformants were resistant to powdery mildew and Botrytis fruit rot. Major conclusions, solutions, achievements and implications The following scientific achievements resulted from this cooperative BARD project: 1. Development and improvement of embryogenesis and tissue culture manipulation in grape, while extending these procedures to several agriculturally important cultivars both in Israel and USA. 2. Development and improvement of novel transformation procedures while developing transformation techniques for grape and other recalcitrant species. 3. Production of transgenic grapevines, characterization of transformed vines while studying the expression patterns of a marker gene under the control of different promoter as the 35S CaMV in different part of the plants including flowers and fruits. 4. Expression of anti-fungal genes in grape: establishment of transgenic plants and evaluation of gene expression. Development of techniques to insert multiple genes. 5. Isolation of novel grape specific promoter to control the expression of future antimicrobial genes. It is of great importance to report that significant progress was made in not only the development of transgenic grapevines, but also in the evaluation of their potential for increased resistance to disease as compared with the non engineered cultivar. In several cases, increased disease resistance was observed. More research and development is still needed before a product can be commercialized, yet our project lays a framework for further investigations.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Shpigel, Nahum, Raul Barletta, Ilan Rosenshine, and Marcelo Chaffer. Identification and characterization of Mycobacterium paratuberculosis virulence genes expressed in vivo by negative selection. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7696510.bard.
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Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of a severe inflammatory bowel disease (IBD) in ruminants, known as Johne’s disease or paratuberculosis. Johne’s disease is considered to be one of the most serious diseases affecting dairy cattle both in Israel and worldwide. Heavy economic losses are incurred by dairy farmers due to the severe effect of subclinical infection on milk production, fertility, lower disease resistance and early culling. Its influence in the United States alone is staggering, causing an estimated loss of $1.5 billion to the agriculture industry every year. Isolation of MAP from intestinal tissue and blood of Crohn's patients has lead to concern that it plays a potential pathogenic role in promoting human IDB including Crohn’s disease. There is great concern following the identification of the organism in animal products and shedding of the organism to the environment by subclinically infected animals. Little is known about the molecular basis for MAP virulence. The goal of the original proposed research was to identify MAP genes that are required for the critical stage of initial infection and colonization of ruminants’ intestine by MAP. We proposed to develop and use signature tag mutagenesis (STM) screen to find MAP genes that are specifically required for survival in ruminants upon experimental infection. This research projected was approved as one-year feasibility study to prove the ability of the research team to establish the animal model for mutant screening and alternative in-vitro cell systems. In Israel, neonatal goat kids were repeatedly inoculated with either one of the following organisms; MAP K-10 strain and three transposon mutants of K-10 which were produced and screened by the US PI. Six months after the commencement of inoculation we have necropsied the goats and taken multiple tissue samples from the jejunum, ileum and mesenteric lymph nodes. Both PCR and histopathology analysis indicated on efficient MAP colonization of all the inoculated animals. We have established several systems in the Israeli PI’s laboratory; these include using IS900 PCR for the identification of MAP and using HSP65-based PCR for the differentiation between MAV and MAP. We used Southern blot analysis for the differentiation among transposon mutants of K-10. In addition the Israeli PI has set up a panel of in-vitro screening systems for MAP mutants. These include assays to test adhesion, phagocytosis and survival of MAP to/within macrophages, assays that determine the rate of MAPinduced apoptosis of macrophages and MAP-induced NO production by macrophages, and assays testing the interference with T cell ã Interferon production and T cell proliferation by MAP infected macrophages (macrophage studies were done in BoMac and RAW cell lines, mouse peritoneal macrophages and bovine peripheral blood monocytes derived macrophages, respectively). All partners involved in this project feel that we are currently on track with this novel, highly challenging and ambitious research project. We have managed to establish the above described research systems that will clearly enable us to achieve the original proposed scientific objectives. We have proven ourselves as excellent collaborative groups with very high levels of complementary expertise. The Israeli groups were very fortunate to work with the US group and in a very short time period to master numerous techniques in the field of Mycobacterium research. The Israeli group has proven its ability to run this complicated animal model. This research, if continued, may elucidate new and basic aspects related to the pathogenesis MAP. In addition the work may identify new targets for vaccine and drug development. Considering the possibility that MAP might be a cause of human Crohn’s disease, better understanding of virulence mechanisms of this organism might also be of public health interest as well.
