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Journal articles on the topic 'Environmental genomic'

To see the other types of publications on this topic, follow the link: Environmental genomic.

Author: Grafiati

Published: 7 July 2024

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1

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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2

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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3

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.

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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.

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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.

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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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Dobrindt, Ulrich, Bianca Hochhut, Ute Hentschel, and Jörg Hacker. "Genomic islands in pathogenic and environmental microorganisms." Nature Reviews Microbiology 2, no. 5 (May 2004): 414–24. http://dx.doi.org/10.1038/nrmicro884.

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Op den Camp, Huub J. M., Tajul Islam, Matthew B. Stott, Harry R. Harhangi, Alexander Hynes, Stefan Schouten, Mike S. M. Jetten, Nils-Kåre Birkeland, Arjan Pol, and Peter F. Dunfield. "Environmental, genomic and taxonomic perspectives on methanotrophicVerrucomicrobia." Environmental Microbiology Reports 1, no. 5 (March 3, 2009): 293–306. http://dx.doi.org/10.1111/j.1758-2229.2009.00022.x.

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Thompson, Samantha L., Galia Konfortova, Richard I. Gregory, Wolf Reik, Wendy Dean, and Robert Feil. "Environmental effects on genomic imprinting in mammals." Toxicology Letters 120, no. 1-3 (March 2001): 143–50. http://dx.doi.org/10.1016/s0378-4274(01)00292-2.

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Liu, Shang, Hailiang Cheng, Youping Zhang, Man He, Dongyun Zuo, Qiaolian Wang, Limin Lv, Zhongxv Lin, and Guoli Song. "Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement." Genes 15, no. 3 (March 19, 2024): 378. http://dx.doi.org/10.3390/genes15030378.

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Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort’s fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future.

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Fourie, Johannes Cornelius Jacobus, Cornelius Carlos Bezuidenhout, Tomasz Janusz Sanko, Charlotte Mienie, and Rasheed Adeleke. "Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features." Journal of Water and Health 18, no. 4 (May 26, 2020): 477–93. http://dx.doi.org/10.2166/wh.2020.029.

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Abstract Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

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Dewell, Sarah, Karen Benzies, and Carla Ginn. "Precision Health and Nursing: Seeing the Familiar in the Foreign." Canadian Journal of Nursing Research 52, no. 3 (September 2020): 199–208. http://dx.doi.org/10.1177/0844562120945159.

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Precision health is the integration of personal genomic data with biological, environmental, behavioral, and other information relevant to the care of a patient. Genetics and genomics are essential components of precision health. Genetics is the study of the effects of individual genes, and genomics is the study of all the components of the genome and interactions between genes, environmental factors, and other psychosocial and cultural factors. Knowledge about the role of genetics and genomics on health outcomes has increased substantially since the completion of the human genome project in 2003. Insights about genetics and genomics obtained from bench science are now having positive clinical implications on patient health outcomes. Nurses have the potential to make distinct contributions to precision health due to their unique role in the health care system. In this article, we discuss gaps in the development of precision health in nursing and how nursing can expand the definition of precision health to actualize its potential. Precision health plays a role in nursing practice. Understanding this connection positions nurses to incorporate genetic and genomic knowledge into their nursing practice.

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Jarquín, Diego, José Crossa, Xavier Lacaze, Philippe Du Cheyron, Joëlle Daucourt, Josiane Lorgeou, François Piraux, et al. "A reaction norm model for genomic selection using high-dimensional genomic and environmental data." Theoretical and Applied Genetics 127, no. 3 (December 12, 2013): 595–607. http://dx.doi.org/10.1007/s00122-013-2243-1.

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Brice, Claire, Zebin Zhang, Devin Bendixsen, and Rike Stelkens. "Hybridization Outcomes Have Strong Genomic and Environmental Contingencies." American Naturalist 198, no. 3 (September 1, 2021): E53—E67. http://dx.doi.org/10.1086/715356.

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Emerson, David, Emily J. Fleming, and Joyce M. McBeth. "Iron-Oxidizing Bacteria: An Environmental and Genomic Perspective." Annual Review of Microbiology 64, no. 1 (October 13, 2010): 561–83. http://dx.doi.org/10.1146/annurev.micro.112408.134208.

