Relevant bibliographies by topics / Functional conservation

Academic literature on the topic 'Functional conservation'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Functional conservation"

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G$aacute$l, Tam$aacute$s. "Functional differentiation under conservation constraints." Journal of Physics A: Mathematical and General 35, no. 28 (July 5, 2002): 5899–905. http://dx.doi.org/10.1088/0305-4470/35/28/309.

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Gál, Tamás. "Functional differentiation under simultaneous conservation constraints." Journal of Physics A: Mathematical and Theoretical 40, no. 9 (February 14, 2007): 2045–52. http://dx.doi.org/10.1088/1751-8113/40/9/010.

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Dolinski, Kara, and David Botstein. "Orthology and Functional Conservation in Eukaryotes." Annual Review of Genetics 41, no. 1 (December 2007): 465–507. http://dx.doi.org/10.1146/annurev.genet.40.110405.090439.

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Pennacchio, Len A., and Axel Visel. "Limits of sequence and functional conservation." Nature Genetics 42, no. 7 (July 2010): 557–58. http://dx.doi.org/10.1038/ng0710-557.

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Rosenfeld, Jordan S. "Functional redundancy in ecology and conservation." Oikos 98, no. 1 (July 2002): 156–62. http://dx.doi.org/10.1034/j.1600-0706.2002.980116.x.

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Rodini, Elizabeth. "Functional Jewels." Art Institute of Chicago Museum Studies 25, no. 2 (2000): 76. http://dx.doi.org/10.2307/4113065.

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Rud, Daniel, Paul Marjoram, Kimberly Siegmund, and Darryl Shibata. "Functional human genes typically exhibit epigenetic conservation." PLOS ONE 16, no. 9 (September 14, 2021): e0253250. http://dx.doi.org/10.1371/journal.pone.0253250.

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Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.
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Paffett-Lugassy, Noëlle, Nelson Hsia, Paula G. Fraenkel, Barry Paw, Irene Leshinsky, Bruce Barut, Nathan Bahary, Jaime Caro, Robert Handin, and Leonard I. Zon. "Functional conservation of erythropoietin signaling in zebrafish." Blood 110, no. 7 (October 1, 2007): 2718–26. http://dx.doi.org/10.1182/blood-2006-04-016535.

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Erythropoietin (Epo) and its cognate receptor (EpoR) are required for maintaining adequate levels of circulating erythrocytes during embryogenesis and adulthood. Here, we report the functional characterization of the zebrafish epo and epor genes. The expression of epo and epor was evaluated by quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization, revealing marked parallels between zebrafish and mammalian gene expression patterns. Examination of the hypochromic mutant, weissherbst, and adult hypoxia-treated hearts indicate that zebrafish epo expression is induced by anemia and hypoxia. Overexpression of epo mRNA resulted in severe polycythemia, characterized by a striking increase in the number of cells expressing scl, c-myb, gata1, ikaros, epor, and βe1-globin, suggesting that both the erythroid progenitor and mature erythrocyte compartments respond to epo. Morpholino-mediated knockdown of the epor caused a slight decrease in primitive and complete block of definitive erythropoiesis. Abrogation of STAT5 blocked the erythropoietic expansion by epo mRNA, consistent with a requirement for STAT5 in epo signaling. Together, the characterization of zebrafish epo and epor demonstrates the conservation of an ancient program that ensures proper red blood cell numbers during normal homeostasis and under hypoxic conditions.
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Colombo, Rinaldo M., and Graziano Guerra. "On the stability functional for conservation laws." Nonlinear Analysis: Theory, Methods & Applications 69, no. 5-6 (September 2008): 1581–98. http://dx.doi.org/10.1016/j.na.2007.07.012.

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Kunkler, J., W. Jack, C. Tyler, U. Chetty, J. Dixon, G. Kerr, A. Rodger, and L. Matheson. "306Structural and functional changes after conservation therapy." Radiotherapy and Oncology 40 (January 1996): S80. http://dx.doi.org/10.1016/s0167-8140(96)80315-x.

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Dissertations / Theses on the topic "Functional conservation"

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Pridham, Phillip. "Functional conservation of transcription activation mechanisms." Thesis, University of Nottingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395631.

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Caufield, J. Harry. "Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4580.

