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1.
Genes (Basel) ; 15(3)2024 03 14.
Article in English | MEDLINE | ID: mdl-38540421

ABSTRACT

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks.


Subject(s)
Vigna , United States , Vigna/genetics , Phylogeny , Polymorphism, Single Nucleotide/genetics , Alleles , United States Department of Agriculture , Plant Breeding , Polymerase Chain Reaction
3.
Front Plant Sci ; 14: 1144681, 2023.
Article in English | MEDLINE | ID: mdl-37035062

ABSTRACT

Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.

4.
Int J Sports Physiol Perform ; 18(9): 901-908, 2023 Sep 01.
Article in English | MEDLINE | ID: mdl-36410336

ABSTRACT

PURPOSE: To examine the effect of match schedule on self-reported wellness and sleep in rugby union referees during the 2019 Rugby World Cup. METHODS: Following an observational design, 18 international-level male referees participating in the 2019 Rugby World Cup completed a daily questionnaire to quantify wellness status (sleep quality, mood, stress, fatigue, muscle soreness, and total wellness) and sleep characteristics (bedtime, wake-up time, and time in bed) from the previous night across the tournament. Linear mixed models and effect sizes (Hedges gav) assessed differences in wellness and sleep characteristics between prematch and postmatch days surrounding single-game and 2-game congested match schedules (prematch1, postmatch1, prematch2, and postmatch2 days). RESULTS: During regular schedules, all self-reported wellness variables except stress were reduced (gav = 0.33-1.05, mean difference -0.32 to -1.21 arbitrary units [AU]) and referees went to bed later (1.08, 1:07 h:min) and spent less time in bed (-0.78, 00:55 h:min) postmatch compared with prematch days. During congested schedules, only wellness variables differed across days, with total wellness reduced on postmatch1 (-0.88, -3.56 AU) and postmatch2 (-0.67, -2.70 AU) days, as well as mood (-1.01, -0.56 AU) and fatigue (-0.90, -1.11 AU) reduced on postmatch1 days compared with prematch days. CONCLUSION: Referees were susceptible to acute reductions in wellness on days following matches regardless of schedule. However, only single-game regular match schedules negatively impacted the sleep characteristics of referees. Targeted strategies to maximize wellness status and sleep opportunities in referees considering the match schedule faced should be explored during future Rugby World Cup competitions.


Subject(s)
Rugby , Humans , Male , Fatigue , Self Report , Sleep
5.
HRB Open Res ; 5: 31, 2022.
Article in English | MEDLINE | ID: mdl-36101871

ABSTRACT

Background: The aim of this study was to measure the impact of post-acute sequelae of COVID-19 (PASC) on quality of life, mental health, ability to work and return to baseline health in an Irish cohort. Methods: We invited individuals with symptoms of COVID-19 lasting more than 14 days to participate in an anonymous online questionnaire. Basic demographic data and self-reported symptoms were recorded. Internationally validated instruments including the patient health questionnaire somatic, anxiety and depressive symptom scales (PHQ-SADS), the Patient Health Questionnaire-15 (PHQ-15) and Chadler fatigue scale (CFQ) were used. Results: We analysed responses from 988 participants with self-reported confirmed (diagnostic/antibody positive; 81%) or suspected (diagnostic/antibody negative or untested; 9%) COVID-19. The majority of respondents were female (88%), white (98%), with a median age of 43.0 (range 15 - 88 years old) and a median BMI of 26.0 (range 16 - 60). At the time of completing this survey, 89% of respondents reported that they have not returned to their pre-COVID-19 level of health. The median number of symptoms reported was 8 (range 0 to 33 symptoms), with a median duration of 12 months (range 1 to 20 months) since time of acute infection. A high proportion of PASC patients reported that they have a moderate or severe limitation in their ability to carry out their usual activities, 38% report their ability to work is severely limited and 33% report a moderate, or higher, level of anxiety or depression. Conclusion: The results of this survey of an Irish cohort with PASC are in line with reports from other settings, and we confirm that patients with PASC reported prolonged, multi-system symptoms which can significantly impact quality of life, affect ability to work and cause significant disability. Dedicated multidisciplinary, cross specialty supports are required to improve outcomes of this patient group.

6.
Front Genet ; 13: 910386, 2022.
Article in English | MEDLINE | ID: mdl-35991553

ABSTRACT

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome-environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat-based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. "I shall endeavor to find out how nature's forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature" Alexander von Humboldt-Letter to Karl Freiesleben, June 1799.

7.
Environ Sci Technol ; 56(21): 14982-14993, 2022 11 01.
Article in English | MEDLINE | ID: mdl-35759608

ABSTRACT

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.


