Set1 Targets Genes With Essential Identity And Tumor-Suppressing Functions In Planarian Stem Cells,
2021
University of Kentucky
Set1 Targets Genes With Essential Identity And Tumor-Suppressing Functions In Planarian Stem Cells, Prince Verma, Courtney K. M. Waterbury, Elizabeth M. Duncan
Biology Faculty Publications
Tumor suppressor genes (TSGs) are essential for normal cellular function in multicellular organisms, but many TSGs and tumor-suppressing mechanisms remain unknown. Planarian flatworms exhibit particularly robust tumor suppression, yet the specific mechanisms underlying this trait remain unclear. Here, we analyze histone H3 lysine 4 trimethylation (H3K4me3) signal across the planarian genome to determine if the broad H3K4me3 chromatin signature that marks essential cell identity genes and TSGs in mammalian cells is conserved in this valuable model of in vivo stem cell function. We find that this signature is indeed conserved on the planarian genome and that the lysine methyltransferase Set1 …
Genetic Parameter Estimates For Bull Prolificacy And Its Relationship With Scrotal Circumference In A Commercial Beef Cattle Population,
2021
University of Nebraska - Lincoln
Genetic Parameter Estimates For Bull Prolificacy And Its Relationship With Scrotal Circumference In A Commercial Beef Cattle Population, Chad A. Russell, E John Pollak, Matthew L. Spangler
Department of Animal Science: Faculty Publications
The commercial beef cattle industry relies heavily on the use of natural service sires. When artificial insemination is deemed difficult to implement, multisire breeding pastures are used to increase reproductive rates in large breeding herds or to safe-guard against bull injury during the breeding season. Although each bull might be given an equal opportunity to produce offspring, evidence suggest that there is substantial variation in the number of calves sired by each bull in a breeding pasture. With the use of DNA-based paternity testing, correctly assigning calves to their respective sires in multisire pastures is possible and presents an opportunity …
Deciphering Symbiotic Interactions Of “Candidatus Aenigmarchaeota” With Inferred Horizontal Gene Transfers And Co-Occurrence Networks,
2021
Sun Yat-Sen University
Deciphering Symbiotic Interactions Of “Candidatus Aenigmarchaeota” With Inferred Horizontal Gene Transfers And Co-Occurrence Networks, Yu-Xian Li, Yang-Zhi Rao, Yan-Ling Qi, Yan-Ni Qu, Ya-Ting Chen, Jian-Yu Jiao, Wen-Sheng Shu, Hongchen Jiang, Brian P. Hedlund, Zheng-Shuang Hua, Wen-Jun Li
Life Sciences Faculty Research
"Candidatus Aenigmarchaeota"("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota"in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota"in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota …
Commentary: Unbiasing Genome-Based Analyses Of Selection: An Example Using Iconic Shark Species,
2021
Drury University
Commentary: Unbiasing Genome-Based Analyses Of Selection: An Example Using Iconic Shark Species, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Vincent P. Richards, Stephen J. O'Brien, Agostinho Antunes, Mahmood S. Shivji
Biology Faculty Articles
No abstract provided.
