Relevant bibliographies by topics / Functionnal genes

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Functionnal genes'

Author: Grafiati
Published: 11 January 2025

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Journal articles on the topic "Functionnal genes"

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Sitnicka, Dorota, Katarzyna Figurska, and Slawomir Orzechowski. "Functional Analysis of Genes." Advances in Cell Biology 2, no. 1 (January 1, 2010): 1–16. http://dx.doi.org/10.2478/v10052-010-0001-y.

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SummaryThe aim of this article is to present the current literature concerning the expression analysis and methods of functional characteristics of genes. The progress in the analysis of gene expression within cells or whole tissues is undisputed and leads to a constant improvement of our understanding of the function of particular gene. The traditional methods of the functional characteristics of genes such as homology, inactivation and overexpression are more frequently being replaced by microarray and DNA chip analysis, which are extensively supported by bioinformatics tools. Knowledge of the functions and changes in gene expression has applications in medical diagnostics, the pharmaceutical industry and in plant and animal biotechnology.
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Jeong, Soon-Seog, and Ridong Chen. "Functional misassignment of genes." Nature Biotechnology 19, no. 2 (February 2001): 95. http://dx.doi.org/10.1038/84480.

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Scott, Rodney J. "Cancer genes: Functional aspects." European Journal of Cancer 33, no. 10 (September 1997): 1706–7. http://dx.doi.org/10.1016/s0959-8049(97)00259-1.

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Carpenter, D., R. S. McIntosh, R. J. Pleass, and J. A. L. Armour. "Functional effects of CCL3L1 copy number." Genes & Immunity 13, no. 5 (April 5, 2012): 374–79. http://dx.doi.org/10.1038/gene.2012.5.

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Klee, Eric W., Stephen C. Ekker, and Lynda B. M. Ellis. "Target selection forDanio rerio functional genomics." genesis 30, no. 3 (2001): 123–25. http://dx.doi.org/10.1002/gene.1045.

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Montgomery, Nathan D. "Functional genomics: A rose by another name." genesis 33, no. 3 (July 2002): 140. http://dx.doi.org/10.1002/gene.10101.

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Purnell, Beverly A. "Functional screen for microcephaly genes." Science 370, no. 6519 (November 19, 2020): 926.3–926. http://dx.doi.org/10.1126/science.370.6519.926-c.

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Camilleri, M., and A. R. Zinsmeister. "Candidate genes and functional dyspepsia." Neurogastroenterology & Motility 21, no. 1 (January 2009): 94. http://dx.doi.org/10.1111/j.1365-2982.2008.01205.x.

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Oliveira, Daniela M., and Margaret A. Goodell. "Transient RNA interference in hematopoietic progenitors with functional consequences." genesis 36, no. 4 (August 2003): 203–8. http://dx.doi.org/10.1002/gene.10212.

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Vudattu, N. K., I. Magalhaes, H. Hoehn, D. Pan, and M. J. Maeurer. "Expression analysis and functional activity of interleukin-7 splice variants." Genes & Immunity 10, no. 2 (December 18, 2008): 132–40. http://dx.doi.org/10.1038/gene.2008.90.

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Dissertations / Theses on the topic "Functionnal genes"

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Heglind, Mikael. "Functional studies of two forkhead genes /." Göteborg : Institute of Biomedicine, Department of Medical and Clinical Genetics, The Sahlgrenska Academy at University of Gothenburg, 2010. http://hdl.handle.net/2077/21481.

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Rice, Kim. "Functional analysis of the HOX11 target genes ALDH1A1 and FHL1." Thesis, Rice, Kim (2004) Functional analysis of the HOX11 target genes ALDH1A1 and FHL1. PhD thesis, Murdoch University, 2004. https://researchrepository.murdoch.edu.au/id/eprint/277/.

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HOX11 is a developmental regulator that plays a crucial role in the normal development of the spleen and is also aberrantly activated by the t(10;14)(q24;q11) and variant t(7;10)(q35;q24) translocations in a subset of T-cell acute lymphoblastic leukaemias (TALLs). The recent finding that HOX11 is deregulated in up to 40% of childhood TALLs when abnormalities not detected by cytogenetics are included, suggests that the over-expression of HOX11 and subsequent deregulation of downstream target genes are critical events in the progression of this tumour type. To date, three candidate HOX11 target genes have been reported, two of which are Aldehyde Dehydrogenase 1a1 (ALDH1A1) and Four and a Half LIM domain Protein 1 (FHL1). This investigation focused on two aspects of HOX11 function, namely its roles as a transcriptional regulator and as a nuclear oncoprotein capable of inducing neoplastic transformation. More specifically, we sought to further understand the role of HOX11 in tumorigenesis by 1) Confirming target gene status of ALDH1A1 and FHL1 by assessing whether their proximal promoter regions are transcriptionally regulated by HOX11, 2) Investigating the regulatory elements/transcriptional complexes involved in the response of ALDH1A1 to HOX11 in both a T-cell and an erythroid cell line in order to gain an insight into the mechanism(s) responsible for mediating a HOX11 activity and 3) Assessing the ability of ALDH1A1 and FHL1 to perturb normal patterns of haematopoiesis, on the basis that the transforming capabilities of HOX11 are thought to derive from its ability to affect haematopoietic cell differentiation. To confirm ALDH1A1 and FHL1 as target genes, they were both characterised in terms of the ability of their proximal promoters to be transcriptionally regulated by HOX11 using luciferase reporter assays. Significant repression of the proximal promoters of ALDH1A1 and FHL1 by HOX11 was observed in PER-117 T-cells which provided further evidence for their status as target genes. In the case of ALDH1A1, a CCAAT box (-74/-70bp) was identified as the primary cis-regulatory element involved in ALDH1A1 transcription and repression by HOX11 appeared to occur, either directly or indirectly, via interactions at the CCAAT box. Electromobility shift assays (EMSAs) revealed the disruption of a specific complex at this site by HOX11, which also altered the formation of complexes at a non-canonical TATA box (a GATA box at -34/-29bp). Significantly, HOX11 was shown to have the potential to interact with TFIIB, a member of the basal transcriptional complex. This, together with the presence of a TFIIB responsive element immediately 5' of the GATA box, suggested that HOX11 may repress transcription by interfering with members of a preinitiation complex on the ALDH1A1 promoter. The transcriptional repression by HOX11 demonstrated in T-cells was dependent on DNA binding helix 3 of the homeodomain, suggesting that repression may require DNA binding. Alternatively, this region may be required for stable protein-protein interactions. In support of this, the in vitro association of HOX11 with TFIIB was disrupted upon deletion of helix 3, and the HOX11 H3 mutant switched from a transcriptional repressor to a potent activator of transcription. Together, this data supports a model whereby HOX11 represses transcription by interfering with activation complexes at the CCAAT box and at the GATA box possibly via protein-protein interactions involving the homeodomain helix 3, whereas deletion of the region disables repressor-specific interactions, resulting in potent activation by HOX11. Luciferase reporter gene assays investigating the response of nested deletions of the ALDH1A1 promoter to HOX11 in the HEL900 erythroleukaemic cell line, also identified the CCAAT box (-74/-70bp) as the primary cis-regulatory element involved in ALDH1A1 transcription. However, in stark contrast to the its effect in T-cells, HOX11 was shown to activate transcription in the HEL cell line, both from the empty pGL3Basic luciferase reporter vector and from the ALDH1A1 promoter, in a manner independent of the homeodomain DNA binding helix 3. HOX11 thus appears to be a dichotomous regulator, capable of both transcriptional activation and repression depending on the circumstances. The mechanisms underlying these two functions are also appear to be distinct, with repression but not activation requiring the presence of homeodomain helix 3. ALDH1A1 encodes an enzyme involved in the irreversible conversion of retinaldehyde to the biologically active metabolite, retinoic acid (RA) and appears to be physiologically regulated by Hox11 in the developing spleen. Since RA is a potent modulator of cellular differentiation, proliferation and apoptosis, the dysregulation of RA synthesis is likely to have severe consequences for the cell and may constitute a mechanism whereby overexpression of HOX11 predisposes T-cells to malignant transformation. FHL1 also appears to have potential relevance to tumorigenesis, given that it encodes protein isoforms with suspected roles in transcriptional regulation. As a starting point to investigate a possible link between these HOX11 target genes and leukaemogenesis, the effect of overexpressing ALDH1A1 and FHL1 on murine haematopoiesis was assessed following reconstitution of lethally irradiated mice with retrovirally-transduced primary murine bone marrow cells. The enforced expression of ALDH1A1 in bone marrow was associated with a marked increase in myelopoiesis and a decrease in B and T-lymphopoiesis. By contrast, overexpression of FHL1 was not associated with perturbations in myelopoiesis or lymphopoiesis, although a slight increase in erythropoiesis was observed in the bone marrow. While further work is required to clarify the possible oncogenic roles of both of these HOX11 target genes, these findings have served to identify ALDH1A1 in particular, as a gene which could potentially be involved in HOX11-mediated tumorigenesis.
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Rice, Kim. "Functional analysis of the HOX11 target genes ALDH1A1 and FHL1 /." Access via Murdoch University Digital Theses Project, 2004. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20051012.93820.

