Готові списки джерел за темами / Environmental genomic

Добірка наукової літератури з теми "Environmental genomic"

Автор: Grafiati

Опубліковано: 7 липня 2024

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Статті в журналах з теми "Environmental genomic":

Zhao, Hao‐Qian, Wen‐Qing Wei, Chao Zhao, and Ze‐Xiong Xie. "Genomic markers on synthetic genomes." Engineering in Life Sciences 21, no. 12 (November 10, 2021): 825–31. http://dx.doi.org/10.1002/elsc.202100030.

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Greer, Charles W. "Genomic Technologies for Environmental Science." Soil and Sediment Contamination: An International Journal 11, no. 3 (May 2002): 403–8. http://dx.doi.org/10.1080/20025891106835.

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Kappil, Maya, Luca Lambertini, and Jia Chen. "Environmental Influences on Genomic Imprinting." Current Environmental Health Reports 2, no. 2 (May 1, 2015): 155–62. http://dx.doi.org/10.1007/s40572-015-0046-z.

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Heidelberg, Karla B., and John F. Heidelberg. "Marine Environmental Genomics: New Secrets from a Mysterious Ocean." Marine Technology Society Journal 39, no. 3 (September 1, 2005): 94–98. http://dx.doi.org/10.4031/002533205787442549.

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Ocean microbes play critical roles in ecosystem dynamics and biogeochemical cycles. For a number of reasons, these organisms have been hard to study; among other characteristics, they are difficult or maybe impossible to culture. The recent application of cultivation-independent genomic techniques to study bacterial communities has begun to fundamentally change our views of microbial ecology and function. These approaches are providing more comprehensive insights into the structure and function of natural assemblages of microbial populations. Genomics-based technologies are revealing previously unknown groups of microorganisms and novel metabolic pathways, leading to a deeper appreciation of the fundamental genetic and potential functional diversity of ocean microbes. When evaluated in the context of observed ecosystem functions, we can begin to understand the complex interactions of individuals and populations with their physical and chemical environment. The continuing study and interpretation of the community genomic data will require a close synergy among interdisciplinary researchers working throughout the world's ocean basins. Community genomic approaches have and will become a powerful tool for understanding marine microbial ecology in the future.

Orsini, Luisa, Ellen Decaestecker, Luc De Meester, Michael E. Pfrender, and John K. Colbourne. "Genomics in the ecological arena." Biology Letters 7, no. 1 (August 11, 2010): 2–3. http://dx.doi.org/10.1098/rsbl.2010.0629.

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This meeting report presents the cutting-edge research that is developing around the waterflea Daphnia , an emerging model system in environmental genomics. Daphnia has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the Daphnia Genomics Consortium (DGC), Daphnia is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.

Mani, Ram-Shankar, and Arul M. Chinnaiyan. "Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences." Nature Reviews Genetics 11, no. 12 (November 3, 2010): 819–29. http://dx.doi.org/10.1038/nrg2883.

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Jirtle, R. L., M. Sander, and J. C. Barrett. "Genomic imprinting and environmental disease susceptibility." Environmental Health Perspectives 108, no. 3 (March 2000): 271–78. http://dx.doi.org/10.1289/ehp.00108271.

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Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M. Westram, and Roger K. Butlin. "Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast." Science Advances 5, no. 12 (December 2019): eaav9963. http://dx.doi.org/10.1126/sciadv.aav9963.

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The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.

Mani, Ram-Shankar, and Arul M. Chinnaiyan. "Erratum: Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences." Nature Reviews Genetics 12, no. 2 (January 18, 2011): 150. http://dx.doi.org/10.1038/nrg2953.

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STANOJEVIĆ, Dragan, Radica Ć. ĐEDOVIĆ, and Nikolija GLIGOVIĆ. "GENOMICS AS A TOOL FOR IMPROVING DAIRY CATTLE POPULATIONS." "Annals of the University of Craiova - Agriculture Montanology Cadastre Series " 53, no. 1 (December 30, 2023): 291–97. http://dx.doi.org/10.52846/aamc.v53i1.1479.

