Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Plant Sciences (50)
- Ecology and Evolutionary Biology (9)
- Genetics and Genomics (4)
- Microbiology (4)
- Plant Biology (3)
-
- Botany (2)
- Cell and Developmental Biology (2)
- Comparative and Evolutionary Physiology (2)
- Entomology (2)
- Evolution (2)
- Physiology (2)
- Social and Behavioral Sciences (2)
- Animal Studies (1)
- Bacteriology (1)
- Biochemistry, Biophysics, and Structural Biology (1)
- Biodiversity (1)
- Bioinformatics (1)
- Developmental Biology (1)
- Education (1)
- Forest Sciences (1)
- Genomics (1)
- Higher Education (1)
- Immunology and Infectious Disease (1)
- Scholarship of Teaching and Learning (1)
- Sociology (1)
- Institution
- Keyword
-
- Student Publications (27)
- Fungi (18)
- Phylogeny (10)
- Drosophila (9)
- Evolution (7)
-
- DNA methylation (5)
- Gene expression (5)
- Transcriptome (5)
- Annelida (4)
- Capitella teleta (4)
- Development (4)
- Dictyostelium (4)
- Genetic variation (4)
- Mosquito (4)
- Phylogenetic analysis (4)
- Plasticity (4)
- Resorption proficiency (4)
- Spiralia (4)
- Anthocyanins (3)
- Autumn migration (3)
- Bees (3)
- Biogeography (3)
- Biomechanics (3)
- Bone Morphogenetic Protein (BMP) (3)
- CcrM (3)
- Cell cycle (3)
- Cyanobacteria (3)
- Genome (3)
- Genomics (3)
- Machine learning (3)
- Publication Year
- Publication Type
- File Type
Articles 61 - 90 of 377
Full-Text Articles in Biology
Proteome Of The Wood Decay Fungus Fomitopsis Pinicola Is Altered By Substrate, Grzegorz Sabat, Steven Ahrendt, Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu V. Vuong, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette, David S. Hibbett, Jennifer Bhatnagar, Daniel Cullen
Proteome Of The Wood Decay Fungus Fomitopsis Pinicola Is Altered By Substrate, Grzegorz Sabat, Steven Ahrendt, Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu V. Vuong, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette, David S. Hibbett, Jennifer Bhatnagar, Daniel Cullen
Biology
The brown rot fungus Fomitopsis pinicola efficiently depolymerizes wood cellulose via the combined activities of oxidative and hydrolytic enzymes. Mass spectrometric analyses of culture filtrates identified specific proteins, many of which were differentially regulated in response to substrate composition.
The Timing And Development Of Infections In A Fish-Cestode Host-Parasite System, Anika M. Wohlleben, Natalie C. Steinel, Néva P. Meyer, John A. Baker, Susan A. Foster
The Timing And Development Of Infections In A Fish-Cestode Host-Parasite System, Anika M. Wohlleben, Natalie C. Steinel, Néva P. Meyer, John A. Baker, Susan A. Foster
Biology
The cestode Schistocephalus solidus is a common parasite in freshwater threespine stickleback populations, imposing strong fitness costs on their hosts. Given this, it is surprising how little is known about the timing and development of infections in natural stickleback populations. Previous work showed that young-of-year stickleback can get infected shortly after hatching. We extended this observation by comparing infection prevalence of young-of-year stickleback from 3 Alaskan populations (Walby, Cornelius and Wolf lakes) over 2 successive cohorts (2018/19 and 2019/20). We observed strong variation between sampling years (2018 vs 2019 vs 2020), stickleback age groups (young-of-year vs 1-year-old) and sampling populations.