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Fernandes, Alinda. "Lentiviral-mediated gene delivery to investigate the functional role of neuropsychiatric genes." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/lentiviralmediated-gene-delivery-to-investigate-the-functional-role-of-neuropsychiatric-genes(b6392e47-e94b-4e64-b343-e7eafd696b26).html.

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Genetic studies have led to the identification of several candidate genes, some novel and others established, that may contribute to the risk of developing neuropsychiatric disorders. For example, dopamine receptor genes are established candidates for a number of psychiatric disorders such as Parkinson’s Disease, alcohol addiction and mood disorders. On the other hand, a gene of unknown function, AUTS2 (Autism susceptibility candidate 2), has recently been associated with alcohol consumption in a GWAS meta-analysis performed by our group. Interestingly, it has been associated with a broad range of neuropsychiatric disorders including autism, epilepsy and schizo-affective disorders. This thesis looked to address two broad aims: to establish lentiviral-mediated gene delivery technique in vivo by delineating the role of two well characterised Dopamine receptors D2R and D3R and to functionally characterise the role of AUTS2. By successfully establishing lentiviral mediated gene manipulation in vitro and in vivo, this thesis presents data for a similar role of nucleus accumbens D2R and D3R in novelty-induced locomotion while these receptors have a differential function in the regulation of light-induced locomotor behaviour in rats. Additionally, using molecular biology and in silica methods, this thesis demonstrates that AUTS2 is a nuclear protein and presents indications of its function as a neurodevelopmental gene with a potential role in neural migration, although its specific role has yet to be corroborated. Collectively, findings from this thesis will increase our understanding of the genetic link with brain function and behavioural traits. This will therefore have implications for overall neuropsychiatric research, as it will help understand molecular mechanisms underlying these conditions and possibly direct in the identification of potential therapeutic targets.
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Kacar, Betül, Eva Garmendia, Nurcan Tuncbag, Dan I. Andersson, and Diarmaid Hughes. "Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs." AMER SOC MICROBIOLOGY, 2017. http://hdl.handle.net/10150/625744.

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Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.
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Fan, Li. "Map based candidate gene cloning and functional analysis of genes involved in VLCFAs synthesis." [Ames, Iowa : Iowa State University], 2007.

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Ashwood, Lauren M. "Characterising the functional venom profiles of sea anemones." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/227457/1/Lauren_Ashwood_Thesis.pdf.

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This project examined the relationship between the ecological roles of venom and patterns of venom production in sea anemones. It was found that sea anemones produce multiple venoms and that these distinct venoms are associated with the ecological functions of envenomating structures. Overall, this information provides insights into the ecological context of venom regulation and provides a rational framework for pharmaceutical bioprospecting in sea anemones.
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Kolle, Gabriel Victor. "Functional analysis of vertebrate Crim1 /." [St. Lucia, Qld.], 2002. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16804.pdf.

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Couldrey, Christine. "A gene trap approach to identify the functional role of genes expressed during murine gametogenesis." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624246.

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Tronnersjö, Susanna. "Functional studies of RNA polymerase II-dependent transcription in yeast Saccharomyces cerevisiae /." Uppsala : Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/2006109.pdf.

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Books on the topic "Functionnal genes"

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Enrico, Mihich, Housman David E, and Pezcoller Symposium on Cancer Genes: Functional Aspects (7th. : 1995 : Trento, Italy), eds. Cancer genes: Functional aspects. New York: Plenum Press, 1996.

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Smoler, Gunilla Kanter. Functional characterisation of conserved checkpoint genes. Göteborg: [s.n.], 1998.

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Schumann, Wolfgang, Prof. Dr. rer. nat., Ehrlich S. Dusko, and Ogasawara Naotake, eds. Functional analysis of bacterial genes: A practical manual. Chichester: J. Wiley, 2001.

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Alonso, Jose M., and Anna N. Stepanova. Plant functional genomics: Methods and protocols. New York: Humana Press, 2015.

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Erjavec, Stephanie O'Toole. Utilizing functional genomics approaches to characterize risk genes in alopecia areata. [New York, N.Y.?]: [publisher not identified], 2020.

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Roepke, Jonathon. Localization and functional characterization of iridoid biosynthetic genes in Catharanthus roseus. St. Catharines, Ont: Brock University, Centre for Biotechnology, 2008.

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Berkowitz, Noah C. Functional importance of polymorphic subregions in the C3H anti I-Ab alloresponse. [New York]: [Columbia University], 1993.

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Erich, Grotewold, ed. Plant functional genomics. Totowa, N.J: Humana Press, 2003.

