Biology subjects

Clark, T. A.

Publications and source records attributed to Clark, T. A..

7 recordsLinked to original sources

bioRxiv2026

Baseline Inventory of the Bryophytes of Grand Staircase-Escalante National Monument, Utah

Abstract summaryThis report presents a preliminary bryoflora for Grand Staircase-Escalante National Monument (GSENM) in southern Utah. The inventory included over 1000 collections made across 40 localities (i.e. macrohabitat types) spanning two ecologically important gradients in bryophyte habitat: shade and moisture availability. At present, the growing checklist contains 117 taxa of liverworts and mosses including 27 families, 65 genera, 116 species, 9 varieties, and 1 subspecies. Noteworthy records include 49 putative taxa new for the state of Utah, and 2 undescribed species in the genera Grimmia and Schistidium. We propose 4 of these species be considered for addition to the recently revised bryoflora of North America. As expected for arid and semiarid environments, the bryophytes of GSENM are predominantly acrocarpous mosses (75%) followed by pleurocarpous mosses (16%), thalloid liverworts (7%), and leafy liverworts (2%). The most diverse families included xeric-soil acrocarpous mosses in the Pottiaceae (35%) and xeric-rock acrocarpous mosses in the Grimmiaceae (15%). Both xeric and mesic species were recovered in the Bryaceae (10% of species) while the pleurocarpous Amblystegiaceae included mesic and hydric species (7%). Most species in the bryoflora have broad global or disjunct distributions, but notably, the known distribution of 17 species appears limited in the United States, or globally, and warrant monitoring in GSENM. Using floristic habitat sampling across 19 macrohabitat types (combinations of 6 topography and 7 vegetation classes), mean site richness was 17.2 {+/-} 9 (SD) and ranged from 4 to 34 species. Six diversity hotspots supported [≥]30 species and were canyons with perennial or ephemeral streams dominated by mixed conifer, hardwood-riparian, riparian, or pinyon-juniper vegetation. High richness is likely supported by greater habitat diversity including xeric, mesic, and hydric conditions on variable substrates (e.g. rock, soil, biocrust, downed wood, seeps, and riparian aquatic/semi-aquatic habitat). Consequently, managing and monitoring diversity under future climate change and land-use alterations will necessitate a habitat-stratified approach that utilizes repeated floristic habitat sampling to document changes in site-level richness and to predict other candidate diversity hotspots on the basis of microhabitat-level diversity, which could be assessed by trained non-bryologists. Collection data are available to the public as georeferenced and photographed observations of half of the bryophyte collections on our iNaturalist.com project, Bryophytes of Grand Staircase Escalante, available for scientific, educational, or outreach activities. Observations are accessible to visitors (via the smartphone app) who wish to know what species have been found along popular trails in GSENM. Landscape-level richness may not reach that of the neighboring Grand Canyon National Park (>155 species), which supports a unique high-elevation bryophyte community sheltered in the mixed conifer and spruce-fir forests of the North Rims Kaibab Plateau. Future collecting by experts will inevitably uncover more species in this ecologically diverse monument important to conserving dryland bryophyte diversity and ecosystem function. This study will serve as a baseline for future research and long-term monitoring related to climate change impacts on dryland bryophytes including biocrust species. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/708354v1_ufig1.gif" ALT="Figure 1"> View larger version (106K): org.highwire.dtl.DTLVardef@c50925org.highwire.dtl.DTLVardef@1db65c3org.highwire.dtl.DTLVardef@f60909org.highwire.dtl.DTLVardef@cb5244_HPS_FORMAT_FIGEXP M_FIG C_FIG Cover photos (by T. A. Clark): View of sandstone canyon wall along the Escalante River Trail taken during a July collection trip in 2015 (top) during which riparian bryophytes were collected by authro, T. A. Clark, (shown in photo) at a sandstone seep (bottom). Bureau of Land Managements National Landscape Conservation System Grant Cooperative Agreement #L14AC00275 issued to P.I. Lloyd R. Stark, UNLV O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/708354v1_ufig2.gif" ALT="Figure 2"> View larger version (88K): org.highwire.dtl.DTLVardef@86109eorg.highwire.dtl.DTLVardef@1ad0efborg.highwire.dtl.DTLVardef@b2c239org.highwire.dtl.DTLVardef@1ed4a4a_HPS_FORMAT_FIGEXP M_FIG C_FIG Copyright 2020 by the authorsAll content contained herein is the property of the authors and all images the property of Theresa A. Clark and should not be used without permission except for education, in which case inclusion of the author/photographers name in citation or superimposed over any image(s) is requested.