Differential Dna Methylation In Pacific Oyster Reproductive Tissue In Response To Ocean Acidification, Yaamini R. Venkataraman, Samuel J. White, Steven B. Roberts
Differential Dna Methylation In Pacific Oyster Reproductive Tissue In Response To Ocean Acidification, Yaamini R. Venkataraman, Samuel J. White, Steven B. Roberts
Biology
Background
There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were …
Its Rdna Barcodes Clarify Molecular Diversity Of Aquatic Hyphomycetes, Ricardo Franco-Duarte, Isabel Fernandes, Vladislav Gulis, Fernanda Cássio, Cláudia Pascoal
Its Rdna Barcodes Clarify Molecular Diversity Of Aquatic Hyphomycetes, Ricardo Franco-Duarte, Isabel Fernandes, Vladislav Gulis, Fernanda Cássio, Cláudia Pascoal
Biology
Aquatic hyphomycetes are key microbial decomposers of allochthonous organic matter in freshwater ecosystems. Although their importance in carbon flow and food webs in streams is widely recognized, there are still gaps in our understanding of their molecular diversity and distribution patterns. Our study utilized the growing database of ITS rDNA barcodes of aquatic hyphomycetes (1252 sequences) and aimed to (i) produce new barcodes for some lesser-known taxa; (ii) clarify the taxonomic placement of some taxa at the class or order level, based on molecular data; and (iii) provide insights into the biogeographical origins of some taxa. This study increased the …
Student Attitudes Contribute To The Effectiveness Of A Genomics Cure, David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. Diangelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E.J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Justin Thackeray
Student Attitudes Contribute To The Effectiveness Of A Genomics Cure, David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. Diangelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E.J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Justin Thackeray
Biology
The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect …
Coordinating Tiny Limbs And Long Bodies: Geometric Mechanics Of Lizard Terrestrial Swimming, Baxi Chong, Tianyu Wang, Eva Erickson, Philip J. Bergmann, Daniel I. Goldman
Coordinating Tiny Limbs And Long Bodies: Geometric Mechanics Of Lizard Terrestrial Swimming, Baxi Chong, Tianyu Wang, Eva Erickson, Philip J. Bergmann, Daniel I. Goldman
Biology
Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body–limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards (Brachymeles and Lerista) and laboratory studies of fully limbed lizards (Uma scoparia and Sceloporus olivaceus) and a snake (Chionactis occipitalis) reveal that body-wave dynamics …
Population Genomics Provides Insights Into The Genetic Basis Of Adaptive Evolution In The Mushroom-Forming Fungus Lentinula Edodes, Jingcheng Zhang, Nan Shen, Chuang Li, Xingjie Xiang, Gaolei Liu, Ying Gui, Sean Patev, David S. Hibbett, Kerrie Barry, William Andreopoulos, Anna Lipzen, Robert Riley, Guifen He, Mi Yan, Igor V. Grigoriev, Hoi Shan Kwan, Man Kit Cheung, Yinbing Bian, Yang Xiao
Population Genomics Provides Insights Into The Genetic Basis Of Adaptive Evolution In The Mushroom-Forming Fungus Lentinula Edodes, Jingcheng Zhang, Nan Shen, Chuang Li, Xingjie Xiang, Gaolei Liu, Ying Gui, Sean Patev, David S. Hibbett, Kerrie Barry, William Andreopoulos, Anna Lipzen, Robert Riley, Guifen He, Mi Yan, Igor V. Grigoriev, Hoi Shan Kwan, Man Kit Cheung, Yinbing Bian, Yang Xiao
Biology
Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of …
The Life History Of Drosophila Sperm Involves Molecular Continuity Between Male And Female Reproductive Tracts, Erin L. Mccullough, Emma Whittington, Akanksha Singh, Scott Pitnick, Mariana F. Wolfner, Steve Dorus