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The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of interactomics. I have employed novel computational methods to provide context for bacterial PUFs and to leverage the rich genomic, proteomic, and interactomic data available for hundreds of bacterial species. The methods employed in this study began with sets of protein complexes. I initially hypothesized that, if protein interactions reveal protein functions and interactions are frequently conserved through protein complexes, then conserved protein functions should be revealed through the extent of conservation of protein complexes and their components. The subsequent analyses revealed how partial protein complex conservation may, unexpectedly, be the rule rather than the exception. Next, I expanded the analysis by combining sets of thousands of experimental protein-protein interactions. Progressing beyond the scope of protein complexes into interactions across full proteomes revealed novel evolutionary consistencies across bacteria but also exposed deficiencies among interactomics-based approaches. I have concluded this study with an expansion beyond bacterial protein interactions and into those involving bacteriophage-encoded proteins. This work concerns emergent evolutionary properties among bacterial proteins. It is primarily intended to serve as a resource for microbiologists but is relevant to any research into evolutionary biology. As microbiomes and their occupants become increasingly critical to human health, similar approaches may become increasingly necessary.
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Oddo, Julia C. (Julia Christine). "Exploring the functional conservation of muscleblind (Mbl) proteins." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/101357.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Biology, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 54-59).
Muscleblind (Mbl) is an evolutionarily conserved family of proteins involved in many aspects of RNA metabolism, including alternative splicing. Disruption of Muscleblind in several animals lends to a variety of defects and disease, including the multi-systemic disorder Myotonic Dystrophy (DM). Though much is known about the involvement of Muscleblind in DM, there is much basic knowledge of the protein's function to be discovered. We approach this problem by exploring the functional conservation of a diverse subset of Muscleblind homologs. The functions of Muscleblinds from a basal metazoan, Trichoplax adhaerens, a primitive chordate, Ciona intestinalis, and the model organisms, Drosophila melanogaster and Caenorhabditis elegans were compared to human Muscleblind-like (MBNL). The zinc finger RNA-binding domains are the most conserved region between homologs, suggesting a conserved role in RNA binding and splicing regulation. To test this, we used splicing reporter assays with validated human MBNL-regulated mini-genes and performed RNA sequencing experiments in mouse embryonic fibroblasts (MEFs). Additionally, we accessed the subcellular localization of the homologs to determine conservation of extra-nuclear functions. Reporter assays in HeLa cells showed that the homologs can positively and negatively regulate splicing. Our RNA-seq experiments led us to discover hundreds of endogenously regulated splicing events, including the identity of the transcripts, direction of splicing regulation, types of splicing events, and the magnitude of alternate exon inclusion in the spliced mRNAs. Additionally, we identified a spectrum of splicing events, from those uniquely regulated by a single Muscleblind, to events regulated by all Muscleblinds, and, characterized the variation in splicing activity that exists between homologs. A subset of events regulated by mammalian Muscleblind were oppositely regulated by non-mammalian homologs. Muscleblinds show nuclear-cytoplasmic localization, which suggests conservation in extra-nuclear functions. In conjunction with exon and intron sequences, this information provides a future tool to discover conserved and novel RNA regulatory elements used by diverse Muscleblinds to regulate splicing and in putative cytoplasmic functions. These data could also be used to determine functionally important residues in Muscleblind proteins and help us better understand the protein family.
by Julia C. Oddo.
S.M.
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Edwards, Martin Tavis. "Comparative prokaryotic genomics : conservation of functional and spatial context." Thesis, Birkbeck (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428024.

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Maloney, Victoria Jane. "Function, functional conservation and interactions of the membrane-bound endo-1,4-beta-glucanases orthologous to Korrigan." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/24242.

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Plant endoglucanses (E.C. 3.2.1.4) encompass multi-gene families across several plant clades, all belonging to the glycosyl hydrolase 9 (GH9) family. One class of GH9 enzymes is unique in that all members possess sequences that encode an N-terminal membrane-anchoring domain. This class of enzymes, termed membrane-bound endo-1,4-beta-glucanases, is the focus of this thesis. The most extensively studied enzyme was first discovered in Arabidopsis and was given the name KORRIGAN (KOR) because of the dwarfed phenotype and cellulose deficiency apparent in plants exhibiting KOR gene mutations. Research has principally focused on Arabidopsis and other non-tree species and the possible role that the enzyme might play in primary cell wall development and cellulose synthesis. However, very little research with KOR has been conducted on trees and secondary cell wall development. Consequently, I investigated the effects of mis-regulating KOR in hybrid poplar and white spruce. I was able to demonstrate that the down-regulation of the hybrid poplar KOR gene increases the crystallinity of the secondary cell wall cellulose and affects the relationship between cellulose and the hemicellulose cell wall components. Concurrently, we were the first to isolate and characterize the KOR gene and suppress KOR gene activity in white spruce. Expression of white spruce KOR in Arabidopsis kor1-1 mutants demonstrated that the gene is able to rescue the mutant phenotype, providing evidence for functional equivalence. Additionally, suppression of the gene in white spruce reduced growth and cellulose content. Since KOR has been demonstrated to be required in cells undergoing cellulose synthesis, we investigated whether or not the KOR protein and the cellulose synthase complex (CSC) interact. Although we were not able to provide evidence for any KOR-protein interaction, we were able to disprove the hypothesis that KOR interacts with CesA7, a member of the secondary cell wall CSC. Collectively, the expression, functional characterization, and interaction data suggest that KOR does not function in direct contact with the CSC, but rather that it plays a role in the later stages of cell wall development, presumably in the relaxation of the stresses around the cellulose microfibril or in the separation of putative cellulose macrofibrils.
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Hua, Jiale. "Glimm type functional and one dimensional systems of hyperbolic conservation laws /." access abstract and table of contents access full-text, 2009. http://libweb.cityu.edu.hk/cgi-bin/ezdb/thesis.pl?phd-ma-b23749921f.pdf.

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Thesis (Ph.D.)--City University of Hong Kong, 2009.
"Submitted to Department of Mathematics in partial fulfillment of the requirements for the degree of Doctor of Philosophy." Includes bibliographical references (leaves 88-95)
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Habberfield, Michael William. "Functional connectivity for wildlife populations across spatially complex landscapes." Thesis, State University of New York at Buffalo, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10163822.

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Integrating animal movement information with the spatial analysis of landscape structure is critical for restoring biological communities in spatially-structured landscapes. This integration can be accomplished by focusing on functional connectivity—a landscape’s potential for the movement of organisms among resource patches—in relation to the spatial and structural connectivity of landscape elements. I carried out three investigations in order to examine how landscape structure interacts with the ecological factors associated with animal movement processes, and thereby produce actionable outcomes for the restoration of wildlife populations. This work combined population- and individual-level data of dispersing wildlife to better resolve the influence of spatial structure on functional connectivity. First, I used a meta-analysis to quantify the relationship between structural and functional connectivity for a broad scope of animal species. Second, I assessed the influence of landscape position and habitat density on colonization, movement, and population dynamics of wood frogs (Lithobates sylvatica) within a network of restored vernal pools. Third, I experimentally evaluated dispersal and habitat selection of green frogs (Lithobates clamitans) within this vernal pool system.