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Wuke. cDNA cloning, sequence analysis, and expression studies of the murine Hox-1.7 and Hox-1.8 homeobox genes and functional studies of the murine Hox-1.4 homeobox gene. [New York]: Columbia University, 1992.

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Issar, Smith, Slepecky Ralph, Setlow Peter, and International Spore Conference, (10th : 1988 : Woods Hole, Mass.), eds. Regulation of procaryotic development: A structural and functional analysis of bacterial sporulation and germination. Washington, D.C: American Society for Microbiology, 1989.

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Book chapters on the topic "Functionnal genes"

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Andleeb, Tayyaba, James Milson, and Philippa Borrill. "The Wheat Transcriptome and Discovery of Functional Gene Networks." In Compendium of Plant Genomes, 75–92. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-38294-9_5.

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AbstractGene expression patterns have been a widely applied source of information to start understanding gene function in multiple plant species. In wheat, the advent of increasingly accurate and complete gene annotations now enables transcriptomic studies to be carried out on a routine basis and studies by groups around the world have compared gene expression changes under an array of environmental and developmental stages. However, associating data from differentially expressed genes to understanding the biological role of these genes and their applications for breeding is a major challenge. Recently, the first steps to apply network-based approaches to characterise gene expression have been taken in wheat and these networks have enabled the prediction of gene functions in wheat but only for a handful of traits. Combining advanced analysis methods with better sequencing technology will increase our capacity to place gene expression in wheat in the context of functions of genes that influence agronomically important traits.
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Ng, Esther Feng Ying, and Franz Meitinger. "Genetic Engineering and Screening Using Base Editing and Inducible Gene Knockout." In Methods in Molecular Biology, 167–87. New York, NY: Springer US, 2024. https://doi.org/10.1007/978-1-0716-4224-5_12.

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AbstractGenetic engineering and screening in human cells are powerful techniques for the precise and comprehensive identification and analysis of gene and protein domain functions. Genome-wide knockout screens have been extensively utilized to discover essential genes, tumor suppressors, and genes that regulate responses to various chemicals, including antimitotic and therapeutic drugs. The advent of base editors, which facilitate the targeted mutation of single amino acids, has advanced the identification of critical and functional domains or motifs. In this context, we outline methods for creating efficient base editor and inducible knockout cell lines for targeted gene manipulation and conducting genetic screens to elucidate the roles of genes and their domains within a specific cell biological context.
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Rasheed, Awais, Humaira Qayyum, and Rudi Appels. "Genome-Informed Discovery of Genes and Framework of Functional Genes in Wheat." In Compendium of Plant Genomes, 165–86. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-38294-9_9.

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AbstractThe complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018), and since then many wheats genomic resources have been developed in a short period of time. These resources include resequencing of several hundred wheat varieties, exome capture from thousands of wheat germplasm lines, large-scale RNAseq studies, and complete genome sequences with de novo assemblies of 17 important cultivars. These genomic resources provide impetus for accelerated gene discovery and manipulation of genes for genetic improvement in wheat. The groundwork for this prospect includes the discovery of more than 200 genes using classical gene mapping techniques and comparative genomics approaches to explain moderate to major phenotypic variations in wheat. Similarly, QTL repositories are available in wheat which are frequently used by wheat genetics researchers and breeding communities for reference. The current wheat genome annotation is currently lagging in pinpointing the already discovered genes and QTL, and annotation of such information on the wheat genome sequence can significantly improve its value as a reference document to be used in wheat breeding. We aligned the currently discovered genes to the reference genome, provide their position and TraesIDs, and present a framework to annotate such genes in future.
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Guo, Hui-jun, Yong-dun Xie, Lin-shu Zhao, Hong-chun Xiong, Jia-yu Gu, Shi-rong Zhao, and Lu-xiang Liu. "Progress of mutant resource development and tilling on starch biosynthesis in wheat." In Mutation breeding, genetic diversity and crop adaptation to climate change, 280–84. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0028.

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Abstract Induced mutations have been widely utilized for the development of plant mutant germplasm and varieties since 1927 and have contributed to genetic diversity enhancement and food security in the world. Mutant resources are essential for gene identification and functional characterization by forward and reverse genetic strategies. The publishing of annotated wheat reference genomes is greatly promoting the progress of wheat functional genomic research. Mutant resources of a broad spectrum and diversified wild- types will be the prerequisites in this process, in part due to the polyploid nature of wheat. This review describes the progress of mutant resource development derived from the winter wheat cultivar 'Jing411'. The segregating M2 population has been used for mining functional mutant alleles of key genes involved in starch biosynthesis and could be further used for allele mining of any other target genes. The morphological mutant resources developed from various mutagens have been, and are going to be, used to develop genetic populations for gene mapping and the genetic analysis of biological functions.
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Andersen, Lise Brock, Ann Lund, Marie Kveiborg, Brian F. C. Clark, and Suresh I. S. Rattan. "From Genes to Functional Gene Products during Ageing." In Molecular Gerontology, 53–73. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4615-5889-7_5.

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Nover, L. "Gene Technology and Functional Analyses of Heat Shock Genes." In Heat Shock Response, 167–220. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367811730-8.

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Murphy, P. J., A. Karakousis, S. E. Smith, and P. Langridge. "Cloning Functional Endomycorrhiza Genes." In Biotechnology of Ectomycorrhizae, 77–83. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-1889-1_7.

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Zhegunov, Gennadiy. "Functional Systems of Genes." In The Dual Nature of Life, 241–50. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-30394-4_23.

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Bhalla, Parinishtha, Anukriti Verma, Bhawna Rathi, Shivani Sharda, and Pallavi Somvanshi. "Exploring Molecular Signatures in Spondyloarthritis: A Step Towards Early Diagnosis." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 142–55. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_15.

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AbstractSpondyloarthritis is an acute inflammatory disorder of the musculoskeletal system often accompanied by pain, stiffness, bone and tissue damage. It majorly consists of ankylosing spondylitis, psoriatic arthritis and reactive arthritis. It follows a differential diagnosis pattern for demarcation between the spondyloarthritis subtypes and other arthritic subtypes such as rheumatoid arthritis, juvenile arthritis and osteoarthritis due to the heterogeneity causing gradual chronicity and complications. Presence of definite molecular markers can not only improve diagnosis efficiency but also aid in their prognosis and therapy. This study is an attempt to compose a refined list of such unique and common molecular signatures of the considered subtypes, by employing a reductionist approach amalgamating gene retrieval, protein-protein interaction network, functional, pathway, micro-RNA-gene and transcription factor-gene regulatory network analysis. Gene retrieval and protein-protein interaction network analysis resulted in unique and common interacting genes of arthritis subtypes. Functional annotation and pathway analysis found vital functions and pathways unique and common in arthritis subtypes. Furthermore, miRNA-gene and transcription factor-gene interaction networks retrieved unique and common miRNA’s and transcription factors in arthritis subtypes. Furthermore, the study identified important signatures of arthritis subtypes that can serve as markers assisting in prognosis, early diagnosis and personalized treatment of arthritis patients requiring validation via prospective experimental studies.
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Saeed, Muhammad Usama, Nazim Hussain, and Muhammad Bilal. "Biomaterials in Gene Delivery." In Functional Biomaterials, 129–48. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-7152-4_5.

