Genetics and Genomics Commons^™

Comparative Genome Analysis Of Fungal Antagonists Marinomonas Ostreistagni 398 And M. Spartinae 468., Jessie L. Fields

Honors Theses

Under certain conditions, the Spartina alterniflora and Juncus roemerianus grasses in marshes undergo progressive decline in an event known as Saltwater Marsh Dieback, which may be attributed to the presence of the plant pathogenic fungi Fusarium. The microbiomes of S. alterniflora and J. roemerianus from Deer Island, MS were characterized and Fusarium suppressing bacteria were identified. Among isolates capable of antagonizing Fusarium were Marinomonas ostreistagni 398 and M. spartinae 468. Despite the progress in understanding the diversity of Marinomonas, our ability to explain ecological, metabolic, and biochemical traits of marinomonads at the genomic sequence level remains limited. Analysis revealed that ...

Characterizing Long Covid: Deep Phenotype Of A Complex Condition, Rachel R. Deer, Feifan Liu, Melissa A. Haendel, Peter N. Robinson

COVID-19 Publications by UMass Chan Authors

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies.

METHODS: The Human Phenotype Ontology ...

Identification Of Biomarker Systems Of Autism Spectrum Disorder And Uterine Cancer, Allison Hickman

All Dissertations

Complex diseases and disorders pose a challenge to scientists due to their variable and often inconsistent genetic and environmental underpinnings across affected individuals. Because of this variability, large condition-specific datasets and corresponding analytical tools and approaches are being curated as resources to investigate potential genetic trends in complex diseases and disorders. In this Dissertation, I used DNA- and RNA-based resources to discover polygenic biosignatures associated with Autism Spectrum Disorder (ASD) or uterine cancer. To explore the intersection of small-effect common DNA variants and regulation in ASD, I discovered and analyzed trends in allelic associations at eQTLs within ASD-affected individuals. Association ...

Divergent Selection For Water Conversion Ratio In Broiler Populations, Joseph Hiltz

Graduate Theses and Dissertations

Water scarcity is a global reality and with the anticipated population growth, freshwater resources will be further strained to meet both human needs and agriculture applications. To ensure a water sustainable and food secure future, all aspects of agriculture must become more efficient. Two strategies were explored. The potential of improving water efficiency in broilers was examined. The first strategy was to develop a more efficient and accurate method for measuring water consumption/inputs in agriculture. To date, water measuring technology has lacked the necessary sophistication to assure accuracy and repeatability of low flow water usage.

After establishing a low ...

Environmental Rnai Pathways In The Two-Spotted Spider Mite, Mosharrof Mondal, Jacob Peter, Obrie Scarbrough, Alex Flynt

Faculty Publications

© 2020, The Author(s).

Background:RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipulation and has applications that includes arthropod pest control. RNAi technologies are dependent on delivery method with the most convenient likely being feeding, which is effective in some animals while others are insensitive. The two-spotted spider mite, Tetranychus urticae, is prime candidate for developing RNAi approaches due to frequent occurrence of conventional pesticide resistance. Using a sequencing-based approach, the fate of ingested RNAs was explored to identify ...

Genome-Wide Analyses Of Genomic Variation Regulating Differential Stress Responses In Japanese Quail, Steven Anthony Shumaker

Graduate Theses and Dissertations

As consumer demands for poultry grow, producers work to improve bird productivity in both meat and egg production. This endeavor is multifaceted, as many different factors play a part in influencing the productivity of birds, including environmental conditions, overall health, and genetic potential. One aspect controlled for in all aspects of poultry production optimization is stress management. Mitigation of stress is of primary concern to producers, as improper stress management can have many deleterious effects on chickens. Stress management requires an understanding of poultry stress responses and their physiological mechanisms, which can be more deeply understood through genomic analysis. Chapter ...

Using Artificial Intelligence To Decipher Epigenetic Code Of Drug Resistance In The Deadliest Human Malaria Parasite, Samira Jahangiri

Graduate Theses and Dissertations

Malaria remains one of the immense global public health challenges, with an estimated ~200 million cases worldwide in 2019 despite the remarkable gains in reducing this deadly disease over the past decade. The recent emergence and spread of artemisinin resistance (ART-R) in Plasmodium falciparum will increasingly impede global efforts to control and eliminate malaria. Previous studies have observed broad transcriptional changes and identified several noncoding genetic variants strongly associated with ART-R. The broad transcriptional variations suggest that the malaria parasite uses sophisticated epigenetic regulation to survive under drug pressure. Therefore, evaluating the regulatory effects of noncoding-variants in malaria parasites is ...