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The dairy industry plays a pivotal role in meeting the global demand for high-quality milk and dairy products. To address the ever-increasing need for efficient and productive dairy cattle populations, the integration of genomics has emerged as a transformative tool. Genomic selection, a revolutionary advancement in cattle breeding, has allowed for the identification of superior individuals at an early age based on their genetic potential. Genomic selection has not only accelerated genetic progress but has also minimized generation intervals, leading to more efficient breeding programs. Furthermore, the incorporation of genomic data in selection decisions has increased the accuracy of breeding values, ultimately resulting in the production of dairy cattle with improved milk yield, fertility, and disease resistance. Beyond traditional breeding goals, genomics has also enabled the identification of genetic variants associated with traits that are difficult to measure, such as feed efficiency, heat tolerance, and environmental adaptability. By deciphering the genetic basis of these traits, it is now possible to develop breeding strategies that enhance the resilience of dairy cattle populations in the face of changing environmental conditions. This paper also explores the role of genomics in addressing health and welfare concerns within the dairy industry. Genetic markers associated with susceptibility to diseases and stress-related conditions have been identified, providing opportunities to select for healthier and more resilient animals. Furthermore, genomics has opened avenues for tailoring nutritional strategies to individual cattle based on their genetic predispositions, optimizing feed efficiency and reducing environmental impacts. The utilization of genomic data is not limited to breeding and production. Genomics has facilitated the development of innovative tools for managing dairy cattle populations. Precision management, including genomic-based early disease detection and personalized healthcare, is becoming increasingly viable, enhancing animal welfare and reducing production losses. In conclusion, genomics has revolutionized dairy cattle breeding and management by providing accurate and efficient tools for selecting animals with superior genetic potential, improving production, health, and welfare, and enhancing the overall sustainability of dairy cattle populations. As genomics continues to evolve, the dairy industry stands to benefit from a more precise and sustainable approach to cattle production, ensuring a resilient and productive future for the dairy sector.

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Дисертації з теми "Environmental genomic":

Yang, Bin, and 杨彬. "A novel framework for binning environmental genomic fragments." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B45789344.

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Jackson, Colin John. "The typing and environmental detection of Campylobacter jejuni." Thesis, Manchester Metropolitan University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262007.

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Herzog, Rebecca [Verfasser]. "Global change genomics - comparative genomic analyses on environmental associated speciation and adaptation processes in Odonata / Rebecca Herzog." Hannover : Gottfried Wilhelm Leibniz Universität, 2021. http://d-nb.info/1238221785/34.

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Finke, Jan Felix. "Environmental and genomic insights into marine virus populations and communities." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/61997.

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The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.
Science, Faculty of
Earth, Ocean and Atmospheric Sciences, Department of
Graduate

Chan, Yu-ki, and 陳裕琪. "Environmental genomic analysis of refuge habitats in hyper-arid deserts." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46917366.

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Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.

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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host. The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population. With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.

Gray, Miranda M. "Genomic differentiation of big bluestem (Andropogon gerardii) along the Great Plains’ environmental gradient." Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/14626.

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Master of Science
Department of Plant Pathology
Eduard D. Akhunov
Loretta C. Johnson
Big bluestem (Andropogon gerardii Vitman) is an ecologically dominant grass of the North American grasslands with precipitation-dependent productivity. However, climatic predictions for big bluestem’s dominant range in the Great Plains include increased periods of drought. The main objectives of this research were to determine the extent of neutral and non-neutral genetic differentiation and diversity among putative big bluestem ecotypes using amplified fragment length polymorphism (AFLP) markers. This is the first study of both neutral and non-neutral genetic diversity of big bluestem which also includes source populations of well-described ecotypes studied in reciprocal common gardens. A total of 378 plants were genotyped from 11 source prairies, originating from one of three ecoregions (Central Kansas, Eastern Kansas, and Illinois). Using two AFLP primer sets, 387 polymorphic markers (error rate 9.18%) were found. Un-rooted neighbor joining tree and principle-component analyses showed continuous genetic differentiation between Kansas and Illinois putative ecotypes, with genetic overlap occurring between Kansas ecotypes. Analysis of molecular variance showed high diversity within-prairie sites (80%) relative to across-prairies (11%), and across- ecoregions (9%) (p<0.001). Within-prairie genetic diversity levels were similar among ecoregions (84-92%), with the highest genetic variation maintained in Illinois prairies (92%). Population structure analyses supported K=6 genetic clusters across the environmental gradient, with Kansas prairies belonging to three main genetic groups, and Illinois prairies having largely divergent allele frequencies from Kansas prairies. Interestingly, BAYESCAN analysis of the three putative ecotypes identified eight F[subscript]ST-outlier AFLP loci under potential diversifying selection. Frequency patterns of loci under diversifying selection were further linked to geo-environmental descriptors including precipitation, temperature severity, diurnal temperature variation, prairie location, and elevation. The observed allele frequency divergence between Kansas and Illinois ecotypes suggests tallgrass restorations should consider possible maladaptation of non-local ecotypes and genetic swamping. However, high within-prairie genetic variation may help individual big bluestem populations withstand climatic variability.