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Guazzaroni, María-Eugenia, Raul Alberto Platero, and Rafael Silva-Rocha. "Genomic and Postgenomic Approaches to Understand Environmental Microorganisms." International Journal of Genomics 2018 (October 24, 2018): 1–2. http://dx.doi.org/10.1155/2018/4915348.

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21

Hanawalt, Philip C. "Genomic instability: environmental invasion and the enemies within." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 400, no. 1-2 (May 1998): 117–25. http://dx.doi.org/10.1016/s0027-5107(98)00084-0.

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22

Mann, Scott, and Yi-Ping Phoebe Chen. "Bacterial genomic G+C composition-eliciting environmental adaptation." Genomics 95, no. 1 (January 2010): 7–15. http://dx.doi.org/10.1016/j.ygeno.2009.09.002.

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23

Silva, Elisabete, Alena Kabil, and Andreas Kortenkamp. "Cross-talk between non-genomic and genomic signalling pathways — Distinct effect profiles of environmental estrogens." Toxicology and Applied Pharmacology 245, no. 2 (June 2010): 160–70. http://dx.doi.org/10.1016/j.taap.2010.02.015.

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24

Vogel, Gretchen. "Human genomic ‘bycatch’ threatens privacy." Science 380, no. 6646 (May 19, 2023): 676–77. http://dx.doi.org/10.1126/science.adi7653.

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Burbano, Hernán A., and Rafal M. Gutaker. "Ancient DNA genomics and the renaissance of herbaria." Science 382, no. 6666 (October 6, 2023): 59–63. http://dx.doi.org/10.1126/science.adi1180.

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Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.

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Li, Xin, Tingting Guo, Qi Mu, Xianran Li, and Jianming Yu. "Genomic and environmental determinants and their interplay underlying phenotypic plasticity." Proceedings of the National Academy of Sciences 115, no. 26 (June 11, 2018): 6679–84. http://dx.doi.org/10.1073/pnas.1718326115.

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Observed phenotypic variation in living organisms is shaped by genomes, environment, and their interactions. Flowering time under natural conditions can showcase the diverse outcome of the gene–environment interplay. However, identifying hidden patterns and specific factors underlying phenotypic plasticity under natural field conditions remains challenging. With a genetic population showing dynamic changes in flowering time, here we show that the integrated analyses of genomic responses to diverse environments is powerful to reveal the underlying genetic architecture. Specifically, the effect continuum of individual genes (Ma1,Ma6,FT, andELF3) was found to vary in size and in direction along an environmental gradient that was quantified by photothermal time, a combination of two environmental factors (photoperiod and temperature). Gene–gene interaction was also contributing to the observed phenotypic plasticity. With the identified environmental index to quantitatively connect environments, a systematic genome-wide performance prediction framework was established through either genotype-specific reaction-norm parameters or genome-wide marker-effect continua. These parallel genome-wide approaches were demonstrated for in-season and on-target performance prediction by simultaneously exploiting genomics, environment profiling, and performance information. Improved understanding of mechanisms for phenotypic plasticity enables a concerted exploration that turns challenge into opportunity.

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Tyrmi, Jaakko S., Jaana Vuosku, Juan J. Acosta, Zhen Li, Lieven Sterck, Maria T. Cervera, Outi Savolainen, and Tanja Pyhäjärvi. "Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting." G3: Genes|Genomes|Genetics 10, no. 8 (June 16, 2020): 2683–96. http://dx.doi.org/10.1534/g3.120.401285.

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Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.

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Bajrami, Emirjeta, and Mirko Spiroski. "Genomic Imprinting." Open Access Macedonian Journal of Medical Sciences 4, no. 1 (February 4, 2016): 181–84. http://dx.doi.org/10.3889/oamjms.2016.028.

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BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics.AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting.RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15.CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder.

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Wickens, H. J., S. Simpson, A. Pope, and J. Allen. "Pharmacy and Genomic Medicine: A UK-wide survey of pharmacy staff assessing their prior education, confidence and educational needs." International Journal of Pharmacy Practice 31, Supplement_2 (November 30, 2023): ii53. http://dx.doi.org/10.1093/ijpp/riad074.066.