Genome-Scale Data Reveal Deep Lineage Divergence And A Complex Demographic History In The Texas Horned Lizard (Phrynosoma Cornutum) Throughout The Southwestern And Central Us, Nicholas Finger, Keaka Farleigh, Jason T. Bracken, Adam D. Leaché, Olivier François, Ziheng Yang, Tomas Flouri, Tristan Charran, Tereza Jezkova, Dean A. Williams, Christopher Blair

Publications and Research

The southwestern and central US serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas Horned Lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat ...

Comparison Of Multiple Imputation Algorithms And Verification Using Whole-Genome Sequencing In The Cmuh Genetic Biobank, Ting-Yuan Liu, Chih-Fan Lin, Hsing-Tsung Wu, Ya-Lun Wu, Yu-Chia Chen, Chi-Chou Liao, Yu-Pao Chou, Dysan Chao, Hsing-Fang Lu, Ya-Sian Chang, Jan-Gowth Chang, Kai-Cheng Hsu, Fuu‑Jen Tsai

BioMedicine

A genome-wide association study (GWAS) can be conducted to systematically analyze the contributions of genetic factors to a wide variety of complex diseases. Nevertheless, existing GWASs have provided highly ethnic specific data. Accordingly, to provide data specific to Taiwan, we established a large-scale genetic database in a single medical institution at the China Medical University Hospital. With current technological limitations, microarray analysis can detect only a limited number of single-nucleotide polymorphisms (SNPs) with a minor allele frequency of >1%. Nevertheless, imputation represents a useful alternative means of expanding data. In this study, we compared four imputation algorithms in terms of ...

On Computing Relative Effective Population Size Estimates And Parameters From An Equilibrium Cycle Of Hermaphrodite Frequency Fluctuation Due To Mixed Reproductive Modes In Filamentous Fungi, Christopher Toomajian

Fungal Genetics Reports

Many filamentous ascomycete fungi reproduce primarily asexually, with only occasional sexual generations. This can lead to a departure from the 1:1 mating type ratio that is expected in obligate sexual populations. The relaxed selection on sexual traits also can lead to a decrease in the frequency of female fertile strains in field populations, while male fertility does not similarly decrease since male gametes also can serve as asexual spores. Both changes ultimately impact the strength of genetic drift in populations. The frequency of female sterility likely increases with the time since the last generation of sexual reproduction, such that ...

Soil Bacteria In Urban Community Gardens Have The Potential To Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer, Abdullah Ibn Mafiz, Yingshu He, Wei Zhang, Yifan Zhang

Agricultural and Environmental Sciences Faculty Research

Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in ...

Relationship Of Cultivated Grain Amaranth Species And Wild Relative Accessions, Ranjita Thapa, Matthew Edwards, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was ...

Neuroanatomical Characterization Of Fruitless P2 Neurons And Assessment Of Their Role In Female Mate Receptivity, William Yeung

Electronic Thesis and Dissertation Repository

In behaviourally isolated species, preferential mate choice for conspecifics over heterospecifics is a primary isolating barrier for reducing interspecific gene flow. Drosophila males court heterospecific females more frequently than females are sexually receptive to courting heterospecific males, emphasizing the importance of female mate preference in reproductive isolation. The neurogenetic bases of female mate preference have been elusive historically, but recent research identified the D. melanogaster fruitless (fru) P2 exon to influence both conspecific and heterospecific female receptivity. I have expanded on these findings by creating a transgenic line that expresses Gal4 under fru^P2 regulation. Driving a fluorescent reporter using ...

Editorial For The Genetics Of Alzheimer’S Disease Special Issue: October 2021, Laura Ibanez, Justin B. Miller

Sanders-Brown Center on Aging Faculty Publications

No abstract provided.

