PMID- 36849912 OWN - NLM STAT- MEDLINE DCOM- 20230301 LR - 20230302 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 23 IP - 1 DP - 2023 Feb 28 TI - Modulation of defense genes and phenolic compounds in wild blueberry in response to Botrytis cinerea under field conditions. PG - 117 LID - 10.1186/s12870-023-04090-5 [doi] LID - 117 AB - Botrytis blight is an important disease of wild blueberry [(Vaccinium angustifolium (Va) and V. myrtilloides (Vm))] with variable symptoms in the field due to differences in susceptibility among blueberry phenotypes. Representative blueberry plants of varying phenotypes were inoculated with spores of B. cinerea. The relative expression of pathogenesis-related genes (PR3, PR4), flavonoid biosynthesis genes, and estimation of the concentration of ten phenolic compounds between uninoculated and inoculated samples at different time points were analyzed. Representative plants of six phenotypes (brown stem Va, green stem Va, Va f. nigrum, tall, medium, and short stems of Vm) were collected and studied using qRT-PCR. The expression of targeted genes indicated a response of inoculated plants to B. cinerea at either 12, 24, 48 or 96 h post inoculation (hpi). The maximum expression of PR3 occurred at 24 hpi in all the phenotypes except Va f. nigrum and tall stem Vm. Maximum expression of both PR genes occurred at 12 hpi in Va f. nigrum. Chalcone synthase, flavonol synthase and anthocyanin synthase were suppressed at 12 hpi followed by an upregulation at 24 hpi. The expression of flavonoid pathway genes was phenotype-specific with their regulation patterns showing temporal differences among the phenotypes. Phenolic compound accumulation was temporally regulated at different post-inoculation time points. M-coumaric acid and kaempferol-3-glucoside are the compounds that were increased with B. cinerea inoculation. Results from this study suggest that the expression of PR and flavonoid genes, and the accumulation of phenolic compounds associated with B. cinerea infection could be phenotype specific. This study may provide a starting point for understanding and determining the mechanisms governing the wild blueberry-B. cinerea pathosystem. CI - © 2023. The Author(s). FAU - Abbey, Joel AU - Abbey J AD - Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, P.O. Box 550, Truro, NS, B2N 2R8, Canada. jaabbey@dal.ca. FAU - Jose, Sherin AU - Jose S AD - Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, P.O. Box 550, Truro, NS, B2N 2R8, Canada. FAU - Percival, David AU - Percival D AD - Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, P.O. Box 550, Truro, NS, B2N 2R8, Canada. FAU - Jaakola, Laura AU - Jaakola L AD - Department of Arctic and Marine Biology, The Arctic University of Norway, Tromso, Norway. AD - NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, NO‑1431, Ås, Norway. FAU - Asiedu, Samuel K AU - Asiedu SK AD - Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, 50 Pictou Road, P.O. Box 550, Truro, NS, B2N 2R8, Canada. LA - eng PT - Journal Article DEP - 20230228 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (Anthocyanins) RN - 0 (Flavonoids) RN - 0 (Phenols) RN - Botrytis cinerea SB - IM MH - *Botrytis MH - *Blueberry Plants/genetics MH - Anthocyanins MH - Flavonoids MH - Phenols PMC - PMC9972761 OTO - NOTNLM OT - Blueberry OT - Botrytis cinerea OT - Gene expression OT - HPLC–DAD OT - Phenolics OT - Real-time RT-PCR COIS- The authors declare no competing interests. EDAT- 2023/03/01 06:00 MHDA- 2023/03/03 06:00 PMCR- 2023/02/28 CRDT- 2023/02/28 00:40 PHST- 2022/09/16 00:00 [received] PHST- 2023/01/27 00:00 [accepted] PHST- 2023/02/28 00:40 [entrez] PHST- 2023/03/01 06:00 [pubmed] PHST- 2023/03/03 06:00 [medline] PHST- 2023/02/28 00:00 [pmc-release] AID - 10.1186/s12870-023-04090-5 [pii] AID - 4090 [pii] AID - 10.1186/s12870-023-04090-5 [doi] PST - epublish SO - BMC Plant Biol. 2023 Feb 28;23(1):117. doi: 10.1186/s12870-023-04090-5. PMID- 36012791 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20240903 IS - 2309-608X (Electronic) IS - 2309-608X (Linking) VI - 8 IP - 8 DP - 2022 Jul 29 TI - Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32. LID - 10.3390/jof8080804 [doi] LID - 804 AB - The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali, which will facilitate further research into the pathogenicity mechanisms of these species. FAU - Hilário, Sandra AU - Hilário S AUID- ORCID: 0000-0002-6463-9757 AD - Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. FAU - Gonçalves, Micael F M AU - Gonçalves MFM AUID- ORCID: 0000-0003-2295-3374 AD - Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. FAU - Fidalgo, Cátia AU - Fidalgo C AUID- ORCID: 0000-0002-7064-4966 AD - Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. FAU - Tacão, Marta AU - Tacão M AUID- ORCID: 0000-0001-7965-4928 AD - Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. FAU - Alves, Artur AU - Alves A AUID- ORCID: 0000-0003-0117-2958 AD - Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal. LA - eng GR - UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020/Fundação para a Ciência e Tecnologia/ GR - SFRH/BD/137394/2018/Fundação para a Ciência e Tecnologia/ GR - SFRH/BD/129020/2017/Fundação para a Ciência e Tecnologia/ GR - CEECIND/01373/2018/Fundação para a Ciência e Tecnologia/ GR - CEECIND/00977/2020/Fundação para a Ciência e Tecnologia/ PT - Journal Article DEP - 20220729 PL - Switzerland TA - J Fungi (Basel) JT - Journal of fungi (Basel, Switzerland) JID - 101671827 PMC - PMC9409727 OTO - NOTNLM OT - CAZymes OT - Diaporthe OT - Fusicoccin A OT - effectors OT - virulence factors OT - whole genome sequencing COIS- The authors declare no conflict of interest. EDAT- 2022/08/27 06:00 MHDA- 2022/08/27 06:01 PMCR- 2022/07/29 CRDT- 2022/08/26 01:26 PHST- 2022/07/13 00:00 [received] PHST- 2022/07/27 00:00 [revised] PHST- 2022/07/28 00:00 [accepted] PHST- 2022/08/26 01:26 [entrez] PHST- 2022/08/27 06:00 [pubmed] PHST- 2022/08/27 06:01 [medline] PHST- 2022/07/29 00:00 [pmc-release] AID - jof8080804 [pii] AID - jof-08-00804 [pii] AID - 10.3390/jof8080804 [doi] PST - epublish SO - J Fungi (Basel). 