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Abstract Introduction Pharmacy teams are key in helping patients to get the most from genomic medicine.1,2 However, genomics has only recently been included in undergraduate curricula, and it has been suggested that all healthcare professionals could benefit from education in pharmacogenomics2. We surveyed pharmacy staff to gather information on previous education, current practice and future educational needs in genomics and pharmacogenomics. Aim This survey aimed to establish existing levels of education and confidence in genomics and pharmacogenomics in pharmacy staff working in any role, in any sector, across the UK, and to investigate respondents’ preferences in delivery of genomic education. Methods The survey was based on a 2021 survey of genomic knowledge among medical staff by Health Education England (HEE)3, and amended to reflect pharmacy roles and practice following discussion with pharmacy leads from the 7 NHS Genomic Medicine Service Alliances in England, and from Scotland, Wales and Northern Ireland. SmartSurvey software was used to host the survey, with data held securely. The survey was open between 1st March and 16th May 2022, and was publicised via pharmacy groups including the Royal Pharmaceutical Society, National Pharmacy Association, Local Pharmaceutical Committees, chief pharmacists networks in primary and secondary care, and social media. This work was assessed using the NHS Health Research Authority Research screening tool and judged as ‘not research’; therefore ethical approval was not required. Results 1,552 responses were received from pharmacists, pharmacy technicians, dispensers and other pharmacy staff across the UK; 68% of responses were from England, 13% from Scotland, 10% from Northern Ireland and 9% from Wales. The majority of responses (69%) were from Pharmacists, with 24% from Pharmacy Technicians and 4% from Pharmacy support workers. Only 13% of respondents had received any formal training in genomics. Most respondents felt unprepared to use genomic testing in their practice; just 8% of pharmacists (including trainees), and 1% of pharmacy technicians (including trainees) felt prepared. However, 65% of respondents thought that genomics would change their practice within the next 5 years, and over 70% of pharmacists, and 56% of pharmacy technicians, could envisage ordering, advising on, or counselling patients on genomic testing in the future after appropriate training. 29% of respondents (mainly pharmacy managers) did not currently see patients and therefore might not train personally in genomics. Discussion/Conclusion This work suggests that pharmacy teams are likely to require educational support to embrace the opportunities of genomic medicine. High survey engagement suggested that respondents were keen to make their voices heard. Pharmacists appeared more confident in their ability to advise patients on genomics than Technicians, however both groups seemed keen to receive training. One limitation is that respondents were likely interested in genomics; those with no interest may not have completed the survey. Additionally, pharmacy managers who do not see patients might not train personally in genomics, but may influence strategy for pharmacy genomics service development and delivery. National bodies should capitalise on enthusiasm across the sector to help drive pharmacy genomics services forward through education and training. References 1. Royal College of Physicians and British Pharmacological Society. Personalised prescribing: using pharmacogenomics to improve patient outcomes. Report of a working party. London: RCP and BPS, 2022. https://www.rcp.ac.uk/projects/outputs/personalised-prescribing-using-pharmacogenomics-improve-patient-outcomes last accessed 1/6/23 2. Royal Pharmaceutical Society. Collaborative Position statement for Pharmacy professionals and Genomic Medicine. London: RPS, 2023 https://www.rpharms.com/development/pharmacogenomics/genomic-statement last accessed 1/6/23 3. Health Education England. Genomics in your practice: a health and social care survey. Birmingham, Health Education England, 2023 https://www.genomicseducation.hee.nhs.uk/documents/genomics-in-your-practice-a-health-and-social-care-survey/ last accessed 1/6/23

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Rosen, G. L., and S. D. Essinger. "Comparison of Statistical Methods to Classify Environmental Genomic Fragments." IEEE Transactions on NanoBioscience 9, no. 4 (December 2010): 310–16. http://dx.doi.org/10.1109/tnb.2010.2081375.

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Phifer-Rixey, Megan, Ke Bi, Kathleen G. Ferris, Michael J. Sheehan, Dana Lin, Katya L. Mack, Sara M. Keeble, Taichi A. Suzuki, Jeffrey M. Good, and Michael W. Nachman. "The genomic basis of environmental adaptation in house mice." PLOS Genetics 14, no. 9 (September 24, 2018): e1007672. http://dx.doi.org/10.1371/journal.pgen.1007672.

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Silva, Francijara Araújo da, Carlos Henrique Schneider, Eliana Feldberg, Fabricio Beggiato Baccaro, Natália Dayane Moura Carvalho, and Maria Claudia Gross. "Genomic Organization Under Different Environmental Conditions:Hoplosternum Littoraleas a Model." Zebrafish 13, no. 3 (June 2016): 197–208. http://dx.doi.org/10.1089/zeb.2015.1237.