Curreem, Oi-ting Shirly. "The study of environmental adaptability of laribacter hongkongensis by genomic and proteomic approach." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43931686.

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Braff, Jennifer C. "Construction and phenotypic screening of mid-size insert marine microbial environmental genomic libraries." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43722.

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Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2008.
Includes bibliographical references (leaves 52-56).
Functional screening of environmental genomic libraries permits the identification of clones expressing activities of interest without requiring prior knowledge of the genes responsible. In this study, protocols were optimized for the construction of mid-size DNA insert, inducible expression environmental genomic plasmid libraries for this purpose. A library with a mean insert size of 5.2 kilobases was constructed with environmental DNA isolated from surface ocean water collected at Hawaii Ocean Time-series station ALOHA in plasmid cloning vector pMCL200 under the inducible control of the PLAC promoter. To begin to evaluate the utility of such libraries for gene expression-based screens, this library was screened phenotypically for clones expressing genes that confer fluorescence or distinctive coloration on colonies of host Escherichia coli cells, and results were compared to those for a fosmid library constructed from the same marine microbial DNA sample. Ecologically relevant sequences were identified in both libraries, and each was observed to offer both advantages and disadvantages. Results of this study suggest that mid-size insert plasmid libraries under the control of inducible promoters can provide a useful and complementary approach for both functional screening and shotgun sequencing of environmental genomic libraries.
by Jennifer C. Braff.
S.M.

Tsai, Yeng-Chieh. "The application of two-dimensional genomic DNA nylon matrix for environmental samples analysis." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 67 p, 2009. http://proquest.umi.com/pqdweb?did=1654501591&sid=1&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Книги з теми "Environmental genomic":

Dick, Gregory. Genomic Approaches in Earth and Environmental Sciences. Chichester, UK: John Wiley & Sons, Ltd, 2018. http://dx.doi.org/10.1002/9781118708231.

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Pool, Robert. Environmental contamination, biotechnology, and the law: The impact of emerging genomic information. Washington, D.C: National Academy Press, 2001.

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Greated, Alicia. The IncP-9 plasmid group: Characterisation of genomic sequences and development of tools for environmental monitoring. Birmingham: University of Birmingham, 2000.

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Martin, C. Cristofre, and C. Cristofre Martin, eds. Environmental Genomics. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-548-0.

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Cristofre, Martin C., ed. Environmental genomics. Totowa, N.J: Humana, 2007.

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Bridge, Paul, David Smith, and Erko Stackebrandt, eds. Trends in the systematics of bacteria and fungi. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0000.

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Abstract There are fundamental differences between the current levels of genomic and proteomic knowledge for bacteria and fungi. With multiple growth forms and over 100,000 known species, the fungi probably present a more complex situation, but genomic studies are hindered by the lack of reliable reference data for many species. As activities such as environmental sampling, and genomic and proteomic profiling, become more important in extending our understanding of ecosystems, there is an increasing imperative for researchers in microbial systematics to develop the methods and concepts required to interpret the information being generated. This volume presents a collection of chapters that provide some insights into how current methods and resources are being used in microbial systematics, together with some thoughts and suggestions about how both methodologies and concepts may develop in the future.

Martin, Francis, and Stephane Uroz, eds. Microbial Environmental Genomics (MEG). New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3369-3.