Rnase Κ Promotes Robust Pirna Production By Generating 2',3'-Cyclic Phosphate-Containing Precursors,
2021
Thomas Jefferson University
Rnase Κ Promotes Robust Pirna Production By Generating 2',3'-Cyclic Phosphate-Containing Precursors, Megumi Shigematsu, Takuya Kawamura, Keisuke Morichika, Natsuko Izumi, Takashi Kiuchi, Shozo Honda, Venetia Pliatsika, Ryuma Matsubara, Isidore Rigoutsos, Susumu Katsuma, Yukihide Tomari, Yohei Kirino
Computational Medicine Center Faculty Papers
In animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2′,3′-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5′-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5′-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors. We identified Bombyx RNase Kappa (BmRNase κ) as a mitochondria-associated endoribonuclease which produces cP-RNAs during piRNA biogenesis. BmRNase κ-depletion elevated transposon levels and disrupted a piRNA-mediated …
Analysis Of The Role Of Akirin Interactions With Nuclear Body Proteins During Myogenesis,
2021
Kennesaw State University
Analysis Of The Role Of Akirin Interactions With Nuclear Body Proteins During Myogenesis, Laura Yorke
Master of Science in Integrative Biology Theses
Akirin is a highly conserved, small nuclear protein of indeterminate structure ubiquitously expressed in non-fungal eukaryotic species. It was first discovered in the innate immune response, but many other functions have since been found, including embryonic muscle patterning and myogenesis. Animals with either nonfunctional or missing Akirin have aberrations in embryonic muscle patterning, along with other defects. Akirin interacts with transcription factors such as Twist to coordinate development through interfacing between Twist and other complexes, such as the Brahma Chromatin Remodeling Complex (BRM). Therefore, Akirin likely plays a general role in transcription during early development, interfacing with other transcriptional machinery …
Mechanisms Of How Diet And Light Interact To Influence Drosophila Longevity Through The Eye,
2021
Dominican University of California
Mechanisms Of How Diet And Light Interact To Influence Drosophila Longevity Through The Eye, Charles H. Lau
Natural Sciences and Mathematics | Biological Sciences Master's Theses
Previous studies in Drosophila melanogaster have established that overexposure to light damages photoreceptors and that photoreceptor degeneration contributes to shortened lifespans. However, the role of diet and circadian rhythms in the eye has not yet been elucidated. Many vital processes in the eye are regulated by circadian rhythms, and circadian misalignment has been proven as a driver of aging. In the eye, one of the most enriched circadian functions is phototransduction. Phototransduction plays a major role in the organism’s ability to detect light. Our lab has previously proven that Dietary Restrictions (DR) can play a role in amplifying circadian rhythms …
Comparative Genomics Reveals Thermal Adaptation And A High Metabolic Diversity In “Candidatus Bathyarchaeia”,
2021
Sun Yat-Sen University
Comparative Genomics Reveals Thermal Adaptation And A High Metabolic Diversity In “Candidatus Bathyarchaeia”, Yan-Ling Qi, Paul N. Evans, Yu-Xian Li, Yang-Zhi Rao, Yan-Ni Qu, Sha Tan, Jian-Yu Jiao, Ya-Ting Chen, Brian P. Hedlund, Wen-Sheng Shu, Zheng-Shuang Hua, Wen Jun Li
Life Sciences Faculty Research
"Candidatus Bathyarchaeia"is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a …
Highly Contiguous Assemblies Of 101 Drosophilid Genomes,
2021
Stanford University
Highly Contiguous Assemblies Of 101 Drosophilid Genomes, Bernard Y. Kim, Jeremy R. Wang, Danny E. Miller, Olga Barmina, Emily Delaney, Ammon Thompson, Aaron A. Comeault, David Peede, Emmanuel R. R. D'Agostino, Julianne Pelaez, Jessica M. Aguilar, Diler Haji, Teruyuki Matsunaga, Ellie E. Armstrong, Molly Zych, Yoshitaka Ogawa, Marina Stamenković-Radak, Mihailo Jelić, Marija Savić Veselinović, Marija Tanasković, Jeremy S. Davis
Biology Faculty Publications
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, …
Highly Contiguous Assemblies Of 101 Drosophilid Genomes,
2021
Stanford University
Highly Contiguous Assemblies Of 101 Drosophilid Genomes, Bernard Y. Kim, Jeremy R. Wang, Danny E. Miller, Olga Barmina, Emily Delaney, Ammon Thompson, Aaron A. Comeault, David Peede, Emmanuel R.R. D’Agostino, Julianne Pelaez, Jessica M. Aguilar, Diler Haji, Teruyuki Matsunaga, Ellie E. Armstrong, Molly Zych, Yoshitaka Ogawa, Marina Stamenković-Radak, Mihailo Jelić, Marija Savić Veselinović, Marija Tanasković, Pavle Erić, Jian Jun Gao, Takehiro K. Katoh, Masanori J. Toda, Hideaki Watabe, Masayoshi Watada, Jeremy S. Davis, Leonie C. Moyle, Giulia Manoli, Enrico Bertolini, Vladimír Košťál, R. Scott Hawley, Aya Takahashi, Corbin D. Jones, Donald K. Price, Noah Whiteman, Artyom Kopp, Daniel R. Matute, Dmitri A. Petrov