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Zhang, Xiao-kun. "Non-genomic responses of nuclear receptors to environmental signals." Toxicology Letters 221 (August 2013): S29—S30. http://dx.doi.org/10.1016/j.toxlet.2013.06.105.

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Ishoey, Thomas, Tanja Woyke, Ramunas Stepanauskas, Mark Novotny, and Roger S. Lasken. "Genomic sequencing of single microbial cells from environmental samples." Current Opinion in Microbiology 11, no. 3 (June 2008): 198–204. http://dx.doi.org/10.1016/j.mib.2008.05.006.

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Millet, Emilie J., Willem Kruijer, Aude Coupel-Ledru, Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Sébastien Lacube, Alain Charcosset, Claude Welcker, Fred van Eeuwijk, and François Tardieu. "Genomic prediction of maize yield across European environmental conditions." Nature Genetics 51, no. 6 (May 20, 2019): 952–56. http://dx.doi.org/10.1038/s41588-019-0414-y.

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Sebat, Jonathan L., Frederick S. Colwell, and Ronald L. Crawford. "Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4927–34. http://dx.doi.org/10.1128/aem.69.8.4927-4934.2003.

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ABSTRACT Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing uncultured microorganisms. However, conventional library-screening techniques permit characterization of relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities. A cosmid library derived from a microcosm of groundwater microorganisms was used to construct a microarray (COSMO) containing ∼1-kb PCR products amplified from the inserts of 672 cosmids plus a set of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance, including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified species of microorganisms.

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Wilson, Robert E., Steven M. Matsuoka, Luke L. Powell, James A. Johnson, Dean W. Demarest, Diana Stralberg, and Sarah A. Sonsthagen. "Implications of Historical and Contemporary Processes on Genetic Differentiation of a Declining Boreal Songbird: The Rusty Blackbird." Diversity 13, no. 3 (February 25, 2021): 103. http://dx.doi.org/10.3390/d13030103.

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The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird (Euphagus carolinus) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change.

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Kleerebezem, Michiel, Herwig Bachmann, Eunice van Pelt-KleinJan, Sieze Douwenga, Eddy J. Smid, Bas Teusink, and Oscar van Mastrigt. "Lifestyle, metabolism and environmental adaptation in Lactococcus lactis." FEMS Microbiology Reviews 44, no. 6 (September 29, 2020): 804–20. http://dx.doi.org/10.1093/femsre/fuaa033.

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ABSTRACT Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.

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López-Gatius, Fernando, Irina Garcia-Ispierto, Sergi Ganau, Robert Wijma, Daniel J. Weigel, and Fernando A. Di Croce. "Effect of Genetic and Environmental Factors on Twin Pregnancy in Primiparous Dairy Cows." Animals 13, no. 12 (June 16, 2023): 2008. http://dx.doi.org/10.3390/ani13122008.

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Twin pregnancies are highly undesirable in dairy cattle; they compromise the health and wellbeing of a cow and dramatically impair the farm economy. Recently, a genomic prediction for twin pregnancies has been developed. The objective of this study was to assess environmental and management risk factors affecting the incidence of twin pregnancies in high-producing dairy cows in their first lactation, with a special emphasis placed on the genomic prediction values of twin pregnancy. Our study population of primiparous cows proved valuable in identifying factors other than genomic predictive values that influence twin pregnancy rates. The odds ratio for twin pregnancies was 0.85 (p < 0.0001) for each unit of a prediction value increase, 3.5 (p = 0.023) for cows becoming pregnant during the negative photoperiod, and 0.33 (p = 0.016) for cows producing ≥42 kg of milk at AI, compared with the remaining cows who produced <42 kg of milk. As a general conclusion, the practical implication of our findings is that genomic prediction values can identify the risk of twin pregnancy at a herd level. Given the cumulative effect of genomic selection, selecting animals with a reduced genetic risk of twin pregnancies can contribute to reducing the incidence of twin pregnancies in dairy herds.

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Turzynski, Victoria, Indra Monsees, Cristina Moraru, and Alexander J. Probst. "Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples." Viruses 13, no. 11 (October 21, 2021): 2126. http://dx.doi.org/10.3390/v13112126.

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Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses—bacteriophages and archaeal viruses—influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage–host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth’s ecosystems.