2022 Jul 29;8(8):804. doi: 10.3390/jof8080804. PMID- 39520394 OWN - NLM STAT- MEDLINE DCOM- 20250212 LR - 20250214 IS - 1938-291X (Electronic) IS - 0022-0493 (Print) IS - 0022-0493 (Linking) VI - 118 IP - 1 DP - 2025 Feb 11 TI - Strategic honey bee hive placement improves honey bee visitation but not pollination in northern highbush blueberry. PG - 282-290 LID - 10.1093/jee/toae267 [doi] AB - Commercial blueberry Vaccinium spp. (Ericales: Ericaceae) production relies on insect-mediated pollination. Pollination is mostly provided by rented honey bees, Apis mellifera L. (Hymenoptera: Apidae), but blueberry crop yields can be limited due to pollination deficits. Various hive placement strategies have been recommended to mitigate pollination shortfalls, but the effect of hive placement has received limited formal investigation. This study explores the effects of clumped and dispersed hive placement strategies on honey bee visitation and pollination outcomes in "Bluecrop" and "Duke" fields over 2 years (2021 and 2022) within 2 economically important regions of production in the United States-the Midwest (Michigan) and Pacific Northwest (Oregon and Washington). Clumping hives consistently increased honey bee visitation rate but did not result in higher fruit set, fruit weight, or seed count. Increases in honey bee visitation through clumping could perhaps improve pollination outcomes in more pollination-limited blueberry cultivars and other pollination-dependent crops. Clumping hives is substantially more efficient and cost-effective for beekeepers due to fewer drop locations and could lead to cost savings for both beekeepers and blueberry growers without growers sacrificing pollination levels and crop yields. CI - © The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America. FAU - Brouwer, Kayla AU - Brouwer K AD - Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA, USA. FAU - Eeraerts, Maxime AU - Eeraerts M AUID- ORCID: 0000-0003-2739-9704 AD - Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA, USA. AD - Department of Environment, Forest and Nature Lab, Ghent University, Melle-Gontrode, Belgium. FAU - Rogers, Emma AU - Rogers E AUID- ORCID: 0000-0003-2739-9704 AD - Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA, USA. FAU - Goldstein, Lauren AU - Goldstein L AUID- ORCID: 0000-0003-2557-9744 AD - Department of Entomology, Michigan State University, East Lansing, MI, USA. FAU - Perkins, Jacquelyn A AU - Perkins JA AUID- ORCID: 0000-0001-5336-1756 AD - Department of Entomology, Michigan State University, East Lansing, MI, USA. FAU - Milbrath, Meghan O AU - Milbrath MO AUID- ORCID: 0000-0002-7726-5854 AD - Department of Entomology, Michigan State University, East Lansing, MI, USA. FAU - Melathopoulos, Andony AU - Melathopoulos A AD - Department of Horticulture, Oregon State University, Corvallis, OR, USA. FAU - Meyer, Jason AU - Meyer J AD - Peerbolt Crop Management, Portland, OR, USA. FAU - Kogan, Clark AU - Kogan C AD - StatsCraft LLC, Spokane, WA, USA. FAU - Isaacs, Rufus AU - Isaacs R AUID- ORCID: 0000-0001-7523-4643 AD - Department of Entomology, Michigan State University, East Lansing, MI, USA. FAU - DeVetter, Lisa Wasko AU - DeVetter LW AUID- ORCID: 0000-0002-4412-385X AD - Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA, USA. LA - eng GR - 2020-51181-32155/National Institute of Food and Agriculture (NIFA), U.S. Department of Agriculture/ GR - Specialty Crops Research Initiative/ GR - 1014919/NIFA Hatch project/ GR - Belgian American Educational Foundation/ GR - 1210723N/FWO/ PT - Journal Article PL - England TA - J Econ Entomol JT - Journal of economic entomology JID - 2985127R SB - IM MH - Animals MH - Bees/physiology MH - *Blueberry Plants MH - *Pollination MH - *Beekeeping PMC - PMC11818375 OTO - NOTNLM OT - Apis mellifera OT - Vaccinium OT - bees OT - crop pollination OT - hive placement EDAT- 2024/11/13 13:59 MHDA- 2025/02/12 18:47 PMCR- 2024/11/09 CRDT- 2024/11/09 09:53 PHST- 2024/06/20 00:00 [received] PHST- 2024/10/14 00:00 [revised] PHST- 2024/10/24 00:00 [accepted] PHST- 2025/02/12 18:47 [medline] PHST- 2024/11/13 13:59 [pubmed] PHST- 2024/11/09 09:53 [entrez] PHST- 2024/11/09 00:00 [pmc-release] AID - 7888869 [pii] AID - toae267 [pii] AID - 10.1093/jee/toae267 [doi] PST - ppublish SO - J Econ Entomol. 