On Critical Relative Distance of DNA Codes for Additive Stem Similarity

We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a thermodynamically motivated similarity measure called an additive stem similarity. These results yield a method to analyze and compare known samples of the nearest neighbor "thermodynamic weights" associated to stacked pairs that occurred in DNA secondary structures.Comment: 5 or 6 pages (compiler-dependable), 0 figures, submitted to 2010 IEEE International Symposium on Information Theory (ISIT 2010), uses IEEEtran.cl

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the "nervous system development" as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity

The morphological, physiological, and genetic underpinnings of intraspecific salinity tolerance in Sorghum bicolor

Decreases in land quality and quantity threaten the efficient production of agriculturally and economically pivotal crops. Such reductions in arable lands are a consequence of population growth and urbanization, and often result in the introduction of various abiotic stresses. The most common abiotic stressors include water limitation (drought), water logging (over watering), poor water quality (salinity), and extreme temperatures (cold, frost, heat). Each of these stressors negatively impact plant growth, development, and yield. Soil salinity, specifically, is a considerable constraint affecting lands used in agriculture. Salts in the soil rise both naturally and through anthropogenic factors making the abundance a threat. Salt toxicity affects plants in two phases, the first of which is osmotic stress. Similar to drought stress, salinity imposed osmotic stress is when soil water potential is lower than the osmotic potential of the plant, therefore limiting water and nutrient extraction. Following osmotic stress, plants accumulate salt ions (e.g. Na+, Cl-, SO42-, NO3-) that can increase to toxic concentrations and disrupt normal metabolic processes. Such toxicity results in reduction of important traits such as root biomass, live aboveground biomass, height, and grain yield. The goals of my dissertation work involved dissecting the various morphological, physiological, and genetic underpinnings of salinity tolerance in Sorghum bicolor. Since research to date demonstrates a significant amount of underlying genetic variation, I designed various projects to investigate the genetic controls associated with phenotypic responses to salinity stress among a diverse group of Sorghum genotypes. In my first research chapter, I screened 21 sorghum accessions and interpreted tolerance as the ability to maintain biomass, similar to plants in control conditions, in response to a long-term treatment of 75 mM NaCl. Findings from this research chapter, when combined with published phylogenetic relationships, suggest that the greater salinity tolerance observed in some accessions of Sorghum bicolor, specifically in the landrace durra, are a byproduct of drought tolerance acquired during domestication. To further expand on these findings, I selected two accessions that showed significant variation in tolerance and used qPCR to investigate expression variation of genes associated with salt detoxification. During the secondary phase of salinity stress (referred to as ion toxicity) Na+ and Cl- ions enter the plant and disrupt normal metabolic processes. If the ions are not effectively managed, the primary evident effect is increased leaf senescence. Tolerant genotypes, however, are able to overcome ion toxicity if they can 1) continue production of new growth and 2) efficiently and effectively exclude, extrude, sequester, and transport ions. Results from this chapter indicate that the tolerant accession experienced an earlier onset of osmotic adjustment, promoting the efficient uptake and transport of water. Additionally, the sensitive accession experienced an earlier onset of ionic stress, suggesting poor exclusion at the root level. These findings suggest that the tolerant genotype has better control over osmotic adjustment and ion transport systems, therefore requiring fewer resources to be diverted for the stress response, providing more available energy that can be utilized for new growth and development. Finally, to further investigate the variation in genetic response to salt exposure, I evaluated the salinity tolerance that existed within a recombinant inbred line (RIL) population produced from a cross between Sorghum bicolor and Sorghum propinquum, two species that differ in response to salt exposure. In this study, I used a high-density genetic map to identify genetic markers correlated with salinity tolerance. I identified 146 candidate genes within the18 QTL intervals. QTL containing candidate genes that aid in the alleviation of osmotic stress (i.e. water acquisition, osmotic adjustment) were significantly associated with live aboveground biomass, and QTL containing candidate genes that aid in ionic detoxification (i.e. sensing, signaling, transporting) were significantly associated with an increase in dead aboveground biomass. Given the QTL and their associated phenotypes observed in the study, I suspect that the increased tolerance observed in S. bicolor is a result of early osmotic adjustment followed by effective sensing and signaling during the ionic phase of salinity response. In summary my dissertation work suggests that salinity stress in sorghum triggers a complex network of tightly regulated response elements, where the accumulation of ions, if properly transported and sequestered, aid in osmotic adjustment and ionic alleviation. Further, given Sorghum bicolor’s domestication history, it appears that increased salinity tolerance arose as a byproduct of the drought tolerance acquired during domestication, therefore aiding in an early osmotic adjustment and subsequent water acquisition