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Conference papers on the topic "Functionnal genes"

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Coorey, H., R. Jayatillaka, N. Jayathilaka, and N. Ambanpola. "Determining Differentially Expressed Genes in Dengue Patients during Disease Progression." In SLIIT International Conference on Advancements in Sciences and Humanities 2023. Faculty of Humanities and Sciences, SLIIT, 2023. http://dx.doi.org/10.54389/ajrm6708.

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Gene expression studies on gene transcription to synthesize functional gene products have been used extensively to understand the biological differences between different disease conditions. Thus, this study determines differentially expressed genes in dengue infection during disease progression following the three phases: Febrile, Defervescence and Convalescent. Integrative data analysis of two publicly available longitudinal datasets in the Gene Expression Omnibus (GEO) database has been employed to accomplish the prime objective of exploring temporal gene expression patterns. The Friedman test was given more emphasis due to the non-normality distributions of data. Since previous studies on gene expression have not primarily relied on normality assumption, repeated measures analysis of variance and linear mixed models were implemented to examine the potential of detecting differentially expressed genes despite non-normality. The Friedman test indicated that gene expression levels differentiate with different phases in dengue disease over time, resulting in a high number of significant differentially expressed genes compared to the other two techniques. The pathway analysis approach consists of significant differentially expressed genes derived from the Friedman test. The results identified 27 and 26 upregulated pathways for the “Febrile and Convalescent” and “Defervescence and Convalescent” groups respectively. Moreover, genes available in pathways were not identified by the two parametric tests for non-normal data implying that the parametric approaches resulted in the least significance for data with non-normal distributions.
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Malyutina, T. A. "NEUROPEPTIDES INVOLVING IN THE REGULATION OF LOCOMOTOR BEHAVIOR OF ROOT-KNOT PLANT-PARASITIC NEMATODES (REVIEW)." In THEORY AND PRACTICE OF PARASITIC DISEASE CONTROL. All-Russian Scientific Research Institute for Fundamental and Applied Parasitology of Animals and Plant – a branch of the Federal State Budget Scientific Institution “Federal Scientific Centre VIEV”, 2023. http://dx.doi.org/10.31016/978-5-6048555-6-0.2023.24.281-284.

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In the last few decades, the attention of researchers has been attracted by endogenous FMRFamide-like neuropeptides found in a number of invertebrates, including species of the Nematoda phylum. A foreign literature review was presented for the functional significance of endogenous FMRFamide-like neuropeptides in locomotor behaviour of root-knot phytonematodes, representatives of the genus Meloidogyne Goldi, 1982, namely, Meloidogyne incognita, M. minor, M. hapla and M. graminicola. In Russia, such studies are not carried out. The main characteristics of phytoparasitic neuropeptides were obtained from the study of genes (flp-genes) that encode these neuropeptides. M. incognita was found to have FMRFamidelike positive immunoreactivity in the central nervous system and 19 flp genes. The Mi-flp-12 and Mi-flp-14 genes encode neuropeptides that stimulate locomotor behaviour, while Mi-flp-32 encodes a neuropeptide that inhibits parasite locomotor behaviour. Nematodes M. incognita and M. hapla were found to have G-proteincoupled receptors (GPCRs) encoded by the flp-32 gene, and their similarity to receptor 1 (C26F1) of the free-living nematode Caenorhabditis elegans was detected. Similar data were presented in the literature for M. graminicola. The peptidergic signaling nervous system of root-knot phytonematodes is similar to the system of nematodes in vertebrates and free-living nematodes, which indicates the conservatism of the system in species of the entire Nematoda phylum.
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Uvarova, A. N., E. A. Tkachenko, K. V. Korneev, and D. V. Kuprash. "FUNCTIONAL ANALYSIS OF SNPS ASSOCIATED WITH SEVERE VIRAL RESPIRATORY DISEASES AND LOCATED IN THE REGULATORY REGIONS OF ANTIVIRAL IMMUNE RESPONSE GENES." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-378.

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We investigated the regulatory regions of the CD55, LGALS1, and IFNAR2 genes in cell models of human macrophages and B-cells and analyzed several SNPs located in the regulatory regions of these genes and associated with severe COVID-19 or flu. In the course of this work, we characterized the IFNAR2 gene enhancer and performed functional annotation of several SNPs in the CD55 and LGALS1 promoters.
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Ploos van Amstel, J. K., A. L. van der Zanden, P. H. Reitsma, and R. M. Bertina. "RESTRICTION ANALYSIS AND SOUTHERN BLOTTING OF TOTAL HUMAN DNA REVEALS THE EXISTENCE OF MORE THAN ONE GENE HOMOLOGOUS WITH PROTEIN S cDNA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644639.

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A deficiency in protein S, the cofactor of activated protein C, is associated with an increased risk for the development of venous thrombosis. It is inherited as an autosomal dominant disorder. To improve the detection of heterozygotes in affected families, we have started to search for restriction fragment length polymorphism (RFLP) in the protein S gene. This study revealed the existence of two genes containing sequences homologous to protein S cDNA.Three non-overlapping fragments of clone pSUL5, which codes for the carboxy-terminal part of protein S and contains the complete 3' untranslated region, were isolated and used as probes in search for RFLP of the protein S gene.Surprisingly the non-overlapping probes shared more than one hybridizing band. The hybridization took place under stringent assay conditions.This observation is contradictory to the intron-exon organization of a gene and suggests the existence of two genes, containing sequences homologous with pSUL5. Both genes could be assigned to chromosome 3 by mapping through somatic cell hybrids. Whether two functional protein S genes are present in the human genome remains to be established.
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Zeng, Erliang, Giri Narasimhan, Lisa Schneper, and Kalai Mathee. "A Functional Network of Yeast Genes Using Gene Ontology Information." In 2008 IEEE International Conference on Bioinformatics and Biomedicine. IEEE, 2008. http://dx.doi.org/10.1109/bibm.2008.60.

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Teixeira, Lívia, Izabela Conceição, Paulo Caramelli, Marcelo Luizon, and Karina Gomes. "ALZHEIMER’S DISEASE AND TYPE 2 DIABETES MELLITUS: COMMON MIRNAS, GENES AND REGULATORY BIOLOGICAL PATHWAYS." In XIII Meeting of Researchers on Alzheimer's Disease and Related Disorders. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1980-5764.rpda066.