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Martin, Francis, and Stephane Uroz, eds. Microbial Environmental Genomics (MEG). New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2871-3.

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Cellura, A. Raymond. The genomic environment and niche-experience. Abbeville, SC: Cedar Springs Press, 2004.

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Cellura, A. Raymond. The genomic environment and niche-experience. Abbeville, SC: Cedar Springs Press, 2005.

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Частини книг з теми "Environmental genomic":

Rajesh, Thangamani, Jeyaprakash Rajendhran, and Paramasamy Gunasekaran. "Genomic Technologies in Environmental Bioremediation." In Microorganisms in Environmental Management, 701–18. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2229-3_31.

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Shintani, Masaki, and Kazuhide Kimbara. "Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders." In Manual of Environmental Microbiology, 5.1.1–1–5.1.1–10. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555818821.ch5.1.1.

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Ahrendt, Steven R., Stephen J. Mondo, Sajeet Haridas, and Igor V. Grigoriev. "MycoCosm, the JGI’s Fungal Genome Portal for Comparative Genomic and Multiomics Data Analyses." In Microbial Environmental Genomics (MEG), 271–91. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2871-3_14.

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Sobti, RC, Apurav Sharma, and Sanjeev Kumar Soni. "Applications of Biotechnological Techniques in Mitigating Environmental Concerns." In Genomic, Proteomics, and Biotechnology, 249–312. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003220831-17.

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Dubrova, Yuri E. "Genomic Instability in the Offspring of Irradiated Parents." In Radiobiology and Environmental Security, 127–39. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-1939-2_12.

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Balkenhol, Niko, Rachael Y. Dudaniec, Konstantin V. Krutovsky, Jeremy S. Johnson, David M. Cairns, Gernot Segelbacher, Kimberly A. Selkoe, et al. "Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations." In Population Genomics, 261–322. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/13836_2017_2.

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Yang, T. C., M. Durante, K. A. George, and S. Yamada. "Genomic Alterations in Radiogenic Cell Transformation." In Fundamentals for the Assessment of Risks from Environmental Radiation, 281–88. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4585-5_36.

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Ramanand, Susmita G., and Ram S. Mani. "Genetic, Environmental, and Nuclear Factors Governing Genomic Rearrangements." In Advances in Experimental Medicine and Biology, 57–66. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-32656-2_3.

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Gürgan, Muazzez, Eylül İrem İrez, and Sevinç Adiloğlu. "Understanding Bioremediation of Metals and Metalloids by Genomic Approaches." In Omics Insights in Environmental Bioremediation, 375–92. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-4320-1_16.

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Habyarimana, Ephrem, and Sofia Michailidou. "Genomic Prediction and Selection in Support of Sorghum Value Chains." In Big Data in Bioeconomy, 207–18. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-71069-9_16.

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AbstractGenomic prediction and selection models (GS) were deployed as part of DataBio project infrastructure and solutions. The work addressed end-user requirements, i.e., the need for cost-effectiveness of the implemented technologies, simplified breeding schemes, and shortening the time to cultivar development by selecting for genetic merit. Our solutions applied genomic modelling in order to sustainably improve productivity and profits. GS models were implemented in sorghum crop for several breeding scenarios. We fitted the best linear unbiased predictions data using Bayesian ridge regression, genomic best linear unbiased predictions, Bayesian least absolute shrinkage and selection operator, and BayesB algorithms. The performance of the models was evaluated using Monte Carlo cross-validation with 70% and 30%, respectively, as training and validation sets. Our results show that genomic models perform comparably with traditional methods under single environments. Under multiple environments, predicting non-field evaluated lines benefits from borrowing information from lines that were evaluated in other environments. Accounting for environmental noise and other factors, also this model gave comparable accuracy with traditional methods, but higher compared to the single environment model. The GS accuracy was comparable in genomic selection index, aboveground dry biomass yield and plant height, while it was lower for the dry mass fraction of the fresh weight. The genomic selection model performances obtained in our pilots are high enough to sustain sorghum breeding for several traits including antioxidants production and allow important genetic gains per unit of time and cost.