The meta-analysis demonstrated that universal scaling relationships of species and the landscapes they are moving through interact as key drivers mediating the level of functional connectivity afforded to wildlife by structural connectivity. Mark-recapture data revealed rapid colonization of the restored vernal pool network by wood frogs, with subsequently moderate levels of frog movement among neighboring pools. Local pool density interacted with the colonization process and terrestrial habitat availability to limit wood frog productivity within a pool cluster. Experimental dispersal data for green frogs artificially translocated within the pool network showed key differences between movement in familiar and novel environments. Differing movement behaviors and habitat selection patterns indicated that a habitat patch for this species is on the scale of a pool cluster rather than an individual pool. Together, the observed spatial dynamics of these vernal pool amphibians contribute a framework for improving amphibian dispersal modeling, potential responses to rapid environmental changes, and predicting colonization and subsequent population dynamics in restored systems. The results of this dissertation improve our understanding of how spatial structure interacts with organism-specific factors to produce observed patterns of functional connectivity.

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Grant, Alesha. "Functional Conservation of Interferon Antagonism among Flaviviruses| Zika Virus Targets Human STAT2." Thesis, Icahn School of Medicine at Mount Sinai, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10270604.

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Flaviviruses are a diverse group of emerging arboviruses capable of infecting an extraordinarily broad range of vertebrate and invertebrate hosts. Nearly half of the viruses in this rapidly expanding genus have been reported to be pathogenic for humans, as well as other vertebrates. The spectrum of human disease includes asymptomatic and febrile illnesses, rash, arthralgia, encephalitis and hemorrhagic fever. The recent outbreak of Zika virus (ZIKV) has uncovered pathology in the form of microcephaly and Guillain-Barré syndrome, cementing the importance of flaviviruses as emerging human pathogens. All vector-borne flaviviruses studied thus far have to overcome type I interferon (IFN) antiviral responses in order to replicate and cause disease in vertebrates. The non-structural protein NS5 is a potent and specific antagonist of IFN signaling for human pathogenic flaviviruses such as dengue virus (DENV), yellow fever virus (YFV), West Nile virus (WNV), and tick-borne encephalitis viruses (TBEVs). Intriguingly, each of these viruses exhibits different mechanisms of IFN antagonism, highlighting the complicated evolutionary nature of flaviviruses. This thesis work presents novel insights into the NS5-mediated antagonism of IFN signaling for several underexamined flaviviruses. Notably, all NS5 proteins examined were able to inhibit IFN-induced gene expression in a mammalian system, indicating a functional conservation of IFN antagonism for flavivirus NS5 proteins. However, mechanistically NS5 function was diverse. Of great interest, ZIKV NS5 bound to the human, but not mouse, IFN-regulated transcriptional activator STAT2 and targeted it for proteasomal degradation. This phenomenon may explain the requirement for IFN deficiency in order to observe ZIKV pathogenesis in mice. Furthermore, the mechanism of ZIKV NS5 resembles that of DENV NS5, but not that of its closer relative Spondweni virus (SPOV). However, unlike DENV NS5, ZIKV NS5 did not require the E3 ubiquitin ligase UBR4 to induce STAT2 degradation. Consequently, flavivirus NS5 proteins exhibit a remarkable functional convergence in IFN antagonism, albeit by virus-specific mechanisms. The potent antagonism of human IFN responses by neglected flaviviruses such as SPOV and Usutu virus (USUV), coupled with similar ecologies to that of known human flavivirus pathogens, suggests their potential for broad emergence into the human population.

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Henscheid, Kristy L. "Functional conservation and RNA binding of the pre-mRNA splicing factor U2AF65 /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1400950821&sid=5&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 129-141). Also available for download via the World Wide Web; free to University of Oregon users.
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McOwen, Chris. "The integration of phylogenetic and functional trait information into monocot biodiversity conservation." Thesis, University of St Andrews, 2012. http://hdl.handle.net/10023/3659.

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It is now widely acknowledged that a high proportion of the world's species are threatened with global extinction in the near future. Conserving all endangered species is impractical due to limited financial resources and manpower. Therefore, there is a real need to understand the mechanisms behind the extinction process in order to develop a proactive rather than reactive conservation strategy. Furthermore, given these limitations there is a need to be selective, prioritising species or areas not just on the basis of extinction risk or the number of species present, but with consideration for their role within the ecosystem. In this thesis, I investigate three aspects of current global extinction: What causes species to become threatened, how we should prioritise those that are, and how such information can be translated into area-based conservation priorities. Firstly, I developed models of plant extinction risk in relation to environmental (anthropogenic, climatic, and physical) variables and used them to show that non- randomness in extinction risk is highly influenced by interactions between the plants traits and their environment. Incorporating such interactions, my models were able to explain ~30% of the variation in plant extinction risk. Results from this large-scale comparative study suggest the biological traits that increase species' susceptibility are dependent upon local environmental conditions. Secondly, I looked at how much unique evolutionary history, a proxy for species value, will be lost under current extinction patterns, whilst investigating how effective current conservation methods are at prioritising species based on their evolutionary value. The results are not promising; species threatened with extinction had disproportionately high quantities of unique evolutionary history. Furthermore, the IUCN Red List makes no allowance for this, for example, species considered Critically Endangered, the highest threat status under the IUCN Red List, may not necessarily be the most evolutionary unique. Finally, I looked at the relationships among species richness, versity (FD) and phylogenetic diversity (PD) as measures of biodiversity and therefore the conservation value of an area. It was found species richness is generally a good surrogate for FD and PD. However, agricultural development and climatic variation bring out discrepancies between species richness, FD and PD, challenging the claim of interchangeability of different diversity measures, with potential consequences for conservation planning.
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Books on the topic "Functional conservation"

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Agency, United States Environmental Protection. Functional profile of black spruce wetlands in Alaska. Seattle, Wash: The Agency, 1996.