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Background: The increased incidence of Type 2 Diabetes Mellitus (T2DM) in the 21st century, along with the higher risk of developing Alzheimer’s disease (AD) in diabetic patients have stimulated the search for pathways that link glycemic disorders to neurodegeneration. MicroRNAs (miRNAs) are non-coding RNAs that play key roles in regulating gene expression. Objective: To identify miRNAs, genes and their regulatory pathways in common in AD and T2DM. Methods: Literature search was carried out to find miRNAs commonly expressed in AD and T2DM. MiRTarBase database was used to provide experimentally validated information on the interactions between miRNAs and their target genes. The functional enrichment of molecular pathways differentially regulated by these miRNAs was performed using EnrichR with Reactome gene set annotation. Results: We found six circulating miRNAs commonly expressed in both diseases (hsa-mir-21; hsamir-103a-1; hsa-mir-103a-2; hsa-mir-107; hsa-mir-146a and hsa-mir-144), which regulate 129 target genes. The common pathways between AD and T2DM were related to inflammatory mediators, cell death and axon formation signalling with p-adjust <10-5. Conclusion: Our study provides evidence that AD and T2DM share common pathophysiological mechanisms and regulators miRNAs, and suggests miRNAs as potential markers related to both diseases.
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Yarshevich, A. V., and P. M. Marozik. "ANALYSIS OF ASSOCIATION OF VDR GENE VARIANTS WITH SERUM VITAMIN D LEVEL IN PATIENTS WITH BONE-MUSCULAR DISEASE." In SAKHAROV READINGS 2021: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2021. http://dx.doi.org/10.46646/sakh-2021-2-146-149.

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Currently, the pathology of the musculoskeletal system is considered in several multifactorial diseases, the pathogenesis of which is complex and is due to the interaction of environmental and endogenous factors. An important role in the progression of pathology is played by disorders in metabolism and a decrease in sensitivity to vitamin D. Studies of the past two decades have shown that the various biological actions of the active metabolite of vitamin D - 1,25-dihydroxy vitamin D (calcitriol) - are carried out by modulating the expression of genes that are mediated by interaction with the intracellular vitamin D receptor (VDR). VDR is a product of the corresponding gene - VDR, which determines its structure and functional activity. In this gene, a certain number of polymorphic variants have been identified that can affect gene expression.
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Teixeira, LCR, JD Pereira, IMCA Conceição, P. Caramelli, MR Luizon, and KB Gomes. "ALZHEIMER’S DISEASE AND TYPE 2 DIABETES MELLITUS: COMMON MIRNAS, GENES AND REGULATORY BIOLOGICAL PATHWAYS." In Resumos do 54º Congresso Brasileiro de Patologia Clínica/Medicina Laboratorial, 43. Zeppelini Editorial e Comunicação, 2022. http://dx.doi.org/10.5327/1516-3180.140s1.6808.

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Objective: The increased incidence of type 2 diabetes mellitus (T2DM) in the 21st century, along with the higher risk of developing Alzheimer’s disease (AD) in diabetic patients have stimulated the search for pathways that link glycemic disorders to neurodegeneration. MicroRNAs (miRNAs) are non-coding RNAs that play key roles in regulating gene expression. To identify miRNAs, genes and their regulatory pathways in common in AD and T2DM. Method: Literature search was carried out to find miRNAs commonly expressed in AD and T2DM. MiRTarBase database was used to provide experimentally validated information on the interactions between miRNAs and their target genes. The functional enrichment of molecular pathways differentially regulated by these miRNAs was performed using EnrichR with Reactome gene set annotation. We found six circulating miRNAs commonly expressed in both diseases (hsa-mir-21; hsa-mir-103a-1; hsa-mir-103a-2; hsa-mir-107; hsa-mir-146a and hsa-mir-144), which regulate 129 target genes. The common pathways between AD and T2DM were related to inflammatory mediators, cell death and axon formation signalling with p-adjust < 10-5. Conclusion: Our study provides evidence that AD and T2DM share common pathophysiological mechanisms and regulators miRNAs, and suggests miRNAs as potential markers related to both diseases. References: 1. Saeidimehr S et al. MicroRNA-based linkage between aging and cancer: from epigenetics view point. Cell J. 2016; 18(2): 117-26
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Pannekok, H., A. J. Van Zonneveid, C. J. M. de vries, M. E. MacDonald, H. Veerman, and F. Blasi. "FUNCTIONAL PROPERTIES OF DELETION-MUTANTS OF TISSUE-TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643724.

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Over the past twenty-five years, genetic methods have generated a wealth of information on the regulation and the structure-function relationship of bacterial genes.These methods are based on the introduction of random mutations in a gene to alter its function. Subsequently, genetic techniques cure applied to localize the mutation, while the nature of the impairedfunction could be determined using biochemical methods. Classic examples of this approach is now considered to be the elucidation of the structure and function of genes, constituting the Escherichia coli lactose (lac) and tryptophan (trp) operons,and the detailed establishment of the structure and function of the repressor (lacl) of the lac operon. Recombinant DNA techniques and the development of appropriate expression systems have provided the means both to study structure and functionof eukaryotic (glyco-) proteins and to create defined mutations with a predestinedposition. The rationale for the construction of mutant genes should preferentiallyrely on detailed knowledge of the three-dimensional structure of the gene product.Elegant examples are the application of in vitro mutagenesis techniques to substitute amino-acid residues near the catalytic centre of subtilisin, a serine proteasefrom Bacillus species and to substituteanamino acid in the reactive site (i.e. Pi residue; methionine) of α-antitrypsin, a serine protease inhibitor. Such substitutions have resulted into mutant proteins which are less susceptible to oxidation and, in some cases, into mutant proteins with a higher specific activity than the wild-type protein.If no data are available on the ternary structure of a protein, other strategies have to be developed to construct intelligent mutants to study the relation between the structure and the function of a eukaryotic protein. At least for a number of gene families, the gene structure is thought to be created by "exon shuffling", an evolutionary recombinational process to insert an exon or a set of exons which specify an additional structural and/or functional domain into a pre-existing gene. Both the structure of the tissue-type plasminogen activator protein(t-PA) and the t-PA gene suggest that this gene has evolved as a result of exon shuffling. As put forward by Gilbert (Science 228 (1985) 823), the "acid test"to prove the validity of the exon shuffling theory is either to delete, insert or to substitute exon(s) (i.e. in the corresponding cDNA) and toassay the properties of the mutant proteins to demonstrate that an exon or a set of adjacent exons encode (s) an autonomousfunction. Indeed, by the construction of specific deletions in full-length t-PA cDNA and expression of mutant proteins intissue-culture cells, we have shown by this approach that exon 2 of thet-PA gene encodes the function required forsecretion, exon 4 encodes the "finger" domain involved in fibrin binding(presumably on undegraded fibrin) and the set of exons 8 and 9 specifies kringle 2, containing a lysine-binding sit(LBS) which interacts with carboxy-terminal lysines, generated in fibrin after plasmic digestion. Exons 10 through 14 encode the carboxy-ter-minal light chain of t-PA and harbor the catalytic centre of the molecule and represents the predominant "target site" for the fast-acting endothelial plasminogen activator inhibitor (PAI-1).As a follow-up of this genetic approach to construct deletion mutants of t-PA, we also created substitution mutants of t-PA. Different mutants were constructed to substitute cDNA encoding thelight chain of t-PA by cDNA encoding the B-chain of urokinase (u-PA), in order to demonstrate that autonomous structural and functional domains of eitherone of the separate molecules are able toexert their intrinsic properties in a different context (C.J.M. de Vries et al., this volume). The possibilities and the limitations of this approach to study the structure and the function of t-PA and of other components of the fibrinolytic process will be outlined.
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Triche, Timothy J., Sheetal A. Mitra, Hyung G. Kang, and Jonathan D. Buckley. "Abstract 402: Gene editing for functional analysis of Ewing sarcoma target genes." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-402.

