Bibliographic reference of tef
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The document discusses elongation factor 1-alpha (EF-1α) gene as a phylogenetic marker. It notes that EF-1α encodes an essential part of the protein translation machinery and has been used successfully to infer species- and genus-level relationships in lepidoptera and fungi. The gene is generally single-copy, shows high sequence variation between closely related species, and has become a standard marker for identification in the fungus Fusarium. The document also provides bibliographic references and accession numbers related to phylogenetic studies using EF-1α.
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[1] PolyPhen-2, PMID:20354512, http://genetics.bwh.harvard.edu/pph2/
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Reference protein sequences from other organisms are already used to predict amino acid conservation scores [1, 2]. These might be improved if protein variants in individual races of certain species could be included in the calculations. When these variants would be annotated with the frequency and their functional effects, this information would be even more valuable. Variants causing disease in animals are currently stored in Online Mendelian Inheritance in Animals (OMIA, http://omia.angis.org.au/). For several species, including dogs, the research community has partially adopted standards resembling HGNC and HGVS nomenclature. Further standardization may contribute to data from other species becoming more FAIR (Findable, Accessible, Interoperable, and Re-usable) (FAIR data, http://www.dtls.nl/fair-data/). As a first step, we have established instances of the variant frequency database Varda (Dog Varda, http://varda.generade.nl) and the LOVD3 gene variant database platform [3] for the dog (Dog LOVD, http://databases. generade.nl/dog/). We demonstrate that variants from VCF files can be stored and annotated with their frequency in Varda. Information about the functional effects of variants and the resulting phenotypes in individual animals can be stored in the Canis familiaris LOVD. We hope that this example will be followed by research and diagnostic centers world-wide for the dog and other species.
[1] PolyPhen-2, PMID:20354512, http://genetics.bwh.harvard.edu/pph2/
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The document discusses genetic and environmental polymorphism, which refers to differences in DNA sequences or phenotypes induced by environmental factors. It provides examples of various types of genetic polymorphism, including phenotypic, biochemical, immunological, chromosomal, and DNA polymorphisms. The manifestation of these polymorphisms can include variations in traits, proteins, antigens, blood groups, length of chromosomes, and DNA sequences. The importance of polymorphism studies is also highlighted for applications like forensics, transplantation, epidemiology, taxonomy, and understanding susceptibility to environmental factors and drugs.
Application of genetic mapping
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Genetics is the study of genes and heredity in living organisms. The document discusses the history and development of genetics from Mendel's early experiments in 1866 to modern large-scale genome sequencing projects. It outlines the three main branches of genetics and describes the importance of genetics for understanding molecular and cellular functions, inheritance patterns, and genetic variation. The application of genetics is discussed in areas like disease prevention, genetically modified crops and organisms, genetic counseling, and developing molecular medicine.
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Genetic variation refers to differences in genes between individuals of a population. It arises due to mutations, recombination during meiosis, gene flow between populations, and environmental factors. Genetic variation is important for evolution and survival of species as it provides raw materials for natural selection. While some genetic variations are harmful, others can provide benefits like disease resistance. Variations in genes involved in drug metabolism can impact individual responses to medications. Understanding genetic diversity is important for personalized medicine and drug development.
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Genetic variation exists at different scales, from single nucleotide polymorphisms within individuals of a species to larger structural differences between species. Genetic variation arises through mutations, recombination, gene flow, genetic drift, and the interaction of these processes over time. The effective population size of a species influences how genetic variation is shaped by these evolutionary forces.
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Gene transfer and genetically modified organisms involve modifying an organism's genes through biotechnology. Some examples include tomatoes modified to delay ripening and transgenic sheep that produce enhanced wool. Potential benefits include increased food supply and quality, but risks include unknown health effects and unintended gene transfer. The sequencing of the human genome allowed for the identification of genes, improved data storage, and discovery of gene locations and evolutionary relationships. Gene transfer between species keeps protein sequences unchanged due to the universal genetic code. One technique uses restriction enzymes to cut genes from genomes, plasmids to transfer genes, and DNA ligase to join genes for insertion into host cells like bacteria.