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Marble, Anne D. A guide to wetland functional design. Boca Raton: Lewis Publishers, 1992.

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Marble, Anne D. A guide to wetland functional design. McLean, Va: Federal Highway Administration, 1991.

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Heemskerk, Ben. Ecosystem and tree attributes affecting the presence of functional wildlife tree types. Victoria: British Columbia Ministry of Forests and Range, Forest Science Program, 2009.

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Heemskerk, Ben. Ecosystem and tree attributes affecting the presence of functional wildlife tree types. Victoria: British Columbia Ministry of Forests and Range, Forest Science Program, 2009.

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Sergey, Belyi, Tsekanovskii Eduard, and SpringerLink (Online service), eds. Conservative Realizations of Herglotz-Nevanlinna Functions. Basel: Springer Basel AG, 2011.

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Moench, Mel. Planet earth home: Introducing the functional, efficient, ecologically balanced, need-oriented, energy-independent, food-independent, simple, durable, non-polluting, single family, universal, minimal existence, living system built in the image of nature itself. Buffalo, MN: Osprey Press, 1995.

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Arlinskii, Yuri, Sergey Belyi, and Eduard Tsekanovskii. Conservative Realizations of Herglotz-Nevanlinna Functions. Basel: Springer Basel, 2011. http://dx.doi.org/10.1007/978-3-7643-9996-2.

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1941-, Schulze E. D., and Mooney Harold A, eds. Biodiversity and ecosystem function. Berlin: Springer-Verlag, 1994.

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S, Smith Daniel, and Hellmund Paul Cawood, eds. Ecology of greenways: Design and function of linear conservation areas. Minneapolis: University of Minnesota Press, 1993.

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Book chapters on the topic "Functional conservation"

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Mitchell, Thomas M. "On the Functional Forms of Technical Change Functions." In Conservation Laws and Symmetry: Applications to Economics and Finance, 275–99. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-017-1145-6_10.

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Volz, Karl. "Structural and Functional Conservation in Response Regulators." In Two-Component Signal Transduction, 53–64. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818319.ch4.

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Moreno-Hagelsieb, Gabriel. "Inferring Functional Relationships from Conservation of Gene Order." In Bioinformatics, 181–99. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-429-6_8.

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Moreno-Hagelsieb, Gabriel. "Inferring Functional Relationships from Conservation of Gene Order." In Methods in Molecular Biology, 41–63. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6613-4_3.

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Ruhí, A., D. Boix, J. Sala, S. Gascón, and X. D. Quintana. "Spatial and temporal patterns of pioneer macrofauna in recently created ponds: taxonomic and functional approaches." In Pond Conservation in Europe, 293–307. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-90-481-9088-1_25.

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Bigalke, R. C. "Functional Relationships Between Protected and Agricultural Areas in South Africa and Namibia." In Wildlife Conservation by Sustainable Use, 169–201. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4012-6_9.

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Nagarajan, Aparna, and Robert L. Burnap. "Patterns of Conservation and Divergence of the Photosystem II Complex." In Functional Genomics and Evolution of Photosynthetic Systems, 317–44. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-1533-2_13.

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Hen, René. "Structural and functional conservation of serotonin receptors throughout evolution." In Comparative Molecular Neurobiology, 266–78. Basel: Birkhäuser Basel, 1993. http://dx.doi.org/10.1007/978-3-0348-7265-2_14.

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Gichohi, Helen. "Functional Relationships Between Parks and Agricultural Areas in East Africa: the Case of Nairobi National Park." In Wildlife Conservation by Sustainable Use, 141–67. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4012-6_8.

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Tinoco-Ojanguren, Clara, José L. Andrade, Oscar Briones, and Alejandro E. Castellanos. "Functional Diversity in Plants: Implications for Conservation Issues of the Mexican Biodiversity." In Mexican Natural Resources Management and Biodiversity Conservation, 519–54. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-90584-6_23.

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Conference papers on the topic "Functional conservation"

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Berry, Pam, Robert Dunford, Alison Smith, and Francis Turkelboom. "Multi-functional production systems: from research to practice." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107783.

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Ferreira, Rui Manuel Alves, Isabel Maria Simão Alves-Pereira, Joana Manuela Capela-Pires, and Marta Sofia Garcia Candeias. "Functional and conservation value of fruits - a lab approach." In Sixth International Conference on Higher Education Advances. Valencia: Universitat Politècnica de València, 2020. http://dx.doi.org/10.4995/head20.2020.11082.

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Fruits are a relevant source of phenols and ascorbate, biomolecules which scavenge reactive oxygen species. For this reason, they are considered as healthy for the human being. Fruits quality depends on their levels of antioxidants and enzyme activities that ensure their conservation. The aim of this work was to plan and execute a laboratory class of Enzymology, a discipline of Biochemistry degree of University of Évora, Portugal, for determining the functional and conservation value of three different fruits types, sold in the market of Évora, Portugal. The development of this activity allowed that students of a pilot class participate in a laboratory activity which intended to compare the content of phenols, ascorbate, and polyphenol oxidase enzyme activity present in apple, peach and blueberries pulp. At Lab activity, the students successfully determined markers of functional and conservation value of selected fruits. The skills acquired by the students, in terms of obtaining fruit pulp and their composition in antioxidants, stimulated their commitment degree on the application of biochemistry in the everyday, acquiring thereby significant learning, with a high degree of satisfaction.
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Takács, Péter, Bálint Bánó, and Tibor Erős. "Functional diversity of the Middle-Danubian fish fauna, the role of non-native species." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/108126.