Тези доповідей конференцій з теми "Environmental genomic":

Afanasyeva, K. P., A. N. Rusakovich, N. E. Kharchenko, I. D. Aleksandrov, and M. V. Aleksandrova. "GENOMIC CHANGES IN THE PROGENY OF DROSOPHILA MELANOGASTER MALES IRRADIATED BY y-RAYS." In SAKHAROV READINGS 2022: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2022. http://dx.doi.org/10.46646/sakh-2022-1-328-331.

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The results of sequencing and bioinformatics analysis of genomic changes in 9 F1 progeny of males from the isogenic line D. melanogaster irradiated by Co60 Y—rays at a dose of 40 Gy (LD85) and in 3 control samples are presented. In 9 progeny from irradiated males, a total of 46 genomic changes (32 significant and 15 mosaic de novo mutations) were found, which is equal to a frequency of 5.2 mutations/genome. The spectrum of changes included 33 deletions (17-78 000 bp in size), 4 duplications (322-1371 bp), 4 reciprocal translocations and 6 inversions in X, 2 and 3 chromosomes. In 3 studied control samples, 2 deletions (98 and 128 bp in length) were found in 3 chromosome (frequency - 0.66 mutations/genome). This shows that in the progeny of irradiated males, the frequency of de novo mutations at the genome level is 7.9 times higher than in the control, even without taking into account base substitutions and indels, the analysis of which is ongoing. Almost half of the identified structural changes in the genome affect coding genes. Thus, the results show that next-generation genome sequencing can detect a much wider range of mutations of any size. This indicates a much higher genetic hazard of sparsely ionizing radiation than previously thought.

Singer, William, Bo Zhang, Dajun Yu, David Holshouser, Haibo Huang, Keren Brooks, Maria Rosso, and Mark Reiter. "Evaluating Breeding and Management Solutions for Methionine Content in Soybean." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/qvdx5082.

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Soybean is widely recognized as a valuable crop and plant protein source due to its ideal amino acid profile. However, deficient methionine content in soybean seeds limits the nutritional utility. Therefore, a genome-wide association study (GWAS) utilizing 311 soybean accessions from maturity groups IV and V was performed alongside genomic prediction models to determine genetic underpinnings and breeding potential. Additionally, sulfur fertilization source and rate were evaluated for their impact on methionine content in soybean seeds. Across four environments, 23 novel single nucleotide polymorphisms (SNPs) were identified as being associated with methionine content, and average prediction accuracy (r2) ranged from 0.03 to 0.62 for genomic prediction models. Across six locations, soybean plots treated with ammonium sulfate (AMS) exhibited statistically increased methionine content when compared to other sulfur fertilizers. When combined, these results highlight the complex genetic and environmental controls for methionine content in soybean seeds and will positively contribute to protein quality improvement in soybean.

Ding, G. H., X. Han, Z. D. Xu, X. X. Jin, C. Y. Chi, and B. D. Liu. "Preliminary report about genomic methylation of twoIva xanthifoliapopulations using MSAP method." In International Conference on Environmental Science and Biological Engineering. Southampton, UK: WIT Press, 2014. http://dx.doi.org/10.2495/esbe140851.

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Dudaniec, Rachael. "Genomic adaptation along an environmental gradient in range-expanding damselflies(Ischnura elegans)." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.93376.

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Boughattas, Sonia, Dana Al Batesh, Bruno Giraldes, Asmaa Al-Thani, and Fatiha Benslimane. "Optimized DNA Extracting Method for Oxford Nanopore- Long reads Sequencing from Marine samples." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0136.