Aug2015 analysis team 13 carroll dnanexus parliament talk
This document summarizes work done to characterize structural variants in a trio using multiple calling methods and the Parliament pipeline. It reports on:
- Mapping 30X Illumina and PacBio genomes for the trio and calling variants individually with short-read callers
- Assessing concordance of individual callers with Mendelian inheritance
- Combining calls with Parliament and forcing genotypes, which achieved higher concordance than individual callers
- Future work including releasing a full Parliament callset for the trio, evaluating additional regions, varying Illumina and PacBio amounts, and applying machine learning.
Genetic factors and periodontal disease
Genetic basis of periodontal disease, Host susceptibility, linkage of genetic susceptibility with periodontal disease
Space Breeding
Space breeding involves sending seeds into low-Earth orbit to induce mutations from cosmic radiation and microgravity. Returning seeds are selected and bred to develop varieties with desirable traits like higher yield, disease resistance, and stress tolerance. China has been a pioneer in this area, sending over 400 plant species to space and developing commercial rice and vegetable varieties from space-bred seeds. The goals of space breeding are to efficiently produce new crop varieties with improved economic traits that are difficult to obtain through traditional breeding methods.
Day 6 September 15th Chapters 3 and 5
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- The endoplasmic reticulum builds proteins and detoxifies toxins. The Golgi apparatus processes and packages cell products for delivery. Vacuoles provide storage and waste management in plant cells. Chloroplasts are the sites of photosynthesis in plant cells.
- Chapter 5 discusses DNA, how it contains genetic instructions, and how those instructions get expressed to build organisms via transcription and translation. Mutations can damage DNA and affect protein production and organismal traits.
Tianjian et al., 1995 (page 1)
This document describes a study where researchers isolated a gain-of-function mutant of Bruton's tyrosine kinase (BTK) called BTK* through random mutagenesis. BTK* results from a single point mutation in the pleckstrin homology (PH) domain that replaces a glutamate with a lysine at residue 41. BTK* shows increased phosphorylation, increased membrane targeting, and can drive cell growth in soft agar. The transforming activity requires kinase activity and an intact PH domain. Expression of BTK* can also relieve interleukin-5 dependence in a B cell line. The results demonstrate that the PH domain critically regulates BTK transformation and activation.
Role of Epigenetics in Heterosis
Epigenetics plays an important role in heterosis. DNA methylation and histone modifications are key epigenetic mechanisms that regulate gene expression without changing DNA sequences. Studies have shown that hybrid plants exhibit increased genome-wide DNA methylation compared to their parental lines, and genes sensitive to epigenetic remodeling are transcriptionally repressed in hybrids. Drought-tolerant rice varieties maintain higher DNA methylation levels than susceptible varieties under drought stress. Histone acetylation levels in maize roots increase under salt stress and are associated with up-regulation of cell wall genes, reducing damage from excess salinity. While epigenetics contributes to heterosis, direct evidence is still needed and questions remain around how epigenetic variation arises
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1. Several studies examined genes that regulate cell proliferation and differentiation in the respiratory epithelium, including Sox2 and SPDEF.
2. GATA-6 was shown to activate transcription of surfactant proteins A and TTF-1.
3. Additional research investigated the roles of surfactant proteins A and D in regulating phospholipid homeostasis and enhancing clearance of pathogens like RSV and bacteria from the lungs.
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Includes over 250 transcriptomics and genomics papers published from 2009 to 2011 in plants, animals, and other non-human species; sorted by species.
Abstracts Of Presentations At The 2015 APS Annual Meeting
This document contains abstracts from presentations given at the 2015 APS Annual Meeting. The abstracts describe various plant pathology research studies and are grouped alphabetically by first author's name. The summaries provided are from three of the abstracts within the document.