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Sessa, Guido, and Gregory B. Martin. molecular link from PAMP perception to a MAPK cascade associated with tomato disease resistance. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597918.bard.
Full textAbstract:
The research problem: The detection of pathogen-associated molecular patterns (PAMPs) by plant pattern recognition receptors (PRRs) is a key mechanism by which plants activate an effective immune response against pathogen attack. MAPK cascades are important signaling components downstream of PRRs that transduce the PAMP signal to activate various defense responses. Preliminary experiments suggested that the receptor-like cytoplasmickinase (RLCK) Mai5 plays a positive role in pattern-triggered immunity (PTI) and interacts with the MAPKKK M3Kε. We thus hypothesized that Mai5, as other RLCKs, functions as a component PRR complexes and acts as a molecular link between PAMP perception and activation of MAPK cascades. Original goals: The central goal of this research was to investigate the molecular mechanisms by which Mai5 and M3Kε regulate plant immunity. Specific objectives were to: 1. Determine the spectrum of PAMPs whose perception is transmitted by M3Kε; 2. Identify plant proteins that act downstream of M3Kε to mediate PTI; 3. Investigate how and where Mai5 interacts with M3Kε in the plant cell; 4. Examine the mechanism by which Mai5 contributes to PTI. Changes in research directions: We did not find convincing evidence for the involvement of M3Kε in PTI signaling and substituted objectives 1 and 3 with research activities aimed at the analysis of transcriptomic profiles of tomato plants during the onset of plant immunity, isolation of the novel tomato PRR FLS3, and investigation of the involvement of the RLCKBSKs in PTI. Main achievements during this research program are in the following major areas: 1. Functional characterization of Mai5. The function of Mai5 in PTI signaling was demonstrated by testing the effect of silencing the Mai5 gene by virus-induced gene silencing (VIGS) experiments and in cell death assays. Domains of Mai5 that interact with MAPKKKs and subcellular localization of Mai5 were analyzed in detail. 2. Analysis of transcriptional profiles during the tomato immune responses to Pseudomonas syringae (Pombo et al., 2014). We identified tomato genes whose expression is induced specifically in PTI or in effector-triggered immunity (ETI). Thirty ETI-specific genes were examined by VIGS for their involvement in immunity and the MAPKKK EPK1, was found to be required for ETI. 3. Dissection of MAP kinase cascades downstream of M3Kε (Oh et al., 2013; Teper et al., 2015). We identified genes that encode positive (SGT and EDS1) and negative (WRKY1 and WRKY2) regulators of the ETI-associated cell death mediated by M3Kε. In addition, the MKK2 MAPKK, which acts downstream of M3Kε, was found to interact with the MPK3 MAPK and specific MPK3 amino acids involved interaction were identified and found to be required for induction of cell death. We also identified 5 type III effectors of the bacterial pathogen Xanthomonaseuvesicatoria that inhibited cell death induced by components of ETI-associated MAP kinase cascades. 4. Isolation of the tomato PRR FLS3 (Hind et al., submitted). FLS3, a novel PRR of the LRR-RLK family that specifically recognizes the flagellinepitope flgII-28 was isolated. FLS3 was shown to bind flgII-28, to require kinase activity for function, to act in concert with BAK1, and to enhance disease resistance to Pseudomonas syringae. 5. Functional analysis of RLCKs of the brassinosteroid signaling kinase (BSK) family.Arabidopsis and tomato BSKs were found to interact with PRRs. In addition, certain ArabidospsisBSK mutants were found to be impaired in PAMP-induced resistance to Pseudomonas syringae. Scientific and agricultural significance: Our research activities discovered and characterized new molecular components of signaling pathways mediating recognition of invading pathogens and activation of immune responses against them. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease.