Wright State University\u27s Symposium of Student Research, Scholarship & Creative Activities from Thursday, October 26, 2023

The student abstract booklet is a compilation of abstracts from students\u27 oral and poster presentations at Wright State University\u27s Symposium of Student Research, Scholarship & Creative Activities on October 26, 2023.https://corescholar.libraries.wright.edu/celebration_abstract_books/1001/thumbnail.jp

Characterisation of sweet sorghum germplasm based on agro-morphological traits, molecular markers and juice related traits.

Master of Science in Plant Breeding. University of KwaZulu-Natal, Pietermaritzburg, 2018.There is rising interest for alternative energy sources because of the decline in fossil fuel production and concern over environmental pollution. Currently most biofuel is based on maize and sugar cane as raw materials. However, the use of feedstocks has triggered concerns related to food security, while sugar cane has a high-water consumption and high production requirements amongst other drawbacks. A crop which meets several requirements for biofuel (such as high biomass yield and growth rate, perennial growth, low input requirements, adaptation to the marginal areas, and tolerance to multiple stresses) is sweet sorghum. This study, therefore, aimed at characterising sweet sorghum germplasm using agro-morphological traits and molecular markers (single nucleotide polymorphisms (SNP) during the 2016-2017 summer season at two sites (Ukulinga farm and Potchefstroom). Fourteen quantitative traits were evaluated in an alpha lattice (10 x 5) design with three replications. Analysis of variance for the quantitative traits revealed high levels of genetic variability. This implies that morphological traits differed greatly with a significant G x E interaction across the two sites. Most of the accessions yielded high at Ukulinga than Potchefstroom on juice yield and %brix with a mean yield of 9 605 l/ha and 16.3%, respectively. Most of the accessions studied were early to medium maturing, as evidenced by the mean number of days to 50% flowering (74 days). Analysis of principle components showed that the first four principle components (PC) accounted for 79.12% of the total variation and that some quantitative traits were significantly positively correlated. The estimates for phenotypic coefficient of variation (PCV) were higher than those of genetic coefficient of variation (GCV) for all the traits, indicating the influence of the environment on these traits. However, GCV values for days to 50% flowering, plant height, stalk diameter and stalk yield were very close to PCV. This indicated minimal influence of the environment on the phenotypic expression of these traits. The highest broad sense heritability (H2) of 99.2% was recorded for plant height. Juice volume had the highest expected genetic advance, expressed as a percentage of mean (GAM) of 131.2%. Days to 50% flowering were significantly and positively correlated to plant height, stalk diameter, number of leaves, stalk yield, brix, juice volume and bagasse weight, but negatively significantly correlated to panicle length, panicle width, panicle weight and 1000 grain weight. Plant height was significantly positively correlated to stalk diameter, number of leaves per plant, stalk yield, juice volume and fresh bagasse weight. Bagasse weight, brix, stalk diameter, plant height and number of leaves had a highly positive and direct contribution on juice yield. Several traits had a highly positively and indirect contribution on juice yield via these traits which had a direct contribution. This revealed primary and secondary traits with practical relevance to sweet sorghum improvement programme, because they showed direct and indirect effects on juice yield (volume), which ultimately translates to sugar yield for ethanol production. Kompetitive Allele Specific Polymorphism (KASP) genotyping using 137 SNP markers revealed a considerable level of genetic diversity among the sweet sorghum accessions. Three populations were generated from the analysis. The expected heterozygosity (He) values ranged from 0.236 to 0.291 with a mean of 0.266. The mean of effective alleles across populations was of 1.438. The percentage of polymorphic loci ranged from 80.29% to 91.24% with a mean of 86.86%. Dissimilarity indices ranged from 0.000 to 0.583 with a mean of 0.296. The highest dissimilarity index was observed between SA 2193 and SA 2014, which implied a considerable amount of genetic diversity. Accessions were clustered into three main groups based on dissimilarity indices. The study identified SA 4490, SA 2400, SA 4495, SA 2193 and SA 4479 as superior accessions in juice yield. These accessions should be used as parents in sweet sorghum improvement programme