Life Sciences Faculty Research
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, …
Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field,
2021
University of the Pacific
Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino
Pacific Journal of Health
The yeast Pichia pastoris (also known as Komagataella pastoris) has been used for over 30 years to produce thousands of valuable, heterologous proteins, such as insulin to treat diabetes and antibodies to prevent migraine headaches. Despite its success, there are some common, stubborn problems encountered by research scientists when they try to use the yeast to produce their recombinant proteins. In order to provide those working in this field with strategies to overcome these common obstacles, nine experts in P. pastoris protein expression field were interviewed to create a written review and video (https://www.youtube.com/watch?v=FyC9xXVLyD0). This review describes …
Understanding Potassium Toxicity Stress Responses Of The Extremophyte Schrenkiella Parvula Using Systems Biology Approaches,
2021
Louisiana State University and Agricultural and Mechanical College
Understanding Potassium Toxicity Stress Responses Of The Extremophyte Schrenkiella Parvula Using Systems Biology Approaches, Pramod Pantha
LSU Doctoral Dissertations
Schrenkiella parvula is an extremophyte model closely related to Arabidopsis thaliana and Brassica crops. Its natural habitat includes shores of saline lakes in the Irano-Turanian region. It has adapted to grow in soils rich in multiple salts including Na+ and K+. I have investigated the genetic basis for high K+ tolerance in plants using S. parvula as a stress tolerant model compared to the premier plant model, Arabidopsis thaliana which is highly sensitive to salt stresses using physiological, ionomic, transcriptomic, and metabolomic approaches. Under high K+ stress, root system architecture changes significantly compared to control …
The Biodiversity Of Freshwater Crustaceans Revealed By Taxonomy And Mitochondrial Dna Barcodes,
2021
Wayne State University
The Biodiversity Of Freshwater Crustaceans Revealed By Taxonomy And Mitochondrial Dna Barcodes, Adrian Amelio Vasquez, Brittany L. Bonnici, Donna R. Kashian, Jorge Trejo-Martinez, Carol J. Miller, Jeffrey L. Ram
Physiology Faculty Research Publications
Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from specimens collected by plankton net in western Lake Erie in 2012 & 2013, along with later specimens collected at various locations and times, including some collected in Belize in 2015. Methods and other details about these sequences are described in a paper by the same authors in a submitted publication (2021: URL to be given here when published). The right columns below contain additional notes on lengths of sequences, GenBank accession ID (when obtained), and annotation as to whether the sequence represents a new barcode for its …
The Role Of Interspecies Recombination In The Evolution Of Antibiotic-Resistant Pneumococci,
2021
Imperial College London, London, United Kingdom
The Role Of Interspecies Recombination In The Evolution Of Antibiotic-Resistant Pneumococci, Joshua C. D'Aeth, Mark Pg Van Der Linden, Lesley Mcgee, Herminia De Lencastre, Paul Turner, Jae-Hoon Song, Stephanie W. Lo, Rebecca A. Gladstone, Gps Consortium, Sadia Shakoor
Department of Pathology and Laboratory Medicine
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking …
Comparative Genomics Methods And Applications,
2021
University of new mexico
Comparative Genomics Methods And Applications, Emily N. Alden
Biomedical Sciences ETDs
Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …
Leveraging Multiple Data Sources: How Catch Data, Metadata, And Genetic Samples Can Aid The Recovery Of Endangered Smalltooth Sawfish (Pristis Pectinata),
2021
Louisiana State University and Agricultural and Mechanical College
Leveraging Multiple Data Sources: How Catch Data, Metadata, And Genetic Samples Can Aid The Recovery Of Endangered Smalltooth Sawfish (Pristis Pectinata), Kelcee Smith
LSU Doctoral Dissertations
