Comparison of protocols for genomic DNA extraction from ‘velame pimenta’ (Croton linearifolius), a native species to the Caatinga, Brazil

The Caatinga biome occupies some 12% of the Brazilian territory, which is present in at least nine states. The species that constitute its biodiversity have the potential to be used as natural resources, among them are approximately 700 species of the genus Croton. As an example of this potential, the Croton linearifolius specie is used by local communities as a natural insecticide. Associated with the economic potential of the Caatinga species, one must stress the risk of extinction or genetic erosion due to the growing deforestation of natural areas of this biome. These factors make it relevant in genetic studies in order to guide conservation strategies. Considering the lack of molecular studies involving C. linearifolius, we compared the efficiency of six protocols for genomic DNA extraction previously described in literature. The DNA extraction buffers [based on the use of Cetyl trimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), mannitol and sorbitol] were different in their efficiency to obtaining the genomic DNA of C. linearifloius. In general, protocols using CTAB buffer were more efficient. The use of liquid nitrogen in the maceration process was also evaluated and its use was considered a no necessary factor in obtaining DNA in adequate quantity and quality for PCR platform procedures.Keywords: DNA Isolation, molecular markers, native species of CaatingaAfrican Journal of Biotechnology Vol. 12(30), pp. 4761-476

Physical activity, sedentary behaviour, and childhood asthma: a European collaborative analysis

