Academic literature on the topic 'Animal genomics'
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Journal articles on the topic "Animal genomics"
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Song, Luting, and Wen Wangs. "Genomes and evolutionary genomics of animals." Current Zoology 59, no. 1 (February 1, 2013): 87–98. http://dx.doi.org/10.1093/czoolo/59.1.87.
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Abstract Alongside recent advances and booming applications of DNA sequencing technologies, a great number of complete genome sequences for animal species are available to researchers. Hundreds of animals have been involved in whole genome sequencing, and at least 87 non-human animal species’ complete or draft genome sequences have been published since 1998. Based on these technological advances and the subsequent accumulation of large quantity of genomic data, evolutionary genomics has become one of the most rapidly advancing disciplines in biology. Scientists now can perform a number of comparative and evolutionary genomic studies for animals, to identify conserved genes or other functional elements among species, genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation. This review deals with the current ge-nomic and evolutionary research on non-human animals, and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals. It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom.
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Tellam, R. "Animal Genomics." Australian Veterinary Journal 82, no. 7 (July 2004): 425. http://dx.doi.org/10.1111/j.1751-0813.2004.tb11134.x.
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Lopez, Jose V., Bishoy Kamel, Mónica Medina, Timothy Collins, and Iliana B. Baums. "Multiple Facets of Marine Invertebrate Conservation Genomics." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 473–97. http://dx.doi.org/10.1146/annurev-animal-020518-115034.
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Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Ponce de León, F. Abel, and Gustavo A. Gutierrez. "Genomics and animal production." Revista Peruana de Biología 27, no. 1 (March 4, 2020): 015–20. http://dx.doi.org/10.15381/rpb.v27i1.17574.
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Developing countries have the challenge of achieving food security in a world context that is affected by climate change and global population growth. Molecular Genetics and genomics are proposed as technologies that will help to achieve sustainable food security. Technologies that have been developed in the last decade such as the development of genetic markers, genetic maps, genomic selection, next-generation sequencing, and DNA editing systems are discussed. Examples of some discoveries and achievements are provided.
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Smith, Timothy P. "226 Genomics in animal agriculture: current technologies and applications." Journal of Animal Science 97, Supplement_3 (December 2019): 55–56. http://dx.doi.org/10.1093/jas/skz258.113.
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Abstract The early impact of genomic research on animal agriculture was relatively modest, as it proved difficult to translate quantitative trait loci mapping to industrial application. Fortunately, developments in technology have facilitated the application of genomics to animal agriculture, which has led to more substantial impacts on many commercially produced animal species. A brief look back on the history of genomic research will be presented, followed by an overview of recent developments in genomic technologies. Examples of application of genomic research, focusing on beef cattle and comparative genomics with other bovinae specie, and the current status of some new genomic resources emerging for sheep, pigs, and goats, will also be presented.
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Burton, Jeanne L., and Guilherme J. M. Rosa. "Physiological genomics special issue on animal functional genomics." Physiological Genomics 28, no. 1 (December 2006): 1–4. http://dx.doi.org/10.1152/physiolgenomics.00220.2006.
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Giuffra, Elisabetta, and Christopher K. Tuggle. "Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap." Annual Review of Animal Biosciences 7, no. 1 (February 15, 2019): 65–88. http://dx.doi.org/10.1146/annurev-animal-020518-114913.
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Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community–driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
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Passamonti, Matilde Maria, Elisa Somenzi, Mario Barbato, Giovanni Chillemi, Licia Colli, Stéphane Joost, Marco Milanesi, et al. "The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock." Animals 11, no. 10 (September 28, 2021): 2833. http://dx.doi.org/10.3390/ani11102833.
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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Hien, Le Thi Thu, Nguyen Tuong Van, Kim Thi Phuong Oanh, Nguyen Dang Ton, Huynh Thi Thu Hue, Nguyen Thuy Duong, Pham Le Bich Hang, and Nguyen Hai Ha. "Genomics and big data: Research, development and applications." Vietnam Journal of Biotechnology 19, no. 3 (October 13, 2021): 393–410. http://dx.doi.org/10.15625/1811-4989/16158.
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Recent years, genomics and big data analytics have been widely applied and have significant impacts in various important areas of social life worldwide. The development of the next-generation sequencing (NGS) technologies, such as whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome, and/or targeted sequencing, has enabled quickly generating the genomes of interested living organisms. Around the world many nations have invested in and promoted the development of genomics and big data analytics. A number of well-established projects on sequencing of human, animal, plant, and microorganism genomes to generate vast amounts of genomic data have been conducted independently or as collaborative efforts by national or international research networks of scientists specializing in different technical fields of genomics, bioinformatics, computational and statistical biology, automation, artificial intelligence, etc. Complicated and large genomic datasets have been effectively established, storage, managed, and used. Vietnam supports this new field of study through setting up governmental authorized institutions and conducting genomic research projects of human and other endemic organisms. In this paper, the research, development, and applications of genomic big data are reviewed with focusing on: (i) Available sequencing technologies for generating genomic datasets; (ii) Genomics and big data initiatives worldwide; (iii) Genomics and big data analytics in selected countries and Vietnam; (iv) Genomic data applications in key areas including medicine for human health care, agriculture - forestry, food safety, and environment.
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van Oers, Kees, and Jakob C. Mueller. "Evolutionary genomics of animal personality." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1560 (December 27, 2010): 3991–4000. http://dx.doi.org/10.1098/rstb.2010.0178.
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Research on animal personality can be approached from both a phenotypic and a genetic perspective. While using a phenotypic approach one can measure present selection on personality traits and their combinations. However, this approach cannot reconstruct the historical trajectory that was taken by evolution. Therefore, it is essential for our understanding of the causes and consequences of personality diversity to link phenotypic variation in personality traits with polymorphisms in genomic regions that code for this trait variation. Identifying genes or genome regions that underlie personality traits will open exciting possibilities to study natural selection at the molecular level, gene–gene and gene–environment interactions, pleiotropic effects and how gene expression shapes personality phenotypes. In this paper, we will discuss how genome information revealed by already established approaches and some more recent techniques such as high-throughput sequencing of genomic regions in a large number of individuals can be used to infer micro-evolutionary processes, historical selection and finally the maintenance of personality trait variation. We will do this by reviewing recent advances in molecular genetics of animal personality, but will also use advanced human personality studies as case studies of how molecular information may be used in animal personality research in the near future.
Dissertations / Theses on the topic "Animal genomics"
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Mendivil, Ramos Olivia. "The origin of the Hox and ParaHox loci and animal homeobox evolution." Thesis, University of St Andrews, 2013. http://hdl.handle.net/10023/6395.
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The homeobox superfamily is one of the most significant gene families in the evolution of developmental processes in animals. Within this superfamily the ANTP class has expanded exclusively in animals and, therefore, the reconstruction of its origin and diversification into the different ‘modern' families have become prominent questions in the ‘evo-devo' field. The current burgeoning availability of animal genome sequences is improving the resolution of these questions, putting them in a genome evolution context, as well as providing the field with a large, detailed and diverse catalogue of animal homeobox complements. Here I have contributed with a new hypothesis on the origin and evolution of the Hox and ParaHox loci and the new term, ghost loci, referring to homologous genome regions that have lost their homeobox genes. This hypothesis proposes that the last common ancestor of all animals had a much more complex genome (i.e. differentiated Hox, ParaHox and NK loci) that underwent a simplification in the early animal lineages of sponges and placozoans. In collaboration with the Adamska group I resolved the orthology of the first ever ParaHox genes reported in calcareous sponges. This finding serves as an independent confirmation of the ghost loci hypothesis and further resolves the events of secondary simplification within the sponge lineage. Finally, I have catalogued the homeobox complement of the newly sequenced arthropod, the myriapod Strigamia maritima, and examined the linkage and clustering of these genes. This has furthered our understanding of the evolution of the ANTP class. The diversity of the homeobox complement and the retention in this myriapod and the retention of some homeobox genes not previously described within arthropods, in combination with the interesting phylogenetic position that this lineage occupies relative to other arthropods, makes this complement an important point of reference for comparison within the arthropods and in a broader perspective in the ecdyzosoans. These findings have provided significant further insights into the origin and evolution of the homeobox superfamily, with important implications for animal evolution and the evolution of development.
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López, Escardó David 1988. "Unveiling new molecular Opisthokonta diversity : A perspective from evolutionary genomics." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/587085.