Stochastic Sensitivity Analysis and Kernel Inference via Distributional Data

AbstractCellular processes are noisy due to the stochastic nature of biochemical reactions. As such, it is impossible to predict the exact quantity of a molecule or other attributes at the single-cell level. However, the distribution of a molecule over a population is often deterministic and is governed by the underlying regulatory networks relevant to the cellular functionality of interest. Recent studies have started to exploit this property to infer network states. To facilitate the analysis of distributional data in a general experimental setting, we introduce a computational framework to efficiently characterize the sensitivity of distributional output to changes in external stimuli. Further, we establish a probability-divergence-based kernel regression model to accurately infer signal level based on distribution measurements. Our methodology is applicable to any biological system subject to stochastic dynamics and can be used to elucidate how population-based information processing may contribute to organism-level functionality. It also lays the foundation for engineering synthetic biological systems that exploit population decoding to more robustly perform various biocomputation tasks, such as disease diagnostics and environmental-pollutant sensing

PROGRAM and PROCEEDINGS THE NEBRASKA ACADEMY OF SCIENCES -- April 22, 2022

Aeronautics & Space Science -- Chairperson(s): Dr. Scott Tarry & Michaela Lucas ANTHROPOLOGY SECTION Chairperson: Dr. Taylor Livingston APPLIED SCIENCE & TECHNOLOGY SECTION Chairperson: Mary Ettel BIOLOGICAL SCIENCES SECTION Chairperson: Therese McGinn BIOMEDICAL SCIENCES SECTION Chairperson: Annemarie Shibata CHEMISTRY SECTION Chairperson: Nathanael Fackler EARTH SCIENCES SECTION Chairperson: Irina Filina ENVIRONMENTAL SCIENCES SECTION Chairperson: Mark Hammer PHYSICS SECTION Chairperson: Adam Davis FRIENDS OF THE ACADEMY 2022 Maiben Lecturer: Dan Sitzman 2022 FRIEND OF SCIENCE AWARD TO: Julie Sigmon and Chris Schabe

The evolutionary genomics of CTCF binding and functional signatures in mouse.

Genetic differences within and between species predominantly lie in the noncoding sequence of the regulatory regions of the genome whose function and significance largely remain poorly understood. Despite significant progress in the field of genomics and the rapid progress in sequencing methods and the subsequent explosion of genomic data, our understanding of the role of the non- coding genetic sequence in the regulation of tissue- and species-specific gene expression is still lagging behind, limiting our comprehension of the evolutionary mechanisms and pressures that shape those expression profiles, and their involvement in the health and disease. The CTCF protein demarcates mammalian genomes into discrete transcriptionally active domains, providing the platform for complex spatial and temporal regulatory processing of genetic information that govern biological processes. In this thesis, I investigate the dynamics and functional implications of evolutionarily novel CTCF binding sites in two Mus genus mouse subspecies, Mus musculus domesticus and Mus musculus castaneus, separated by a short evolutionary time of only one million years. The project investigated the subspecies-specific binding of CTCF in terms of the repeat content, evolution, functional impact and involvement in chromatin conformation. The key findings of this investigation are: (1) the incorporation of young CTCF sites into the non-coding genome via action of transposable elements is followed rapidly with the exhibition of various characteristics of biological function; (2) Unlike other tissue-specific transcription factors, allele- specific CTCF occupancy is affected by cis- and trans-acting regulatory mechanisms that exhibit similar functional characteristics; (3) CTCF evolutionary dynamics support both maintenance of pre-existing structures and functions and provide template for novel ones. In summary, this thesis discusses the evolutionary dynamics of CTCF genomic occupancy and functional signatures in short evolutionary time, and illustrates how either novel species-specific CTCF sites, or common sites with newly-acquired genotypic variants integrate into existing genomic architecture and begin to exert their effects