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Elek, Zoltan, Sándor Bérces, Szlavko Ackov, and Peter Odor. "Functional plasticity of ground beetles can presume the changes in their community composition by forestry treatments." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107495.

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Moran Rodas, Virna Estefania. "Influence of vegetation and land use on functional soil conditions and soil erosion in the western coastal plain of El Salvador." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107883.

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Jamieson, Annie. "What Are We Conserving? Functional Conservation for Music Technology in Museums." In Rethinking the History of Technology-based Music. University of Huddersfield, 2022. http://dx.doi.org/10.5920/functionalconservation.

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Keeton, William, Garrett Meigs, Sabina Burrascano, Francesco Sabatini, Miroslav Svoboda, and Georg Gratzer. "European Old-growth Forests in a Global Context: Expanding our Conception of Late-Successional Forests to Account for Structural and Functional Variability." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107326.

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Surnina, E. N., and et al. "Structural and functional features of lettuce plants under dynamic lighting conditions." In Botanical Gardens as Centers for Study and Conservation of Phyto-Diversity. TSU Press, 2020. http://dx.doi.org/10.17223/978-5-94621-956-3-2020-57.

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Yang, Zhenyu, and David Sankoff. "Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters." In 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2011. http://dx.doi.org/10.1109/bibm.2011.54.

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Maiti, Shyantani, and Pralay Mitra. "Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis." In 2018 International Conference on Bioinformatics and Systems Biology (BSB). IEEE, 2018. http://dx.doi.org/10.1109/bsb.2018.8770546.

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Reports on the topic "Functional conservation"

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

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The original objectives of the approved proposal were: 1. To construct a YFP fused Arabidopsis cDNA library in a mammalian expression vector. 2. To infect the library into a host fibroblast cell line and to screen for new cytoskeletal associated proteins using an automated microscope. 3. Isolate the new genes. 4. Characterize their role in plants. The project was approved as a feasibility study to allow proof of concept that would entail building the YFP library and picking up a couple of positive clones using the fluorescent screen. We report here on the construction of the YFP library, the development of the automatic microscope, the establishment of the screen and the isolation of positive clones that are plant cDNAs encoding cytoskeleton associated proteins. The rational underling a screen of plant library in fibroblasts is based on the high conservation of the cytoskeleton building blocks, actin and tubulin, between the two kingdoms (80-90% homology at the level of amino acids sequence). In addition, several publications demonstrated the recognition of mammalian cytoskeleton by plant cytoskeletal binding proteins and vice versa. The major achievements described here are: 1. The development of an automated microscope equipped with fast laser auto-focusing for high magnification and a software controlling 6 dimensions; X, Y position, auto focus, time, color, and the distribution and density of the fields acquired. This system is essential for the high throughput screen. 2. The construction of an extremely competent YFP library efficiently cloned (tens of thousands of clones collected, no empty vectors detected) with all inserts oriented 5't03'. These parameters render it well representative of the whole transcriptome and efficient in "in-frame" fusion to YFP. 3. The strategy developed for the screen allowing the isolation of individual positive cDNA clones following three rounds of microscopic scans. The major conclusion accomplished from the work described here is that the concept of using mammalian host cells for fishing new plant cytoskeletal proteins is feasible and that screening system developed is complete for addressing one of the major bottlenecks of the plant cytoskeleton field: the need for high throughput identification of functionally active cytoskeletal proteins. The new identified plant cytoskeletal proteins isolated in the pilot screen and additional new proteins which will be isolated in a comprehensive screen will shed light on cytoskeletal mediated processes playing a major role in cellular activities such as cell division, morphogenesis, and functioning such as chloroplast positioning, pollen tube and root hair elongation and the movement of guard cells. Therefore, in the long run the screen described here has clear agricultural implications.
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McCoy-Sulentic, Miles, Diane Menuz, and Rebecca Lee. Central Basin and Range Ecoregion Wetland Assessment and Landscape Analysis. Utah Geological Survey, November 2021. http://dx.doi.org/10.34191/ofr-738.

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Wetlands in the arid Central Basin and Range (“Central Basin”) ecoregion of Utah are scarce but provide important functions including critical habitat for wildlife including Species of Greatest Conservation Need and migratory birds, water quality improvement, and recreational and aesthetic values. The Utah Geological Survey (UGS) conducted a study in 2019 and 2020 to better understand the location, type, condition, and potential function of wetlands in the ecoregion. This study focused on areas in the Great Salt Lake and Escalante Desert-Sevier Lake (“Sevier Basin”) HUC6 watersheds within the Central Basin to complement previous work by the UGS that focused on other watersheds in the ecoregion.
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Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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Li, Li, Joseph Burger, Nurit Katzir, Yaakov Tadmor, Ari Schaffer, and Zhangjun Fei. Characterization of the Or regulatory network in melon for carotenoid biofortification in food crops. United States Department of Agriculture, April 2015. http://dx.doi.org/10.32747/2015.7594408.bard.