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Opisthokonta is an eukaryotic supergroup that contains Metazoa, Fungi and their unicellular relatives. Therefore, this group provides an ideal framework to study distinct unicellular-multicellular transitions, among them, the transition towards animal multicellularity. This thesis aims to describe new Opisthokonta diversity at many different levels, a very neeeded starting point to better understand the evolution of opisthokonts and the origin of multicellularity in animals. In particular, we here described a new genus and species at the onset of Holomycota (Parvularia atlantis), detected new molecular metazoan diversity through a metabarcoding approach, and evaluated the power of single-cell genomics to increment the genomic diversity of choanoflagellates. Overall, this thesis provided new insights into the diversity of Opisthokonta and into the power of single-cell genomics technologies. Finally, our results also have reshaped the phylogeny of choanoflagellates and increased the knowledge of the pre-metazoan genetic tool-kit.Els Opistoconts són el supergroup d'eucariotes que engloba els animals, els fongs i els seus respectius parents unicel·lulars. Ofereixen, per tant, un marc ideal on estudiar la transició d'organismes unicel·lulars a pluricel·lulars, entre elles, la transició a la pluricel·lularitat animal. Aquesta tesis pretén entendre millor la diversitat dels Opistoconts a diferents nivells, com a primer pas imprescindible, per poder entendre millor la seva evolució i obtenir noves dades que ajudin a compendre els processos que van precedir l'origen de la pluricel·lularitat animal. Concretament, els resultats obtinguts corresponen a: la descripció d'un nou génere i una nova espècie a la base dels holomycots (Parvularia atlantis), la detecció de nova diversitat animal gràcies a un estudi metagenètic (metabarcoding) i l'avaluació de l'ús de técniques de genòmica unicel·lular (Single-cell genomics) per poder expandir la diversitat genòmica dels coanoflagel·lats. Amb tot, els resultats donen una millor comprensió de la diversitat dels Opistoconts i del potencial de la genòmica unicel·lular. Finalment, els resultats han permés també remodelar la filogènia dels coanoflagel·lats i incrementar el conexiement sobre el contingut genètic que va precedir l'aparició dels animals.
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Jennings, Robert M. (Robert Michael). "Mitochondrial genomics and northwestern Atlantic population genetics of marine annelids." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/39191.
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Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005.Includes bibliographical references.
The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics.
(cont.) Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that selection operating at the post- settlement stage may be extremely important in structuring genetic differentiation between populations and life stages. Further, it demonstrates how combined genetic analysis of sub-adult and adult samples can provide more information about population dynamics than either could alone.
by Robert M. Jennings.
Ph.D.
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Oliveira, Daniele Portela de. "Predição genômica para o peso ao sobreano via norma de reação em bovinos de corte /." Jaboticabal, 2016. http://hdl.handle.net/11449/132931.
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Orientador: Humberto TonhatiCoorientador: Rusbel Raul Aspilcueta Borquis
Banca: Newton Tamassia Pégolo
Banca: Francisco Ribeiro de Araújo Neto
Banca: Danísio Prado Munari
Banca: Henrique Nunes de Oliveira
Resumo: A expansão dos programas de melhoramento de gado de corte buscam animais com maior peso ao abate em idades mais jovens associados a diversidade de climas aumentou o interesse por estudos com interação genótipo ambiente (G x A). Uma alternativa para identificar animais de maior potencial genético em idade jovens é a inclusão das informações genômicas nas avaliações genéticas. Com este trabalho objetivou-se analisar modelos de normas de reação com a inclusão da informação genômica por meio da matriz de relacionamento com pedigree e genótipos e identificar regiões genômicas associadas com o peso ao sobreano. Foram utilizados registros de peso de bovinos da raça Nelore com aproximadamente 520 dias de idade. Foram genotipados 5.091 animais com um painel de 777.962 SNPs (Illumina BovineHD Beadchip). As estimativas dos componentes de variância foram obtidas pela máxima verossimilhança restrita para os modelos com a matriz A-1 e H-1. Para comparar a habilidade de predição dos métodos no gradiente ambiental (GA) foram calculadas: a correlação entre o valor genômico (GEBV) e o fenótipo predito; a correlação foi dividida pela raiz quadrada da herdabilidade referente ao GA. A população de validação foi composta por animais nascidos entre 2009 e 2011. Os resultados das análises de associação genômica ampla foram apresentados com base na proporção de variância explicada em janelas de 200 SNPs adjacentes, e foram consideradas as duas janelas de maior valor. No Capítulo 2, os GAs foram considerados por fazenda e ano de nascimento dos animais. Os resultados para os parâmetros genéticos indicam que houve G x A, e que o modelo com a matriz H foi, em média, 19% superior ao modelo com a matriz A. Os cromossomos 14 e 27 se destacaram nos GAs. No capítulo 3, foi utilizado um processo iterativo proposto na literatura na definição dos GA. Os resultados dos componentes...
Abstract: The growing of beef cattle breeding programs and the demand for animals for slaughter at young ages related with variety of climates conduced researches in genotype environmental interaction (GxE). The way to choose the top animals in young ages is include the genomic information on genetic evaluations. The aim of this study was to examine reaction norm models with genomic information by the relationship matrix with pedigree plus genotypes and looking for related genes with the yearling weight. The yearling weights from Nellore animals with about 520 days of age were used. A total of 5.091 animals were genotyped with a panel of 777,962 SNPs (IlluminaBovineHDBeadchip). The variance components were estimated through restricted maximum likelihood with A -1 and H -1 matrix. To compare the predictive ability of the methods, the following procedures were used: correlation between the genomic values (GEBV) and the predicted phenotypes and the correlation value divided by the square root of the heritability for each GA. Genotyped animals born between 2009 and 2011 were the test population. The results of the genome association analysis (GWAS) have been presented based on the proportion of variance explained by windows of 200 adjacent SNPs; and the top of two windows were studied. In chapter 2 the environmental gradients (EG) were composed by farm and birth age effects. Estimates of genetic parameters suggest the GxE; and the model with H matrix was 19% higher compared with the model with only pedigree on relationship matrix. Chromosomes 14 and 27 were the most important on the EG. In chapter 3 the EG were based on iterative process proposed in prior researches. The results of variance components for intercept and slope were almost the same for both models. The CSDM3 was the most important gene identified on reaction norm slope, because it was found in beef cattle before
Doutor
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Silparasetty, Shobha Lavanya. "Cloning of "Animal Cryptochrome" cDNA from the Model Organism CHLAMYDOMONAS REINHARDTII for Functional Analysis of Its Protein Product." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/117.
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reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases are involved in the repair of UV light-induced DNA damage using the energy of blue light. In order to determine, if the “animal cryptochrome” gene of C. reinhardtii actually encodes a 6-4 DNA photolyase rather than a photoreceptor, an experimental design was developed to test whether the protein product is able to rescue an E. coli mutant defective in its DNA photolyase gene. The design is as follows: In a first step, the coding region of the “animal cryptochrome” cDNA is cloned. In a second step, the cDNA is inserted in-frame into an E. coli expression vector. In a third step, the construct is transformed into an E. coli photolyase mutant, its expression induced, and the strain tested for better survival after UV light exposure. To accomplish the first step, the cloning of “animal cryptochrome” cDNA, total RNA was successfully extracted from C. reinhardtii 4 hrs into the light phase of a 12 h light/12 h dark cycle and reverse transcribed into cDNA using oligo(dT) primers. After initially unsuccessful attempts at amplifying animal cryptochrome from cDNA or genomic template with a variety of primers and conditions, a short fragment with the expected size of 186 bp was amplifiable with both templates. However, even this fragment was not reliably obtained in every PCR assay. Because of this difficulty, real-time PCR was finally performed in the presence of DMSO (Dimethylsulfoxide) and Betaine. These two adjuvants were reported to improve amplifications particularly for GC-rich templates. C. reinhardtii DNA is especially GC-rich with an average of 64% Gs and Cs. The improved conditions allowed the reliable amplification of the 186 bp fragment from genomic template. It also enabled the amplification of a larger fragment of 528 bp from the same template. The results suggest that a combination of 5% DMSO and 1M Betaine is optimal for the amplification of C. reinhardtii DNA and thus can serve as the basis for successful amplification of the entire 1788 bp coding region of the animal cryptochrome cDNA.
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Gouliouris, Theodore. "The relative importance of human and animal sources of vancomycin-resistant Enterococcus faecium in immunocompromised patients in hospital." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/288742.
