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Comparison of Three Macroinvertebrate Sampling Methods for Use in Assessment of Water Quality Changes in Flashy Urban Streams

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Journal of Environmental Protection 2020年第8期11卷 585-609页

作者： Roger Yeardley Jr. scott jacobs Ken Fritz William Thoeny Office of Research and Development U.S. Environmental Protection Agency Cincinnati USA Pegasus Technical Services c/o U.S. Environmental Protection Agency Cincinnati USA

The unique challenges associated with sampling of macroinvertebrates in flashy urban streams create a methods gap. These streams form isolated pools for much of the year, interspersed with spates that scour and deposit excessive amounts of sediment. Commonly used stream grab sampling methods, such as nets and Hess and Surber fixed-area samplers, work well in wadable streams with perennial flow. Deployed samplers (Hester-Dendy, gravel tray) can be used in waters with or without flow. We evaluated three methods which don’t require stream flow: modified Hester-Dendy (MHD), gravel tray, and bucket (a type of cylinder grab sample method), for their potential use in bioassessment of a project involving daylighting of a 180-m culvert on Congress Run, a flashy urban tributary to Mill Creek in Cincinnati, Ohio. Method efficacy was measured using three criteria: usability (level of effort and recoverability of samplers), variability, and community retrieval completeness. The bucket method required the lowest level of effort and had the highest sample recovery. The bucket sampler had the lowest variability for most metrics, including the critical metric of taxa richness, with a coefficient of variation (CV) of 20.9%. The MHD and tray samplers had taxa richness CVs of 42.9% and 53.9%, respectively. The bucket sampler also had the lowest CV (27.4%) for a multi-metric index. The bucket sampler performed best with respect to community retrieval completeness, with higher pooled and average taxa richness. The total number of taxa collected from all the replicate bucket grab samples (42) was greater than that collected by the HD and tray samplers combined (27). Multivariate analyses showed significant grouping with respect to methods and location. This study supports the bucket grab sampler method as a candidate for sampling of flashy urban streams.

关键词： Macroinvertebrate Methods Stream Urban Sampling Flow Hydrology

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Nationwide retrospective study of hepatitis B virological response and liver stiffness improvement in 465 patients on nucleos(t)ide analogue

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World Journal of Gastroenterology 2022年第31期28卷 4390-4398页

作者： Alnoor Ramji Karen Doucette Curtis Cooper Gerald Yosel Minuk Mang Ma Alexander Wong David Wong Edward Tam Brian Conway David Truong Philip Wong Lisa Barrett Hin Hin Ko Sarah Haylock-jacobs Nishi Patel Gilaad G Kaplan scott Fung Carla S Coffin Department of Medicine University of British ColumbiaVancouver v6t 1z3Canada Department of Medicine University of AlbertaEdmonton t6g 2r7Canada Department of Medicine The Ottawa Hospital Research InstituteUniversity of OttawaOttawa ON K1H 8L6Canada Department of Medicine University of ManitobaWinnipeg r3e 3j7Canada Department of Medicine University of SaskatchewanSaskatoon s7n 5e5Canada Department of Medicine University Health NetworkToronto m5g 2c4Canada Pacific Gastroenterology Associates Vancouver v6z 2k5Canada Vancouver Infectious Disease Centre Vancouver v6z 2c7Canada Department of Medicine McGill UniversityMontreal h3a 0g4Canada Department of Microbiology and Immunology Dalhousie UniversityHalifax b3h 4r2Canada Cumming School of Medicine University of CalgaryCalgary t2n 1n4Canada

BACKGROUND Hepatitis B virus(HBV)nucleos(t)ide analog(NA)therapy reduces liver disease but requires prolonged therapy to achieve hepatitis B surface antigen(HBsAg)*** is limited North American real-world data using non-invasive tools for fibrosis assessment and few have compared 1st generation NA or lamivudine(LAM)to tenofovir disoproxil fumarate(TDF).AIM To assess impact of NA on virological response and fibrosis regression using liver stiffness measurement(LSM)(i.e.,FibroScan®).METHODS Retrospective,observational cohort study from the Canadian HBV *** collected included demographics,NA,HBV DNA,alanine aminotransferase(ALT),and *** were HBV monoinfected patients,treatment naïve,and received 1 NA with minimum 1 year *** In 465(median 49 years,37%female,35%hepatitis B e antigen+at baseline,84%Asian,6%White,and 9%Black).Percentage of 64(n=299)received TDF and 166 were LAM-treated with similar median duration of 3.9 and 3.7 years,*** mean baseline LSM was 11.2 kPa(TDF)vs 8.3 kPa(LAM)(P=0.003).At 5-year follow-up,the mean LSM was 7.0 kPa in TDF vs 6.7 kPa in LAM(P=0.83).There was a significant difference in fibrosis regression between groups(i.e.,mean-4.2 kPa change in TDF and-1.6 kPa in LAM,P<0.05).The last available data on treatment showed that all had normal ALT,but more TDF patients were virologically suppressed(<10 IU/mL)(n=170/190,89%)vs LAM-treated(n=35/58,60%)(P<0.05).None cleared *** In this real-world North American study,approximately 5 years of NA achieves liver fibrosis regression rarely leads to HBsAg loss.