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Lindow, Steven, Isaac Barash, and Shulamit Manulis. Relationship of Genes Conferring Epiphytic Fitness and Internal Multiplication in Plants in Erwinia herbicola. United States Department of Agriculture, July 2000. http://dx.doi.org/10.32747/2000.7573065.bard.
Full textAbstract:
Most bacterial plant pathogens colonize the surface of healthy plants as epiphytes before colonizing internally and initiating disease. The epiphytic phase of these pathogens is thus an important aspect of their epidemiology and a stage at which chemical and biological control is aimed. However, little is known of the genes and phenotypes that contribute to the ability of bacteria to grow on leaves and survive the variable physical environment in this habitat. In addition, while genes such as hrp awr and others which confer pathogenicity and in planta growth ability have been described, their contribution to other aspects of bacterial epidemiology such as epiphytic fitness have not been addressed. We hypothesized that bacterial genes conferring virulence or pathogenicity to plants also contribute to the epiphytic fitness of these bacteria and that many of these genes are preferentially located on plasmids. We addressed these hypotheses by independently identifying genes that contribute to epiphytic fitness, in planta growth, virulence and pathogenicity in the phytopathogenic bacterium Erwinia herbicola pv gypsophilae which causes gall formation on gypsophila. This species is highly epiphytically fit and has acquired a plasmid (pPATH) that contains numerous pathogenicity and virulence determinants, which we have found to also contribute to epiphytic fitness. We performed saturation transposon mutagenesis on pPATH as well as of the chromosome of E.h. gypsophilae, and identified mutants with reduced ability to grow in plants and/or cause disease symptoms, and through a novel competition assay, identified mutants less able to grow or survive on leaves. The number and identity of plasmid-borne hrp genes required for virulence was determined from an analysis of pPATH mutants, and the functional role of these genes in virulence was demonstrated. Likewise, other pPATH-encoded genes involved in IAA and cytokinin biosynthesis were characterized and their pattern of transcriptional activity was determined in planta. In both cases these genes involved in virulence were found to be induced in plant apoplasts. About half of avirulent mutants in pPATH were also epiphytically unfit whereas only about 10% of chromosomal mutants that were avirulent also had reduced epiphytic fitness. About 18% of random mutants in pPATH were avirulent in contrast to only 2.5% of random chromosomal mutants. Importantly, as many as 28% of pPATH mutants had lower epiphytic fitness while only about 10% of random chromosomal mutants had lower epiphytic fitness. These results support both of our original hypotheses, and indicate that genes important in a variety of interactions with plant have been enriched on mobile plasmids such as pPATH. The results also suggest that the ability of bacteria to colonize the surface of plants and to initiate infections in the interior of plants involves many of the same traits. These traits also appear to be under strong regulatory control, being expressed in response to the plant environment in many cases. It may be possible to alter the pattern of expression of such genes by altering the chemical environment of plants either by genetic means or by additional or chemical antagonists of the plant signals. The many novel bacterial genes identified in this study that are involved in plant interactions should be useful in further understanding of bacterial plant interactions.
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Prusky, Dov B., Tesfaye Mengiste, and Robert Fluhr. Mechanisms activated by fungal-based host pH modulators during quiescent infections and active postharvest disease development. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7597911.bard.
Full textAbstract:
This project aims were to provide new insights on the mechanisms activated during alkalinization and acidification of the infection court by Colletotrichum and Botrytis spp. respectively that will lead to quiescent infection-development on tomato fruits. We have chosen these pathogens due to their contrasting life style of alkalinization and acidification, respectively. We will study the roles of these fungal-based host-pH modulators in modulating host gene expression during quiescent infection development and compare these roles with those governing active colonization as a basis for developing novel strategies for control of postharvest diseases. The aims will be pursued through: Characterization of the effects of pH modulation on fungal-plant cell-cell signaling and on the fungal and plant transcriptome during the initial stages of fungal quiescence. The unpublished material that is presented as short abstract is considered one of the key point modulating Characterization of expression profiles of tomato fruits affected by acidifying and alkalinizing pathogensduring the transformation of quiescent to active infections by Colletotrichum and Botrytis. Functional analysis of selected genes involved in signaling pathways that affects the quiescent and active infections of Colletotrichum and Botrytis.