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The general goals of the BARD research grant US-4423-11 are to understand how Or regulates carotenoid accumulation and to reveal novel strategies for breeding agricultural crops with enhanced β-carotene level. The original objectives are: 1) to identify the genes and proteins in the Or regulatory network in melon; 2) to genetically and molecularly characterize the candidate genes; and 3) to define genetic and functional allelic variation of these genes in a representative germplasm collection of the C. melo species. Or was found by the US group to causes provitamin A accumulation in chromoplasts in cauliflower. Preliminary genetic study from the Israeli group revealed that the melon Or gene (CmOr) completely co-segregated with fruit flesh color in a segregating mapping population and in a wide melon germplasm collection, which set the stage for the funded research. Major conclusions and achievements include: 1). CmOris proved to be the gene that controls melon fruit flesh color and represents the previously described gflocus in melon. 2). Genetic and molecular analyses of CmOridentify and confirm a single SNP that is responsible for the orange and non-orange phenotypes in melon fruit. 3). Alteration of the evolutionarily conserved arginine in an OR protein to both histidine or alanine greatly enhances its ability to promote carotenoid accumulation. 4). OR promotes massive carotenoid accumulation due to its dual functions in regulating both chromoplast biogenesis and carotenoid biosynthesis. 5). A bulk segregant transcriptome (BSRseq) analysis identifies a list of genes associated with the CmOrregulatory network. 6). BSRseq is proved to be an effective approach for gene discovery. 7). Screening of an EMS mutation library identifies a low β mutant, which contains low level of carotenoids due to a mutation in CmOrto produce a truncated form of OR protein. 8). low β exhibits lower germination rate and slow growth under salt stress condition. 9). Postharvest storage of fruit enhances carotenoid accumulation, which is associated with chromoplast development. Our research uncovers the molecular mechanisms underlying the Or-regulated high level of carotenoid accumulation via regulating carotenoidbiosynthetic capacity and storage sink strength. The findings provide mechanistic insights into how carotenoid accumulation is controlled in plants. Our research also provides general and reliable molecular markers for melon-breeding programs to select orange varieties, and offers effective genetic tools for pro-vitamin A enrichment in other important crops via the rapidly developed genome editing technology. The newly discovered low β mutant could lead to a better understanding of the Or gene function and its association with stress response, which may explain the high conservation of the Or gene among various plant species.
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Wright, Kirsten. Collecting Plant Phenology Data In Imperiled Oregon White Oak Ecosystems: Analysis and Recommendations for Metro. Portland State University, March 2020. http://dx.doi.org/10.15760/mem.64.

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Highly imperiled Oregon white oak ecosystems are a regional conservation priority of numerous organizations, including Oregon Metro, a regional government serving over one million people in the Portland area. Previously dominant systems in the Pacific Northwest, upland prairie and oak woodlands are now experiencing significant threat, with only 2% remaining in the Willamette Valley in small fragments (Hulse et al. 2002). These fragments are of high conservation value because of the rich biodiversity they support, including rare and endemic species, such as Delphinium leucophaeum (Oregon Department of Agriculture, 2020). Since 2010, Metro scientists and volunteers have collected phenology data on approximately 140 species of forbs and graminoids in regional oak prairie and woodlands. Phenology is the study of life-stage events in plants and animals, such as budbreak and senescence in flowering plants, and widely acknowledged as a sensitive indicator of environmental change (Parmesan 2007). Indeed, shifts in plant phenology have been observed over the last few decades as a result of climate change (Parmesan 2006). In oak systems, these changes have profound implications for plant community composition and diversity, as well as trophic interactions and general ecosystem function (Willis 2008). While the original intent of Metro’s phenology data-collection was to track long-term phenology trends, limitations in data collection methods have made such analysis difficult. Rather, these data are currently used to inform seasonal management decisions on Metro properties, such as when to collect seed for propagation and when to spray herbicide to control invasive species. Metro is now interested in fine-tuning their data-collection methods to better capture long-term phenology trends to guide future conservation strategies. Addressing the regional and global conservation issues of our time will require unprecedented collaboration. Phenology data collected on Metro properties is not only an important asset for Metro’s conservation plan, but holds potential to support broader research on a larger scale. As a leader in urban conservation, Metro is poised to make a meaningful scientific contribution by sharing phenology data with regional and national organizations. Data-sharing will benefit the common goal of conservation and create avenues for collaboration with other scientists and conservation practitioners (Rosemartin 2013). In order to support Metro’s ongoing conservation efforts in Oregon white oak systems, I have implemented a three-part master’s project. Part one of the project examines Metro’s previously collected phenology data, providing descriptive statistics and assessing the strengths and weaknesses of the methods by which the data were collected. Part two makes recommendations for improving future phenology data-collection methods, and includes recommendations for datasharing with regional and national organizations. Part three is a collection of scientific vouchers documenting key plant species in varying phases of phenology for Metro’s teaching herbarium. The purpose of these vouchers is to provide a visual tool for Metro staff and volunteers who rely on plant identification to carry out aspects of their job in plant conservation. Each component of this project addresses specific aspects of Metro’s conservation program, from day-to-day management concerns to long-term scientific inquiry.
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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.

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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.
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Elias, Emile, Caiti Steele, Kris Havstad, Kerri Steenwerth, Jeanne Chambers, Helena Deswood, Amber Kerr, et al. Assessment of Climate Change Vulnerability and Adaptation and Mitigation Strategies in the Southwest and California. USDA Southwest Climate Hub, October 2017. http://dx.doi.org/10.32747/2017.6965582.ch.

