Association Genetics for Agronomic Traits in Rice and Cloning of ALS Herbicide Resistant Genes from Coreopsis Tinctoria Nutt

We have evaluated the potential of discriminant analysis (DA) to detect candidate markers associated with twelve economically important traits in a large population of unrelated U.S. and Asian inbred lines of rice. Associated marker alleles detected by DA mapped within the same genetic intervals when compared with previous traditional QTL mapping experiments that evaluated progeny derived from various controlled crosses. New markers identified by DA suggest that the procedure can also uncover relevant genetic regions not possible by standard genetic tests. With the same dataset, we also compared different modern regression approaches for selecting molecular markers associated with the twelve agronomic traits. These methods included stepwise forward regression (SFR), least angle regression (LAR) and least absolute shrinkage and selection operator (LASSO) selection. The epistatic model based on stepwise forward regression did successfully identify several interacting loci that explained a relatively high proportion of the observed variation for all the twelve agronomically important traits. Moreover, the loci identified by the epistatic model mapped within previously known QTL regions that underscores the genetic basis of the selected markers. It was concluded that stepwise forward regression with consideration for population structure, epistatic interactions, and missing data (multiple imputation) was a robust method, compared to the general linear model, to identify markers associated with complex agronomic traits. Acetolactate synthase (ALS), also known as acetohydroxy acid synthase (AHAS), which catalyzes the first step in the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine in plants, is a target of five herbicide groups, including sulfonylurea and imidazolinone. A recently discovered group of Coreopsis tinctoria Nutt. mutants from the field showed high levels of resistance to both sulfonylurea and imidazolinone herbicides. In this study the mutants were compared by chemical, genetic, and molecular analyses with “normal” or wild-type Coreopsis. A phylogenetic analysis revealed that the ALS gene can serve as a useful molecular tool for evaluating evolutionary relationships among plant species. Due to pending patent applications by the Louisiana State University Agricultural Center and restrictions of patent applications, specific results from this research cannot be presented in this dissertation

Identification of molecular markers and association mapping of selected loci associated with agronomic traits in rice

Discriminate Analysis as a procedure was evaluated to select molecular markers associated with complex traits in US rice germplasm. Markers for percent head rice, percent total rice, and grain yield were identified with high levels of correct classification that mapped within or near traditional Quantitative Trait Loci (QTL). Mixed model-regression procedure to identify molecular markers that predict phenotypic variance associated with four agronomic traits was created and validated in two distinct rice inbred populations. Main and epistatic effects were identified by standard hypothesis testing and Bayesian information criteria in a multivariate format. The new procedure increased power and enhanced prediction ability of markers in validation samples from both populations. A new SNP discovery and genotyping protocol referred to as Alternative Ecotilling has identified four previously reported and 14 new SNPs in the alk and waxy genes among 57 accessions based on comparisons with sequencing results. The new procedure has been published in 2006 in the journal Plant Molecular Biology Reporter. Application of haplotype-specific markers in exon 7 of the BAD2 gene for marker-assisted identification and introgression of the aroma gene in U.S. rice was evaluated. Aromatic/non-aromatic phenotypes were consistent with corresponding marker haplotypes for all progeny tested which shows the potential of this procedure for marker assisted breeding of new aromatic varieties. Similarly, an allele-specific PCR assays were developed to distinguish between homozygous and heterozygous imazethapyr-resistant S653D and G654E SNP alleles of the rice ALS gene. Field collections were successfully screened for the presence of S653D SNP, and F2 progeny lines of natural CL 121 x red rice outcrosses were screened for the presence of the G654E SNP. These assays were proven successful and are currently used for detection of outcrossing and seed purity for the LSU AgCenter Rice Breeding Project

2010 GREAT Day Program

SUNY Geneseo’s Fourth Annual GREAT Day. This file has a supplement of three additional pages, linked in this record.https://knightscholar.geneseo.edu/program-2007/1004/thumbnail.jp

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

The dynamics of complex systems. Studies and applications in computer science and biology