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Sustaining social and economic growth is impossible without a holistic environmental vision that places environmental preservation for Qatar’s future generations at the forefront. According to the Ministry of Development and Planning and Statistics, the Qatar National Vision (QNV) 2030 aims to direct Qatar towards a balance between developmental needs and the protection of its natural environment, whether land, sea or air. As such, the QNV 2030 includes an emphasis on establishing environmental institutions that can serve as the guardians of Qatar’s environmental heritage. The QNV 2030 also emphasizes the importance of increasing citizens’ awareness of their role in protecting the country’s environment for their children and the nation’s future generations. The State of Qatar has chosen to pursue the path of sustainable development, making it the focus of the Qatar National Development Strategy. Given the large-scale industrialization and the limited land availability, the urban environment will be crucial in maintaining native species. The presence of heavy petrochemical firms in Qatar necessitates stressing on researches related to biomonitoring of environmental ecosystem with the aim to understand and provide impactful solution for different environmental challenges affecting Qatari health, and damages to local ecosystem. Due to the extreme temperatures and salinities in the Gulf region, the national biodiversity has adapted to survive under extreme conditions. Furthermore, the barriers that isolate the Arabian Gulf have created an environment that is rich with endemic species that are specific to the region. As such, this project aimed to cover the gap in the genomic analysis of Qatar’s rich environment. The goal was to decipher the genetic background of different animal species, marine and environmental species specific to the Qatari environmental landscape that has been previously described by Qatar University’s environmental science center. The study also deciphered the microflora in marine environment that is an important building block of the environment and an indicator of its richness. The outcome from this study is to help in preservation of important species in Qatar and will guide the establishment of a national genomic habitat platform in Qatar

Reva, Oleg N., and Oliver Bezuidt. "Visualization of Distribution of Pathogenicity Genomic Islands between Pathogenic, Nosocomial and Environmental Bacteria." In 2012 16th International Conference on Information Visualisation (IV). IEEE, 2012. http://dx.doi.org/10.1109/iv.2012.98.

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Petrosyan, M. S., and L. S. Nersesova. "THE EFFECT OF CREATINE AS DIETARY SUPPLEMENT ON GENOMIC INSTABILITY OF MONONUCLEAR CELLS OF PERIFERAL BLOOD AND HEPATOCYTES OF RATS IMPACTED BY X-RAY RADIATION." In SAKHAROV READINGS 2021: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute, 2021. http://dx.doi.org/10.46646/sakh-2021-1-310-313.

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The effect of creatine (Cr) as a dietary supplement (creatine monohydrate in a 0.9% glucose solution per os at the 1g/kg of rat weight dosage, for two weeks prior to and two weeks after the irradiation) on the post-radiation DNA damage of peripheral blood mononuclear cells and the distribution disorders per rats’ hepatocyte ploidy, induced by the total one-time irradiation in the dosage of 4,5 and 6.5 Gy, has been studied. The results have demonstrated that Cr has a protective effect per the parameters observed, which helps reduce the radiation-induced genomic instability of the respective cells, thus testifying to the radioprotective activity of Cr.

Makanjuola, B. O., G. Rovere, B. C. D. Cuyabano, S. H. Lee, and C. Gondro. "283. Including environmental variables in genomic models for carcass traits in Hanwoo beef cattle." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_283.

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Yang, Bin, Yu Peng, Henry C. M. Leung, S. M. Yiu, J. C. Chen, and Francis Y. L. Chin. "Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers." In Proceeding of the third international workshop. New York, New York, USA: ACM Press, 2009. http://dx.doi.org/10.1145/1651318.1651322.

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M, HAMED, HELMS V, and ZAPP A. "SnvDMiR Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions." In Second International Conference on Advances in Bio-Informatics and Environmental Engineering - ICABEE 2015. Institute of Research Engineers and Doctors, 2015. http://dx.doi.org/10.15224/978-1-63248-043-9-127.

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Звіти організацій з теми "Environmental genomic":

Holden, Lindsay. Investigating the Role of Genomic Variation in Susceptibility to Environmental Chemicals across Populations. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.6255.

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Gabrielle N. Pecora, Francine C. Reid, Lauren M. Tom, Yvette M. Piceno, and Gary L. Andersen. DNA Everywhere. A Guide for Simplified Environmental Genomic DNA Extraction Suitable for Use in Remote Areas. Office of Scientific and Technical Information (OSTI), May 2016. http://dx.doi.org/10.2172/1249500.

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Seroussi, E., L. Ma, and G. Liu. Genetic analyses of recombination and PRDM9 alleles and their implications in dairy cattle breeding. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134158.bard.