2025 Feb 11;118(1):282-290. doi: 10.1093/jee/toae267. PMID- 39996525 OWN - NLM STAT- Publisher LR - 20250225 IS - 1523-1739 (Electronic) IS - 0888-8892 (Linking) DP - 2025 Feb 25 TI - Integrating data to assess occupancy patterns of an endangered bumble bee. PG - e14458 LID - 10.1111/cobi.14458 [doi] AB - There is growing interest in integrating community science data with structured monitoring data to estimate changes in distribution patterns of imperiled species, including pollinators. However, significant challenges remain in determining how unstructured community science data should be incorporated into formal analyses of species distributions. We developed a dynamic framework for combining community science and structured monitoring data of bumble bees to estimate changes in occupancy of rusty-patched bumble bees (Bombus affinis), a federally endangered species in the United States. We applied traditional metapopulation theory and accounted for imperfect detection to estimate site-specific extirpation risk and colonization rates across the known distribution of B. affinis in the Upper Midwest (USA). Despite a 144% increase in presence-only detections from 2017 to 2022, occupancy probabilities and the estimated number of occupied sites remained static or declined slightly across a 4-state region during this period. Our results provide preliminary evidence that the probability of local extirpation risk of B. affinis increased in response to drought, but that effect was tempered with a high number of neighboring patches occupied by B. affinis (i.e., rescue effect). Our framework can be used by managers to track population recovery goals for B. affinis and other bumble bees of conservation concern. In addition, our study highlights the importance of accounting for imperfect detection and addressing spatial sampling biases in bumble bee monitoring efforts, particularly those for which a portion of the monitoring data are generated from community science projects. CI - © 2025 Society for Conservation Biology. FAU - Ellis, Kristen S AU - Ellis KS AUID- ORCID: 0000-0003-2759-3670 AD - Northern Prairie Wildlife Research Center, U.S. Geological Survey, Jamestown, North Dakota, USA. FAU - Otto, Clint R V AU - Otto CRV AUID- ORCID: 0000-0002-7582-3525 AD - Northern Prairie Wildlife Research Center, U.S. Geological Survey, Jamestown, North Dakota, USA. FAU - Bailey, Larissa L AU - Bailey LL AD - Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA. AD - Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA. FAU - Smith, Tamara A AU - Smith TA AUID- ORCID: 0000-0002-5433-0254 AD - Minnesota-Wisconsin Ecological Services Field Office, U.S. Fish and Wildlife Service, Bloomington, Minnesota, USA. FAU - Choy, Steven AU - Choy S AD - Minnesota-Wisconsin Ecological Services Field Office, U.S. Fish and Wildlife Service, Bloomington, Minnesota, USA. FAU - Hatch, Lauren AU - Hatch L AD - Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA. LA - eng GR - Great Lakes Restoration Initiative/ GR - Midwest Climate Adaptation Science Center/ GR - USGS/USFWS Science Support Partnership/ PT - Journal Article DEP - 20250225 PL - United States TA - Conserv Biol JT - Conservation biology : the journal of the Society for Conservation Biology JID - 9882301 SB - IM OTO - NOTNLM OT - autologistic model OT - bee conservation OT - conservación de abejas OT - declinación de polinizadores OT - dinámica de ocupación OT - dinámicas metapoblacionales OT - dynamic occupancy OT - extirpation risk OT - metapopulation dynamics OT - modelo autologístico OT - pollinator decline OT - riesgo de extirpación EDAT- 2025/02/25 12:25 MHDA- 2025/02/25 12:25 CRDT- 2025/02/25 07:13 PHST- 2024/10/07 00:00 [revised] PHST- 2024/05/14 00:00 [received] PHST- 2024/11/22 00:00 [accepted] PHST- 2025/02/25 12:25 [medline] PHST- 2025/02/25 12:25 [pubmed] PHST- 2025/02/25 07:13 [entrez] AID - 10.1111/cobi.14458 [doi] PST - aheadofprint SO - Conserv Biol. 2025 Feb 25:e14458. doi: 10.1111/cobi.14458. PMID- 39775923 OWN - NLM STAT- MEDLINE DCOM- 20250108 LR - 20250205 IS - 1432-2242 (Electronic) IS - 0040-5752 (Print) IS - 0040-5752 (Linking) VI - 138 IP - 1 DP - 2025 Jan 7 TI - Identification and validation of two quantitative trait loci for dwarf bunt in the resistant cultivar 'UI Silver'. PG - 18 LID - 10.1007/s00122-024-04795-7 [doi] LID - 18 AB - Two dwarf bunt resistance QTLs were mapped to chromosome 6D, and KASP markers associated with the loci were developed and validated in a panel of regionally adapted winter wheats. UI Silver is an invaluable adapted resistant cultivar possessing the two identified QTL potentially associated with genes Bt9 and Bt10 and will be useful in future cultivar development to improve dwarf bunt resistance. Dwarf bunt, caused by Tilletia controversa, is a fungal disease of wheat that can cause complete loss of grain yield and quality during epidemics. Traditional breeding for dwarf bunt resistance requires many years of field screening under stringent conditions with disease assessment possible only near or after plant maturity. Molecular marker-assisted selection (MAS) offers a more efficient alternative. This study identified quantitative trait loci (QTL) and associated molecular markers for dwarf bunt resistance in wheat. A doubled haploid (DH) mapping population of 135 lines, derived from bunt-resistant cultivar 'UI Silver' and susceptible line 'Shaan89150', was evaluated in field nursery in Logan, Utah in 2017, 2018, and 2023. The population was genotyped using Illumina 90 K SNP iSelect marker platform. Using inclusive composite interval mapping (ICIM), the major QTL Qdb.ssdhui-6DL was consistently identified on chromosome arm 6DL across all environments, explaining phenotypic variations ranging from 15.29% to 35.40%. Another QTL, Qdb.ssdhui-6DS, was detected on chromosome arm 6DS, explaining approximately 11% of the phenotypic variation. These two QTLs exhibit additive-by-additive effects for increased resistance within the DH population. Kompetitive allele-specific PCR (KASP) markers were developed within QTL intervals and used in a validation panel of regionally adapted winter wheat lines to confirm the association between the two QTL and dwarf bunt resistance. Thus, 'UI Silver' and additional resistant cultivars with these two QTLs are valuable parental lines for improving dwarf bunt resistance through marker-assisted selection. These genetic resources