The Life History Of Drosophila Sperm Involves Molecular Continuity Between Male And Female Reproductive Tracts, Erin L. Mccullough, Emma Whittington, Akanksha Singh, Scott Pitnick, Mariana F. Wolfner, Steve Dorus
Biology
Interactions between sperm and the female reproductive tract (FRT) are critical to reproductive success and yet are poorly understood. Because sperm complete their functional maturation within the FRT, the life history of sperm is likely to include a molecular “hand-off” from males to females. Although such intersexual molecular continuity is likely to be widespread among all internally fertilizing species, the identity and extent of female contributions are largely unknown. We combined semiquantitative proteomics with sex-specific isotopic labeling to catalog the posttesticular life history of the sperm proteome and determine the extent of molecular continuity between male and FRTs. We show …
What Are The Primary Cues Used By Mammalian Predators To Locate Freshwater Turtle Nests? A Critical Review Of The Evidence, Gregory A. Geller, Scott L. Parker
What Are The Primary Cues Used By Mammalian Predators To Locate Freshwater Turtle Nests? A Critical Review Of The Evidence, Gregory A. Geller, Scott L. Parker
Biology
Turtle biologists have long been interested in the biotic and abiotic factors that influence the detection of freshwater turtle nests by mammalian predators. Increased knowledge of nest predation dynamics may help develop conservation strategies to increase turtle nesting success by altering or reducing the signal strength of predominant nest location cues. However, despite this long-standing interest, the related research has produced inconsistent and sometimes conflicting results across studies. Here we review much of the existing literature on freshwater turtle nest predation by mammalian predators and attempt to synthesize some general, underlying themes. Available data suggest that raccoons (Procyon lotor) primarily …
Invertebrate Grazing On Live Turtlegrass (Thalassia Testudinum): A Common Interaction That May Facilitate Fungal Growth, Anjali D. Boyd, Nia S. Walker, Stephanie R. Valdez, Y. Stacy Zhang, Andrew H. Altieri, Vladislav Gulis, Caitlin Crain, Brian Silliman
Invertebrate Grazing On Live Turtlegrass (Thalassia Testudinum): A Common Interaction That May Facilitate Fungal Growth, Anjali D. Boyd, Nia S. Walker, Stephanie R. Valdez, Y. Stacy Zhang, Andrew H. Altieri, Vladislav Gulis, Caitlin Crain, Brian Silliman
Biology
In coastal wetlands and tropical reefs, snails can regulate foundation species by feeding on marsh grasses and hard corals. In many cases, their impacts are amplified because they facilitate microbial infection in grazer-induced wounds. Whether snails commonly graze live plants and facilitate microbial growth on plants in tropical seagrass systems is less explored. On a Belizean Caye, we examined patterns in snail-generated grazer scars on the abundant turtlegrass (Thalassia testudinum). Our initial survey showed the occurrence of snail-induced scarring on live turtlegrass blades was common, with 57% of live leaves scarred. Feeding trials demonstrated that two of five common snails …
Evolutionary Morphogenesis Of Sexual Fruiting Bodies In Basidiomycota: Toward A New Evo-Devo Synthesis, Máté Virágh, Zsolt Merényi, Árpád Csernetics, Csenge Földi, Neha Sahu, Xiao Bin Liu, David S. Hibbett, László G. Nagy
Evolutionary Morphogenesis Of Sexual Fruiting Bodies In Basidiomycota: Toward A New Evo-Devo Synthesis, Máté Virágh, Zsolt Merényi, Árpád Csernetics, Csenge Földi, Neha Sahu, Xiao Bin Liu, David S. Hibbett, László G. Nagy
Biology
SUMMARY The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body …