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This report describes the potential vulnerability of specialty crops, field crops, forests, and animal agriculture to climate-driven environmental changes. Here, vulnerability is defined as a function of exposure to climate change effects, sensitivity to these effects, and adaptive capacity. The exposure of specific sectors of the agricultural and forestry industries varies across the region because the Southwest is climatically and topographically diverse. There is also variability in the sensitivity of different systems to the effects of climate change. Most significantly, there is potential within agricultural and forestry systems to adjust to climate-related effects either through inherent resilience or through conservative management practices. The purpose of this analysis is to describe regional vulnerabilities to climate change and adaptive actions that can be employed to maintain productivity of working lands in the coming decades.
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Börjesson, Patrik, Maria Eggertsen, Lachlan Fetterplace, Ann-Britt Florin, Ronny Fredriksson, Susanna Fredriksson, Patrik Kraufvelin, et al. Long-term effects of no-take zones in Swedish waters. Edited by Ulf Bergström, Charlotte Berkström, and Mattias Sköld. Department of Aquatic Resources, Swedish University of Agricultural Sciences, 2023. http://dx.doi.org/10.54612/a.10da2mgf51.

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Marine protected areas (MPAs) are increasingly established worldwide to protect and restore degraded ecosystems. However, the level of protection varies among MPAs and has been found to affect the outcome of the closure. In no-take zones (NTZs), no fishing or extraction of marine organisms is allowed. The EU Commission recently committed to protect 30% of European waters by 2030 through the updated Biodiversity Strategy. Importantly, one third of these 30% should be of strict protection. Exactly what is meant by strict protection is not entirely clear, but fishing would likely have to be fully or largely prohibited in these areas. This new target for strictly protected areas highlights the need to evaluate the ecological effects of NTZs, particularly in regions like northern Europe where such evaluations are scarce. The Swedish NTZs made up approximately two thirds of the total areal extent of NTZs in Europe a decade ago. Given that these areas have been closed for at least 10 years and can provide insights into long-term effects of NTZs on fish and ecosystems, they are of broad interest in light of the new 10% strict protection by 2030 commitment by EU member states. In total, eight NTZs in Swedish coastal and offshore waters were evaluated in the current report, with respect to primarily the responses of focal species for the conservation measure, but in some of the areas also ecosystem responses. Five of the NTZs were established in 2009-2011, as part of a government commission, while the other three had been established earlier. The results of the evaluations are presented in a synthesis and also in separate, more detailed chapters for each of the eight NTZs. Overall, the results suggest that NTZs can increase abundances and biomasses of fish and decapod crustaceans, given that the closed areas are strategically placed and of an appropriate size in relation to the life cycle of the focal species. A meta-regression of the effects on focal species of the NTZs showed that CPUE was on average 2.6 times higher after three years of protection, and 3.8 times higher than in the fished reference areas after six years of protection. The proportion of old and large individuals increased in most NTZs, and thereby also the reproductive potential of populations. The increase in abundance of large predatory fish also likely contributed to restoring ecosystem functions, such as top-down control. These effects appeared after a 5-year period and in many cases remained and continued to increase in the longer term (>10 years). In the two areas where cod was the focal species of the NTZs, positive responses were weak, likely as an effect of long-term past, and in the Kattegat still present, recruitment overfishing. In the Baltic Sea, predation by grey seal and cormorant was in some cases so high that it likely counteracted the positive effects of removing fisheries and led to stock declines in the NTZs. In most cases, the introduction of the NTZs has likely decreased the total fishing effort rather than displacing it to adjacent areas. In the Kattegat NTZ, however, the purpose was explicitly to displace an unselective coastal mixed bottom-trawl fishery targeting Norway lobster and flatfish to areas where the bycatches of mature cod were smaller. In two areas that were reopened to fishing after 5 years, the positive effects of the NTZs on fish stocks eroded quickly to pre-closure levels despite that the areas remained closed during the spawning period, highlighting that permanent closures may be necessary to maintain positive effects. We conclude from the Swedish case studies that NTZs may well function as a complement to other fisheries management measures, such as catch, effort and gear regulations. The experiences from the current evaluation show that NTZs can be an important tool for fisheries management especially for local coastal fish populations and areas with mixed fisheries, as well as in cases where there is a need to counteract adverse ecosystem effects of fishing. NTZs are also needed as reference for marine environmental management, and for understanding the effects of fishing on fish populations and other ecosystem components in relation to other pressures. MPAs where the protection of both fish and their habitats is combined may be an important instrument for ecosystembased management, where the recovery of large predatory fish may lead to a restoration of important ecosystem functions and contribute to improving decayed habitats. With the new Biodiversity Strategy, EUs level of ambition for marine conservation increases significantly, with the goal of 30% of coastal and marine waters protected by 2030, and, importantly, one third of these areas being strictly protected. From a conservation perspective, rare, sensitive and/or charismatic species or habitats are often in focus when designating MPAs, and displacement of fisheries is then considered an unwanted side effect. However, if the establishment of strictly protected areas also aims to rebuild fish stocks, these MPAs should be placed in heavily fished areas and designed to protect depleted populations by accounting for their home ranges to generate positive outcomes. Thus, extensive displacement of fisheries is required to reach benefits for depleted populations, and need to be accounted for e.g. by specific regulations outside the strictly protected areas. These new extensive EU goals for MPA establishment pose a challenge for management, but at the same time offer an opportunity to bridge the current gap between conservation and fisheries management.
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Friedman, Haya, Julia Vrebalov, James Giovannoni, and Edna Pesis. Unravelling the Mode of Action of Ripening-Specific MADS-box Genes for Development of Tools to Improve Banana Fruit Shelf-life and Quality. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592116.bard.