are essential for understanding gene function via map-based gene cloning. CI - © 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply. FAU - Joshi, Pabitra AU - Joshi P AUID- ORCID: 0000-0003-2521-4104 AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. FAU - Dhillon, Guriqbal Singh AU - Dhillon GS AUID- ORCID: 0000-0001-6766-810X AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. FAU - Gao, Yaotian AU - Gao Y AUID- ORCID: 0009-0008-4754-0975 AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. FAU - Kaur, Amandeep AU - Kaur A AUID- ORCID: 0000-0002-9140-3424 AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. FAU - Wheeler, Justin AU - Wheeler J AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. FAU - Chen, Xianming AU - Chen X AUID- ORCID: 0000-0002-9013-5974 AD - Department of Plant Pathology, USDA-ARS, Wheat Health, Genetics, and Quality Research Unit and, Washington State University, Pullman, WA, 99164-6430, USA. FAU - Krause, William AU - Krause W AD - Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. FAU - Krause, Margaret R AU - Krause MR AUID- ORCID: 0000-0003-1154-337X AD - Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. FAU - Chen, Jianli AU - Chen J AUID- ORCID: 0000-0001-5932-0816 AD - Department of Plant Sciences, University of Idaho Aberdeen, R and E Center, Aberdeen, ID, 83210, USA. jchen@uidaho.edu. LA - eng GR - R21 DA021180/DA/NIDA NIH HHS/United States GR - 2021-07602-IDA021180CG/National Institute of Food and Agriculture/ PT - Journal Article DEP - 20250107 PL - Germany TA - Theor Appl Genet JT - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JID - 0145600 RN - 0 (Genetic Markers) SB - IM MH - *Quantitative Trait Loci MH - *Disease Resistance/genetics MH - *Plant Diseases/genetics/microbiology MH - *Chromosome Mapping/methods MH - *Triticum/genetics/microbiology/growth & development MH - Genetic Markers MH - *Phenotype MH - Genotype MH - Genetic Linkage MH - Plant Breeding MH - Polymorphism, Single Nucleotide MH - Haploidy MH - Basidiomycota PMC - PMC11706883 COIS- Declarations. Conflict of interest: The author(s) declare no conflict of interest. EDAT- 2025/01/08 18:21 MHDA- 2025/01/09 00:23 PMCR- 2025/01/07 CRDT- 2025/01/08 17:21 PHST- 2024/07/15 00:00 [received] PHST- 2024/12/02 00:00 [accepted] PHST- 2025/01/09 00:23 [medline] PHST- 2025/01/08 18:21 [pubmed] PHST- 2025/01/08 17:21 [entrez] PHST- 2025/01/07 00:00 [pmc-release] AID - 10.1007/s00122-024-04795-7 [pii] AID - 4795 [pii] AID - 10.1007/s00122-024-04795-7 [doi] PST - epublish SO - Theor Appl Genet. 2025 Jan 7;138(1):18. doi: 10.1007/s00122-024-04795-7. PMID- 40056346 OWN - NLM STAT- Publisher LR - 20250308 IS - 1614-7499 (Electronic) IS - 0944-1344 (Linking) DP - 2025 Mar 8 TI - Acaricides in agriculture: balancing livestock health and environmental well-being in Trans-Nzoia County, Kenya. LID - 10.1007/s11356-025-36187-9 [doi] AB - Extensive use of chemicals in food production, although useful, has profound implications. Acaricides, extensively used to control ticks and mites in livestock farming, can leave harmful residues that pose risks to unintended organisms such as plants, insects, people, and other animals. Thus, limiting non-target exposure to acaricides is critical. This study is aimed at assessing acaricide knowledge, use, and disposal methods among farmers and agrochemical dealers in Trans-Nzoia County, Kenya, which is well-known for livestock farming. A purposive survey of stakeholders, including 100 farmers and 45 agrochemical shop attendants, revealed concerning practices. The findings revealed insufficient personal protection during acaricide application, with a minority of responders using gloves (33%), safety goggles (0%), masks (42%), or overalls (51%) for agrochemical dealers and gloves (8%), overalls (48%), safety goggles (2%), and masks (28%) for farmers. Furthermore, used acaricide containers and residues were not properly disposed of after spraying, potentially contaminating water sources, soil, and plants. Insects, particularly bees and house flies, were spotted consuming leftovers from unprotected disposal sites, entering food webs. Furthermore, animal drying sections in spraying regions included grass, allowing animals to ingest residues. Recommendations include improved acaricide monitoring and management by extension field staff and educating farmers and pesticide dealers about health concerns, proper disposal techniques, and the importance of wearing personal protective equipment. A regulation requiring agrochemical dealers to sell acaricides together with protective gear is recommended to limit dangers effectively. CI - © 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. FAU - Sifuna, Douglas Bukhebi AU - Sifuna DB AUID- ORCID: 0009-0008-8590-088X AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. dougy302@gmail.com. FAU - Pembere, Anthony AU - Pembere A AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. FAU - Lagat, Silas AU - Lagat S AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. FAU - Barasa, Godfrey AU - Barasa G AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. FAU - Manda, Timothy AU - Manda T AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. FAU - Ngeno, Emily AU - Ngeno E AD - Department of Physical Sciences, Kaimosi Friends University, P.O Box 385, Kaimosi, 50309, Kenya. FAU - Ssebugere, Patrick AU - Ssebugere P AD - Department of Chemistry, Makerere University, P.O Box 7260, Kampala, Uganda. FAU - Nagawa, Christine Betty AU - Nagawa CB AD - Department of Forestry, Bio-Diversity and Tourism, Makerere University, P.O Box 