Empowering Melatonin Therapeutics With Drosophila Models, Cassandra Millet-Boureima, Caroline C. Ennis, Jurnee Jamison, Shana Mcsweeney, Anna Park, Chiara Gamberi
Empowering Melatonin Therapeutics With Drosophila Models, Cassandra Millet-Boureima, Caroline C. Ennis, Jurnee Jamison, Shana Mcsweeney, Anna Park, Chiara Gamberi
Biology
Melatonin functions as a central regulator of cell and organismal function as well as a neurohormone involved in several processes, e.g., the regulation of the circadian rhythm, sleep, aging, oxidative response, and more. As such, it holds immense pharmacological potential. Receptor-mediated melatonin function mainly occurs through MT1 and MT2, conserved amongst mammals. Other melatonin-binding proteins exist. Non-receptor-mediated activities involve regulating the mitochondrial function and antioxidant cascade, which are frequently affected by normal aging as well as disease. Several pathologies display diseased or dysfunctional mitochondria, suggesting melatonin may be used therapeutically. Drosophila models have extensively been employed to study disease pathogenesis …
A Docked Mutation Phenocopies Dumpy Oblique Alleles Via Altered Vesicle Trafficking, Suresh Kandasamy, Kiley Couto, Justin Thackeray
A Docked Mutation Phenocopies Dumpy Oblique Alleles Via Altered Vesicle Trafficking, Suresh Kandasamy, Kiley Couto, Justin Thackeray
Biology
The Drosophila extracellular matrix protein Dumpy (Dpy) is one of the largest proteins encoded by any animal. One class of dpy mutations produces a characteristic shortening of the wing blade known as oblique (dpyo), due to altered tension in the developing wing. We describe here the characterization of docked (doc), a gene originally named because of an allele producing a truncated wing. We show that doc corresponds to the gene model CG5484, which encodes a homolog of the yeast protein Yif1 and plays a key role in ER to Golgi vesicle transport. Genetic analysis is consistent with a similar role …
Linking Ecomechanical Models And Functional Traits To Understand Phenotypic Diversity, Timothy E. Higham, Lara A. Ferry, Lars Schmitz, Duncan J. Irschick, Samuel Starko, Philip S.L. Anderson, Philip J. Bergmann, Heather A. Jamniczky, Leandro R. Monteiro, Dina Navon, Julie Messier, Emily Carrington, Stacy C. Farina, Kara L. Feilich, L. Patricia Hernandez, Michele A. Johnson, Sandy M. Kawano, Chris J. Law, Sarah J. Longo, Christopher H. Martin, Patrick T. Martone, Alejandro Rico-Guevara, Sharlene E. Santana, Karl J. Niklas
Linking Ecomechanical Models And Functional Traits To Understand Phenotypic Diversity, Timothy E. Higham, Lara A. Ferry, Lars Schmitz, Duncan J. Irschick, Samuel Starko, Philip S.L. Anderson, Philip J. Bergmann, Heather A. Jamniczky, Leandro R. Monteiro, Dina Navon, Julie Messier, Emily Carrington, Stacy C. Farina, Kara L. Feilich, L. Patricia Hernandez, Michele A. Johnson, Sandy M. Kawano, Chris J. Law, Sarah J. Longo, Christopher H. Martin, Patrick T. Martone, Alejandro Rico-Guevara, Sharlene E. Santana, Karl J. Niklas
Biology
Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This ‘ecomechanical approach’ integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, …
Modeling Neoplastic Growth In Renal Cell Carcinoma And Polycystic Kidney Disease, Cassandra Millet-Boureima, Stephanie He, Thi Bich Uyen Le, Chiara Gamberi
Modeling Neoplastic Growth In Renal Cell Carcinoma And Polycystic Kidney Disease, Cassandra Millet-Boureima, Stephanie He, Thi Bich Uyen Le, Chiara Gamberi
Biology