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Enterococcus faecium is a leading cause of hospital-acquired infection, disproportionally affecting immunocompromised and critically ill patients. Despite infection control measures, rates of vancomycin-resistant E. faecium (VREfm) bacteraemias have failed to decline in the United Kingdom, and Cambridge University Hospitals (CUH) report the highest numbers nationally. The aims of my PhD were to use epidemiological and genomic surveillance data to establish risk factors for acquisition and infection with E. faecium in patients at CUH, and to use a One Health approach to consider possible sources for hospital patients by relating bloodstream-associated isolates with those cultured from livestock and the environment in the same geographic region. A retrospective matched nested case control study was performed to determine risk factors for VRE bacteraemia relating to antibiotic exposure. 235 cases were matched to 220 controls for length of admission, year, specialty and ward type. Multivariable analysis demonstrated that duration of exposure to parenteral vancomycin, fluoroquinolones and meropenem were independently associated with VRE bacteraemia. This provides evidence for the importance of antimicrobial stewardship targeting high-risk antibiotics in patients at risk of VRE bacteraemia. VREfm bacteraemia may be complicated by disease recurrence. Whole genome sequencing was used to distinguish between relapse and reinfection in 14 episodes of recurrent VREfm bacteraemia. This demonstrated that 10 (71%) episodes were due to reinfection with a new strain, with reinfection being more likely with increasing time between two positive cultures. This study also evaluated 9 patients with blood cultures positive for both VREfm and vancomycin-susceptible E. faecium (VSEfm), the majority (78%) of which were found to be unrelated strains. More than half of all study isolates from these two patient groups were closely related to another isolate causing bacteraemia at CUH, suggesting that hospital acquisition of VREfm is a driver for infection and recurrence. A cross-sectional study of E. faecium in raw and treated wastewater from 20 municipal water treatment plants across the East of England revealed widespread dissemination of healthcare-associated lineages of VREfm in all sampled locations including rural areas, and environmental release in treated wastewater in 17/20 locations. Wastewater isolates were genetically intermixed with isolates causing bacteraemia at CUH, including highly related isolates indicating recent transmission between the two reservoirs. These findings are consistent with widespread distribution of healthcare-associated VREfm in community populations. A One Health approach incorporating sampling from livestock (10 pork, 10 cattle, 9 poultry farms) detected no VREfm in animals whilst 2 independent meat surveys demonstrated VREfm in 1-2% of uncooked products. Genomic comparison of >1400 E. faecium isolates from livestock, meat, wastewater and almost 800 people with bloodstream infection demonstrated that livestock and human isolates were genetically distinct. Analysis of the accessory genome added further evidence for distinct gene content associated with niche adaptation. An analysis of mobile genes encoding antibiotic resistance revealed limited evidence of sharing between human and animal populations. A prospective longitudinal study in haematology patients at CUH over 6 months revealed high rates of VREfm carriage (63% of cases) and environmental contamination (49% of samples). Genomic analysis elucidated complex colonisation dynamics with frequent loss and acquisition of subtypes, including unsuspected acquisition of new VREfm subtypes in patients already colonised with VREfm, and multiple transmission chains involving patients and the environment, including some leading to bacteraemia. These findings highlight the shortcomings of infection control and environmental cleaning and provide the basis for revised interventions.
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Matos, Márcia Cristina [UNESP]. "Associação genômica ampla para características reprodutivas em bovinos da raça Nelore." Universidade Estadual Paulista (UNESP), 2013. http://hdl.handle.net/11449/105922.
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matos_mc_dr_jabo.pdf: 4821384 bytes, checksum: 0c887753a87a7ee387b394c1e0625fe2 (MD5)Análises de associação genômica ampla (GWAS) para idade ao primeiro parto (IPP) e duração do período gestacional (PG) em bovinos da raça Nelore foram conduzidas utilizando painel de ~ 777.000 polimorfismos de nucleotídeo de sítio único (SNP). As análises de associação foram conduzidas em três grupos amostrais distintos com seus respectivos dados fenotípicos: 1) IPP em meses para 96 fêmeas, 2) valores genéticos preditos (EBVs) para IPP e PG para 831 touros, e 3) EBVs para IPP e PG para 1.278 fêmeas. Para cada conjunto de dados e para cada marcador, efeitos de substituição alélica foram estimados por meio do método dos quadrados mínimos ponderados e corrigidos para estratificação populacional. Os marcadores apresentando maiores efeitos estimados foram considerados como indicativos de evidência da associação da região cromossômica com o fenótipo investigado. Realizou-se a prospecção de genes candidatos nas regiões detectadas por diferentes metodologias (busca de SNP intragênicos, mapeamento de genes potencialmente em LD com SNP e construção de redes de termos funcionais, além de revisão manual para evidência em processo reprodutivo baseado em literatura científica). Grande número de regiões genômicas foram indicadas pelos efeitos de substituição alélica estimados, os quais apresentaram distribuição esperada para uma característica poligênica. Os resultados obtidos revelaram funções biológicas relacionadas a processos reprodutivos e sugeriram os genes PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (inter-alphatrypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium...
Genome-wide scans for age at first calving (AFC) and gestation length (GL) in Nellore cattle were performed using a panel of over 777,000 single nucleotide polymorphisms (SNP). Association analyses were carried out in three distinct sample groups and their respective phenotypic data: 1) AFC, in months, for 96 cows, 2) AFC and GL estimated breeding values (EBVs) for 831 sires, and 3) AFC and GL EBVs for 1,278 cows. For each dataset and each marker, allele substitution effects were estimated via ordinary least squares and corrected for population stratification. Markers exhibiting high estimated effects were considered as indicative of evidence of association between the chromosomal region and phenotype investigated. Different methodologies were applied for the prospection of candidate genes within the detected regions (intragenic SNP mining, mapping of genes potentially in linkage disequilibrium with SNP, networking of functional terms, and manual review of genes previously found to be involved in reproductive processes). Large amounts of genomic regions were indicated by the estimated allele substitution effects, which presented a distribution consistent with a polygenic trait. The results obtained revealed biological functions related to reproductive processes and suggested PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (interalpha- trypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium ATPase 3), EFCAB6 (uncharacterized gene), TPT1 (translationally-controlled tumor protein) and AMH (muellerian-inhibiting factor precursor), and ZBTB16 (zinc finger and BTB domain-containing protein 16) and PIK3R1 (Phosphatidylinositol 3-kinase... (Complete abstract click electronic access below)
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Matos, Márcia Cristina. "Associação genômica ampla para características reprodutivas em bovinos da raça Nelore /." Jaboticabal, 2013. http://hdl.handle.net/11449/105922.
Full textAbstract:
Orientador: Wilter Ricardo Russiano VicenteCoorientador: Alexeia Barufatti Grisolia
Coorientador: José Fernando Garcia
Banca: Roberto Carvalheiro
Banca: Joaquim Mansano Garcia
Banca: Fernando Sebastián Baldi Rey
Banca: Lenira El Faro
Resumo: Análises de associação genômica ampla (GWAS) para idade ao primeiro parto (IPP) e duração do período gestacional (PG) em bovinos da raça Nelore foram conduzidas utilizando painel de ~ 777.000 polimorfismos de nucleotídeo de sítio único (SNP). As análises de associação foram conduzidas em três grupos amostrais distintos com seus respectivos dados fenotípicos: 1) IPP em meses para 96 fêmeas, 2) valores genéticos preditos (EBVs) para IPP e PG para 831 touros, e 3) EBVs para IPP e PG para 1.278 fêmeas. Para cada conjunto de dados e para cada marcador, efeitos de substituição alélica foram estimados por meio do método dos quadrados mínimos ponderados e corrigidos para estratificação populacional. Os marcadores apresentando maiores efeitos estimados foram considerados como indicativos de evidência da associação da região cromossômica com o fenótipo investigado. Realizou-se a prospecção de genes candidatos nas regiões detectadas por diferentes metodologias (busca de SNP intragênicos, mapeamento de genes potencialmente em LD com SNP e construção de redes de termos funcionais, além de revisão manual para evidência em processo reprodutivo baseado em literatura científica). Grande número de regiões genômicas foram indicadas pelos efeitos de substituição alélica estimados, os quais apresentaram distribuição esperada para uma característica poligênica. Os resultados obtidos revelaram funções biológicas relacionadas a processos reprodutivos e sugeriram os genes PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (inter-alphatrypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Genome-wide scans for age at first calving (AFC) and gestation length (GL) in Nellore cattle were performed using a panel of over 777,000 single nucleotide polymorphisms (SNP). Association analyses were carried out in three distinct sample groups and their respective phenotypic data: 1) AFC, in months, for 96 cows, 2) AFC and GL estimated breeding values (EBVs) for 831 sires, and 3) AFC and GL EBVs for 1,278 cows. For each dataset and each marker, allele substitution effects were estimated via ordinary least squares and corrected for population stratification. Markers exhibiting high estimated effects were considered as indicative of evidence of association between the chromosomal region and phenotype investigated. Different methodologies were applied for the prospection of candidate genes within the detected regions (intragenic SNP mining, mapping of genes potentially in linkage disequilibrium with SNP, networking of functional terms, and manual review of genes previously found to be involved in reproductive processes). Large amounts of genomic regions were indicated by the estimated allele substitution effects, which presented a distribution consistent with a polygenic trait. The results obtained revealed biological functions related to reproductive processes and suggested PRKCD (protein kinase C delta type), PRKCE (protein kinase C epsilon type), ITHI-1 (inter-alpha-trypsin inhibitor heavy chain H1 precursor), ITHI-3 (interalpha- trypsin inhibitor heavy chain H3), ITHI-4 (inter-alpha-trypsin inhibitor heavy chain H4 precursor), BT.62377 (sarcoplasmic/endoplasmic reticulum calcium ATPase 3), EFCAB6 (uncharacterized gene), TPT1 (translationally-controlled tumor protein) and AMH (muellerian-inhibiting factor precursor), and ZBTB16 (zinc finger and BTB domain-containing protein 16) and PIK3R1 (Phosphatidylinositol 3-kinase... (Complete abstract click electronic access below)
Doutor
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Toro, Ospina Alejandra Maria. "Estudo do desequilíbrio de ligação e estimativa do tamanho efetivo em uma população da raça gir selecionada para crescimento pós-desmama /." Jaboticabal, 2017. http://hdl.handle.net/11449/149847.