Subject(s)
Sewage , Wastewater , RNA, Ribosomal, 16S/genetics , Genes, Bacterial , Anti-Bacterial Agents/pharmacology
9.
Mol Hortic ; 2(1): 8, 2022 Mar 28.
Article in English | MEDLINE | ID: mdl-37789473

ABSTRACT

The species Vigna unguiculata L. (Walp), commonly known as cowpea, is a multi-purpose legume that has been selected into three subspecies that are divided into grain, fodder and pod (yardlong bean) types. However, genetic bases for distinctions are not well understood. The purpose of this study was to apply genotyping-by-sequencing (GBS) and current reference genome for V. unguiculata to distinguish three subspecies and identify signatures of divergence. The collection of 130 accessions included 128 cultivated from: 1) ssp. cylindrica, fodder type; 2) ssp. sesquipedalis, pod vegetable type; and 3) ssp. unguiculata, grain type. Two wilds genotypes from spp. dekindtiana and spp. pubescens, were used to anchor phylogeny. A total of 11,083 highly informative single nucleotide polymorphisms (SNPs) were discovered. Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies. Principal component analysis showed closer relationship between ssp. unguiculata and ssp. cylindrica compared to ssp. sesquipedalis. Relative differentiation of cultivated subspecies (with Fixation Index, FST) indicated the existence of discrete signatures of selection. This work clarifies the population structure, phylogeny, and domestication of cultivated cowpeas. Furthermore, significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.

10.
Genes (Basel) ; 12(12)2021 11 23.
Article in English | MEDLINE | ID: mdl-34946796

ABSTRACT

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 to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies.


Subject(s)
Amaranthus/genetics , Edible Grain/genetics , Crops, Agricultural/genetics , Domestication , Genome, Plant/genetics , Genotype , Phylogeny , Plant Breeding/methods , Polymorphism, Single Nucleotide/genetics , Seeds/genetics
12.
Front Plant Sci ; 12: 628687, 2021.
Article in English | MEDLINE | ID: mdl-34249030

ABSTRACT

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 µM) compared to a control (0 µM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

13.
Plants (Basel) ; 10(5)2021 May 17.
Article in English | MEDLINE | ID: mdl-34067661

ABSTRACT

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region.

14.
Theor Appl Genet ; 134(8): 2379-2398, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34128089

ABSTRACT

KEY MESSAGE: Methyl esterase (MES), PvMES1, contributes to the defense response toward Fusarium wilt in common beans by regulating the salicylic acid (SA) mediated signaling pathway from phenylpropanoid synthesis and sugar metabolism as well as others. Common bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-borne diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: (a) phenylpropanoid synthesis; (b) sugar metabolism; and (c) interaction between host and pathogen as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease.


Subject(s)
Disease Resistance/immunology , Fusarium/physiology , Oxidoreductases, O-Demethylating/metabolism , Phaseolus/immunology , Plant Diseases/immunology , Plant Proteins/metabolism , Salicylic Acid/metabolism , Disease Resistance/genetics , Gene Expression Regulation, Plant , Oxidoreductases, O-Demethylating/genetics , Phaseolus/genetics , Phaseolus/growth & development , Phaseolus/microbiology , Plant Diseases/genetics , Plant Diseases/microbiology , Plant Proteins/genetics , Signal Transduction
15.
Genes (Basel) ; 12(4)2021 04 12.
Article in English | MEDLINE | ID: mdl-33921270

ABSTRACT

Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions.


Subject(s)
Phaseolus/growth & development , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methods , Acclimatization , Crops, Agricultural/classification , Crops, Agricultural/genetics , Crops, Agricultural/growth & development , Droughts , Gene Expression Regulation, Plant , Gene-Environment Interaction , Mexico , Phaseolus/classification , Phaseolus/genetics , Stress, Physiological , United States
16.
Environ Sci Technol ; 55(6): 3775-3785, 2021 03 16.
Article in English | MEDLINE | ID: mdl-33645970

ABSTRACT

Maria made a landfall in Puerto Rico on September 20, 2017 as a category 4 hurricane, causing severe flooding, widespread electricity outages, damage to infrastructure, and interruptions in water and wastewater treatment. Small rural community water systems face unique challenges in providing drinking water, which intensify after natural disasters. The purpose of this study was to evaluate the functionality of six very small rural public water systems and one large regulated system in Puerto Rico six months after Maria and survey a broad sweep of fecal, zoonotic, and opportunistic pathogens from the source to tap. Samples were collected from surface and groundwater sources, after water treatment and after distribution to households. Genes indicative of pathogenic Leptospira spp. were detected by polymerase chain reaction (PCR) in all systems reliant on surface water sources. Salmonella spp. was detected in surface and groundwater sources and some distribution system water both by culture and PCR. Legionella spp. and Mycobacteria spp. gene numbers measured by quantitative PCR were similar to nonoutbreak conditions in the continental U.S. Amplicon sequencing provided a nontarget screen for other potential pathogens of concern. This study aids in improving future preparedness, assessment, and recovery operations for small rural water systems after natural disasters.