7260, Kampala, Uganda. FAU - Kyarimpa, Christine AU - Kyarimpa C AD - Department of Chemistry, Kyambogo University, P.O. Box 1, Kyambogo, Uganda. FAU - Omwoma, Solomon AU - Omwoma S AD - Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210, Bondo (Main) CampusBondo, 40601, Kenya. LA - eng PT - Journal Article DEP - 20250308 PL - Germany TA - Environ Sci Pollut Res Int JT - Environmental science and pollution research international JID - 9441769 SB - IM OTO - NOTNLM OT - Acaricide residues OT - Disposal methods OT - Environmental contamination OT - Non-target exposure OT - Personal protection COIS- Declarations. Ethical approval: The study was approved by the Jaramogi Oginga Odinga University of Science and Technology Research Ethics Committee. Consent to participate: Informed consent was obtained from all individual participants included in the study. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. EDAT- 2025/03/09 15:07 MHDA- 2025/03/09 15:07 CRDT- 2025/03/08 11:21 PHST- 2024/04/23 00:00 [received] PHST- 2025/02/22 00:00 [accepted] PHST- 2025/03/09 15:07 [medline] PHST- 2025/03/09 15:07 [pubmed] PHST- 2025/03/08 11:21 [entrez] AID - 10.1007/s11356-025-36187-9 [pii] AID - 10.1007/s11356-025-36187-9 [doi] PST - aheadofprint SO - Environ Sci Pollut Res Int. 2025 Mar 8. doi: 10.1007/s11356-025-36187-9. PMID- 34161125 OWN - NLM STAT- Publisher LR - 20240222 IS - 0191-2917 (Print) IS - 0191-2917 (Linking) DP - 2021 Jun 23 TI - First Report of Dickeya fangzhongdai causing soft rot in Orchids in Canada. LID - 10.1094/PDIS-04-21-0771-PDN [doi] AB - Dickeya fangzhongdai was originally described as the causal agent of bleeding canker of pear tree in China. Recently, D. fangzhongdai was isolated and identified as the causal agent of soft rot in an orchid plant purchased in a local supermarket in Prince Edward Island, Canada. A water-soaked dark green spot on the leaf surface was observed and later became larger soft rot symptom. The origin of the orchid plants was traced back to a producer in Ontario, Canada who propagated them from with cuttings originally imported from the Netherlands and Taiwan. Bacterial isolations were made from a soft rot lesion on an orchid leaf by surface sterilization of small pieces of marginal tissue of the diseased leaf in 70% alcohol. The small pieces of leaf tissue were then washed three time using sterile water, and immersed in drops of sterile water. Bacterial streaming was observed under the microscope and non-fluorescing bacterial colonies were isolated on King's B and casamino acid-peptone-glucose agar plates and purified as isolates 908, 909, 910 and 911. The DNA samples were extracted from the four isolates, as well as the diseased leaf tissue, and tested by using a qPCR assay with the specific primer/probe set (DfF/DfR/DfP) for D. fangzhongdai (Tian et al. 2020). The assay yielded PCR amplicons of 135 bp with a melting temperature of 86.5±0.6 °C as did two control reactions using genomic DNA from D. fangzhongdai strains JS5T and QZH3 originally isolated in China, providing presumptive identification of the orchid isolates as D. fangzhongdai. To fulfill Koch's postulates, freshly purchased healthy orchid plants (n=4) were inoculated by leaf injection with the bacterial isolates obtained in this study and strains JS5 T and QZH3 at ~107 CFU/ml. Three leaves of the same side of the plants were inoculated with the same strains as triplicates. Sterile water was used as the negative control. Inoculated plants were incubated in a growth chamber with a 16 h photoperiod at 23 °C. Water soaked lesions developed in 3-5 days after inoculation followed by soft rotting in leaves inoculated with the new bacterial strains from orchid plants while strain QZH3 caused soft rot in 10 days after inoculation (Fig. S1). The non-fluorescing bacteria on King's B plates with colony morphology similar to those inoculated were re-isolated from the inoculated leaves and confirmed to be D. fangzhongdai by qPCR. Phylogenetic analysis of the assembled 16S rRNA sequence of isolate 908 (GenBank accession number: MT984340), together with GenBank data of all Dickeya spp. and some Pectobacterium spp, using neighbor-joining (NJ) method inferred with MEGA X software (Kumar et al. 2018) showed that isolate 908 clustered with strains JS5T and QZH3 at a phylogenetic distance of 0.0007. This clearly indicated that isolate 908 and JS5T and QZH3 belong to the same genus. Species-level identification of isolate 908 was achieved by genome sequencing and analysis based on average nucleotide identity (ANI). Genomic DNA of isolate 908 was sequenced with Illumina MiSeq to provide approximately 180X genome coverage. After quality checking using FastQC (Andrews 2010), de-novo assembly was performed with VelvetOptimiser v2.2.6 (Zerbino and Birney 2008). The draft genome size of strain 908 was 4,938,027 bp consisting of 76 contigs with 56.8% G+C content and 63,801 bp as N50. The draft genome was checked for misassembled fragments using QUAST v5.0.2 (Gurevich et al. 2013) and found to be of good quality. The draft genome sequence is deposited in GenBank under the accession number of JADCNJ000000000. The draft genome sequence of strain 908 was compared to that of D. fangzhongdai JS5T type strain genome using FastANI v1.2 (Jain et al. 2018) resulting in an ANI value of 98.9%, which is above the 95% cut-off for the same species. Previously, it was reported that D. fangzhongdai caused soft rot in orchid in Europe (Alič et al. 2018) and in onions in New York (Ma et al. 2020). The difference in virulence among D. fangzhongdai strains warrants further investigation and