Full textAbstract:
Orientador: Josineudson Augusto II de Vasconcelos SilvaBanca: Lenira El faro Zadra
Banca: Rusbel Raul Aspilcueta Borquis
Resumo: O objetivo deste estudo foi estimar o desequilíbrio de ligação (r2) nas distâncias de 25-50kb, 50-100kb, 100-500kb, 0,5-1Mb e o tamanho efetivo (Ne) nas gerações 0, 5, 10, 15, 20 em população da raça Gir selecionada para crescimento pós-desmama. Os animais utilizados no presente estudo foram provenientes do rebanho fechado do Instituto de Zootecnia, Sertãozinho, SP. Foram obtidos os genótipos de 155 animais com o painel BovineDL 33kb e 18 com painel HD imputado onde realizou-se controle de qualidade (CQ) para alelo de menor frequência (MAF) < 0,02 e call rate < 0,1. Depois do CQ permaneceram 27.236 SNPs e 155 animais do painel de 33 kb e 732.962 SNPs e 173 animais do painel HD Imputado. As análises de r2 foram realizadas pelo programa Plink e programa estatístico R Studio e o Ne por meio do DL. Os resultados das distâncias 25-50kb, 50-100kb, 100-500kb e 0,5-1Mb do r2 para o painel 33kb foram iguais a 0,29, 0,25, 0,16 e 0,032 respectivamente, e 0,35, 0,29, 0,18, 0,032 para o painel HD imputado demostrando que o DL permaneceu nas distâncias menores a 100kb, decaindo com o aumento das distâncias. Estes resultados foram maiores aos descritos na literatura para animais zebuínos, sugerindo como causa os segmentos longos de haplótipos que compartilham os animais aparentados. O Ne foi igual a 9, 17, 24, 30 e 30 animais nas gerações 0, 5, 10, 15, 20, observa-se que o Ne é maior na geração 20, com 30 animais, e decai drasticamente a partir da 5 geração com 17 animais, e sendo de 9 an... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The aim of this study was to estimate the linkage disequilibrium (r2) at distances of 25-50kb, 50-100kb, 100-500kb, 0,5-1Mb and the effective population size (Ne) in generations 0, 5, 10, 15, 20 in population of the selected Gir for yearling growth. The animals used in this study were from the closed herd Animal Science Institute, Sertãozinho, SP. the genotypes of 155 animals were obtained with BovineDL 33kb and 18 animals of panel HD, where quality control was held (QC) for minor allele frequency (MAF) <0.02 and call rate <0.1. After QC remained 27,236 SNPs and 155 animals to panel 33 kb, 732.962 SNPs and 173 the panel HD imputation. The r2 analyzes were performed by Plink program and R Studio statistical program and Ne through the DL. The results of r2 for distances 25-50kb, 50-100kb, 100-500kb and 0,5-1Mb were equal to 0.29, 0.25, 0.16 and 0.032, respectively, showing that the DL remained in smaller distances 100kb, decreasing with increasing distances. These results were higher than those reported in the literature for Zebu animals, suggesting a cause to long haplotype segments that share the related animals. Ne is equal to 9, 17, 24, 30 and 30 in the generations 0, 5, 10, 15, 20, it is observed that Ne is higher in generation 20 with 30 animals and decays sharply from 5 Generation 17 animals, and with 9 animals the latest generation, small size for a population. The values found in this study to DL and Ne, explain the selection system and the structure of the populatio... (Complete abstract click electronic access below)
Mestre
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Tramonte, Nicole Colucci. "Relações genéticas entre índices de biotipo animal e características de importância econômica em bovinos Nelore /." Jaboticabal, 2018. http://hdl.handle.net/11449/161899.
Full textAbstract:
Orientador: Fernando Sebastian Baldi ReyCoorientador: William Koury Filha
Coorientador: Claudio de Ulhoa Magnabosco
Coorientador: Rafael Lara Tonussi
Banca: Danísio Prado Munari
banca: Carina Ubirajara Faria
Resumo: O objetivo do presente estudo foi reunir as características morfológicas de estrutura (ES), precocidade (PS) e musculosidade (MS) ao sobreano em características únicas indicadoras de biotipo animal, estimar seus parâmetros genéticos e para características de importância econômica como peso ajustado aos 450 dias de idade (P450), área de olho de lombo (AOL), espessura de gordura subcutânea na costela (EG), espessura de gordura subcutânea na garupa (EGP8), ES, PS, MS, perímetro escrotal ajustado aos 365 (PE365) e 450 (PE450) dias de idade, idade ao primeiro parto (IPP), probabilidade de parto precoce (PPP) e stayability(STAY), a fim de verificar a possibilidade da utilização das características indicadoras biotipo em programas de melhoramento genético de bovinos de corte da raça Nelore. Os dados analisados foram fornecidos pela Associação Nacional de Criadores e Pesquisadores (ANCP). O modelo utilizado para a estimativa de parâmetros genéticos incluiu o efeito aleatório genético aditivo direto e o efeito fixo de grupo de contemporâneos. Para as análises foi utilizada a metodologia ssGBLUP. Métodos multivariados foram empregados para análises de componentes principais pelo procedimento PROC PRINCOMP do software SAS. Foram utilizados dados de ES, PS, MS e P450. O primeiro e o segundo componentes da análise explicaram 82,08% da variabilidade dos dados de e foram utilizados como autovalores para obtenção dos índices de biotipo animal PCA1 e PCA2. A característica SAM foi formada pel... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The aim of this study was to gather the morphological characteristics after yearling of body structure (BS), finishing precocity (FP) and muscling (MS) in unique traits indicative of animal biotype and estimate its genetic parameters and for the characteristics of economic importance of body weight at 450 days of age (W450), ribeye area (REA), backfat thickness (BF), rump fat thickness (RF), BS, FP, MS, scrotal circumference at 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), heifer pregnancy (HP) and stayability (STAY) in order to verify the possibility of using the animal biotype indicator characteristics in breeding programs for Nelore beef cattle. The data analyzed were provided by the National Association of Breeders and Researchers (ANCP). The model used for the estimation of genetic parameters included the additive genetic direct random effect and the fixed group effect of contemporaries. For the analyzes, the ssGBLUP methodology was used. Multivariate methods were used for principal component analyzes by the PROC PROCOMP procedure of the SAS software. Data from BS, FP, MS and W450 were used. The first and second components of the analysis explained 82.08% of the variability of the data and were used as eigenvalues to obtain the indices of animal biotype PCA1 and PCA2. The SAM characteristic was formed by the combination of BS, FP and MS scores, penalizing or subsidizing late or early animals, respectively. The animal biotype indexes presented high ... (Complete abstract click electronic access below)
Mestre
Books on the topic "Animal genomics"
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Chowdhary, Bhanu P. Equine genomics. Ames, Iowa: Wiley-Blackwell, 2013.