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Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, it is not well studied in livestock including cattle. The general objectives of this project were to perform genetic analyses of recombination and PRDM9 alleles and study their implications in dairy cattle breeding. The specific objectives were: 1. Analyze variation in recombination across individuals, breeds, and environments; 1.1.Construct individual-level recombination maps; 1.2.Compare recombination features between bulls held under different environmental conditions in US and Israeli; 2. Examine genetic basis of recombination variation in cattle; 2.1.Characterize PRDM9 alleles and their impacts on total and locus-specific recombination features; 2.2.Validate pedigree-based recombination maps using single sperm sequencing and typing; 3. Investigate the impacts of recombination on dairy cattle breeding; 3.1.Evaluate correlation between recombination and dairy production and health traits; 3.2.Evaluate the benefits of incorporating recombination as novel quantitative trait into genomic selection scheme.

Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.

Dudareva, Natalia, Alexander Vainstein, Eran Pichersky, and David Weiss. Integrating biochemical and genomic approaches to elucidate C6-C2 volatile production: improvement of floral scent and fruit aroma. United States Department of Agriculture, September 2007. http://dx.doi.org/10.32747/2007.7696514.bard.

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The specific objectives of approved proposal include to: 1. Elucidate the C6-C2 biochemical pathways leading to the biosynthesis of phenylacetaldehyde, phenylethyl alcohol and phenylethyl acetate in floral tissues of ornamentally important plants, pefunia and roses. 2. Isolate and characterrze genes responsible for the production of these C6-C2 compounds and those involved in the regulation of the pathway using genomic and transcriptomic tools. 3. Determine whether altering the expression of key genes of this pathway can result in changing the aroma characteristics of flowers. Aldehydes are intermediates in a variety of biochemical pathways including those involved in the metabolism of carbohydrates, vitamins, steroids, amino acids, benzylisoquinoline alkaloids, hormones, and lipids. In plants they are also synthesized in response to environmental stresses such as salinity, cold, and heat shock or as flavors and aromas in fruits and flowers. Phenylacetaldehyde along with 2-phenylethanol and its acetate ester, are important scent compounds in numerous flowers, including petunias and roses. However, little is known about the biosynthesis of these volatile compounds in plants. We have shown that the formation PHA and 2-phenylethanol from Phe does not occur via trans-cinnamic acid and instead competes with the key enzyme of phenypropanoid metabolism Pheammonia-lyase (PAL) for Phe utilization. Using functional genomic approach and comparative gene expression profiling, we have isolated and characterized a novel enzyme from petunia and rose flowers that catalyzes the formation of the Ca-Czcompound phenylacetaldehyde (PHA) from L-phenylalanine (Phe) by the removal of both the carboxyl and amino groups. This enzyme, designated as phenylacetaldehyde synthases (PAAS), is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts. Down-regulation of PAAS expression via RNA interference-based (RNAi) technology in petunia resulted in no PHA emission when compared with controls. These plants also produced no 2-phenylethanol, supporting our conclusion that PHA is a precursor of 2-phenylethanol. To understand the regulation of scent formation in plants we have also generated transgenic petunia and tobacco plants expressing the rose alcohol acetyltransferase (RhAAT) gene under the control of a CaMV-35S promoter. Although the preferred substrate of RhAAT in vitro is geraniol, in transgenic petunia flowers, it used phenylethyl alcohol and benzyl alcohol to produce the corresponding acetate esters, not generated by control flowers. These results strongly point to the dependence of volatile production on substrate availability. Analysis of the diurnal regulation of scent production in rose flowers revealed that although the daily emission of most scent compounds is synchronized, various independently evolved mechanisms control the production, accumulation and release of different volatiles. This research resulted in a fundamental discovery of biochemical pathway, enzymes and genes involved in biosynthesis of C6-C2s compounds, and provided the knowledge for future engineering plants for improved scent quality.

Seale, Maria, R. Salter, Natàlia Garcia-Reyero,, and Alicia Ruvinsky. A fuzzy epigenetic model for representing degradation in engineered systems. Engineer Research and Development Center (U.S.), September 2022. http://dx.doi.org/10.21079/11681/45582.