their pathogenicity on potato is being investigated to evaluate any threat to the potato industry. To our knowledge, this is the first report of D. fangzhongdai causing soft rot disease on orchids in Canada and North America. FAU - Zhou, Aiguo AU - Zhou A AD - CFIA, Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, Prince Edward Island, Canada. AD - South China Agricultural University, 12526, College of Marine Sciences, Guangzhou, Guangdong, China; scauzhouaiguo@163.com. FAU - Nie, Jingbai AU - Nie J AD - CFIA, Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, Prince Edward Island, Canada; jingbai.Nie@canada.ca. FAU - Tian, Yanli AU - Tian Y AD - Nanjing Agricultural University, College of Plant protection, 1#Weigang, Nanjing, Jiangsu, China, 210095; tianyanli@njau.edu.cn. FAU - Chuan, Jiacheng AU - Chuan J AD - CFIA, Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, Prince Edward Island, Canada. AD - University of Prince Edward Island, 2359, Biology Department, Charlottetown, Prince Edward Island, Canada; jiacheng.chuan@canada.ca. FAU - Hu, Baishi AU - Hu B AD - College of Plant protection, Nanjing Agricultural University, No.1 Weigang, Nanjing, Nanjing, Jiangsu, China, 210095; hbs@njau.edu.cn. FAU - Zou, Jixing AU - Zou J AD - South China Agricultural University, 12526, College of Marine Sciences, Guangzhou, Guangdong, China; zoujixing@scau.edu.cn. FAU - Li, Xiang AU - Li X AD - CFIA, Canadian Food Inspection Agency, Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, Charlottetown, Prince Edward Island, Canada, C1A5T1; Sean.Li@inspection.gc.ca. LA - eng PT - Journal Article DEP - 20210623 PL - United States TA - Plant Dis JT - Plant disease JID - 9882809 SB - IM OTO - NOTNLM OT - Average Nucleic Identity OT - Causal Agent OT - Dickeya fangzhongdai OT - Prokaryotes OT - Soft rot disease of orchid OT - qPCR EDAT- 2021/06/24 06:00 MHDA- 2021/06/24 06:00 CRDT- 2021/06/23 17:13 PHST- 2021/06/23 17:13 [entrez] PHST- 2021/06/24 06:00 [pubmed] PHST- 2021/06/24 06:00 [medline] AID - 10.1094/PDIS-04-21-0771-PDN [doi] PST - aheadofprint SO - Plant Dis. 2021 Jun 23. doi: 10.1094/PDIS-04-21-0771-PDN. PMID- 20709691 OWN - NLM STAT- MEDLINE DCOM- 20110216 LR - 20240924 IS - 1367-4811 (Electronic) IS - 1367-4803 (Linking) VI - 26 IP - 19 DP - 2010 Oct 1 TI - Search and clustering orders of magnitude faster than BLAST. PG - 2460-1 LID - 10.1093/bioinformatics/btq461 [doi] AB - MOTIVATION: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. RESULTS: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. AVAILABILITY: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch. FAU - Edgar, Robert C AU - Edgar RC AD - Tiburon, CA 94920, USA. robert@drive5.com LA - eng PT - Journal Article DEP - 20100812 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (Proteins) SB - IM MH - *Algorithms MH - Cluster Analysis MH - Computational Biology/*methods MH - Databases, Protein MH - Proteins/chemistry MH - Sequence Alignment/*methods MH - Sequence Analysis, Protein/*methods EDAT- 2010/08/17 06:00 MHDA- 2011/02/17 06:00 CRDT- 2010/08/17 06:00 PHST- 2010/08/17 06:00 [entrez] PHST- 2010/08/17 06:00 [pubmed] PHST- 2011/02/17 06:00 [medline] AID - btq461 [pii] AID - 10.1093/bioinformatics/btq461 [doi] PST - ppublish SO - Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12. PMID- 23955772 OWN - NLM STAT- MEDLINE DCOM- 20131211 LR - 20240924 IS - 1548-7105 (Electronic) IS - 1548-7091 (Linking) VI - 10 IP - 10 DP - 2013 Oct TI - UPARSE: highly accurate OTU sequences from microbial amplicon reads. PG - 996-8 LID - 10.1038/nmeth.2604 [doi] AB - Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community. FAU - Edgar, Robert C AU - Edgar RC AD - Independent Investigator, Tiburon, California, USA. LA - eng PT - Journal Article DEP - 20130818 PL - United States TA - Nat Methods JT - Nature methods JID - 101215604 RN - 0 (RNA, Ribosomal, 16S) SB - IM MH - Algorithms MH - Databases, Genetic MH - Humans MH - Metagenomics MH - Microbiota/*genetics MH - *Phylogeny MH - RNA, Ribosomal, 16S/*genetics MH - Research Design MH - Sensitivity and Specificity MH - Software EDAT- 2013/08/21 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/20 06:00 PHST- 2012/12/07 00:00 [received] PHST- 2013/07/15 00:00 [accepted] PHST- 2013/08/20 06:00 [entrez] PHST- 2013/08/21 06:00 [pubmed] PHST- 2013/12/16 06:00 [medline] AID - nmeth.2604 [pii] AID - 10.1038/nmeth.2604 [doi] PST - ppublish SO - Nat Methods. 2013 Oct;10(10):996-8. doi: 10.1038/nmeth.2604. Epub 2013 Aug 18. PMID- 33961008 OWN - NLM STAT- MEDLINE DCOM- 20230413 LR - 20230416 IS - 1367-4811 (Electronic) IS - 1367-4803 (Linking) VI - 37 IP - 21 DP - 2021 Nov 5 TI - CONSTAX2: improved taxonomic classification of environmental DNA markers. PG - 3941-3943 LID - 10.1093/bioinformatics/btab347 [doi] AB - SUMMARY: CONSTAX-the CONSensus TAXonomy classifier-was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. AVAILABILITY AND IMPLEMENTATION: CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CI - © The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. FAU - Liber, Julian A AU - Liber JA AUID- ORCID: 0000-0002-9941-8268 AD - Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA. FAU - Bonito, Gregory AU - Bonito G AD - Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA. AD - Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. FAU - Benucci, Gian Maria Niccolò AU - Benucci GMN AD - Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA. AD - Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DNA, Environmental) SB - IM MH - *Software MH - *DNA, Environmental MH - Algorithms MH - Eukaryota MH - Documentation EDAT- 2021/05/08 06:00 MHDA- 2023/04/13 06:42 CRDT- 2021/05/07 12:48 PHST- 2021/02/15 00:00 [received] PHST- 2021/04/28 00:00 [revised] PHST- 2021/05/05 00:00 [accepted] PHST- 2023/04/13 06:42 [medline] PHST- 2021/05/08 06:00 [pubmed] PHST- 2021/05/07 12:48 [entrez] AID - 6271412 [pii] AID - 10.1093/bioinformatics/btab347 [doi] PST - ppublish SO - Bioinformatics. 