关键词： Nucleos(t)ide analog therapy Functional cure Hepatitis B virus surface antigen loss Fibrosis regression Liver stiffness measurement Transient elastography

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Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry

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Horticulture Research 2023年第10期10卷 25-36页

作者： MacKenzie jacobs Samantha Thompson Adrian E.Platts Melanie J.A.Body Alexys Kelsey Amanda Saad Patrick Abeli scott J.Teresi Anthony Schilmiller Randolph Beaudry Mitchell J.Feldmann Steven J.Knapp Guo-qing Song Timothy Miles Patrick P.Edger Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI 48824USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Molecular Plant Science Program Michigan State UniversityEast LansingMI 48824USA Department of Plant Soil and Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Department of Horticulture and Natural Resources Kansas State UniversityOlatheKS 66061USA Genetics and Genome Sciences Program Michigan State UniversityEast LansingMI 48824USA Mass Spectrometry&Metabolomics Core Michigan State UniversityEast LansingMI 48824USA Department of Plant Sciences University of CaliforniaDavisCA 95616USA

Anthracnose fruit rot(AFR),caused by the fungal pathogen Colletotrichum fioriniae,is among the most destructive and widespread fruit disease of blueberry,impacting both yield and overall fruit *** cultivars have highly variable resistance against *** date,this pathogen is largely controlled by applying various fungicides;thus,a more cost-effective and environmentally conscious solution for AFR is *** we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry(Vaccinium corymbosum).Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids(***)and resistance against ***,we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar,which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways(*** biosynthesis)and pathogen *** non-targeted metabolite profiling,we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping *** analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two ***,individuals within each group displayed considerable overlapping variation in this compound,suggesting that its abundance may only be partially associated with resistance against *** findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.

关键词： applying resistance specialized

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Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

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Horticulture Research 2023年第11期10卷 96-105页

作者： Alan E.Yocca Adrian Platts Elizabeth Alger scott Teresi Molla F.Mengist Juliana Benevenuto Luis Felipe V.Ferrão MacKenzie jacobs Michal Babinski Maria Magallanes-Lundback Philipp Bayer Agnieszka Golicz Jodi L.Humann Dorrie Main Richard V.Espley David Chagné Nick W.Albert Sara Montanari Nicholi Vorsa James Polashock Luis Díaz-Garcia Juan Zalapa Nahla V.Bassil Patricio R.Munoz Massimo Iorizzo Patrick P.Edger Department of Horticulture Michigan State UniversityEast LansingMI48824United States Department of Plant Biology Michigan State UniversityEast LansingMI48824United States Genetics and Genome Sciences Michigan State UniversityEast LansingMI48824United States Plants for Human Health Institute North Carolina State UniversityKannapolisNC United States Horticultural Sciences Department University of FloridaGainesvilleFL 32611United States Department of Biochemistry and Molecular Biology Michigan State UniversityEast LansingMI48824United States University of Western Australia Perth 6009 Australia Justus Liebig University Giessen35390 Germany Department of Horticulture Washington State UniversityPullmanWA99163United States The New Zealand Institute for Plant and Food Research Limited(PFR) AucklandNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) PalmerstonNew Zealand The New Zealand Institute for Plant and Food Research Limited(PFR) MotuekaNew Zealand SEBS Plant BiologyRutgers UniversityNew Brunswick NJ 01019 United States Department of Viticulture and Enology University of CaliforniaDavisDavisCA 95616United States National Clonal Germplasm Repository USDA-ARSCorvallisOR 97333United States Department of Horticulture North Carolina State UniversityKannapolisNC United States MSU AgBioResearch Michigan State UniversityEast LansingMI48824United States

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed *** industry continues to face a wide variety of production challenges(*** pressures),as well as a demand for higher-yielding cultivars with improved fruit quality ***,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value ***,we describe the construction and analysis of the first pangenome for both blueberry and *** analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in *** genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality *** discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding *** pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational ***,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

关键词： breeding cultivar crops

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