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Jayapal, Manikandan, Rabindra N. Bhattacharjee, Alirio J. Melendez, and M. Prakash Hande. "RETRACTED: Environmental toxicogenomics: A post-genomic approach to analysing biological responses to environmental toxins." International Journal of Biochemistry & Cell Biology 42, no. 2 (February 2010): 230–40. http://dx.doi.org/10.1016/j.biocel.2009.10.007.

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Bay, Rachael A., Ryan J. Harrigan, Vinh Le Underwood, H. Lisle Gibbs, Thomas B. Smith, and Kristen Ruegg. "Genomic signals of selection predict climate-driven population declines in a migratory bird." Science 359, no. 6371 (January 4, 2018): 83–86. http://dx.doi.org/10.1126/science.aan4380.

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The ongoing loss of biodiversity caused by rapid climatic shifts requires accurate models for predicting species’ responses. Despite evidence that evolutionary adaptation could mitigate climate change impacts, evolution is rarely integrated into predictive models. Integrating population genomics and environmental data, we identified genomic variation associated with climate across the breeding range of the migratory songbird, yellow warbler (Setophaga petechia). Populations requiring the greatest shifts in allele frequencies to keep pace with future climate change have experienced the largest population declines, suggesting that failure to adapt may have already negatively affected populations. Broadly, our study suggests that the integration of genomic adaptation can increase the accuracy of future species distribution models and ultimately guide more effective mitigation efforts.

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Joubert, Bonnie R., Kiros Berhane, Jonathan Chevrier, Gwen Collman, Brenda Eskenazi, Julius Fobil, Cathrine Hoyo, et al. "Integrating environmental health and genomics research in Africa: challenges and opportunities identified during a Human Heredity and Health in Africa (H3Africa) Consortium workshop." AAS Open Research 2 (August 27, 2019): 159. http://dx.doi.org/10.12688/aasopenres.12983.1.

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Individuals with African ancestry have extensive genomic diversity but have been underrepresented in genomic research. There is also extensive global diversity in the exposome (the totality of human environmental exposures from conception onwards) which should be considered for integrative genomic and environmental health research in Africa. To address current research gaps, we organized a workshop on environmental health research in Africa in conjunction with the H3Africa Consortium and the African Society of Human Genetics meetings in Kigali, Rwanda. The workshop was open to all researchers with an interest in environmental health in Africa and involved presentations from experts within and outside of the Consortium. This workshop highlighted innovative research occurring on the African continent related to environmental health and the interplay between the environment and the human genome. Stories of success, challenges, and collaborative opportunities were discussed through presentations, breakout sessions, poster presentations, and a panel discussion. The workshop informed participants about environmental risk factors that can be incorporated into current or future epidemiology studies and addressed research design considerations, biospecimen collection and storage, biomarkers for measuring chemical exposures, laboratory strategies, and statistical methodologies. Inclusion of environmental exposure measurements with genomic data, including but not limited to H3Africa projects, can offer a strong platform for building gene-environment (G x E) research in Africa. Opportunities to leverage existing resources and add environmental exposure data for ongoing and planned studies were discussed. Future directions include expanding the measurement of both genomic and exposomic risk factors and incorporating sophisticated statistical approaches for analyzing high dimensional G x E data. A better understanding of how environmental and genomic factors interact with nutrition and infection is also needed. Considering that the environment represents many modifiable risk factors, these research findings can inform intervention and prevention efforts towards improving global health.

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Ketchum, Remi N., Edward G. Smith, Melissa B. DeBiasse, Grace O. Vaughan, Dain McParland, Whitney B. Leach, Noura Al-Mansoori, Joseph F. Ryan, John A. Burt, and Adam M. Reitzel. "Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient." Genome Biology and Evolution 12, no. 10 (July 22, 2020): 1819–29. http://dx.doi.org/10.1093/gbe/evaa150.

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Abstract Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ’s life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

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Bashir, Muhammad Rizwan, Ahsan Mohyo ud Din, Muhammad Sajid, Ejaz ul Hassan, Qamar Anser Tufail Khan, Muhammad Rizwan Khurshid, Hafiz Saad Bin Mustafa, Ahmad Nawaz Gill, Hafeez ur Rehman, and Umer Iqbal. "The application of genomics and bioinformatics to recognize soybean pathogen interaction in a changing climate." Plant Bulletin 2, no. 2 (January 2, 2024): 88–92. http://dx.doi.org/10.55627/pbulletin.002.02.0391.