The small population sizes characteristic of many imperiled species means that they are vulnerable to both demographic and genetic extinction threats. Responses to these threats (e.g., population trends, genetic diversity estimates) are often difficult to obtain, but critical for conservation. Thus, researchers studying imperiled species may have to consult multiple data sources, collaborate with a wide variety of stakeholders, or ask new questions about previously collected data. I used this approach to understand more about the United States (U.S.) population of Pristis pectinata, an endangered elasmobranch that has declined up to 95% due to habitat loss and bycatch in …
Availability And Structure Of Coarse Woody Debris In Hemiboreal Mature To Old-Growth Aspen Stands And Its Implications For Forest Carbon Pool,
2021
Latvian State Forest Research Institute Silava
Availability And Structure Of Coarse Woody Debris In Hemiboreal Mature To Old-Growth Aspen Stands And Its Implications For Forest Carbon Pool, Silva Šēnhofa, Guntars Šnepsts, Kārlis Bičkovskis, Ieva Jaunslaviete, Līga Liepa, Inga Straupe, Āris Jansons
Aspen Bibliography
European aspen deadwood is extensively studied as a habitat for saproxylic species, while less is known of its dynamics and role in carbon sequestration. We studied unmanaged mature (41–60 years), moderately overmature (61–80 years), overmature (81–100 years), and old-growth (101–140 years) and managed mature and moderately overmature aspen stands on fertile mineral soils. In unmanaged stands, marginal mean CWD volume was from 67.3 ± 12.1 m3 ha−1 in moderately overmature to 92.4 ± 5.1 m3 ha−1 in old-growth stands, with corresponding marginal mean CWD carbon pool 8.2 ± 1.6 t ha−1 and 12.5 ± 0.7 …
The Effects Of Climate And Demographic History In Shaping Genomic Variation Across Populations Of The Desert Horned Lizard (Phrynosoma Platyrhinos),
2021
Miami University - Oxford
The Effects Of Climate And Demographic History In Shaping Genomic Variation Across Populations Of The Desert Horned Lizard (Phrynosoma Platyrhinos), Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe, Tereza Jezkova
Publications and Research
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization …
Biallelic Variants In Pcdhgc4 Cause A Novel Neurodevelopmental Syndrome With Progressive Microcephaly, Seizures, And Joint Anomalies,
2021
University of Cologne and University Hospital Cologne, Cologne, Germany
Biallelic Variants In Pcdhgc4 Cause A Novel Neurodevelopmental Syndrome With Progressive Microcephaly, Seizures, And Joint Anomalies, Maria Iqbal, Reza Maroofian, Büşranur Çavdarlı, Florence Riccardi, Michael Field, Siddharth Banka, Dalal K. Bubshait, Yun Li, Jozef Hertecant, Shahid Mahmood Baig
Department of Biological & Biomedical Sciences
Purpose: We aimed to define a novel autosomal recessive neurodevelopmental disorder, characterize its clinical features, and identify the underlying genetic cause for this condition.
Methods: We performed a detailed clinical characterization of 19 individuals from nine unrelated, consanguineous families with a neurodevelopmental disorder. We used genome/exome sequencing approaches, linkage and cosegregation analyses to identify disease-causing variants, and we performed three-dimensional molecular in silico analysis to predict causality of variants where applicable.
Results: In all affected individuals who presented with a neurodevelopmental syndrome with progressive microcephaly, seizures, and intellectual disability we identified biallelic disease-causing variants in Protocadherin-gamma-C4 (PCDHGC4). Five variants were …
Coarse Woody Debris Decomposition Assessment Tool: Model Validation And Application,
2021
USDA Forest Service
Coarse Woody Debris Decomposition Assessment Tool: Model Validation And Application, Zhaohua Dai, Carl C. Trettin, Andrew J. Burton, Martin F. Jurgensen, Deborah S. Page-Dumroese, Brian T. Forschler, Jonathan S. Schilling, Daniel L. Lindner
Aspen Bibliography
Coarse woody debris (CWD) is a significant component of the forest biomass pool; hence a model is warranted to predict CWD decomposition and its role in forest carbon (C) and nutrient cycling under varying management and climatic conditions. A process-based model, CWDDAT (Coarse Woody Debris Decomposition Assessment Tool) was calibrated and validated using data from the FACE (Free Air Carbon Dioxide Enrichment) Wood Decomposition Experiment utilizing pine (Pinus taeda), aspen (Populous tremuloides) and birch (Betula papyrifera) on nine Experimental Forests (EF) covering a range of climate, hydrology, and soil conditions across the continental USA. …