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Whitham, Steven A., Amit Gal-On, and Victor Gaba. Post-transcriptional Regulation of Host Genes Involved with Symptom Expression in Potyviral Infections. United States Department of Agriculture, June 2012. http://dx.doi.org/10.32747/2012.7593391.bard.
Full textAbstract:
Understanding how RNA viruses cause disease symptoms in their hosts is expected to provide information that can be exploited to enhance modern agriculture. The helper component-proteinase (HC-Pro) protein of potyviruses has been implicated in symptom development. Previously, we demonstrated that symptom expression is associated with binding of duplex small-interfering-RNA (duplex-siRNA) to a highly conserved FRNK amino acid motif in the HC-Pro of Zucchini yellow mosaic virus (ZYMV). This binding activity also alters host microRNA (miRNA) profiles. In Turnip mosaic virus (TuMV), which infects the model plant Arabidopsis, mutation of the FRNK motif to FINK was lethal providing further indication of the importance of this motif to HC-Pro function. In this continuation project, our goal was to further investigate how ZYMV and TuMV cause the mis-expression of genes in cucurbits and Arabidopsis, respectively, and to correlate altered gene expression with disease symptoms. Objective 1 was to examine the roles of aromatic and positively charged residues F164RNH and K215RLF adjacent to FR180NK in small RNA binding. Objective 2 was to determine the target genes of the miRNAs which change during HC-Pro expression in infected tissues and transgenic cucumber. Objective 3 was to characterize RNA silencing mechanisms underlying differential expression of host genes. Objective 4 was to analyze the function of miRNA target genes and differentially expressed genes in potyvirus-infected tissues. We found that the charged K/R amino acid residues in the FKNH and KRLF motifs are essential for virus viability. Replacement of K to I in FKNH disrupted duplex-siRNA binding and virus infectivity, while in KRLF mutants duplex-siRNA binding was maintained and virus infectivity was limited: symptomless following a recovery phenomenon. These findings expanded the duplex-siRNA binding activity of HC-Pro to include the adjacent FRNK and FRNH sites. ZYMV causes many squash miRNAs to hyper-accumulate such as miR166, miR390, mir168, and many others. Screening of mir target genes showed that only INCURVATA-4 and PHAVOLUTA were significantly upregulated following ZYMVFRNK infection. Supporting this finding, we found similar developmental symptoms in transgenic Arabidopsis overexpressing P1-HC-Pro of a range of potyviruses to those observed in miR166 mutants. We characterized increased transcription of AGO1 in response to infection with both ZYMV strains. Differences in viral siRNA profiles and accumulation between mild and severe virus infections were characterized by Illumina sequencing, probably due to the differences in HC-Pro binding activity. We determined that the TuMV FINK mutant could accumulate and cause symptoms in dcl2 dcl4 or dcl2 dcl3 dcl4 mutants similar to TuMV FRNK in wild type Arabidopsis plants. These dcl mutant plants are defective in antiviral defenses, and the results show that factors other than HC-ProFRNK motif can induce symptoms in virus-infected plants. As a result of this work, we have a better understanding of the FRNK and FKNH amino acid motifs of HC-Pro and their contributions to the duplex-siRNA binding functions. We have identified plant genes that potentially contribute to infectivity and symptoms of virus infected plants when they are mis-expressed during potyviral infections. The results establish that there are multiple underlying molecular mechanisms that lead viral pathogenicity, some dependent on HC-Pro. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
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Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.