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The changing climate and continuously increasing global population has posed immense pressure on plant scientists to ensure per capita availability of food under scarcity of natural resources. The present circumstances also enforce to understand how rising CO2 level caused greenhouse effect in the environment which causes rise in the temperature and consequently influence the development of plant disease epidemic, to predict the genomic-based models under changing environmental conditions and to ensure continued food production. The application of genomics and bioinformatics tools are the innovative approaches to understand plant pathogen interaction and prediction that offers unique opportunities to enhance plant yield, stability in quality and production, boost the resilience of soybean to integrate resistance genes in present cultivars to sustain yield under epidemic disease conditions in abruptly changing climate. However, genomics data can be used for genomic based selections and advanced bioinformatics tools can be used to make predictions for genotype by pathogen interaction whereas it had ever been remained a great challenge to homogenize the diverse genomic data to which advanced skills and expertise are required in handling bioinformatics tools. Bioinformatics and genomics have the potential to sustain yield for food security by selection of tolerant or resistant genetic combination for disease sensitive environments as well as to facilitate for maintaining food security and mitigate the effect of inversely changing climatic conditions.

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Benayoun, Bérénice A., Elizabeth A. Pollina, and Anne Brunet. "Epigenetic regulation of ageing: linking environmental inputs to genomic stability." Nature Reviews Molecular Cell Biology 16, no. 10 (September 16, 2015): 593–610. http://dx.doi.org/10.1038/nrm4048.

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Divizia, Maurizio, Leonardo Palombi, Ersilia Buonomo, Domenica Donia, Vito Ruscio, Michele Equestre, Luljeta Leno, Augusto Panà, and Anna Marta Degener. "Genomic Characterization of Human and Environmental Polioviruses Isolated in Albania." Applied and Environmental Microbiology 65, no. 8 (August 1, 1999): 3534–39. http://dx.doi.org/10.1128/aem.65.8.3534-3539.1999.

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ABSTRACT Between April and December 1996, a serious outbreak of poliomyelitis occurred in Albania; almost 140 subjects were involved, and the episode presented an unusually high mortality rate (12%). During the outbreak, water samples from the Lana River in Tirana, Albania, and stool samples from two cases of paralytic poliomyelitis were collected and analyzed for the presence of polioviruses. Six polioviruses were isolated from the environmental and human samples, according to standard methods. All the samples were characterized by partial genomic sequencing of 330 bases across the 5′ untranslated region (5′-UTR) (nucleotide positions 200 to 530) and of 300 bases across the VP1 region (nucleotide positions 2474 to 2774). Comparison of these sequences with those present in data banks permitted the identification of environmental isolates Lana A and Lana B as, respectively, a Sabin-like type 2 poliovirus and an intertypic recombinant poliovirus (Sabin-like type 2/wild type 1), both bearing a G instead of an A at nucleotide position 481. The two other environmental polioviruses were similar to the isolates from the paralytic cases. They were characterized by a peculiar 5′-UTR and by a VP1 region showing 98% homology with the Albanian epidemic type 1 isolates reported by other authors. This study confirms the environmental circulation in Albania of recombinant poliovirus strains, likely sustained by a massive vaccination effort and by the presence in the environment of a type 1 poliovirus, as isolated from the Lana River in Tirana about 2 months before the first case of symptomatic acute flaccid paralysis was reported in this town.

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Christiani, David C., Richard R. Sharp, Gwen W. Collman, and William A. Suk. "Applying Genomic Technologies in Environmental Health Research: Challenges and Opportunities." Journal of Occupational and Environmental Medicine 43, no. 6 (June 2001): 526–33. http://dx.doi.org/10.1097/00043764-200106000-00003.

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Hanawalt, Philip. "PL 1 Genomic instability: Environmental invasion and the enemies within." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 379, no. 1 (September 1997): S1. http://dx.doi.org/10.1016/s0027-5107(97)82606-1.

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Perera, Bambarendage P. U., Laurie K. Svoboda, and Dana C. Dolinoy. "Genomic tools for environmental epigenetics and implications for public health." Current Opinion in Toxicology 18 (December 2019): 27–33. http://dx.doi.org/10.1016/j.cotox.2019.02.008.

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