2021 Nov 5;37(21):3941-3943. doi: 10.1093/bioinformatics/btab347. PMID- 24076764 OWN - NLM STAT- MEDLINE DCOM- 20140203 LR - 20240109 IS - 1548-7105 (Electronic) IS - 1548-7091 (Print) IS - 1548-7091 (Linking) VI - 10 IP - 12 DP - 2013 Dec TI - Differential abundance analysis for microbial marker-gene surveys. PG - 1200-2 LID - 10.1038/nmeth.2658 [doi] AB - We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling-a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field. FAU - Paulson, Joseph N AU - Paulson JN AD - 1] Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland, College Park, Maryland, USA. [2] Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA. FAU - Stine, O Colin AU - Stine OC FAU - Bravo, Héctor Corrada AU - Bravo HC FAU - Pop, Mihai AU - Pop M AUID- ORCID: 0000000196175304 LA - eng GR - R01 HG004885/HG/NHGRI NIH HHS/United States GR - R01 HG005220/HG/NHGRI NIH HHS/United States PT - Journal Article DEP - 20130929 PL - United States TA - Nat Methods JT - Nature methods JID - 101215604 RN - 0 (Genetic Markers) RN - 0 (RNA, Ribosomal, 16S) SB - IM CIN - Nat Methods. 2014 Apr;11(4):359. doi: 10.1038/nmeth.2897. PMID: 24681719 MH - Algorithms MH - Animals MH - Area Under Curve MH - Cluster Analysis MH - Computer Simulation MH - Databases, Genetic MH - Gene Expression Profiling/methods MH - *Genetic Markers MH - Genetic Variation MH - Humans MH - Intestines/microbiology MH - Metagenomics/*methods MH - Mice MH - *Microbiota MH - Models, Genetic MH - Models, Statistical MH - Normal Distribution MH - Phenotype MH - RNA, Ribosomal, 16S/*genetics MH - Sequence Analysis, DNA MH - Software PMC - PMC4010126 MID - NIHMS521579 COIS- Competing financial interests The authors declare no competing financial interests. EDAT- 2013/10/01 06:00 MHDA- 2014/02/04 06:00 PMCR- 2014/06/01 CRDT- 2013/10/01 06:00 PHST- 2013/03/04 00:00 [received] PHST- 2013/08/16 00:00 [accepted] PHST- 2013/10/01 06:00 [entrez] PHST- 2013/10/01 06:00 [pubmed] PHST- 2014/02/04 06:00 [medline] PHST- 2014/06/01 00:00 [pmc-release] AID - nmeth.2658 [pii] AID - 10.1038/nmeth.2658 [doi] PST - ppublish SO - Nat Methods. 2013 Dec;10(12):1200-2. doi: 10.1038/nmeth.2658. Epub 2013 Sep 29. PMID- 23630581 OWN - NLM STAT- MEDLINE DCOM- 20131112 LR - 20240924 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 4 DP - 2013 TI - phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PG - e61217 LID - 10.1371/journal.pone.0061217 [doi] LID - e61217 AB - BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. RESULTS: Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. CONCLUSIONS: The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor. FAU - McMurdie, Paul J AU - McMurdie PJ AD - Department of Statistics, Stanford University, Stanford, California, United States of America. FAU - Holmes, Susan AU - Holmes S LA - eng GR - R01 GM086884/GM/NIGMS NIH HHS/United States GR - R01GM086884/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130422 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM MH - Data Interpretation, Statistical MH - Humans MH - *Metagenome MH - Multivariate Analysis MH - Phylogeny MH - Principal Component Analysis MH - Sequence Analysis, DNA MH - *Software PMC - PMC3632530 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2013/05/01 06:00 MHDA- 2013/11/13 06:00 PMCR- 2013/04/22 CRDT- 2013/05/01 06:00 PHST- 2012/10/17 00:00 [received] PHST- 2013/03/06 00:00 [accepted] PHST- 2013/05/01 06:00 [entrez] PHST- 2013/05/01 06:00 [pubmed] PHST- 2013/11/13 06:00 [medline] PHST- 2013/04/22 00:00 [pmc-release] AID - PONE-D-12-31789 [pii] AID - 10.1371/journal.pone.0061217 [doi] PST - epublish SO - PLoS One. 2013 Apr 22;8(4):e61217. doi: 10.1371/journal.pone.0061217. Print 2013. PMID- 14597658 OWN - NLM STAT- MEDLINE DCOM- 20040112 LR - 20250204 IS - 1088-9051 (Print) IS - 1088-9051 (Linking) VI - 13 IP - 11 DP - 2003 Nov TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks. PG - 2498-504 AB - Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models. FAU - Shannon, Paul AU - Shannon P AD - Institute for Systems Biology, Seattle, Washington 98103, USA. FAU - Markiel, Andrew AU - Markiel A FAU - Ozier, Owen AU - Ozier O FAU - Baliga, Nitin S AU - Baliga NS FAU - Wang, Jonathan T AU - Wang JT FAU - Ramage, Daniel AU - Ramage D FAU - Amin, Nada AU - Amin N FAU - Schwikowski, Benno AU - Schwikowski B FAU - Ideker, Trey AU - Ideker T LA - eng GR - P20 GM064361/GM/NIGMS NIH HHS/United States GR - P20 GM64361/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Genome Res JT - Genome research JID - 9518021 RN - 0 (Archaeal Proteins) SB - IM MH - Algorithms MH - Archaeal Proteins/chemistry/metabolism MH - Bacteriophage lambda/physiology MH - Computational Biology/*methods MH - Halobacterium/chemistry/cytology/physiology MH - Internet MH - *Models, Biological MH - *Neural Networks, Computer MH - Phenotype MH - Software/*trends MH - *Software Design MH - Stochastic Processes PMC - PMC403769 EDAT- 2003/11/05 05:00 MHDA- 2004/01/13 05:00 PMCR- 2004/05/01 CRDT- 2003/11/05 05:00 PHST- 2003/11/05 05:00 [pubmed] PHST- 2004/01/13 05:00 [medline] PHST- 2003/11/05 05:00 [entrez] PHST- 2004/05/01 00:00 [pmc-release] AID - 13/11/2498 [pii] AID - 0132498 [pii] AID - 10.1101/gr.1239303 [doi] PST - ppublish