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Reports on the topic "Functionnal genes"

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Meir, Shimon, Michael Reid, Cai-Zhong Jiang, Amnon Lers, and Sonia Philosoph-Hadas. Molecular Studies of Postharvest Leaf and Flower Abscission. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696523.bard.

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Original objectives: Understanding the regulation of abscission competence by exploring the nature and function of auxin-related gene expression changes in the leaf and pedicelAZs of tomato (as a model system), was the main goal of the previously submitted proposal. We proposed to achieve this goal by using microarray GeneChip analysis, to identify potential target genes for functional analysis by virus-induced gene silencing (VIGS). To increase the potential of accomplishing the objectives of the previously submitted proposal, we were asked by BARD to show feasibility for the use of these two modern techniques in our abscission system. Thus, the following new objectives were outlined for the one-year feasibility study: 1.to demonstrate the feasibility of the VIGS system in tomato to perform functional analysis of known abscission-related genes; 2. to demonstrate that by using microarray analysis we can identify target genes for further VIGS functional analysis. Background to the topic: It is a generally accepted model that auxin flux through the abscission zone (AZ) prevents organ abscission by rendering the AZ insensitive to ethylene. However, the molecular mechanisms responsible for acquisition of abscission competence and the way in which the auxin gradient modulates it are still unknown. Understanding this basic stage of the abscission process may provide us with future tools to control abscission for agricultural applications. Based on our previous study, performed to investigate the molecular changes occurring in leaf and stem AZs of MirabillisJalapaL., we have expanded our research to tomato, using genomic approaches that include modern techniques for gene discovery and functional gene characterization. In our one-year feasibility study, the US team has established a useful system for VIGS in tomato, using vectors based on the tobacco rattle virus (TRV), a Lcreporter gene for silencing (involved in regulation of anthocyanin biosynthesis), and the gene of interest. In parallel, the Israeli team has used the newly released Affymetrix Tomato GeneChip to measure gene expression in AZ and non-AZ tissues at various time points after flower removal, when increased sensitivity to ethylene is acquired prior to abscission (at 0-8 h), and during pedicelabscission (at 14 h). In addition, gene expression was measured in the pedicel AZ pretreated with the ethylene action inhibitor, 1-methylcyclopropene (1-MCP) before flower removal, to block any direct effects of ethylene. Major conclusions, solutions and achievements: 1) The feasibility study unequivocally established that VIGS is an ideal tool for testing the function of genes with putative roles in abscission; 2) The newly released Affymetrix Tomato GeneChip was found to be an excellent tool to identify AZ genes possibly involved in regulation and execution of abscission. The VIGS-based study allowed us to show that TAPG, a polygalacturonase specifically associated with the tomato AZ, is a key enzyme in the abscission process. Using the newly released Affymetrix Tomato GeneChip we have identified potential abscission regulatory genes as well as new AZ-specific genes, the expression of which was modified after flower removal. These include: members of the Aux/IAAgene family, ethylene signal transduction-related genes, early and late expressed transcription factors, genes which encode post-translational regulators whose expression was modified specifically in the AZ, and many additional novel AZ-specific genes which were previously not associated with abscission. This microarray analysis allowed us to select an initial set of target genes for further functional analysis by VIGS. Implications: Our success in achieving the two objectives of this feasibility study provides us with a solid basis for further research outlined in the original proposal. This will significantly increase the probability of success of a full 3-year project. Additionally, our feasibility study yielded highly innovative results, as they represent the first direct demonstration of the functional involvement of a TAPG in abscission, and the first microarray analysis of the abscission process. Using these approaches we could identify a large number of genes involved in abscission regulation, initiation and execution, and in auxin-ethylene cross-talk, which are of great importance, and could enable their potential functional analysis by VIGS.
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Mawassi, Munir, Baozhong Meng, and Lorne Stobbs. Development of Virus Induced Gene Silencing Tools for Functional Genomics in Grapevine. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7613887.bard.

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Grapevine is perhaps the most widely grown fruit crop. To understand the genetic make-up so as to improve the yield and quality of grapes and grape products, researchers in Europe have recently sequenced the genomes of Pinot noir and its inbred. As expected, function of many grape genes is unknown. Functional genomics studies have become the major focus of grape researchers and breeders. Current genetic approaches for gene function studies include mutagenesis, crossing and genetic transformation. However, these approaches are difficult to apply to grapes and takes long periods of time to accomplish. It is thus imperative to seek new ways for grape functional genomics studies. Virus-induced gene silencing (VIGS) offers an attractive alternative for this purpose and has proven highly effective in several herbaceous plant species including tomato, tobacco and barley. VIGS offers several advantages over existing functional genomics approaches. First, it does not require transformation to silence a plant gene target. Instead, it induces silencing of a plant gene through infection with a virus that contains the target gene sequence, which can be accomplished within a few weeks. Second, different plant genes can be readily inserted into the viral genome via molecular cloning and functions of a large number of genes can be identified within a short period of time. Our long-term goal of this research is to develop VIGS-based tools for grapevine functional genomics, made of the genomes of Grapevine virus A (GVA) from Israel and Grapevine rupestris stem pitting-associated virus (GRSPaV) from Canada. GVA and GRSPaV are members of the Flexiviridae. Both viruses have single-stranded, positive sense RNA genomes, which makes them easy to manipulate genetically and excellent candidates as VIGS vectors. In our three years research, several major breakthroughs have been made by the research groups involved in this project. We have engineered a cDNA clone of GVA into a binary vector that is infectious upon delivery into plantlets of micropropagated Vitis viniferacv. Prime. We further developed the GVA into an expression vector that successfully capable to silence endogenous genes. We also were able to assemble an infectious full-length cDNA clones of GRSPaV. In the following sections Achievements and Detailed description of the research activities, we are presenting the outcome and results of this research in details.
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Levin, Ilan, John W. Scott, Moshe Lapidot, and Moshe Reuveni. Fine mapping, functional analysis and pyramiding of genes controlling begomovirus resistance in tomato. United States Department of Agriculture, November 2014. http://dx.doi.org/10.32747/2014.7594406.bard.