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Gòdia, Francesc, and Martin Fussenegger, eds. Animal Cell Technology Meets Genomics. Dordrecht: Springer Netherlands, 2005. http://dx.doi.org/10.1007/1-4020-3103-3.
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Bovine genomics. Ames, Iowa: Wiley-Blackwell, 2012.
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International Symposium on Animal Genomics for Animal Health (2007 Paris, France). Animal genomics for animal health: Paris, France, 25-27 October 2007. Edited by Pinard Marie-Hélène and United States. Agricultural Research Service. Basel: Karger, 2008.
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1959-, Jiang Zhihua, and Ott Troy L, eds. Reproductive genomics in domestic animals. Ames, Iowa: Wiley-Blackwell, 2010.
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Der Experimentator: Molekularbiologie/ Genomics. 6th ed. Heidelberg: Spektrum Akademischer Verlag, 2009.
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Nene, Vishvanath, and Chittaranjan Kole, eds. Genome Mapping and Genomics in Animal-Associated Microbes. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-74042-1.
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Chittaranjan, Kole, and SpringerLink (Online service), eds. Genome Mapping and Genomics in Animal-Associated Microbes. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009.
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Animal genomes under the focus of cytogenetics. New York: Nova Science Publishers, 2011.
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Coordination of programs on domestic animal genomics: The federal framework : progress report. Washington, D.C: Executive Office of the President, National Science and Technology Council, 2004.
Find full textBook chapters on the topic "Animal genomics"
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Lyons, Leslie A. "Companion Animal Genetics." In Comparative Genomics, 367–99. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4309-7_34.
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Irving-Pease, Evan K., Hannah Ryan, Alexandra Jamieson, Evangelos A. Dimopoulos, Greger Larson, and Laurent A. F. Frantz. "Paleogenomics of Animal Domestication." In Population Genomics, 225–72. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2018_55.
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Smits, M. A., J. M. J. Rebel, M. F. W. te Pas, and M. M. Hulst. "Exploiting Genomics to Improve Animal Health." In Animal Genomics for Animal Health, 27–33. Basel: KARGER, 2008. http://dx.doi.org/10.1159/000317141.
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Mishra Shukla, Swati. "Functional Genomics." In Encyclopedia of Animal Cognition and Behavior, 1–7. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-47829-6_1337-1.
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Lalonde, Christine, and Steven Arnocky. "Behavioral Genomics." In Encyclopedia of Animal Cognition and Behavior, 737–42. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_1402.
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Mishra Shukla, Swati. "Functional Genomics." In Encyclopedia of Animal Cognition and Behavior, 2828–34. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_1337.
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Lalonde, Christine, and Steven Arnocky. "Behavioral Genomics." In Encyclopedia of Animal Cognition and Behavior, 1–6. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-319-47829-6_1402-1.
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Pinard-Van Der Laan, M. H., and C. G. Gay. "The Future Impact of Animal Genomics in Animal Health Research." In Animal Genomics for Animal Health, 3–11. Basel: KARGER, 2008. http://dx.doi.org/10.1159/000317139.
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Mellencamp, M. A., L. Galina-Pantoja, C. D. Gladney, and M. Torremorell. "Improving Pig Health through Genomics: a View from the Industry." In Animal Genomics for Animal Health, 35–41. Basel: KARGER, 2008. http://dx.doi.org/10.1159/000317142.
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Singh, Birbal, Gorakh Mal, Sanjeev K. Gautam, and Manishi Mukesh. "Animal Genomics—A Current Perspective." In Advances in Animal Biotechnology, 311–31. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-21309-1_28.
Full textConference papers on the topic "Animal genomics"
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Gutiérrez-Gil, Beatriz, Aroa Suárez-Vega, Yolanda Bayón, Luis Fernando de la Fuente, and Juan-José Arranz. "MICROBLOGGING ON TWITTER IN ANIMAL BREEDING AND ANIMAL GENOMICS RELATED COURSES AS A NETWORKING TOOL TO DEVELOP STUDENTS´ COMMUNICATION SKILLS." In 13th International Conference on Education and New Learning Technologies. IATED, 2021. http://dx.doi.org/10.21125/edulearn.2021.2365.
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YIn, Lu. "Beyond Labels: Knowledge Elicitation using Deep Metric Learning and Psychometric Testing." In Twenty-Ninth International Joint Conference on Artificial Intelligence and Seventeenth Pacific Rim International Conference on Artificial Intelligence {IJCAI-PRICAI-20}. California: International Joint Conferences on Artificial Intelligence Organization, 2020. http://dx.doi.org/10.24963/ijcai.2020/747.
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Knowledge present in a domain is well expressed as relationships between corresponding concepts. For example, in zoology, animal species form complex hierarchies; in genomics, the different (parts of) molecules are organized in groups and subgroups based on their functions; plants, molecules, and astronomical objects all form complex taxonomies. Nevertheless, when applying supervised machine learning (ML) in such domains, we commonly reduce the complex and rich knowledge to a fixed set of labels. This oversimplifies and limits the potential impact that the ML solution can deliver. The main reason for such a reductionist approach is the difficulty in eliciting the domain knowledge from the experts. Developing a label structure with sufficient fidelity and providing comprehensive multi-label annotation can be exceedingly labor-intensive in many real-world applications. Here, we provide a method for efficient hierarchical knowledge elicitation (HKE) from experts working with high-dimensional data such as images or videos. Our method is based on psychometric testing and active deep metric learning. The developed models embed the high-dimensional data in a metric space where distances are semantically meaningful, and the data can be organized in a hierarchical structure.
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Eynck, Christina. "Camelina breeding and development- a Canadian perspective." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/bsmv8815.
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Climate change is predicted to have a more profound impact on the Canadian Prairies compared to other regions in the world, with higher relative temperatures, longer periods of water stress and increased frequency of droughts. Camelina sativa (camelina) is a promising alternative, climate-resilient oilseed that could become part of a Canadian strategy to battle climate change and its detrimental effects on agriculture. Albeit currently a small crop, camelina has enormous potential for growth: favorable agronomics, like early maturity, frost and drought tolerance, pest and disease resistance, as well as exceptional winter hardiness in true winter types in combination with a unique oil profile render it an excellent feedstock crop not only for biofuel, but also high value feed and food uses. Uses for camelina oil and meal include industrial applications (e.g. biodiesel, lubricants, and polymers) and higher value areas such as cosmetics, Omega-3 supplements for human and companion animal nutrition, and applications in the livestock, poultry and aquaculture feed sectors. As a relatively undeveloped crop, there is significant potential for improvement of both agronomic and seed quality characteristics. This presentation will provide an overview of current camelina breeding and crop development efforts underway at the AAFC Research and Development Center in Saskatoon in collaboration with industry. This includes variety and germplasm development in spring- and winter-type camelina, insights into the genomics of camelina as well as recent developments in the Canadian camelina industry.
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Zapara, Tatyana, Alexander Romashchenko, Anna Proskura, Alexander Ratushnyak, and Svetlana Vechkapova. "Mechanisms and functions of neurogenesis in the limbic system of adult animals." In 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB). IEEE, 2020. http://dx.doi.org/10.1109/csgb51356.2020.9214729.
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High, K. A., J. P. Evans, J. L. Ware, D. W. Stafford, and H. R. Roberts. "HEMOPHILIA B IN CANINES IS DUE TO A POST-TRANSCRIPTIONAL DEFECT." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644017.
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Factor IX is a vitamin K dependent plasma proteinsynthesized in the liver; a deficiency of Factor IX results in hemophilia B. An animal model for hemophilia B exists in dogs; affected animals have severe disease, with activity levels of less than 1%. The purpose of the current study is to determine the molecular basis of canine hemophilia. In previous work, we had shown that the Factor IX gene in hemophilic dogs appeared to be at least partly intact; thus, genomic DNA from normal, carrier and hemophilic dogs, when probed with sequences from the 4th, 7th, and 8th exons of the human gene, gave identical patterns on Southern blot. We have now completed the mapping of the hemophilic gene, using probes from the first, second, third and sixth exons, and have shown it to beentirely intact, that is, free of any large deletions or rearrangements, as determined by Southern blotting. In addition, using the guanidinium thiocyanate technique, we h^ve prepared total RNA from normal and -hemophilic dog livers add analyzed these samples by Northern blotting. The results show that the hemophilic dog synthesizes a Factor IX transcript of approximately 3 kilobases, that is, of the same size asthe normal dog. In addition, baaed on signal intensity, the transcript appears to be produced in roughlyequivalent amounts in the normal and hemophilic dogs.We conclude that the defect responsible for canine hemophilia B interferes with the production of the normal Factor IX protein at a post-transcriptional level. Moreover, since the hemophilic dogs produce Factor IX mRNA it should be possible to elucidate the gene defect in the hemophilic animals by preparing normal and hemophilic canine liver cDNA libraries and isolating and characterizing the respective Factor IX cDNAs.