Our research has focused on the study of complex dynamics and on their use in both information security and bioinformatics. Our first work has been on chaotic discrete dynamical systems, and links have been established between these dynamics on the one hand, and either random or complex behaviors. Applications on information security are on the pseudorandom numbers generation, hash functions, informationhiding, and on security aspects on wireless sensor networks. On the bioinformatics level, we have applied our studies of complex systems to theevolution of genomes and to protein folding

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Characterisation of small RNAs in response to human vaccination and infection

Background Heterogeneity in host responses plays a role in vaccine failure, vaccine-related adverse events and infection outcomes and undermines efforts to produce universally effective vaccines and treatments. Gene expression analyses have provided insights into the immune response, but a deeper understanding requires a broader view encompassing gene regulation. MicroRNAs (miRNAs) are small RNAs (sRNAs) that post-transcriptionally regulate protein-coding genes. Small RNA sequencing (sRNA-seq) has revealed the presence of other small RNA molecules ~20 to 30 nucleotides long, which arise from RNAs classes, including tRNAs, small nucleolar RNAs and yRNAs. The action of these so-called sRNA-derived fragments (sRNA-dfs) is poorly understood; they may play a role in gene regulation. Their role in the immune system is not known. Research questions: 1. Does vaccination and infection alter miRNA expression? 2. Can miRNA expression predict or shape the response to vaccination and/or infection? 3. What is the role of miRNAs in the immune response to infection/vaccination? Methods sRNA-seq was run on samples from three studies: an infant vaccine study involving the reactogenic 4CMenB vaccine, a randomised controlled trial of two typhoid vaccines set within a typhoid vaccine-challenge study, and a ChAdOx1 nCoV-19 vaccine study that followed participants through COVID-19 infection. Results This thesis found vaccination and infection strongly influence miRNAs and sRNA-df expression in plasma, whole blood and PBMCs. In total, 1846 sRNAs were DE after vaccination or infection in at least one study. These features comprised miRNAs and sRNA-dfs derived from tRNAs, snoRNAs, lncRNAs and protein-coding genes. Associations were found between aspects of the immune response and sRNA expression. The infant vaccine study revealed an association between vaccine fever and post-vaccination expression of hsa-miR-122-5p at 4 months of age. Integration of miRNA, mRNA expression, and proteomics revealed a possible link between liver-derived miRNAs and the acute phase response to vaccination via the action of IL6 on hepatocytes. An in-vitro model supported this. The typhoid vaccine-challenge study revealed a divergent pattern of miRNA expression 10 days after vaccination is associated with vaccine-mediated protection from typhoid, and that a hypo-responsiveness to S. Typhi challenge is associated with susceptibility to typhoid fever. Finally, the COVID-19 study showed downregulation of miRNAs at COVID-19 onset was associated with wide-scale upregulation of pro-inflammatory genes and pathways. Amelioration of COVID-19 disease severity after ChAdOx1 nCoV-19 vaccination was reflected at the sRNA level, with less perturbation occurring compared with COVID-19 infection in unvaccinated individuals. Conclusion This thesis reports for the first time that vaccination and infection alter the expression of sRNA fragments derived from snoRNA, lncRNAs and protein-coding genes. This thesis opens up exciting avenues for investigating the role of miRNAs and sRNA-dfs as purveyors of the acute phase response and correlates of vaccine-mediated protection, whose dysregulation may contribute to disease pathogenesis, aspects hitherto overlooked

Prevention and Treatment of Atherosclerosis

This open access book is supported by the European Atherosclerosis Society Association (EAS). This follow-up edition of the well-received Handbook volume 'Atherosclerosis: Diet and Drugs' reflects the state-of-the-art and most recent developments in atherosclerosis research. Outstanding international experts give a comprehensive overview of the field covering topics, such as improving the treatment focusing on established targets, novel drug developments addressing pre-defined targets, hypothesis-based and hypothesis-free approaches to unravel novel targets

Pacific Symposium on Biocomputing 2023

The Pacific Symposium on Biocomputing (PSB) 2023 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2023 will be held on January 3-7, 2023 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2023 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field