plant biology↗

bioRxiv2023

Can biocrust moss hide from climate change? Multiscale habitat buffering improves summer-stress resistance in Syntrichia caninervis

PremiseMosses provide many ecosystem functions and are the most vulnerable of biocrust organisms to climate change due to their sensitive water relations stressed by summer aridity. Given their small size, moss stress resistance may be more dependent on fine-scale habitat than macroscale (climate and community), but this sheltering role of habitat (i.e. habitat buffering) has never been compared to macroclimate and may have important implications for predicting critical biocrust refugia in changing climates. MethodsWe located three populations of a keystone biocrust moss, Syntrichia caninervis, spanning 1200-m of altitude comprising three plant communities (elevation-plant zones) in the Mojave Desert. We stratified 96 microsites along three habitat aridity gradients: elevation-zone, topography (aspect), and microhabitat (shrub proximity). We estimated summer photosynthetic stress (Fv/Fm) and aridity exposure (macroclimate, irradiance, and shade). ResultsMicrosite aridity exposure varied greatly revealing exposed and buffered microhabitats in all elevation-zones. Moss stress did not differ by elevation zone despite the extensive macroclimate gradient, failing to support the high-elevation refugia hypothesis. Instead, stress was lowest on N-facing slopes and microhabitats with higher shrub shading, while the importance of (and interactions between) topography, irradiance, and shade varied by elevation zone. ConclusionsWe demonstrate fine-scale habitat buffering is physiologically more protective than high-elevation climate, and thus, may allow some mosses to hide from the brunt of climate change in widespread microrefugia throughout their current ranges. Our findings support a scale-focused vulnerability paradigm: microrefugia may be more important than macrorefugia for bolstering biocrust moss resistance to summer climate stress.

plant biology↗

bioRxiv2023

Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation

Tardigrades, commonly known as waterbears, are eight-legged microscopic invertebrates renowned for their ability to withstand extreme stressors, including high osmotic pressure, freezing temperatures, and complete desiccation. Limb retraction and expelling their internal water stores results in the tun state, greatly increasing their ability to survive. Emergence from the tun state and/or activity regain follows stress removal, where resumption of life cycle occurs as if stasis never occurred. However, the mechanism(s) through which tardigrades initiate tun formation is yet to be uncovered. Herein, we use chemobiosis to demonstrate that tardigrade tun formation is mediated by reactive oxygen species (ROS). We further reveal that tuns are dependent on reversible cysteine oxidation, and that this reversible cysteine oxidation is facilitated by the release of intracellular reactive oxygen species (ROS). We provide the first empirical evidence of chemobiosis and map the initiation and survival of tardigrades via osmobiosis, chemobiosis, and cryobiosis. In vivo electron paramagnetic spectrometry suggests an intracellular release of reactive oxygen species following stress induction; when this release is quenched through the application of exogenous antioxidants, the tardigrades can no longer survive osmotic stress. Together, this work suggests a conserved dependence of reversible cysteine oxidation across distinct tardigrade cryptobioses.

biochemistry↗

bioRxiv2019

High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations

High throughput DNA sequencing technologies have undergone tremendous development over the past decade. Although optical detection-based sequencing has constituted the majority of data output, it requires a large capital investment and aggregation of samples to achieve optimal cost per sample. We have developed a novel electronic detection-based platform capable of accurately detecting single base incorporations. The GenapSys technology with its electronic detection modality allows the system to be compact, accessible, and affordable. We demonstrate the performance of the system by sequencing several different microbial genomes with varying GC content. The platform is capable of generating up to 2 Gb of high-quality nucleic acid sequence in a single run. We routinely generate sequence data that exceeds 99% raw accuracy with read lengths of up to 175 bp. Average quality scores remain above Q30 (99.9% raw sequencing accuracy) beyond 150 bp, with more than 85% of total bases at or above Q30. The utility of the platform is highlighted by targeted sequencing of the human genome. We show high concordance of SNP detection on the human NA12878 HapMap cell line with data generated on the Illumina sequencing platform. In addition, we sequenced a targeted panel of cancer-associated genes in a well characterized reference standard. With multiple library preparation approaches on this sample, we were able to identify low frequency mutations at expected allele frequencies.