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Gustaw, Klaudia, Anita Gorczyca, and Patrycja Wojdyło. "Insights into the genomes of Apilactobacillus kunkeeei strains isolated from flowers." In 1st International PhD Student’s Conference at the University of Life Sciences in Lublin, Poland: ENVIRONMENT – PLANT – ANIMAL – PRODUCT. Publishing House of The University of Life Sciences in Lublin, 2022. http://dx.doi.org/10.24326/icdsupl1.p007.
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Rubtsov, N. V. "Lessons of studies of karyotypic and genomic evolution in animals, application of developed technique in the studies of karyotype and genome organization in plants." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.207.
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The present report is devoted to analysis of results obtained with modern molecular and molecular-cytogenetic methods in studies of karyotype and genome organization in various animal species. Perspectives of their application for the study of karyotype and genome organization in plants are considered and discussed.
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Pereira, Rordana Gomes Fernandes, and Paulo Roberto Martins Queiroz. "ANÁLISE MOLECULAR, BIOLÓGICA E FILOGENÉTICA DO NOVO CORONAVÍRUS SARS-COV-2." In II Congresso Brasileiro de Biologia Molecular On-line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/2313.
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Introdução: Os coronavírus são uma família de vírus que possuem RNA de fita simples e são capazes de contaminar homens e animais. São conhecidos por sua alta frequência de recombinação e altas taxas de mutação, permitindo que se adaptem a novos hospedeiros e nichos ecológicos. Os níveis virais elevados fornecem um ambiente adequado para a replicação viral, levando a persistência viral, por sua vez, pode originar novas estirpes virais. Objetivo: O objetivo deste trabalho foi analisar o aspecto molecular, biológico e filogenético do SARS-CoV-2. Material e Métodos: Para isso, foi feito um levantamento dos estudos relacionados com o tema ao longo dos anos de 2019 e 2021 e a utilização de vários softwares para a análise filogenética de 105 genomas completos do SARS-Cov-2 provenientes do Brasil, China, Índia, Itália e Estados Unidos e de morcegos de Wuhan (WIV). Resultados: Apenas duas sequências do SARS-Cov-2 isolados no Brasil tiveram semelhança com as sequências WIV, demonstrando que as estirpes brasileiras da pesquisa possuem uma alta variabilidade genética. Já os isolados do SARS-Cov-2 isolados na China apresentam o maior número de sequências relacionadas com as WIV. Nos isolados virais da Índia observou-se uma relação de afinidade por um ancestral comum e os isolados WIV, porém, não possuem uma similaridade direta com as sequências WIV pois a análise mostrou mais ramificações isoladas confirmando achados de estudos que revelaram que a Europa e o Sudeste Asiático são as duas principais rotas de introdução da doença na Índia. Os vírus dos Estados Unidos, da China e da Índia ficaram reunidos com as estirpes do próprio país demostrando através do alinhamento de sequências que mutações diferentes ocorrem pelo mundo. Além disso, algumas estirpes apresentaram proximidade com outras sequências de outros países devido a circulação de pessoas entre as nacionalidades estudadas neste trabalho. Conclusão: O novo Coronavírus foi originado de um processo de coevolução com início em um animal não humano e atingiu os hospedeiros humanos através do salto de espécies. Dessa forma, com base na filogenia molecular do genoma viral essa capacidade zoonótica traz consigo o alerta para possíveis novos surtos ou epidemias devido à evolução e adaptações desse vírus em outros hospedeiros animais.
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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
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"Tandem repeats are selfish elements which mark the level of hidden recombination in animal mitochondrial genomes." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-159.
Full textReports on the topic "Animal genomics"
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Short, Samuel, Bernhard Strauss, and Pantea Lotfian. Emerging technologies that will impact on the UK Food System. Food Standards Agency, June 2021. http://dx.doi.org/10.46756/sci.fsa.srf852.
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Rapid technological innovation is reshaping the UK food system in many ways. FSA needs to stay abreast of these changes and develop regulatory responses to ensure novel technologies do not compromise food safety and public health. This report presents a rapid evidence assessment of the emerging technologies considered most likely to have a material impact on the UK food system and food safety over the coming decade. Six technology fields were identified and their implications for industry, consumers, food safety and the regulatory framework explored. These fields are: Food Production and Processing (indoor farming, 3D food printing, food side and byproduct use, novel non-thermal processing, and novel pesticides); Novel Sources of Protein, such as insects (for human consumption, and animal feedstock); Synthetic Biology (including lab-grown meat and proteins); Genomics Applications along the value chain (for food safety applications, and personal “nutrigenomics”); Novel Packaging (active, smart, biodegradable, edible, and reusable solutions); and, Digital Technologies in the food sector (supporting analysis, decision making and traceability). The report identifies priority areas for regulatory engagement, and three major areas of emerging technology that are likely to have broad impact across the entire food industry. These areas are synthetic biology, novel food packaging technologies, and digital technologies. FSA will need to take a proactive approach to regulation, based on frequent monitoring and rapid feedback, to manage the challenges these technologies present, and balance increasing technological push and commercial pressures with broader human health and sustainability requirements. It is recommended FSA consider expanding in-house expertise and long-term ties with experts in relevant fields to support policymaking. Recognising the convergence of increasingly sophisticated science and technology applications, alongside wider systemic risks to the environment, human health and society, it is recommended that FSA adopt a complex systems perspective to future food safety regulation, including its wider impact on public health. Finally, the increasing pace of technological
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Zeng, Jian, Ali Toosi, Rohan L. Fernando, Jack C. M. Dekkers, and Dorian J. Garrick. Genomic Selection of Purebred Animals for Crossbred Performance in the Presence of Dominant Gene Action. Ames (Iowa): Iowa State University, January 2013. http://dx.doi.org/10.31274/ans_air-180814-1249.
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McCarthy, Noel, Eileen Taylor, Martin Maiden, Alison Cody, Melissa Jansen van Rensburg, Margaret Varga, Sophie Hedges, et al. Enhanced molecular-based (MLST/whole genome) surveillance and source attribution of Campylobacter infections in the UK. Food Standards Agency, July 2021. http://dx.doi.org/10.46756/sci.fsa.ksj135.
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This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the contributions of the main sources of human infection and to identify any changes over time. An extension to the project focussed on antimicrobial resistance in study isolates and older archived isolates. These older isolates were from earlier years at the Oxfordshire site and the earliest available coherent set of isolates from the national archive at Public Health England (1997/8). The aim of this additional work was to analyse the emergence of the antimicrobial resistance that is now present among human isolates and to describe and compare antimicrobial resistance in recent food animal isolates. Having identified the presence of bias in population genetic attribution, and that this was not addressed in the published literature, this study developed an approach to adjust for bias in population genetic attribution, and an alternative approach to attribution using sentinel types. Using these approaches the study estimated that approximately 70% of Campylobacter jejuni and just under 50% of C. coli infection in our sample was linked to the chicken source and that this was relatively stable over time. Ruminants were identified as the second most common source for C. jejuni and the most common for C. coli where there was also some evidence for pig as a source although less common than ruminant or chicken. These genomic attributions of themselves make no inference on routes of transmission. However, those infected with isolates genetically typical of chicken origin were substantially more likely to have eaten chicken than those infected with ruminant types. Consumption of lamb’s liver was very strongly associated with infection by a strain genetically typical of a ruminant source. These findings support consumption of these foods as being important in the transmission of these infections and highlight a potentially important role for lamb’s liver consumption as a source of Campylobacter infection. Antimicrobial resistance was predicted from genomic data using a pipeline validated by Public Health England and using BIGSdb software. In C. jejuni this showed a nine-fold increase in resistance to fluoroquinolones from 1997 to 2018. Tetracycline resistance was also common, with higher initial resistance (1997) and less substantial change over time. Resistance to aminoglycosides or macrolides remained low in human cases across all time periods. Among C. jejuni food animal isolates, fluoroquinolone resistance was common among isolates from chicken and substantially less common among ruminants, ducks or pigs. Tetracycline resistance was common across chicken, duck and pig but lower among ruminant origin isolates. In C. coli resistance to all four antimicrobial classes rose from low levels in 1997. The fluoroquinolone rise appears to have levelled off earlier and among animals, levels are high in duck as well as chicken isolates, although based on small sample sizes, macrolide and aminoglycoside resistance, was substantially higher than for C. jejuni among humans and highest among pig origin isolates. Tetracycline resistance is high in isolates from pigs and the very small sample from ducks. Antibiotic use following diagnosis was relatively high (43.4%) among respondents in the human surveillance study. Moreover, it varied substantially across sites and was highest among non-elderly adults compared to older adults or children suggesting opportunities for improved antimicrobial stewardship. The study also found evidence for stable lineages over time across human and source animal species as well as some tighter genomic clusters that may represent outbreaks. The genomic dataset will allow extensive further work beyond the specific goals of the study. This has been made accessible on the web, with access supported by data visualisation tools.