Full textAbstract:
Research problem: Bread wheat (Triticumaestivum) provides approximately 20% of the calories and proteins consumed by humankind. As the world population continues to increase, it is necessary to improve wheat yields, increase grain quality, and minimize the losses produced by biotic and abiotic stresses. Stripe rust, caused by Pucciniastriiformisf. sp. tritici(Pst), is one of the most destructive diseases of wheat. The new pathogen races are more virulent and aggressive than previous ones and have produced large economic losses. A rich source for stripe-rust resistance genes (Yr) was found in wild emmer wheat populations from Israel. Original Project goals: Our long term goal is to identify, map, clone, characterize and deploy in breeding, novel wild emmer Yr genes, and combine them with multiple beneficial traits. The current study was aiming to map and clone YrG303 and Yr15, located on chromosome 1BS and combine them with drought resistance and grain quality genes. Positional cloning of YrG303/Yr15: Fine mapping of these genes revealed that YrG303 is actually allelic to Yr15. Fine genetic mapping using large segregating populations resulted in reduction of the genetic interval spanning Yr15 to less than 0.1 cM. Physical mapping of the YrG303/Yr15 locus was based on the complete chromosome 1BS physical map of wheat constructed by our group. Screening of 1BS BAC library with Yr15 markers revealed a long BAC scaffold covering the target region. The screening of T. dicoccoidesaccession-specific BAC library with Yr15 markers resulted in direct landing on the target site. Sequencing of T. dicoccoidesBAC clones that cover the YrG303/Yr15 locus revealed a single candidate gene (CG) with conserved domains that may indicate a role in disease resistance response. Validation of the CG was carried out using EMS mutagenesis (loss-of- function approach). Sequencing of the CG in susceptible yr15/yrG303 plants revealed three independent mutants that harbour non-functional yr15/yrG303 alleles within the CG conserved domains, and therefore validated its function as a Pstresistance gene. Evaluation of marker-assisted-selection (MAS) for Yr15. Introgressions of Yr15 into cultivated wheat are widely used now. Recently, we have shown that DNA markers linked to Yr15 can be used as efficient tools for introgression of Yr15 into cultivated wheat via MAS. The developed markers were consistent and polymorphic in all 34 tested introgressions and are the most recommended markers for the introgression of Yr15. These markers will facilitate simultaneous selection for multiple Yr genes and help to avoid escapees during the selection process. Engineering of improved chromosome 1BS that harbors multiple beneficial traits. We have implemented the knowledge and genetic resources accumulated in this project for the engineering of 1B "super-chromosome" that harbors multiple beneficial traits. We completed the generation of a chromosome including the rye 1RS distal segment associated with improved drought tolerance with the Yr gene, Yr15, and the strong gluten allele 7Bx-over-expressor (7Bxᴼᴱ). We have completed the introgression of this improved chromosome into our recently released variety Patwin-515HP and our rain fed variety Kern, as well as to our top breeding lines UC1767 and UC1745. Elucidating the mechanism of resistance exhibited by Yr36 (WKS1). The WHEAT KINASE START1 (WKS1) resistance gene (Yr36) confers partial resistance to Pst. We have shown that wheat plants transformed with WKS1 transcript are resistant to Pst. WKS1 is targeted to the chloroplast where it phosphorylates the thylakoid-associatedascorbateperoxidase (tAPX) and reduces its ability to detoxify peroxides. Based on these results, we propose that the phosphorylation of tAPX by WKS1 reduces the ability of the cells to detoxify ROS and contributes to cell death. Distribution and diversity of WKS in wild emmer populations. We have shown that WKS1 is present only in the southern distribution range of wild emmer in the Fertile Crescent. Sequence analysis revealed a high level of WKS1 conservation among wild emmer populations, in contrast to the high level of diversity observed in NB-LRR genes. This phenomenon shed some light on the evolution of genes that confer partial resistance to Pst. Three new WKS1 haplotypes displayed a resistance response, suggesting that they can be useful to improve wheat resistance to Pst. In summary, we have improved our understanding of cereals’ resistance mechanisms to rusts and we have used that knowledge to develop improved wheat varieties.