OBJECTIVES: To investigate the associations of physical activity (PA) and sedentary behaviour in early childhood with asthma and reduced lung function in later childhood within a large collaborative study. DESIGN: Pooling of longitudinal data from collaborating birth cohorts using meta-analysis of separate cohort-specific estimates and analysis of individual participant data of all cohorts combined. SETTING: Children aged 0-18 years from 26 European birth cohorts. PARTICIPANTS: 136 071 individual children from 26 cohorts, with information on PA and/or sedentary behaviour in early childhood and asthma assessment in later childhood. MAIN OUTCOME MEASURE: Questionnaire-based current asthma and lung function measured by spirometry (forced expiratory volume in 1 s (FEV1), FEV1/forced vital capacity) at age 6-18 years. RESULTS: Questionnaire-based and accelerometry-based PA and sedentary behaviour at age 3-5 years was not associated with asthma at age 6-18 years (PA in hours/day adjusted OR 1.01, 95% CI 0.98 to 1.04; sedentary behaviour in hours/day adjusted OR 1.03, 95% CI 0.99 to 1.07). PA was not associated with lung function at any age. Analyses of sedentary behaviour and lung function showed inconsistent results. CONCLUSIONS: Reduced PA and increased sedentary behaviour before 6 years of age were not associated with the presence of asthma later in childhood. © Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.The authors received no specific funding for this article. Funding information per cohort: ABCD: The ABCD study has been supported by grants from The Netherlands Organisation for Health Research and Development (ZonMW) and The Netherlands Heart Foundation. ABIS: Special thanks to the participating families in the ABIS study, and all staff at Obstetric departments and Well-Baby Clinics. ABIS has been supported by Swedish Research Council (K2005-72X-11242-11A and K2008-69X-20826-01-4) and the Swedish Child Diabetes Foundation (Barndiabetesfonden), JDRF Wallenberg Foundation (K 98-99D-12813-01A), Medical Research Council of Southeast Sweden (FORSS), and the Swedish Council for Working Life and Social Research (FAS2004-1775) and Östgöta Brandstodsbolag. BAMSE: This BAMSE birth cohort was supported by grants from the Swedish Research Council, the Swedish Research Council for Health, Working Life and Welfare, Formas, the Swedish Heart-Lung Foundation, the Swedish Asthma and Allergy Research Foundation, Region Stockholm (ALF project, and for cohort and database maintenance), and the European Research Council (TRIBAL, grant agreement 757919). CHOP: The CHOP study reported herein have been carried out with partial financial support from the Commission of the European Community, specific RTD Programme 'Quality of Life and Management of Living Resources', within the European Union's Seventh Framework Programme (FP7/2007-2013), project EarlyNutrition under grant agreement no. 289346, partial financial support from Polish Ministry of Science and Higher Education (2571/7.PR/2012/2), the EU H2020 project PHC-2014-DynaHealth under grant no. 633595 and the European Research Council Advanced Grant META-GROWTH (ERC-2012-AdG-no.322605). COPSAC2000: All funding received by COPSAC is listed on www.copsac.com. The Lundbeck Foundation (Grant no R16-A1694); The Ministry of Health (Grant no 903516); Danish Council for Strategic Research (Grant no 0603-00280B) and The Capital Region Research Foundation have provided core support to the COPSAC research center. DNBC: The Danish National Birth Cohort was established with a significant grant from the Danish National Research Foundation. Additional support was obtained from the Danish Regional Committees, the Pharmacy Foundation, the Egmont Foundation, the March of Dimes Birth Defects Foundation, the Health Foundation and other minor grants. The DNBC Biobank has been supported by the Novo Nordisk Foundation and the Lundbeck Foundation. EDEN: EU FP7 Framework MedAll project, National Institute for Research in Public Health (IRESP TGIR Cohorte Santé 2008 Program); National Agency for Research (ANR non-thematic programme); French Speaking Association for the Study of Diabetes and Metabolism (Alfediam); Mutuelle Générale de l’Éducation Nationale; Nestlé; French National Institute for Health Education (INPES); Paris‐Sud University; French National Istitute for Population Health Surveillance (InVS); French Agency for Environment Security (AFFSET); French Ministry of Health Perinatal Program; Inserm Nutrition Research Program; Institut Fédératif de Recherche and Cohort Program; French Ministry of Research; EURIP and FIRE doctoral school–Programme Bettencourt; Fondation pour la Recherche Médicale (FRM). G21: Generation XXI was supported by the European Regional Development Fund (ERDF) through the Operational Programme Competitiveness and Internationalisation and national funding from the Foundation for Science and Technology (FCT), Portuguese Ministry of Science, Technology and Higher Education under the project 'HIneC: When do health inequalities start? Understanding the impact of childhood social adversity on health trajectories from birth to early adolescence' (POCI-01-0145-FEDER-029567; Reference PTDC/SAU-PUB/29567/2017). It is also supported by the Unidade de Investigação em Epidemiologia–Instituto de Saúde Pública da Universidade do Porto (EPIUnit) (UIDB/04750/2020), Administração Regional de Saúde Norte (Regional Department of Ministry of Health) and Fundação Calouste Gulbenkian; PhD Grant SFRH/BD/108742/2015 (to SS) co-funded by FCT and the Human Capital Operational Programme (POCH/FSE Program); ACS is founded by a FCT Investigator contracts IF/01060/2015. Generation R: The Generation R Study is made possible by financial support from the Erasmus Medical Centre, Rotterdam, the Erasmus University Rotterdam and The Netherlands Organization for Health Research and Development. The project received funding for projects from the European Union's Horizon 2020 research and innovation programme (LIFECYCLE, grant agreement No 733206, 2016; EUCAN-Connect grant agreement No 824989; ATHLETE, grant agreement No 874583). LD received funding from the European Union's Horizon 2020 cofunded programme ERA-Net on Biomarkers for Nutrition and Health (ERA HDHL) (ALPHABET project (no 696295; 2017), ZonMW The Netherlands (no 529051014; 2017)). GINIplus: The GINIplus study was mainly supported for the first 3 years of the Federal Ministry for Education, Science, Research and Technology (interventional arm) and Helmholtz Zentrum Munich (former GSF) (observational arm). The 4 years, 6 years, 10 years and 15 years follow-up examinations of the GINIplus study were covered from the respective budgets of the five study centres (Helmholtz Zentrum Munich (former GSF), Research Institute at Marien-Hospital Wesel, LMU Munich, TU Munich and from 6 years onwards also from IUF - Leibniz Research-Institute for Environmental Medicine at the University of Düsseldorf) and a grant from the Federal Ministry for Environment (IUF Düsseldorf, FKZ 20462296). Further, the 15-year follow-up examination of the GINIplus study was supported by the Commission of the European Communities, the 7th Framework Program: MeDALL project, and as well by the companies Mead Johnson and Nestlé. The authors thank all the families for their participation in the GINIplus study. Furthermore, we thank