genomics↗

bioRxiv2019

Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3

BackgroundClinical sequencing has traditionally focused on genomic DNA through the use of targeted panels and exome sequencing, rather than investigating the potential transcriptomic consequences of disease-associated variants. RNA sequencing has recently been shown to be an effective additional tool for identifying disease-causing variants. We here use targeted long-read genome and transcriptome sequencing to efficiently and economically identify molecular consequences of a rare, disease-associated variant in hypertrophic cardiomyopathy (HCM).\n\nMethods and ResultsOur study, which employed both Pacific Biosciences SMRT sequencing and Oxford Nanopore Technologies MinION sequencing, as well as two RNA targeting strategies, identified alternatively-spliced isoforms that resulted from a splice-site variant containing allele in HCM. These included a predicted in-frame exon-skipping event, as well as an abundance of additional isoforms with unexpected intron-inclusion, exon-extension, and pseudo-exon events. The use of long-read RNA sequencing allowed us to not only investigate full length alternatively-spliced transcripts but also to phase them back to the variant-containing allele.\n\nConclusionsWe suggest that targeted, long-read RNA sequencing in conjunction with genome sequencing may provide additional molecular evidence of disease for rare or de novo variants in cardiovascular disease, as well as providing new information about the consequence of these variants on downstream RNA and protein expression.

genetics↗

bioRxiv2017

Amplification-free, CRISPR-Cas9 Targeted Enrichment and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions

Targeted sequencing has proven to be an economical means of obtaining sequence information for one or more defined regions of a larger genome. However, most target enrichment methods require amplification. Some genomic regions, such as those with extreme GC content and repetitive sequences, are recalcitrant to faithful amplification. Yet, many human genetic disorders are caused by repeat expansions, including difficult to sequence tandem repeats.\n\nWe have developed a novel, amplification-free enrichment technique that employs the CRISPR-Cas9 system for specific targeting multiple genomic loci. This method, in conjunction with long reads generated through Single Molecule, Real-Time (SMRT) sequencing and unbiased coverage, enables enrichment and sequencing of complex genomic regions that cannot be investigated with other technologies. Using human genomic DNA samples, we demonstrate successful targeting of causative loci for Huntingtons disease (HTT; CAG repeat), Fragile X syndrome (FMR1; CGG repeat), amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72; GGGGCC repeat), and spinocerebellar ataxia type 10 (SCA10) (ATXN10; variable ATTCT repeat). The method, amenable to multiplexing across multiple genomic loci, uses an amplification-free approach that facilitates the isolation of hundreds of individual on-target molecules in a single SMRT Cell and accurate sequencing through long repeat stretches, regardless of extreme GC percent or sequence complexity content. Our novel targeted sequencing method opens new doors to genomic analyses independent of PCR amplification that will facilitate the study of repeat expansion disorders.

genomics↗

bioRxiv2017

Universal Alternative Splicing Of Noncoding Exons

The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation by RNA sequencing (RNA-Seq), we are yet to resolve its true dimensions. RNA-Seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. We performed targeted single-molecule and short-read RNA-Seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. Our analysis reaches the lower limits of the transcriptome, identifying a fundamental distinction between protein-coding and noncoding gene content: almost every noncoding exon undergoes alternative splicing, producing a seemingly limitless variety of isoforms. Analysis of syntenic regions of the mouse genome shows that few noncoding exons are shared between human and mouse, yet human splicing profiles are recapitulated on Hsa21 in mouse cells, indicative of regulation by a deeply conserved splicing code. We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

genomics↗