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Abstract. Tomato yellow leaf curl virus (TYLCV), a monopartitebegomovirus, is one of the most devastating viruses of cultivated tomatoes and poses increasing threat to tomato production worldwide. Because all accessions of the cultivated tomato are susceptible to these viruses, wild tomato species have become a valuable resource of resistance genes. QTL controlling resistance to TYLCV and other begomoviruses (Ty loci) were introgressed from several wild tomato species and mapped to the tomato genome. Additionally, a non-isogenic F₁diallel study demonstrated that several of these resistance sources may interact with each other, and in some cases generate hybrid plants displaying lower symptoms and higher fruit yield compared to their parental lines, while their respective resistance genes are not necessarily allelic. This suggests that pyramiding genes originating from different resistance sources can be effective in obtaining lines and cultivars which are highly resistant to begomoviruses. Molecular tools needed to test this hypothesis have been developed by our labs and can thus significantly improve our understanding of the mechanisms of begomovirus resistance and how to efficiently exploit them to develop wider and more durable resistance. Five non-allelic Ty loci with relatively major effects have been mapped to the tomato genome using molecular DNA markers, thereby establishing tools for efficient marker assisted selection, pyramiding of multiple genes, and map based gene cloning: Ty-1, Ty-2, Ty-3, Ty-4, and ty-5. This research focused on Ty-3 and Ty-4 due to their broad range of resistance to different begomoviruses, including ToMoV, and on ty-5 due to its exceptionally high level of resistance to TYLCV and other begomoviruses. Our aims were: (1) clone Ty-3, and fine map Ty-4 and Ty-5 genes, (2)introgress each gene into two backgroundsand develop semi isogenic lines harboring all possible combinations of the three genes while minimizing linkage-drag, (3) test the resulting lines, and F₁ hybrids made with them, for symptom severity and yield components, and (4) identify and functionally characterize candidate genes that map to chromosomal segments which harbor the resistance loci. During the course of this research we have: (1) found that the allelic Ty-1 and Ty-3 represent two alternative alleles of the gene coding DFDGD-RDRP; (2) found that ty-5is highly likely encoded by the messenger RNA surveillance factor PELOTA (validation is at progress with positive results); (3) continued the map-based cloning of Ty-4; (4) generated all possible gene combinations among Ty-1, Ty-3 and ty-5, including their F₁ counterparts, and tested them for TYLCV and ToMoV resistance; (5) found that the symptomless line TY172, carrying ty-5, also carries a novel allele of Ty-1 (termed Ty-1ⱽ). The main scientific and agricultural implications of this research are as follows: (1) We have developed recombination free DNA markers that will substantially facilitate the introgression of Ty-1, Ty-3 and ty-5 as well as their combinations; (2) We have identified the genes controlling TYLCV resistance at the Ty-1/Ty-3 and ty-5 loci, thus enabling an in-depth analyses of the mechanisms that facilitate begomovirus resistance; (3) Pyramiding of Ty resistance loci is highly effective in providing significantly higher TYLCV resistance.
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Lifschitz, Eliezer, and Elliot Meyerowitz. The Relations between Cell Division and Cell Type Specification in Floral and Vegetative Meristems of Tomato and Arabidopsis. United States Department of Agriculture, February 1996. http://dx.doi.org/10.32747/1996.7613032.bard.

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Meristems were the central issue of our project. Genes that are required for cell division, cell elongation, cell proliferation and cell fate were studied in the tomato system. The analysis of the dUTPase and threonine deaminase genes, along with the dissection of their regulatory regions is completed, while that of the RNR2 and PPO genes is at an advanced stage. All these genes were isolated in our laboratory. In addition, 8 different MADS box genes were studied in transgenic plants and their genetic relevances discovered. We have also shown that a given MADS box gene can modify the polarity of cell division without affecting the fate of the organ. In vivo interaction between two MADS box genes was demonstrated and the functional dependency of the tomato agamous gene on the TM5 gene product established. We have exploited the Knotted1 meristematic gene in conjunction with tomato leaf meristematic genes to show that simple and compound leaves and, for that matter, sepals and compound leaves, are formed by two different developmental programs. In this context we have also isolated and characterized the tomato Knotted1 gene (TKnl) and studied its expression pattern. A new program in which eight different meristematic genes in tomato will be studied emerged as a result of these studies. In essence, we have shown that it is possible to study and manipulate plant developmental systems using reverse genetic techniques and have provided a wealth of new molecular tools to interested colleagues working with tomato. Similarly, genes responsible for cell division, cell proliferation and cell fate were studied in Arabidopsis floral meristems. Among these genes are the TSO1, TSO2, HANABA TARANU and UNUSUAL FLORAL ORGANS genes, each affecting in its own way the number of pattern of cell divisions, and cell fate, in developing Arabodopsis flowers. In addition, new methods have been established for the assessment of the function of regulatory gene action in the different clonal layers of developing floral meristems.
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Lichter, Amnon, Gopi K. Podila, and Maria R. Davis. Identification of Genetic Determinants that Facilitate Development of B. cinerea at Low Temperature and its Postharvest Pathogenicity. United States Department of Agriculture, March 2011. http://dx.doi.org/10.32747/2011.7592641.bard.

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Botrytis cinerea is the postharvest pathogen of many agricultural produce with table grapes, strawberries and tomatoes as major targets. The high efficiency with which B. cinerea causes disease on these produce during storage is attributed in part due to its exceptional ability to develop at very low temperature. Our major goal was to understand the genetic determinants which enable it to develop at low temperature. The specific research objectives were: 1. Identify expression pattern of genes in a coldenriched cDNA library. 2. Identify B. cinerea orthologs of cold-induced genes 3. Profile protein expression and secretion at low temperature on strawberry and grape supplemented media. 4. Test novel methods for the functional analysis of coldresponsive genes. Objective 1 was modified during the research because a microarray platform became available and it allowed us to probe the whole set of candidate genes according to the sequence of 2 strains of the fungus, BO5.10 and T4. The results of this experiment allowed us to validate some of our earlier observations which referred to genes which were the product of a SSH suppression-subtraction library. Before the microarray became available during 2008 we also analyzed the expression of 15 orthologs of cold-induced genes and some of these results were also validated by the microarray experiment. One of our goals was also to perform functional analysis of cold-induced genes. This goal was hampered for 3 years because current methodology for transformation with ‘protoplasts’ failed to deliver knockouts of bacteriordopsin-like (bR) gene which was our primary target for functional analysis. Consequently, we developed 2 alternative transformation platforms, one which involves an air-gun based technique and another which involves DNA injection into sclerotia. Both techniques show great promise and have been validated using different constructs. This contribution is likely to serve the scientific community in the near future. Using these technologies we generated gene knockout constructs of 2 genes and have tested there effect on survival of the fungus at low temperature. With reference to the bR genes our results show that it has a significant effect on mycelial growth of the B. cinerea and the mutants have retarded development at extreme conditions of ionic stress, osmotic stress and low temperature. Another gene of unknown function, HP1 is still under analysis. An ortholog of the yeast cold-induced gene, CCH1 which encodes a calcium tunnel and was shown to be cold-induced in B. cinerea was recently cloned and used to complement yeast mutants and rescue them from cold-sensitivity. One of the significant findings of the microarray study involves a T2 ribonuclease which was validated to be cold-induced by qPCR analysis. This and other genes will serve for future studies. In the frame of the study we also screened a population of 631 natural B. cinerea isolates for development at low temperature and have identified several strains with much higher and lower capacity to develop at low temperature. These strains are likely to be used in the future as candidates for further functional analysis. The major conclusions from the above research point to specific targets of cold-induced genes which are likely to play a role in cold tolerance. One of the most significant observations from the microarray study is that low temperature does not induce ‘general stress response in B. cinerea, which is in agreement to its exceptional capacity to develop at low temperature. Due to the tragic murder of the Co-PI Maria R. Davis and GopiPodila on Feb. 2010 it is impossible to deliver their contribution to the research. The information of the PI is that they failed to deliver objective 4 and none of the information which relates to objective 3 has been delivered to the PI before the murder or in a visit to U. Alabama during June, 2010. Therefore, this report is based solely on the IS data.
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Busov, Victor. Functional Gene Discovery and Characterization of Genes and Alleles Affecting Wood Biomass Yield and Quality in Populus. Office of Scientific and Technical Information (OSTI), February 2017. http://dx.doi.org/10.2172/1343386.