all members of the GINIplus Study Group for their excellent work. The GINIplus Study group consists of the following: Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg (Heinrich J, Brüske I, Schulz H, Flexeder C, Zeller C, Standl M, Schnappinger M, Ferland M, Thiering E, Tiesler C); Department of Pediatrics, Marien-Hospital, Wesel (Berdel D, von Berg A); Ludwig-Maximilians-University of Munich, Dr von Hauner Children’s Hospital (Koletzko S); Child and Adolescent Medicine, University Hospital rechts der Isar of the Technical University Munich (Bauer CP, Hoffmann U); IUF- Environmental Health Research Institute, Düsseldorf (Schikowski T, Link E, Klümper C, Krämer U, Sugiri D). HUMIS: HUMIS is supported by the Research Council of Norway (NevroNor, grant number 226402). INMA Asturias: This study was funded by grants from, FIS-FEDER: PI04/2018, PI09/02311, PI13/02429, PI18/00909; Obra Social Cajastur/Fundación Liberbank, and Universidad de Oviedo. We thank Fundación NOE Alimerka. INMA Gipuzkoa: This study was funded by grants from Instituto de Salud Carlos III (FIS-PI06/0867, FIS-PI09/00090, FIS-PI13/02187 include FEDER funds), CIBERESP, Department of Health of the Basque Government (2005111093, 2009111069, 2013111089 and 2015111065), and the Provincial Government of Gipuzkoa (DFG06/002, DFG08/001 and DFG15/221) and annual agreements with the municipalities of the study area (Zumarraga, Urretxu, Legazpi, Azkoitia y Azpeitia y Beasain). INMA Menorca: This study was funded by grants from Instituto de Salud Carlos III (Red INMA G03/176; CB06/02/0041; 97/0588; 00/0021-2; PI061756; PS0901958; PI14/00677 incl. FEDER funds), CIBERESP, Beca de la IV convocatoria de Ayudas a la Investigación en Enfermedades Neurodegenerativas de La Caixa, and EC Contract No. QLK4-CT-2000-00263. INMA Sabadell: This study was funded by grants from Instituto de Salud Carlos III (Red INMA G03/176; CB06/02/0041; PI041436; PI081151 incl. FEDER funds; CPII/00018), CIBERESP, Generalitat de Catalunya-CIRIT 1999SGR 00241, Generalitat de Catalunya-AGAUR 2009 SGR 501, Fundació La marató de TV3 (090430), EU Commission (261357). ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya. INMA Valencia: This study was funded by grants from UE (FP7-ENV-2011 cod 282957 and HEALTH.2010.2.4.5-1), Spain: ISCIII (Red INMA G03/176, CB06/02/0041; FIS-FEDER: PI03/1615, PI04/1509, PI04/1112, PI04/1931, PI05/1079, PI05/1052, PI06/1213, PI07/0314, PI09/02647, PI11/01007, PI11/02591, PI11/02038, PI13/1944, PI13/2032, PI14/00891, PI14/01687, PI16/1288, PI17/00663, and 19/1338; Miguel Servet-FEDER CP11/00178, CP15/00025 and CPII16/00051), Generalitat Valenciana: FISABIO (UGP 15-230, UGP-15-244, UGP-15-249, and AICO 2020/285), and Alicia Koplowitz Foundation 2017. KOALA: The KOALA cohort study was cofinanced by Friesland Foods (now FrieslandCampina), Netherlands Asthma Foundation (grant numbers 3.2.07.022 and 3.2.03.48) and Netherlands Heart Foundation (grant number 2014 T037), the Netherlands Organization for Health Research and Development (ZonMw Prevention Program number 1.210-00-090). The funding sources had no role in the study design and the collection, analysis and interpretation of data and the writing of the article and the decision to submit it for publication. Lifeways: The Lifeways study has been funded by the Health Research Board, Ireland, and the Irish Department of Health and Children’s Health Promotion Policy Unit. LISA: The LISA study was mainly supported by grants from the Federal Ministry for Education, Science, Research and Technology and in addition from Helmholtz Zentrum Munich (former GSF), Helmholtz Centre for Environmental Research—UFZ, Leipzig, Research Institute at Marien-Hospital Wesel, Pediatric Practice, Bad Honnef for the first 2 years. The 4 years, 6 years, 10 years and 15 years follow-up examinations of the LISA study were covered from the respective budgets of the involved partners (Helmholtz Zentrum Munich (former GSF), Helmholtz Centre for Environmental Research—UFZ, Leipzig, Research Institute at Marien-Hospital Wesel, Pediatric Practice, Bad Honnef, IUF—Leibniz-Research Institute for Environmental Medicine at the University of Düsseldorf) and in addition by a grant from the Federal Ministry for Environment (IUF Düsseldorf, FKZ 20462296). Further, the 15-year follow-up examination of the LISA study was supported by the Commission of the European Communities, the 7th Framework Program: MeDALL project. The authors thank all the families for their participation in the LISA study. Furthermore, we thank all members of the LISA Study Group for their excellent work. The LISA Study group consists of the following: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Epidemiology, Munich (Heinrich J, Schnappinger M, Brüske I, Ferland M, Schulz H, Zeller C, Standl M, Thiering E, Tiesler C, Flexeder C); Department of Pediatrics, Municipal Hospital 'St. Georg', Leipzig (Borte M, Diez U, Dorn C, Braun E); Marien Hospital Wesel, Department of Pediatrics, Wesel (von Berg A, Berdel D, Stiers G, Maas B); Pediatric Practice, Bad Honnef (Schaaf B); Helmholtz Centre of Environmental Research—UFZ, Department of Environmental Immunology/Core Facility Studies, Leipzig (Lehmann I, Bauer M, Röder S, Schilde M, Nowak M, Herberth G, Müller J); Technical University Munich, Department of Pediatrics, Munich (Hoffmann U, Paschke M, Marra S); Clinical Research Group Molecular Dermatology, Department of Dermatology and Allergy, Technische Universität München (TUM), Munich (Ollert M, J. Grosch). LRC: All phases of this study were supported by the Swiss National Science Foundation (grants: SNF 320030_182628, 32003B_162820, PDFMP3 137033, 32003B_162820, 32003B_144068, PZ00P3_147987) and Asthma UK 07/048. LUCKI: This study was supported by Maastricht University and the Public Health Service South Limburg. PIAMA: The Prevention and Incidence of Asthma and Mite Allergy Study has been funded by grants from the Netherlands Organization for Health Research and Development; the Netherlands Organization for Scientific Research; the Lung Foundation of the Netherlands; the Netherlands Ministry of Planning, Housing and the Environment; the Netherlands Ministry of Health, Welfare and Sport; and the National Institute for Public Health and the Environment. SEATON: Medical Research Council, Grant number: 80219, MR/K001035/1; Asthma UK, Grant numbers: 00/011, 02/017. STEPS Study: The Academy of Finland (grant no. 123571 and 121659); the Juho Vainio Foundation; the Foundation for Pediatric Research; the Finnish Medical Foundation. SWS: The SWS was supported by grants from the Medical Research Council (MC_UU_12011/4), Dunhill Medical Trust, British Heart Foundation, Food Standards Agency (contract no N05071), British Lung Foundation. National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service Foundation Trust, the European Union’s Seventh Framework Programme (FP7/2007-2013), project EarlyNutrition (grant 289346) and European Union’s Horizon 2020 research and innovation programme under grant agreement No 733206 (LifeCycle). WHISTLER: The authors (from the WHISTLER birth cohort) received no specific funding for this article. The WHISTLER birth cohort was supported with a grant from the Netherlands Organization for Health Research and Development (grant no. 2001-1-1322) and by an unrestricted grant from GlaxoSmithKline Netherlands