Wormcat 2.0 Defines Characteristics And Conservation Of Poorly Annotated Genes In Caenorhabditis Elegans [Preprint], Daniel P. Higgins, Caroline M. Weisman, Dominique Lui, Frank A. D’Agostino, Amy K. Walker

UMass Chan Medical School Faculty Publications

Genome-wide measurement of mRNA or protein levels provides broad data sets for biological discovery. However, subsequent computational methods are essential for uncovering the functional implications of the data as well as intuitively visualizing the findings. Current computational tools are biased toward well-described pathways, limiting their utility for novel discovery. Recently, we developed an annotation and category enrichment tool for Caenorhabditis elegans genomic data, WormCat, that provides an intuitive visualization output. Unlike GO, which excludes genes with no annotation information, WormCat 2.0 retains these genes as a special UNASSIGNED category. Here, we show that the UNASSIGNED gene category enrichment exhibits ...

Two New Species Of Byrrhinus Motschulsky, 1858 (Coleoptera, Limnichidae, Limnichinae) From Negros, Philippines, Emmanuel D. Delocado, Hendrik Freitag

Biology Faculty Publications

Two new species of Limnichidae beetles, Byrrhinus negrosensis sp. nov. and Byrrhinus villarini sp. nov., are described from the Island of Negros in the Philippines. The adult specimens of the new species can be differentiated by patterns of body punctation, colour and orientation of elytral pubescence, posterolateral angle of pronotum, tarsomere length ratio and aedeagal form. Two clades, representing the two new species, were retrieved in the Maximum Likelihood gene tree using the 3’-end of the COI gene. Maximum genetic divergence within B. negrosensis sp. nov. and B. villarini sp. nov. were recorded to be 2.3% and 1 ...

Genomics Of Postprandial Lipidomics In The Genetics Of Lipid-Lowering Drugs And Diet Network Study, Marguerite R. Irvin, May E. Montasser, Tobias Kind, Sili Fan, Dinesh K. Barupal, Amit Patki, Rikki M. Tanner, Nicole D. Armstrong, Kathleen A. Ryan, Steven A. Claas, Jeffrey R. O’Connell, Hemant K. Tiwari, Donna K. Arnett

Epidemiology Faculty Publications

Postprandial lipemia (PPL) is an important risk factor for cardiovascular disease. Inter-individual variation in the dietary response to a meal is known to be influenced by genetic factors, yet genes that dictate variation in postprandial lipids are not completely characterized. Genetic studies of the plasma lipidome can help to better understand postprandial metabolism by isolating lipid molecular species which are more closely related to the genome. We measured the plasma lipidome at fasting and 6 h after a standardized high-fat meal in 668 participants from the Genetics of Lipid-Lowering Drugs and Diet Network study (GOLDN) using ultra-performance liquid chromatography coupled ...

Sampling Bias Exaggerates A Textbook Example Of A Trophic Cascade, Elaine M. Brice, Eric J. Larsen, Daniel R. Macnulty

Aspen Bibliography

Understanding trophic cascades in terrestrial wildlife communities is a major challenge because these systems are difficult to sample properly. We show how a tradition of non-random sampling has confounded this understanding in a textbook system (Yellowstone National Park) where carnivore [Canis lupus (wolf)] recovery is associated with a trophic cascade involving changes in herbivore [Cervus canadensis (elk)] behaviour and density that promote plant regeneration. Long-term data indicate a practice of sampling only the tallest young plants overestimated regeneration of overstory aspen (Populus tremuloides) by a factor of 4–7 compared to random sampling because it favoured plants taller than the ...

Estimation Of Genetic Diversity Among Canola Accessions Using Simple Sequence Repeat Markers, Jaleel Ahmad, Muhammad Baber, Wajid Nazeer, Sana Hamdullah, Aleena Ahmad Somroo, Shaiza Ali, Rameen Fatima, Seema Aslam

Journal of Bioresource Management

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068 ...

Decoding The Equine Genome: Lessons From Encode, Sichong Peng, Jessica L. Petersen, Rebecca R. Bellone, Theodore S. Kalbfleisch, N. B. Kingsley, Alexa M. Barber, Eleonora Cappelletti, Elena Giulotto, Carrie J. Finno

Veterinary Science Faculty Publications

The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has ...