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Splitter, Gary, and Menachem Banai. Microarray Analysis of Brucella melitensis Pathogenesis. United States Department of Agriculture, 2006. http://dx.doi.org/10.32747/2006.7709884.bard.
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Original Objectives 1. To determine the Brucella genes that lead to chronic macrophage infection. 2. To identify Brucella genes that contribute to infection. 3. To confirm the importance of Brucella genes in macrophages and placental cells by mutational analysis. Background Brucella spp. is a Gram-negative facultative intracellular bacterium that infects ruminants causing abortion or birth of severely debilitated animals. Brucellosis continues in Israel, caused by B. melitensis despite an intensive eradication campaign. Problems with the Rev1 vaccine emphasize the need for a greater understanding of Brucella pathogenesis that could improve vaccine designs. Virulent Brucella has developed a successful strategy for survival in its host and transmission to other hosts. To invade the host, virulent Brucella establishes an intracellular niche within macrophages avoiding macrophage killing, ensuring its long-term survival. Then, to exit the host, Brucella uses placenta where it replicates to high numbers resulting in abortion. Also, Brucella traffics to the mammary gland where it is secreted in milk. Missing from our understanding of brucellosis is the surprisingly lillie basic information detailing the mechanisms that permit bacterial persistence in infected macrophages (chronic infection) and dissemination to other animals from infected placental cells and milk (acute infection). Microarray analysis is a powerful approach to determine global gene expression in bacteria. The close genomic similarities of Brucella species and our recent comparative genomic studies of Brucella species using our B. melitensis microarray, suqqests that the data obtained from studying B. melitensis 16M would enable understanding the pathogenicity of other Brucella organisms, particularly the diverse B. melitensis variants that confound Brucella eradication in Israel. Conclusions Results from our BARD studies have identified previously unknown mechanisms of Brucella melitensis pathogenesis- i.e., response to blue light, quorum sensing, second messenger signaling by cyclic di-GMP, the importance of genomic island 2 for lipopolysaccharide in the outer bacterial membrane, and the role of a TIR domain containing protein that mimics a host intracellular signaling molecule. Each one of these pathogenic mechanisms offers major steps in our understanding of Brucella pathogenesis. Strikingly, our molecular results have correlated well to the pathognomonic profile of the disease. We have shown that infected cattle do not elicit antibodies to the organisms at the onset of infection, in correlation to the stealth pathogenesis shown by a molecular approach. Moreover, our field studies have shown that Brucella exploit this time frame to transmit in nature by synchronizing their life cycle to the gestation cycle of their host succumbing to abortion in the last trimester of pregnancy that spreads massive numbers of organisms in the environment. Knowing the bacterial mechanisms that contribute to the virulence of Brucella in its host has initiated the agricultural opportunities for developing new vaccines and diagnostic assays as well as improving control and eradication campaigns based on herd management and linking diagnosis to the pregnancy status of the animals. Scientific and Agricultural Implications Our BARD funded studies have revealed important Brucella virulence mechanisms of pathogenesis. Our publication in Science has identified a highly novel concept where Brucella utilizes blue light to increase its virulence similar to some plant bacterial pathogens. Further, our studies have revealed bacterial second messengers that regulate virulence, quorum sensing mechanisms permitting bacteria to evaluate their environment, and a genomic island that controls synthesis of its lipopolysaccharide surface. Discussions are ongoing with a vaccine company for application of this genomic island knowledge in a Brucella vaccine by the U.S. lab. Also, our new technology of bioengineering bioluminescent Brucella has resulted in a spin-off application for diagnosis of Brucella infected animals by the Israeli lab by prioritizing bacterial diagnosis over serological diagnosis.
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Weller, Joel I., Ignacy Misztal, and Micha Ron. Optimization of methodology for genomic selection of moderate and large dairy cattle populations. United States Department of Agriculture, March 2015. http://dx.doi.org/10.32747/2015.7594404.bard.
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The main objectives of this research was to detect the specific polymorphisms responsible for observed quantitative trait loci and develop optimal strategies for genomic evaluations and selection for moderate (Israel) and large (US) dairy cattle populations. A joint evaluation using all phenotypic, pedigree, and genomic data is the optimal strategy. The specific objectives were: 1) to apply strategies for determination of the causative polymorphisms based on the “a posteriori granddaughter design” (APGD), 2) to develop methods to derive unbiased estimates of gene effects derived from SNP chips analyses, 3) to derive optimal single-stage methods to estimate breeding values of animals based on marker, phenotypic and pedigree data, 4) to extend these methods to multi-trait genetic evaluations and 5) to evaluate the results of long-term genomic selection, as compared to traditional selection. Nearly all of these objectives were met. The major achievements were: The APGD and the modified granddaughter designs were applied to the US Holstein population, and regions harboring segregating quantitative trait loci (QTL) were identified for all economic traits of interest. The APGD was able to find segregating QTL for all the economic traits analyzed, and confidence intervals for QTL location ranged from ~5 to 35 million base pairs. Genomic estimated breeding values (GEBV) for milk production traits in the Israeli Holstein population were computed by the single-step method and compared to results for the two-step method. The single-step method was extended to derive GEBV for multi-parity evaluation. Long-term analysis of genomic selection demonstrated that inclusion of pedigree data from previous generations may result in less accurate GEBV. Major conclusions are: Predictions using single-step genomic best linear unbiased prediction (GBLUP) were the least biased, and that method appears to be the best tool for genomic evaluation of a small population, as it automatically accounts for parental index and allows for inclusion of female genomic information without additional steps. None of the methods applied to the Israeli Holstein population were able to derive GEBV for young bulls that were significantly better than parent averages. Thus we confirm previous studies that the main limiting factor for the accuracy of GEBV is the number of bulls with genotypes and progeny tests. Although 36 of the grandsires included in the APGD were genotyped for the BovineHDBeadChip, which includes 777,000 SNPs, we were not able to determine the causative polymorphism for any of the detected QTL. The number of valid unique markers on the BovineHDBeadChip is not sufficient for a reasonable probability to find the causative polymorphisms. Complete resequencing of the genome of approximately 50 bulls will be required, but this could not be accomplished within the framework of the current project due to funding constraints. Inclusion of pedigree data from older generations in the derivation of GEBV may result is less accurate evaluations.
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Splitter, Gary, and Menachem Banai. Attenuated Brucella melitensis Rough Rev1 Vaccine. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7585199.bard.