Renal cell carcinoma (RCC) and autosomal dominant polycystic kidney disease (ADPKD) share several characteristics, including neoplastic cell growth, kidney cysts, and limited therapeu-tics. As well, both exhibit impaired vasculature and compensatory VEGF activation of angiogenesis. The PI3K/AKT/mTOR and Ras/Raf/ERK pathways play important roles in regulating cystic and tumor cell proliferation and growth. Both RCC and ADPKD result in hypoxia, where HIF-α signaling is activated in response to oxygen deprivation. Primary cilia and altered cell metabolism may play a role in disease progression. Non-coding RNAs may regulate RCC carcinogenesis and ADPKD through their varied effects. Drosophila exhibits remarkable conservation of the …
Creepy Crawly Compensation: Examining The Costs Of Ectoparasite-Induced Compensatory Growth In Late-Stage Nestlings, Elliot Lusk
Creepy Crawly Compensation: Examining The Costs Of Ectoparasite-Induced Compensatory Growth In Late-Stage Nestlings, Elliot Lusk
Biology
When normal growth rates are suppressed, organisms may undergo a rapid period of increased growth in order to match the physical requirements of a developmental benchmark. This compensatory growth, however, is not without its costs, which can have varying consequences. In nestlings, a major benchmark is that of fledging, which requires advanced physical maturation. In previous studies, compensatory growth and some of its associated costs have been shown in prefledging nestlings but fledging-aged nestlings and the costs they may have sustained needs further study. Here we examine the costs of compensatory growth in late-stage European starling (Sturnus vulgaris) nestlings under …
Niche Partitioning Of Low-Light Adapted Prochlorococcus Subecotypes Across Oceanographic Gradients Of The North Pacific Subtropical Front, Anne W. Thompson, Kathleen Kouba, Nathan A. Ahlgren
Niche Partitioning Of Low-Light Adapted Prochlorococcus Subecotypes Across Oceanographic Gradients Of The North Pacific Subtropical Front, Anne W. Thompson, Kathleen Kouba, Nathan A. Ahlgren
Biology
The cyanobacterium Prochlorococcus is the most abundant photosynthetic cell on Earth and contributes to global ocean carbon cycling and food webs. Prochlorococcus is known for its extensive diversity that falls into two groups of ecotypes, the low-light (LL) and high-light (HL) adapted ecotypes. Previous work has shown niche partitioning of the very abundant HL adapted ecotypes and subecotypes across oceanographic gradients including temperature, nutrients, and day length. However, niche partitioning of subecotypes within the LL adapted ecotypes has not been studied as well because they are less abundant and less accessible than surface, HL populations. Through high-throughput, cyanobacterial-specific, sequencing of …
Genomic Analysis Enlightens Agaricales Lifestyle Evolution And Increasing Peroxidase Diversity, Francisco J. Ruiz-Dueñas, José M. Barrasa, Marisol Sánchez-García, Susana Camarero, Shingo Miyauchi, Ana Serrano, Dolores Linde, Rashid Babiker, Elodie Drula, Iván Ayuso-Fernández, Remedios Pacheco, Guillermo Padilla, Patricia Ferreira, Jorge Barriuso, Harald Kellner, Raúl Castanera, Manuel Alfaro, Lucía Ramírez, Antonio G. Pisabarro, Robert Riley, Alan Kuo, William Andreopoulos, Kurt Labutti, Jasmyn Pangilinan, Andrew Tritt, Anna Lipzen, Guifen He, Mi Yan, Vivian Ng, Igor V. Grigoriev, Daniel Cullen, Francis Martin, David Hibbett
Genomic Analysis Enlightens Agaricales Lifestyle Evolution And Increasing Peroxidase Diversity, Francisco J. Ruiz-Dueñas, José M. Barrasa, Marisol Sánchez-García, Susana Camarero, Shingo Miyauchi, Ana Serrano, Dolores Linde, Rashid Babiker, Elodie Drula, Iván Ayuso-Fernández, Remedios Pacheco, Guillermo Padilla, Patricia Ferreira, Jorge Barriuso, Harald Kellner, Raúl Castanera, Manuel Alfaro, Lucía Ramírez, Antonio G. Pisabarro, Robert Riley, Alan Kuo, William Andreopoulos, Kurt Labutti, Jasmyn Pangilinan, Andrew Tritt, Anna Lipzen, Guifen He, Mi Yan, Vivian Ng, Igor V. Grigoriev, Daniel Cullen, Francis Martin, David Hibbett