Subject(s)
Cyclonic Storms , Drinking Water , Humans , Puerto Rico , Rural Population , Water Quality
17.
Am J Nephrol ; 52(2): 85-97, 2021.
Article in English | MEDLINE | ID: mdl-33735856

ABSTRACT

BACKGROUND: Recent studies have identified the combination of vancomycin with piperacillin-tazobactam (VPT) to be associated with increased nephrotoxicity. Multiple, large cohort studies have found this widely used combination to have a higher risk of nephrotoxicity than other regimens in a variety of populations. SUMMARY: This review summarizes the epidemiology and clinical features of VPT-associated acute kidney injury (AKI). Potential mechanisms involved in the pathogenesis of this phenomenon are also discussed. Key Message: VPT-associated nephrotoxicity is a recently recognized clinical entity. Clinical strategies to minimize the risk of toxicity in this setting include antimicrobial stewardship, monitoring of kidney function, and emerging data supporting the potential role for novel biomarkers in predicting and managing AKI.


Subject(s)
Acute Kidney Injury/chemically induced , Acute Kidney Injury/complications , Anti-Bacterial Agents/adverse effects , Piperacillin, Tazobactam Drug Combination/adverse effects , Vancomycin/adverse effects , Acute Kidney Injury/epidemiology , Anti-Bacterial Agents/administration & dosage , Antimicrobial Stewardship , Creatinine/metabolism , Critical Illness , Drug Therapy, Combination/adverse effects , Humans , Kidney Tubules/metabolism , Nephritis/chemically induced , Nephritis/immunology , Patient Acuity , Piperacillin, Tazobactam Drug Combination/administration & dosage , Risk Factors , Vancomycin/administration & dosage
18.
Water Res ; 194: 116907, 2021 Apr 15.
Article in English | MEDLINE | ID: mdl-33610927

ABSTRACT

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.


Subject(s)
Cyanobacteria , High-Throughput Nucleotide Sequencing , Cyanobacteria/genetics , Harmful Algal Bloom , Wastewater , Water
19.
J Sci Med Sport ; 24(4): 386-390, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33176984

ABSTRACT

OBJECTIVES: Quantify the on-field movements, heart rate and perceived exertion (RPE) of lead referees during Rugby World Cup matches. DESIGN: Descriptive, observational. METHODS: On-field movements (distance, average speed, high-speed running [>5ms-1]), heart rate and RPE of 11 lead referees were assessed during 29 Rugby World Cup (Knockout and Pool) matches. Average speed and heart rate were assessed using rolling average methods (1-10min epochs). Linear mixed models and Cohen's effect size (d) were used to compare match variables between Pool and Knockout matches. RESULTS: Referees covered on average 6674±566m (65.8±6.3mmin-1), with 586±290m in high-speed running. Mean heart rate was 146±9 beatsmin-1, summated-heart-rate-zones was 235±36AU, and sRPE load was 577±205AU. A large reduction (d=1.40) in high-speed running distance and moderate reductions in average speed over 1 (d=0.81) and 2min (d=0.83) epochs were found during Knockout, compared to Pool matches. Differences between Pool and Knockout matches on other measures of referee movement, heart rate and RPE were trivial. CONCLUSIONS: This is the first investigation to examine the effect of competition stage on rugby union referees on-field performance. Individual and match contextual factors may explain the reduction in high-speed running during Knockout matches, however more detailed examination of the factors influencing referee performance is required for greater insight into the key performance indicators in rugby union. Nonetheless, these data provide practitioners with knowledge to assist in preparation of rugby union referees for future Rugby World Cup competitions.


Subject(s)
Football , Heart Rate/physiology , Occupations , Physical Exertion/physiology , Running/physiology , Adult , Geographic Information Systems , Humans , Male
20.
Front Genet ; 11: 656, 2020.
Article in English | MEDLINE | ID: mdl-32670356

ABSTRACT

Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of its consumption for human health and nutrition. While mung bean is rich in a range of nutritional components, such as protein, carbohydrates and vitamins, it remains less well studied than other legume crops in terms of micronutrients. In addition, mung bean genomics and genetic resources are relatively sparse. The objectives of this research were three-fold, namely: to develop a genome-wide marker system for mung bean based on genotyping by sequencing (GBS), to evaluate diversity of mung beans available to breeders in the United States and finally, to perform a genome-wide association study (GWAS) for nutrient concentrations based on a seven mineral analysis using inductively coupled plasma (ICP) spectroscopy. All parts of our research were performed with 95 cultivated mung bean genotypes chosen from the USDA core collection representing accessions from 13 countries. Overall, we identified a total of 6,486 high quality single nucleotide polymorphisms (SNPs) from the GBS dataset and found 43 marker × trait associations (MTAs) with calcium, iron, potassium, manganese, phosphorous, sulfur or zinc concentrations in mung bean grain produced in either of two consecutive years' field experiments. The MTAs were scattered across 35 genomic regions explaining on average 22% of the variation for each seed nutrient in each year. Most of the gene regions provided valuable candidate loci to use in future breeding of new varieties of mung bean and further the understanding of genetic control of nutritional properties in the crop. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) for nutritional improvement in mung bean and to analyze cultivars of mung bean.

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