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Degradation processes are implicated in a large number of system failures, and are crucial to understanding issues related to reliability and safety. Systems typically degrade in response to stressors, such as physical or chemical environmental conditions, which can vary widely for identical units that are deployed in different places or for different uses. This situational variance makes it difficult to develop accurate physics-based or data-driven models to assess and predict the system health status of individual components. To address this issue, we propose a fuzzy set model for representing degradation in engineered systems that is based on a bioinspired concept from the field of epigenetics. Epigenetics is concerned with the regulation of gene expression resulting from environmental or other factors, such as toxicants or diet. One of the most studied epigenetic processes is methylation, which involves the attachment of methyl groups to genomic regulatory regions. Methylation of specific genes has been implicated in numerous chronic diseases, so provides an excellent analog to system degradation. We present a fuzzy set model for characterizing system degradation as a methylation process based on a set-theoretic representation for epigenetic modeling of engineered systems. This model allows us to capture the individual dynamic relationships among a system, environmental factors, and state of health.

Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.

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The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)

Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.

Abbott, Albert G., Doron Holland, Douglas Bielenberg, and Gregory Reighard. Structural and Functional Genomic Approaches for Marking and Identifying Genes that Control Chilling Requirement in Apricot and Peach Trees. United States Department of Agriculture, September 2009. http://dx.doi.org/10.32747/2009.7591742.bard.

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Structural and functional genomic approaches for marking and identifying genes that control chilling requirement in apricot and peach trees. Specific aims: 1) Identify and characterize the genetic nature of chilling requirement for flowering and dormancy break of vegetative shoots in Prunusgermplasm through the utilization of existing apricot (NeweYa'ar Research Center, ARO) and peach (Clemson University) genetic mapping populations; 2) Use molecular genetic mapping techniques to identify markers flanking genomic regions controlling chilling; 3) Comparatively map the regions controlling chilling requirement in apricot and peach and locate important genomic regions influencing chilling requirement on the Prunus functional genomic database as an initial step for identification of candidate genes; 4) Develop from the functional genomics database a set of markers facilitating the development of cultivars with optimized chilling requirements for improved and sustained fruit production in warm-winter environments. Dormant apricot (prunus armeniaca L.) and peach [Prunus persica (L.) Batsch] trees require sustained exposure to low, near freezing, temperatures before vigorous floral and vegetative bud break is possible after the resumption of warm temperatures in the spring. The duration of chilling required (the chilling requirement, CR) is determined by the climatic adaptation of the particular cultivar, thus limiting its geographic distribution. This limitation is particularly evident when attempting to introduce superior cultivars to regions with very warm winter temperatures, such as Israel and the coastal southern United States. The physiological mechanism of CR is not understood and although breeding programs deliberately manipulate CR in apricot and peach crosses, robust closely associated markers to the trait are currently not available. We used segregating populations of apricot (100 Fl individuals, NeweYa'ar Research Center, ARO) and peach (378 F2 individuals, Clemson University) to discover several discreet genomic loci that regulate CR and blooming date. We used the extensive genomic/genetic resources available for Prunus to successfully combine our apricot and peach genetic data and identify five QTL with strong effects that are conserved between species as well as several QTL that are unique to each species. We have identified markers in the key major QTL regions for testing in breeding programs which we are carrying out currently; we have identified an initial set of candidate genes using the peach physical/transcriptome map and whole peach genome sequences and we are testing these currently to identify key target genes for manipulation in breeding programs. Our collaborative work to date has demonstrated the following: 1) CR in peach and apricot is predominantly controlled by a limited number ofQTL loci, seven detected in a peach F2 derived map comprising 65% of the character and 12 in an apricot Fl map comprising 71.6% and 55.6% of the trait in the Perfection and A. 1740 parental maps, respectively and that peach and apricot appear in our initial maps to share five genomic intervals containing potentially common QTL. 2) Application of common anchor markers of the Prunus/peach, physical/genetic map resources has allowed us not only to identify the shared intervals but also to have immediately available some putative candidate gene information from these intervals, the EVG region on LG1 in peach the TALY 1 region in apricot on LG2 in peach; and several others involved in vernalization pathways (LGI and LG7). 3) Mapped BACcontigs are easily defined from the complete physical map resources in peach through the common SSR markers that anchor our CR maps in the two species, 4) Sequences of BACs in these regions can be easily mined for additional polymorphic markers to use in MAS applications.

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.