Biology
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates - namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose-methanol-choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases - we reconstructed the lifestyles of …
Exotic Legume's Leaf Litter Beneficial To Prairie Plants, Asher Gardner
Exotic Legume's Leaf Litter Beneficial To Prairie Plants, Asher Gardner
Biology
Lespedeza cuneata is an invasive, non-native species of bush clover that is invading prairies where the native Lespedeza capitata grows. Both species of bush clover are legumes, which are nitrogen fixers. Legumes and their senescent leaves (i.e., “litter”) are well known for increasing levels of available nitrogen in the soil. However, the exotic L. cuneata also produces tannins that reduce the rate of germination in some prairie plants. The purpose of this study was to clarify whether these compounds in the litter of the invasive species of bush clover deter early growth in its native competitors, and to determine whether …
Resolving Transcriptional States And Predicting Lineages In The Annelid Capitella Teleta Using Single-Cell Rnaseq, Abhinav Sur, Néva P. Meyer
Resolving Transcriptional States And Predicting Lineages In The Annelid Capitella Teleta Using Single-Cell Rnaseq, Abhinav Sur, Néva P. Meyer
Biology
Evolution and diversification of cell types has contributed to animal evolution. However, gene regulatory mechanisms underlying cell fate acquisition during development remains largely uncharacterized in spiralians. Here we use a whole-organism, single-cell transcriptomic approach to map larval cell types in the annelid Capitella teleta at 24- and 48-h post gastrulation (stages 4 and 5). We identified eight unique cell clusters (undifferentiated precursors, ectoderm, muscle, ciliary-band, gut, neurons, neurosecretory cells, and protonephridia), thus helping to identify uncharacterized molecular signatures such as previously unknown neurosecretory cell markers in C. teleta. Analysis of coregulatory programs in individual clusters revealed gene interactions that can …
Fishes Of The Cypress Creek System, Tennessee River Drainage, Jeffery M. Ray, Mitchell S. Lovell, Benjamin S. Wilson, Stuart W. Mcgregor, Gary A. Hastert
Fishes Of The Cypress Creek System, Tennessee River Drainage, Jeffery M. Ray, Mitchell S. Lovell, Benjamin S. Wilson, Stuart W. Mcgregor, Gary A. Hastert
Biology
Cypress Creek is a northern tributary to the Tennessee River (Pickwick Lake) in Lauderdale County, Alabama, and Wayne County, Tennessee, with a drainage area of 214 square miles. Although repeatedly sampled for fishes such as Slackwater Darter, Etheostoma boschungi, Tuscumbia Darter, E. tuscumbia, and Flame Chub, Hemitremia flammea, over the past several decades, the last comprehensive fish survey of the watershed was conducted in 1971, and changes in the fish fauna and community composition may have occurred. Historical data (1845‐ 2019) containing 5,105 records was compiled for 109 species reported at least once from the Cypress Creek system. Samples from …
Fruiting Body Form, Not Nutritional Mode, Is The Major Driver Of Diversification In Mushroom-Forming Fungi, Marisol Sánchez-García, Martin Ryberg, Faheema Kalsoom Khan, Torda Varga, László G. Nagy, David S. Hibbett
Fruiting Body Form, Not Nutritional Mode, Is The Major Driver Of Diversification In Mushroom-Forming Fungi, Marisol Sánchez-García, Martin Ryberg, Faheema Kalsoom Khan, Torda Varga, László G. Nagy, David S. Hibbett
Biology