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The original objectives of the proposal were: 1. Compare mutants 444 and 710 to Rev1 (parent strain), and 16M (field strain) in murine and human macrophage lines for phenotypic differences. 2. Determine in vivo virulence and survival of the mutants 444 and 710 in guinea pigs and mice. 3. Determine humoral and cell-mediated immune responses induced by mutants 444 and 710 in guinea pigs and mice. 4. Determine in vivo protection of mice and guinea pigs provided by mutants 444 and 710 compared to Rev1. Background: While human and animal brucellosis are rare in the U.S., brucellosis caused by B. melitensis remains relatively constant in Israel. Despite a national campaign to control brucellosis in Israel, the misuse of Rev1 Elberg vaccine strain among pregnant animals has produced abortion storms raising concern of human infection due to vaccine excretion in the milk. Further, some commercial Rev1 vaccine lots can: a) produce persistent infection, b) infect humans, c) be horizontally transmitted, d) cause abortion, and e) induce a persistent anti-O-polysaccharide antibody response confounding the distinction between infected and vaccinated animals. In Israel, vaccination practices have not optimally protected the milk supply from Brucella and Rev 1 vaccine can exacerbate the problem. In addition, cattle vaccinated against B. abortus are not protected against B. melitensis supporting the need for an improved vaccine. A safe vaccine used in adult animals to produce herd resistance to infection and a vaccine that can be distinguished from virulent infection is needed. A rough Rev1 vaccine would be less virulent than the parental smooth strain and permit serologic distinction between vaccinated and infected animals. Advantages of the Rev1 vaccine foundation are: 1) Rev1 vaccination of sheep and goats against B. melintensisis approved; therefore, vaccines derived from the Rev1 foundation may be readily accepted by licensing agencies as well as commercial companies, and 2) considerable data exists on Rev1vaccination and Rev1 proteins. Therefore, a post-genomic vaccine against B. melitensis based on the Rev1 foundation would provide a great advantage. Major conclusions from our work are: 1) We have determined that mutant 710 is highly attenuated in macrophages compared to virulent field strain 16M and mutant 444. 2) We have confirmed that mutant 710 is highly attenuated in guinea pigs and mice. 3) We have determined immune responses induced by mutant 710 in animals. 4) We have determined in vivo protection of mice and guinea pigs provided by mutants 444 and 710 compared to Rev1, and importantly, mutant 710 provides a high level of protection against challenge with virulent B. melitensis 16M. Thus, our data support the goals of the grant and provide the foundation for a future vaccine useful against B. melitensis in Israel. Because of patent considerations, many of our findings with 444 and 710 have not yet been published. Scientific and Agricultural Implications: Our findings support the development of a vaccine against B. melitensis based on the mutant 710. Because strain 710 is a mutant of the Elberg Rev1 vaccine, commercialization is more likely than development of an entirely new, uncharacterized Brucella mutant or strain.
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Fluhr, Robert, and Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7696517.bard.
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Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.
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Yogev, David, Ricardo Rosenbusch, Sharon Levisohn, and Eitan Rapoport. Molecular Pathogenesis of Mycoplasma bovis and Mycoplasma agalactiae and its Application in Diagnosis and Control. United States Department of Agriculture, April 2000. http://dx.doi.org/10.32747/2000.7573073.bard.
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Mycoplasma bovis and M. agalactiae are two phylogenetically related mycoplasmas which cause economically significant diseases in their respective bovine or small ruminant hosts. These organisms cause persistent asymptomatic infections that can result in severe outbreaks upon introduction of carrier animals into susceptible herds. Little is known about the mechanisms underlying mycoplasma-host interaction, variation in virulence, or of the factors enabling avoidance of the host immune system. In recent years it has become apparent that the ability of pathogenic microorganisms to rapidly alter surface antigenic structures and to fine tune their antigenicity, a phenomena called antigenic variation, is one of the most effective strategies used to escape immune destruction and to establish chronic infections. Our discovery of a novel genetic system, mediating antigenic variation in M. bovis (vsp) as well as in M. agalactiae (avg) served as a starting point for our proposal which included the following objectives: (i) Molecular and functional characterization of the variable surface lipoproteins (Vsp) system of M. bovis and comparison with the Vsp-counterpart in M. agalactiae (ii) Determination of the role of Vsp proteins in the survival of M. bovis when confronted by host defense factors, (iii) Assessment of Vsp-based genetic and antigenic typing of M. bovis and M. agalactiae for epidemiology of infection and (iv) Improvement of diagnostic tests for M. bovis and M. agalactiae based on the vsp-and vsp-analogous systems. We have carried out an extensive molecular characterization of the vsp system and unravelled the precise molecular mechanism responsible for the generation of surface antigenic variation in M. bovis. Our data clearly demonstrated that the two pathogenic mycoplasma species possess large gene families encoding variable lipoprotein antigens that apparently play an important role in immune evasion and in pathogen-host interaction during infection. Phase variable production of these antigens was found to be mediated by a novel molecular mechanism utilizing double site-specific DNA inversions via an intermediate vsp configuration. Studies in model systems indicate that phase variation of VspA is relevant in interaction between M. bovis and macrophages or monocytes, a crucial stage in pathogenesis. Using an ELISA test with captured VspA as an antigen, phase variation was shown to occur in vivo and under field conditions. Genomic rearrangements in the avg gene family of M. agalactiae were shown to occur in vivo and may well have a role in evasion of host defences and establishment of chronic infection. An epidemiological study indicated that patterns of vsp-related antigenic variation diverge rapidly in an M. bovis infected herd. Marked divergence was also found with avg-based genomic typing of M. agalactiae in chronically infected sheep. However, avg-genomic fingerprints were found to be relatively homogeneous in different animals during acute stages of an outbreak of Contagious Agalactiae, and differ between unrelated outbreaks. These data support the concept of vsp-based genomic typing but indicate the necessity for further refinement of the methodology. The molecular knowledge on these surface antigens and their encoding genes provides the basis for generating specific recombinant tools and serological methods for serodiagnosis and epidemiological purposes. Utilization of these methods in the field may allow differentiating acutely infected herds from chronic herds and disease-free herds. In addition the highly immunogenic nature of these lipoproteins may facilitate the design of protective vaccine against mycoplasma infections.
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Ohad, Nir, and Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695858.bard.
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Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.
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Cytryn, Eddie, Mark R. Liles, and Omer Frenkel. Mining multidrug-resistant desert soil bacteria for biocontrol activity and biologically-active compounds. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598174.bard.
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Control of agro-associated pathogens is becoming increasingly difficult due to increased resistance and mounting restrictions on chemical pesticides and antibiotics. Likewise, in veterinary and human environments, there is increasing resistance of pathogens to currently available antibiotics requiring discovery of novel antibiotic compounds. These drawbacks necessitate discovery and application of microorganisms that can be used as biocontrol agents (BCAs) and the isolation of novel biologically-active compounds. This highly-synergistic one year project implemented an innovative pipeline aimed at detecting BCAs and associated biologically-active compounds, which included: (A) isolation of multidrug-resistant desert soil bacteria and root-associated bacteria from medicinal plants; (B) invitro screening of bacterial isolates against known plant, animal and human pathogens; (C) nextgeneration sequencing of isolates that displayed antagonistic activity against at least one of the model pathogens and (D) in-planta screening of promising BCAs in a model bean-Sclerotiumrolfsii system. The BCA genome data were examined for presence of: i) secondary metabolite encoding genes potentially linked to the anti-pathogenic activity of the isolates; and ii) rhizosphere competence-associated genes, associated with the capacity of microorganisms to successfully inhabit plant roots, and a prerequisite for the success of a soil amended BCA. Altogether, 56 phylogenetically-diverse isolates with bioactivity against bacterial, oomycete and fungal plant pathogens were identified. These strains were sent to Auburn University where bioassays against a panel of animal and human pathogens (including multi-drug resistant pathogenic strains such as A. baumannii 3806) were conducted. Nineteen isolates that showed substantial antagonistic activity against at least one of the screened pathogens were sequenced, assembled and subjected to bioinformatics analyses aimed at identifying secondary metabolite-encoding and rhizosphere competence-associated genes. The genome size of the bacteria ranged from 3.77 to 9.85 Mbp. All of the genomes were characterized by a plethora of secondary metabolite encoding genes including non-ribosomal peptide synthase, polyketidesynthases, lantipeptides, bacteriocins, terpenes and siderophores. While some of these genes were highly similar to documented genes, many were unique and therefore may encode for novel antagonistic compounds. Comparative genomic analysis of root-associated isolates with similar strains not isolated from root environments revealed genes encoding for several rhizospherecompetence- associated traits including urea utilization, chitin degradation, plant cell polymerdegradation, biofilm formation, mechanisms for iron, phosphorus and sulfur acquisition and antibiotic resistance. Our labs are currently writing a continuation of this feasibility study that proposes a unique pipeline for the detection of BCAs and biopesticides that can be used against phytopathogens. It will combine i) metabolomic screening of strains from our collection that contain unique secondary metabolite-encoding genes, in order to isolate novel antimicrobial compounds; ii) model plant-based experiments to assess the antagonistic capacities of selected BCAs toward selected phytopathogens; and iii) an innovative next-generation-sequencing based method to monitor the relative abundance and distribution of selected BCAs in field experiments in order to assess their persistence in natural agro-environments. We believe that this integrated approach will enable development of novel strains and compounds that can be used in large-scale operations.