SO - Genome Res. 2003 Nov;13(11):2498-504. doi: 10.1101/gr.1239303. PMID- 22422314 OWN - NLM STAT- MEDLINE DCOM- 20121207 LR - 20220330 IS - 1750-2799 (Electronic) IS - 1750-2799 (Linking) VI - 7 IP - 4 DP - 2012 Mar 15 TI - Topological analysis and interactive visualization of biological networks and protein structures. PG - 670-85 LID - 10.1038/nprot.2012.004 [doi] AB - Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ∼2 h. FAU - Doncheva, Nadezhda T AU - Doncheva NT AD - Max Planck Institute for Informatics, Saarbrücken, Germany. FAU - Assenov, Yassen AU - Assenov Y FAU - Domingues, Francisco S AU - Domingues FS FAU - Albrecht, Mario AU - Albrecht M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120315 PL - England TA - Nat Protoc JT - Nature protocols JID - 101284307 RN - 0 (Proteins) SB - IM MH - Models, Biological MH - Protein Interaction Mapping/*methods MH - Protein Interaction Maps MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - *Software EDAT- 2012/03/17 06:00 MHDA- 2012/12/12 06:00 CRDT- 2012/03/17 06:00 PHST- 2012/03/17 06:00 [entrez] PHST- 2012/03/17 06:00 [pubmed] PHST- 2012/12/12 06:00 [medline] AID - nprot.2012.004 [pii] AID - 10.1038/nprot.2012.004 [doi] PST - epublish SO - Nat Protoc. 2012 Mar 15;7(4):670-85. doi: 10.1038/nprot.2012.004. PMID- 39267150 OWN - NLM STAT- MEDLINE DCOM- 20240913 LR - 20240915 IS - 2072-1315 (Electronic) IS - 1606-0997 (Print) IS - 1606-0997 (Linking) VI - 43 IP - 1 DP - 2024 Sep 12 TI - Global hotspots and trends of nutritional supplements in sport and exercise from 2000 to 2024: a bibliometric analysis. PG - 146 LID - 10.1186/s41043-024-00638-9 [doi] LID - 146 AB - BACKGROUND: Nutritional supplements for sports and exercise (NSSE) can facilitate the exogenous replenishment of the body. This study provides the first extensive overview of NSSE research through bibliometric and visual analyses. METHODS: We searched the Web of Science Core Collection database for literature related to "NSSE" from 1st January 2000 to 8th March 2024. A total of 1744 articles were included. CiteSpace, VOSviewer, and Bibliometrix R package software were used to analyze the data. RESULTS: Research in the NSSE can be divided into steady growth, exponential growth, fluctuating stage, and surge stages. The United States is the most active country in this field. In recent years, the leading countries have been Croatia, Colombia, Slovenia, Chile, Egypt, China, and Thailand. The Australian Institute of Sports is the top research institution in terms of number of publications. Burke, LM from Australia published the most articles. Research in this area has primarily been published in Nutrients in Switzerland. The study population mainly consisted of men, and postmenopausal women were the main focus of the female group. Coronary heart and cardiovascular diseases continue to dominate research. CONCLUSION: Research on the NSSE is developing rapidly, with an annual growth trend. Insulin resistance, sports nutrition, inflammation, alpha-linolenic acid, limb strength performance, female sex, and gut microbiota are the focus of the current research and trends for future research. Future research should focus on improving the scientific training system for athletes and quality of training and life for the general public. CI - © 2024. The Author(s). FAU - Fu, Te AU - Fu T AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. FAU - Liu, Haitao AU - Liu H AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. 10180110@vip.henu.edu.cn. AD - Research Center of Sports Reform and Development, Henan University, Kaifeng, Henan, 475001, China. 10180110@vip.henu.edu.cn. AD - Institute of Physical Fitness and Health, Henan University, Kaifeng, Henan, 475001, China. 10180110@vip.henu.edu.cn. FAU - Shi, Chaofan AU - Shi C AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. FAU - Zhao, Haichang AU - Zhao H AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. FAU - Liu, Feiyue AU - Liu F AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. FAU - Xia, Yingjian AU - Xia Y AD - College of Physical Education, Henan University, Kaifeng, Henan, 475001, China. LA - eng GR - 2023GGJS023/Training Program for Young Core Teachers in Higher Education Institutions of Henan Province/ GR - 2024SJGLX0265/Education and Teaching Reform Project in Higher Education of Henan Province/ GR - YJSJG2023XJ062/Henan University Graduate Education and Teaching Reform Project/ GR - SYLAL2022011/Henan University Graduate Education Innovation and Quality Improvement Plan Project/ PT - Journal Article PT - Review DEP - 20240912 PL - Bangladesh TA - J Health Popul Nutr JT - Journal of health, population, and nutrition JID - 100959228 SB - IM MH - Humans MH - *Dietary Supplements MH - *Bibliometrics MH - *Exercise MH - *Sports/statistics & numerical data MH - Male MH - Female MH - Global Health MH - Chile MH - Colombia MH - Sports Nutritional Physiological Phenomena MH - Croatia MH - Thailand PMC - PMC11397053 OTO - NOTNLM OT - Bibliometric analysis OT - Dietary supplements OT - Exercise OT - Nutritional supplements OT - Sport COIS- The authors declare no competing interests. EDAT- 2024/09/13 00:46 MHDA- 2024/09/14 10:43 PMCR- 2024/09/12 CRDT- 2024/09/12 23:53 PHST- 2024/07/11 00:00 [received] PHST- 2024/09/04 00:00 [accepted] PHST- 2024/09/14 10:43 [medline] PHST- 2024/09/13 00:46 [pubmed] PHST- 2024/09/12 23:53 [entrez] PHST- 2024/09/12 00:00 [pmc-release] AID - 10.1186/s41043-024-00638-9 [pii] AID - 638 [pii] AID - 10.1186/s41043-024-00638-9 [doi] PST - epublish SO - J Health Popul Nutr. 2024 Sep 12;43(1):146. doi: 10.1186/s41043-024-00638-9.