With ∼36,000 described species, Agaricomycetes are among the most successful groups of Fungi. Agaricomycetes display great diversity in fruiting body forms and nutritional modes. Most have pileate-stipitate fruiting bodies (with a cap and stalk), but the group also contains crust-like resupinate fungi, polypores, coral fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some Agaricomycetes enter into ectomycorrhizal symbioses with plants, while others are decayers (saprotrophs) or pathogens. We constructed a megaphylogeny of 8,400 species and used it to test the following five hypotheses regarding the evolution of morphological and ecological traits in Agaricomycetes and their impact on diversification: 1) resupinate …
Large-Scale Genome Sequencing Of Mycorrhizal Fungi Provides Insights Into The Early Evolution Of Symbiotic Traits, Shingo Miyauchi, Enikő Kiss, Alan Kuo, Elodie Drula, Annegret Kohler, Marisol Sánchez-García, Emmanuelle Morin, Bill Andreopoulos, Kerrie W. Barry, Gregory Bonito, Marc Buée, Akiko Carver, Cindy Chen, Nicolas Cichocki, Alicia Clum, David Culley, Pedro W. Crous, Laure Fauchery, Mariangela Girlanda, Richard D. Hayes, Zsófia Kéri, Kurt Labutti, Anna Lipzen, Vincent Lombard, Jon Magnuson, François Maillard, Claude Murat, Matt Nolan, Robin A. Ohm, Jasmyn Pangilinan, Maíra De Freitas Pereira, Silvia Perotto, David Hibbett
Large-Scale Genome Sequencing Of Mycorrhizal Fungi Provides Insights Into The Early Evolution Of Symbiotic Traits, Shingo Miyauchi, Enikő Kiss, Alan Kuo, Elodie Drula, Annegret Kohler, Marisol Sánchez-García, Emmanuelle Morin, Bill Andreopoulos, Kerrie W. Barry, Gregory Bonito, Marc Buée, Akiko Carver, Cindy Chen, Nicolas Cichocki, Alicia Clum, David Culley, Pedro W. Crous, Laure Fauchery, Mariangela Girlanda, Richard D. Hayes, Zsófia Kéri, Kurt Labutti, Anna Lipzen, Vincent Lombard, Jon Magnuson, François Maillard, Claude Murat, Matt Nolan, Robin A. Ohm, Jasmyn Pangilinan, Maíra De Freitas Pereira, Silvia Perotto, David Hibbett
Biology
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve …
Ocean Acidification Induces Subtle Shifts In Gene Expression And Dna Methylation In Mantle Tissue Of The Eastern Oyster (Crassostrea Virginica), Alan M. Downey-Wall, Louise P. Cameron, Brett M. Ford, Elise M. Mcnally, Yaamini R. Venkataraman, Steven B. Roberts, Justin B. Ries, Katie E. Lotterhos
Ocean Acidification Induces Subtle Shifts In Gene Expression And Dna Methylation In Mantle Tissue Of The Eastern Oyster (Crassostrea Virginica), Alan M. Downey-Wall, Louise P. Cameron, Brett M. Ford, Elise M. Mcnally, Yaamini R. Venkataraman, Steven B. Roberts, Justin B. Ries, Katie E. Lotterhos
Biology
Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (Crassostrea virginica) exposed to experimental OA over 80 days. Oysters were reared under three experimental pCO2 treatments (“control,” 580 μatm; “moderate OA,” 1,000 μatm; “high OA,” 2,800 μatm) and sampled at 6 time points (24 h−80 days). We found that high OA initially induced …
Genome Sequences Of Synechococcus Sp. Strain Mit S9220 And Cocultured Cyanophage Synmits9220m01, B. Shafer Belisle, Andres A.Avila Paz, Angelina R. Carpenter, Tayla C. Cormier, Adam J. Lewis, Linnea S. Menin, Daniel R. Oliveira, Bukyung Song, Amy Szeto, Elizabeth I. Tchantouridze, Kayleigh A. Watson, Mary T. Yohannes, Nathan A. Ahlgren
Genome Sequences Of Synechococcus Sp. Strain Mit S9220 And Cocultured Cyanophage Synmits9220m01, B. Shafer Belisle, Andres A.Avila Paz, Angelina R. Carpenter, Tayla C. Cormier, Adam J. Lewis, Linnea S. Menin, Daniel R. Oliveira, Bukyung Song, Amy Szeto, Elizabeth I. Tchantouridze, Kayleigh A. Watson, Mary T. Yohannes, Nathan A. Ahlgren
Biology
Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.