Gutell 078.mbe.2001.18.1810
This document summarizes a study on the evolution of two plastid genes - rrn16 encoding the plastid small-subunit rRNA and tufA encoding elongation factor Tu - in two species of nonphotosynthetic chlorophyte algae in the genus Polytoma. The study finds that these two genes retain function after the loss of photosynthesis in Polytoma, but show substantially accelerated rates of base substitution in one Polytoma species, P. uvella. In P. uvella, the accelerated evolution of tufA is partly due to relaxed codon bias. Relaxed selection due to a lower protein synthetic load in the nonphotosynthetic plastid (leucoplast) provides a plausible
Functional Genomics of Plant Pathogen interactions in Wheat Rust Pathosystem
Cereal rust fungi are pathogens of major importance to agriculture, threatening cereal production worldwide. Targeted breeding for resistance, based on information from fungal surveys and population structure analyses of virulence, has been effective. Nevertheless, breakdown of resistance occurs frequently and continued efforts are needed to understand how these fungi overcome resistance and to determine the range of available resistance genes. The development of genomic resources for these fungi and their comparison has released a torrent of new ideas and approaches to use this information to assist pathologists and agriculture in general. The sequencing of gene transcripts and the analysis of proteins from haustoria has yielded candidate virulence factors among which could be defence-triggering avirulence genes. Genome-wide computational analyses, including genetic mapping and transcript analyses by RNA sequencing of many fungal isolates, will predict many more candidates (Bakkeren et al., 2012)
Dissecting the mechanisms of host-pathogen systems like wheat-rust, including pathogen counter-defenses will ensure a step ahead towards understanding current outcomes of interactions from a co-evolutionary point of view, and eventually move a step forward in building more durable strategies for management of diseases caused by fungi (Hadrami et al.,2012)
Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...
‘NATIONAL CONFERENCE ON MAN AND ENVIRONMENT’ October 15 – 16, 2012
Organized by
Department of Zoology and Environmental Sciences, Punjabi University, Patiala (Pb.) – 147 002, India
Precision in Plant Immune Expression: Not Lost in Translation
Xinnian Dong, HHMI Investigator, Arts & Sciences Professor of Biology, Duke University
• Expression of broad-spectrum disease resistance in plants often results in fitness penalty.
• Plant immune responses are normally regulated at both transcriptional and translational levels.
• Transcriptional and translational regulatory mechanisms of plant immune genes can be manipulated to engineer broad-spectrum resistance in crops.
CV_JRA
This document is a CV for Jeppe Reitan Andersen, who is currently a wheat breeder at Nordic Seed. The CV provides details on his education, professional positions, research focus, and publications. It summarizes that he has a PhD in plant molecular biology and genetics from the Danish Institute of Agricultural Sciences and is responsible for Nordic Seed's wheat breeding program, with a focus on developing high-yielding and disease-resistant wheat varieties for Denmark and Northern Europe. He has over 15 publications on topics related to flowering time control, vernalization response, and cell wall biosynthesis in grasses.
Epigenomics gyanika
The document discusses epigenetics and epigenomics in plants, describing the main epigenetic modifications including DNA methylation, histone modifications, and non-coding RNAs. It reviews several ongoing research projects applying epigenomics to improve crop traits and stress resistance in important crops like wheat, rice, and maize. Going forward, further research is needed to better understand how epigenetic changes influence plant development and physiology, their degree of heritability, and how epigenomics can be used to enhance crop breeding.
Essay On Arabidopsis Thaliaa
This summarizes an essay on the plant Arabidopsis thaliana and its response to environmental stresses like drought and high salt levels. When stressed, the plant hormone ABA is produced, which triggers adaptive responses to help the plant survive. ABA regulates many transcriptional factors, including members of the bZIP family that are expressed during stress. The essay discusses the domains of AREB/ABF transcription factors and how they are phosphorylated and regulated in response to ABA and stresses.
DNA methylation and Diet
The document discusses the relationship between development, environment, and genetics. It notes that the environment plays an important role in development and can initiate alternative developmental trajectories leading to different phenotypes. Diet in particular is highlighted as influencing development, with examples given of how diet determines caste in insects and horn length in beetles. The document then focuses on DNA methylation, explaining how diet can influence methylation patterns through components like folate, vitamins, and minerals. Several studies are cited showing how changes in diet alter DNA methylation and gene expression in animals. In conclusion, DNA methylation is influenced by dietary interactions with the genome and plays a role in health and disease.
molecular basis of heterosis.pptx
this ppt made for molecular basis of heterosis of crop plant and it has also incuded heterosis on basis of estimation and genetics basis of heterosis. but these points are not properly explation becarse this ppt main aim to explain the heterosis on the basis of heterosis. thank you....