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King, Mary-Claire, and Piri L. Welcsh. Novel Functional Screen for New Breast Cancer Genes. Fort Belvoir, VA: Defense Technical Information Center, June 2004. http://dx.doi.org/10.21236/ada433029.

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Katzir, Nurit, James Giovannoni, Marla Binzel, Efraim Lewinsohn, Joseph Burger, and Arthur Schaffer. Genomic Approach to the Improvement of Fruit Quality in Melon (Cucumis melo) and Related Cucurbit Crops II: Functional Genomics. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592123.bard.

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Background: Genomics tools for enhancement of melon research, with an emphasis on fruit, were developed through a previous BARD project of the PIs (IS -333-02). These included the first public melon EST collection, a database to relay this information to the research community and a publicly available microarray. The current project (IS-3877- 06) aimed to apply these tools for identification of important genes for improvement of melon (Cucumis melo) fruit quality. Specifically, the research plans included expression analysis using the microarray and functional analyses of selected genes. The original project objectives, as they appeared in the approved project, were: Objective 1: Utilization of a public melon microarray developed under the existing project to characterize melon transcriptome activity during the ripening of normal melon fruit (cv. Galia) in order to provide a basis for both a general view of melon transcriptome activity during ripening and for comparison with existing transcriptome data of developing tomato and pepper fruit. Objective 2: Utilization of the same public melon microarray to characterize melon transcriptome activity in lines available in the collection of the Israeli group, focusing on sugar, organic acids and aroma metabolism, so as to identify potentially useful candidates for functional analysis and possible manipulation, through comparison with the general fruit development profile resulting from (1) above. Objective 3: Expansion of our existing melon EST database to include publicly available gene expression data and query tools, as the US group has done with tomato. Objective 4: Selection of 6-8 candidate genes for functional analysis and development of DNA constructs for repression or over-expression. Objective 5: Creation of transgenic melon lines, or transgenic heterologous systems (e.g. E. coli or tomato), to assess putative functions and potential as tools for molecular enhancement of melon fruit quality, using the candidate gene constructs from (4).
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Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.

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High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.
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10

Lers, Amnon, and Gan Susheng. Study of the regulatory mechanism involved in dark-induced Postharvest leaf senescence. United States Department of Agriculture, January 2009. http://dx.doi.org/10.32747/2009.7591734.bard.

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Postharvest leaf senescence contributes to quality losses in flowers and leafy vegetables. The general goal of this research project was to investigate the regulatory mechanisms involved in dark-induced leaf senescence. The regulatory system involved in senescence induction and control is highly complex and possibly involves a network of senescence promoting pathways responsible for activation of the senescence-associated genes. Pathways involving different internal signals and environmental factors may have distinctive importance in different leaf senescence systems. Darkness is known to have a role in enhancement of postharvest leaf senescence and for getting an insight into its regulatory mechanism/s we have applied molecular genetics and functional genomics approaches. The original objectives were: 1. Identification of dark-induced SAGs in Arabidopsis using enhancer/promoter trap lines and microarray approaches; 2. Molecular and functional characterization of the identified genes by analyzing their expression and examining the phenotypes in related knockout mutant plants; 3. Initial studies of promoter sequences for selected early dark-induced SAGs. Since genomic studies of senescence, with emphasis on dark-induced senescence, were early-on published which included information on potential regulatory genes we decided to use this new information. This is instead of using the uncharacterized enhancer/promoter trap lines as originally planned. We have also focused on specific relevant genes identified in the two laboratories. Based on the available genomic analyses of leaf senescence 10 candidate genes hypothesized to have a regulatory role in dark-induced senescence were subjected to both expression as well as functional analyses. For most of these genes senescence-specific regulation was confirmed, however, functional analyses using knock-out mutants indicated no consequence to senescence progression. The transcription factor WARK75 was found to be specifically expressed during natural and dark-induced leaf senescence. Functional analysis demonstrated that in detached leaves senescence under darkness was significantly delayed while no phenotypic consequences could be observed on growth and development, including no effect on natural leaf senescence,. Thus, WARKY75 is suggested to have a role in dark-induced senescence, but not in natural senescence. Another regulatory gene identified to have a role in senescence is MKK9 encoding for a Mitogen-Activated Protein Kinase Kinase 9 which is upregulated during senescence in harvested leaves as well as in naturally senescing leaves. MKK9 can specifically phosphorylate another kinase, MPK6. Both knockouts of MKK9 and MPK6 displayed a significantly senescence delay in harvested leaves and possibly function as a phosphorelay that regulates senescence. To our knowledge, this is the first report that clearly demonstrates the involvement of a MAP kinase pathway in senescence. This research not only revealed a new signal transduction pathway, but more important provided significant insights into the regulatory mechanisms underlying senescence in harvested leaves. In an additional line of research we have employed the promoter of the senescence-induced BFN1 gene as a handle for identifying components of the regulatory mechanism. This gene was shown to be activated during darkinduced senescence of detached leaves, as well as natural senescence. This was shown by following protein accumulation and promoter activity which demonstrated that this promoter is activated during dark-induced senescence. Analysis of the promoter established that, at least some of the regulatory sequences reside in an 80 bps long fragment of the promoter. Overall, progress was made in identification of components with a role in dark-induced senescence in this project. Further studies should be done in order to better understand the function of these components and develop approaches for modulating the progress of senescence in crop plants for the benefit of agriculture.
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