Investigating Cellular And Molecular Mechanisms Of Neurogenesis In Capitella Teleta Sheds Light On The Ancestor Of Annelida, A. Sur, A. Renfro, P. J. Bergmann, N. P. Meyer
Investigating Cellular And Molecular Mechanisms Of Neurogenesis In Capitella Teleta Sheds Light On The Ancestor Of Annelida, A. Sur, A. Renfro, P. J. Bergmann, N. P. Meyer
Biology
Background: Diverse architectures of nervous systems (NSs) such as a plexus in cnidarians or a more centralized nervous system (CNS) in insects and vertebrates are present across Metazoa, but it is unclear what selection pressures drove evolution and diversification of NSs. One underlying aspect of this diversity lies in the cellular and molecular mechanisms driving neurogenesis, i.e. generation of neurons from neural precursor cells (NPCs). In cnidarians, vertebrates, and arthropods, homologs of SoxB and bHLH proneural genes control different steps of neurogenesis, suggesting that some neurogenic mechanisms may be conserved. However, data are lacking for spiralian taxa. Results: To that …
Uv Radiation Increases Flavonoid Protection But Decreases Reproduction In Silene Littorea, José Carlos Del Valle, Mª Luisa Buide, Justen B. Whittall, Fernando Valladares, Eduardo Narbona
Uv Radiation Increases Flavonoid Protection But Decreases Reproduction In Silene Littorea, José Carlos Del Valle, Mª Luisa Buide, Justen B. Whittall, Fernando Valladares, Eduardo Narbona
Biology
Plants respond to changes in ultraviolet (UV) radiation both morphologically and physiologically. Among the variety of plant UV-responses, the synthesis of UV-absorbing flavonoids constitutes an effective non-enzymatic mechanism to mitigate photoinhibitory and photooxidative damage caused by UV stress, either reducing the penetration of incident UV radiation or acting as quenchers of reactive oxygen species (ROS). In this study, we designed a UV-exclusion experiment to investigate the effects of UV radiation in Silene littorea. We spectrophotometrically quantified concentrations of both anthocyanins and UV-absorbing phenolic compounds in petals, calyces, leaves and stems. Furthermore, we analyzed the UV effect on the photosynthetic …
A Network-Based Integrated Framework For Predicting Virus–Prokaryote Interactions, Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, Nathan A. Ahlgren
A Network-Based Integrated Framework For Predicting Virus–Prokaryote Interactions, Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, Nathan A. Ahlgren
Biology
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (s2∗ and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, …
Genome Skimming And Microsatellite Analysis Reveal Contrasting Patterns Of Genetic Diversity In A Rare Sandhill Endemic (Erysimum Teretifolium, Brassicaceae), José Carlos Del Valle, Julie A. Herman, Justen B. Whittall
Genome Skimming And Microsatellite Analysis Reveal Contrasting Patterns Of Genetic Diversity In A Rare Sandhill Endemic (Erysimum Teretifolium, Brassicaceae), José Carlos Del Valle, Julie A. Herman, Justen B. Whittall
Biology
Barriers between islands often inhibit gene flow creating patterns of isolation by distance. In island species, the majority of genetic diversity should be distributed among isolated populations. However, a self-incompatible mating system leads to higher genetic variation within populations and very little between-population subdivision. We examine these two contrasting predictions in Erysimum teretifolium, a rare self-incompatible plant endemic to island-like sandhill habitats in Santa Cruz County, California. We used genome skimming and nuclear microsatellites to assess the distribution of genetic diversity within and among eight of the 13 remaining populations. Phylogenetic analyses of the chloroplast genomes revealed a deep …
Phylogeny And Floral Character Evolution Of Mentzelia Section Bicuspidaria (Loasaceae), Joshua M. Brokaw, John J. Schenk, Jessica K. Devitt, Destiny J. Brokaw
Phylogeny And Floral Character Evolution Of Mentzelia Section Bicuspidaria (Loasaceae), Joshua M. Brokaw, John J. Schenk, Jessica K. Devitt, Destiny J. Brokaw
Biology
Mentzelia section Bicuspidaria (Loasaceae) is a monophyletic group of desert ephemerals that inhabit the complex, heterogeneous landscapes of the southwestern United States and northwestern Mexico. To investigate species circumscriptions and evolutionary relationships in M. sect. Bicuspidaria, we employed phylogeny reconstructions based on DNA sequences from the plastid trnL-trnF, trnS-trnfM, ndhF-rpl32, and rpl32-trnL regions and the nuclear ribosomal ITS and ETS regions. Due to evidence of discordant relationships reconstructed from the plastid and nuclear partitions, we used coalescent-based methods in addition to concatenated data sets to estimate the species tree. Maximum likelihood reconstructions based on the combined …