Opinion_FOXP3_Frontiers in Genetics
This document discusses the FOXP3 gene as a promising candidate gene in susceptibility to generalized vitiligo. It summarizes that FOXP3 is the master transcription factor that regulates regulatory T cells, which play an important role in preventing autoimmunity. Studies have found associations between polymorphisms in the FOXP3 gene and an increased risk of vitiligo. The document argues that further investigation of FOXP3 genetic variants and their effects on regulatory T cell development and function could provide insights into vitiligo pathogenesis and potential new therapeutic approaches targeting the FOXP3 gene/regulatory T cell network.
Advances in Nomenclature of Fungi.pptx
This document discusses the past, present, and future of identifying and naming plant-pathogenic fungi. In the past, fungi were classified based on spore and morphological characteristics, which led to inconsistencies. The development of molecular techniques like DNA sequencing in the 1990s allowed for more accurate polyphasic taxonomy using multiple data sources. DNA barcoding using the ITS region is now commonly used, along with secondary protein-coding gene markers for species-level identification. Databases like MycoBank were created to link fungal names and data across sources and help modernize nomenclatural practices.
Similar to Bibliographic reference of tef (20)
Molecular basis of plant resistance and defense responses to pathogens
Molecular basis of plant resistance and defense responses to pathogens
Abstracts Of Presentations At The 2015 APS Annual Meeting
Abstracts Of Presentations At The 2015 APS Annual Meeting
Functional Genomics of Plant Pathogen interactions in Wheat Rust Pathosystem
Functional Genomics of Plant Pathogen interactions in Wheat Rust Pathosystem
Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...
Rapid Impact Assessment of Climatic and Physio-graphic Changes on Flagship G...
Precision in Plant Immune Expression: Not Lost in Translation
Precision in Plant Immune Expression: Not Lost in Translation
Bibliographic reference of tef
- 1. BIBLIOGRAPHIC REFERENCE. Elongation factor 1α (EF-1α) is a highly conservated ubiqituos protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. (Roger et al., 1999). This gene, which encodes an essential part of the protein translation machinery, has highly phylogenetic utility because it is non-orthologous copies of the gene have not been detected in the genus and universal primers have been designed that work across the phylogenetic breadth of the genus. This gene was first used as a phylogenetic markers to infer species- and generic-level relationships among lepidoptera (Cho et al., 1995). Primers was first developed in the fungi to investigate lineages within the Fusarium oxysporum complex (O´Donell et al., 1998). This gene appears to be consistently single-copy in Fusarium and it shows a high level of sequence polymorphism among closely related species, even in compararison to the intron-rich portions of protein-coding genes such calmoduline, beta-tubulina and histone H3. For these reason, TEF has become the marker of choice as a single-locus identification tool in Fusarium (Geiser et al., 2004). Cho SW, Mitchell A, Regier JC, Mitter C, Poole RW, Friedlander TP and Zhao SW (1995). A highly conserved nuclear gene fow low-level phylogenetics-Elongation-Factor-1-Alpha recovers morphology-based tree for Heliothine moths. Molecular Biology and Evolution 12: 650-656. Geiser DM, Jimenz Gasco MM, Kang S, Mkalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, and O’Donnell K (2004). FUSARIUM-IDv.1.0: A DNA sequence database for identifying Fusarium. European Journal of Plant Pathology 110: 473-479. O´Donell K, Kistler HC. Cigelnik E and Ploetz RC (1998). Multiple evolutionary origins of the fungus causing Panama disease of banana: Concordant evidence from nuclear and mitochondrial gene genealogies. Proceedings of the National Academy of Sciences of the United States of America 95:2044-2049. Roger AJ, Sandblom O, Doolittle WF and Philippe H (1999). An Evaluation of Elongation Factor 1- Alpha as a Phylogenetic Marker for Eukaryotes. Mol. Biol. Evol. 16(2):218-233. Accession number. JN806238 JN806239 JN806240 JN806241 JN806242 JN806243 JN806244 JN806245