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Fruit deterioration is a consequence of a genetically-determined fruit ripening and senescence programs, in which developmental factors lead to a climacteric rise of ethylene production in ethylene-sensitive fruits such as tomato and banana. Breeding of tomato with extended fruit shelf life involves the incorporation of a mutation in RIN, a MADS-box transcription factor participating in developmental control signalling of ripening. The RIN mode of action is not fully understood, and it may be predicted to interact with other MADS-box genes to execute its effects. The overall goal of this study was to demonstrate conservation of ripening control functions between banana and tomato and thus, the potential to genetically extend shelf-life in banana based on tools developed in tomato. The specific objectives were: 1. To increase the collection of potential RIN-like genes from banana; 2. To verify their action as developmental regulators; 3. To elucidate MADS-box gene mode of action in ripening control; 4. To create transgenic banana plants that express low levels of endogenous Le-RIN- like, MaMADS- gene(s). We have conducted experiments in banana as well as in tomato. In tomato we have carried out the transformation of the tomato rin mutant with the MaMADS1 and MaMADS2 banana genes. We have also developed a number of domain swap constructs to functionally examine the ripening-specific aspects of the RIN gene. Our results show the RIN-C terminal region is essential for the gene to function in the ripening signalling pathway. We have further explored the tomato genome databases and recovered an additional MADS-box gene necessary for fruit ripening. This gene has been previously termed TAGL1 but has not been functionally characterized in transgenic plants. TAGL1 is induced during ripening and we have shown via RNAi repression that it is necessary for both fleshy fruit expansion and subsequent ripening. In banana we have cloned the full length of six MaMADS box genes from banana and determined their spatial and temporal expression patterns. We have created antibodies to MaMADS2 and initiated ChI assay. We have created four types of transgenic banana plants designed to reduce the levels of two of the MaMADS box genes. Our results show that the MaMADS-box genes expression in banana is dynamically changing after harvest and most of them are induced at the onset of the climacteric peak. Most likely, different MaMADS box genes are active in the pulp and peel and they are differently affected by ethylene. Only the MaMADS2 box gene expression is not affected by ethylene indicating that this gene might act upstream to the ethylene response pathway. The complementation analysis in tomato revealed that neither MaMADS1 nor MaMADS2 complement the rin mutation suggesting that they have functionally diverged sufficiently to not be able to interact in the context of the tomato ripening regulatory machinery. The developmental signalling pathways controlling ripening in banana and tomato are not identical and/or have diverged through evolution. Nevertheless, at least the genes MaMADS1 and MaMADS2 constitute part of the developmental control of ripening in banana, since transgenic banana plants with reduced levels of these genes are delayed in ripening. The detailed effect on peel and pulp, of these transgenic plants is underway. So far, these transgenic bananas can respond to exogenous ethylene, and they seem to ripen normally. The response to ethylene suggest that in banana the developmental pathway of ripening is different than that in tomato, because rin tomatoes do not ripen in response to exogenous ethylene, although they harbor the ethylene response capability This study has a major contribution both in scientific and agricultural aspects. Scientifically, it establishes the role of MaMADS box genes in a different crop-the banana. The developmental ripening pathway in banana is similar, but yet different from that of the model plant tomato and one of the major differences is related to ethylene effect on this pathway in banana. In addition, we have shown that different components of the MaMADS-box genes are employed in peel and pulp. The transgenic banana plants created can help to further study the ripening control in banana. An important and practical outcome of this project is that we have created several banana transgenic plants with fruit of extended shelf life. These bananas clearly demonstrate the potential of MaMADS gene control for extending shelf-life, enhancing fruit quality, increasing yield in export systems and for improving food security in areas where Musaspecies are staple food crops.
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Elroy-Stein, Orna, and Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, December 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated synthesis of multiple gene products from a single transcription unit, and thereby enables to bypass the need for sequential transformation with multiple independent transgenes. The key goal of this project was to identify and analyze the IRES-trans-acting factors (ITAFs) that mediate the activity of a crucifer-infecting tobamovirus (crTMV148) IRES. The remarkable conservation of the IRES activity across the phylogenetic spectrum (yeast, plants and animals) strongly suggests that key ITAFs that mediate its activity are themselves highly conserved. Thus, crTMV148 IRES offers opportunity for elucidation of the fundamental mechanisms underlying internal translation in higher plants in order to enable its rational manipulation for the purpose of agricultural biotechnology. Major conclusions and achievements. - CrTMV IRES requires PABP for maximal activity. This conclusion was achieved by PABP depletion and reconstitution of wheat germ- and Krebs2-derived in-vitro translation assays using Arabidopsis-derived PABP2, 3, 5, 8 and yeast Pab1p. - Mutations in the internal polypurine tract of the IRES decrease the high-affinity binding of all phylogenetically divergent PABPs derived from Arabidopsis and yeast in electro mobility gel shift assays. - Mutations in the internal polypurine tract decrease IRES activity in-vivo. - The 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap. - In-vivo assembled RNPs containing proteins specifically associated with the IRES were purified from HEK293 cells using the RNA Affinity in Tandem (RAT) approach followed by their identification by mass spectroscopy. - This study yielded a list of potential protein candidates that may serve as ITAFs of crTMV148 IRES activity, among them are a/b tubulin, a/g actin, GAPDH, enolase 1, ribonuclease/angiogenin inhibitor 1, 26S proteasome subunit p45, rpSA, eEF1Bδ, and proteasome b5 subunit. Implications, both scientific and agriculture. The fact that the 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap suggests a potential joint interaction between PABP, the IRES sequence and the 3'-poly(A). This has an important scientific implication related to IRES function in general.
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