New polymorphic microsatellite loci for Theobroma cacao: isolation and characterization of microsatellites from enriched genomic libraries

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Seventeen polymorphic microsatellite markers were isolated from enriched genomic libraries for Theobroma cacao, providing additional tools for studying the genetic diversity and map saturation of this species. These markers were characterized in 32 accessions of the T. cacao germplasm collection from the Centro de Pesquisas do Cacau. The number of alleles at each locus varied from 2 to 8, with an average of 4.41 alleles per locus. The polymorphism information content varied from 0.060 to 0.695, with an average of 0.333. The markers characterized in this study will be employed in map saturation studies and diversity assessments of cacao genotypes.564789792Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)CAPES [PROCAD-NF2008

Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitoria da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.9424212428Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)UESCConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs.111731738Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)UESCConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

DEVELOPMENT AND CHARACTERIZATION OF MICROSATELLITE MARKERS FOR THE WILD SOUTH AMERICAN PASSIFLORA CINCINNATA (PASSIFLORACEAE)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Premise of the study: We developed the first set of microsatellite markers for the passion fruit, Passiflora cincinnata, to provide tools for further study of its genetic diversity and to support current conservation and genetic studies. Methods and Results: We used a microsatellite-enriched library approach to isolate and characterize 25 new molecular markers. Seven primer pairs successfully amplified polymorphic microsatellite regions, with an average of five alleles per locus. The mean values of expected and observed levels of heterozygosity were 0.516 and 0.525, respectively. Conclusions: The microsatellite markers identified in this study may be valuable tools for population genetic studies, and this set of markers also may be useful in the design of a genetic conservation strategy, mating system, and hybridization studies.994E170E172Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)CAPES [PROCAD-NF2008

Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus.942123213

Early-life respiratory tract infections and the risk of school-age lower lung function and asthma: a meta-analysis of 150 000 European children.

BACKGROUND: Early-life respiratory tract infections might affect chronic obstructive respiratory diseases, but conclusive studies from general populations are lacking. OBJECTIVE: To examine if children with early-life respiratory tract infections had increased risks of lower lung function and asthma at school-age. METHODS: We used individual-participant data of 150 090 children primarily from the EU Child Cohort Network to examine the associations of upper and lower respiratory tract infections from age 6 months to 5 years with forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC, forced expiratory flow at 75% of FVC (FEF75), and asthma at a median age of 7 (range 4 to 15) years. RESULTS: Children with early-life lower, not upper, respiratory tract infections had a lower school-age FEV1, FEV1/FVC and FEF75 (Z-score (95% CI): ranging from -0.09 (-0.14, -0.04) to -0.30 (-0.36, -0.24)). Children with early-life lower respiratory tract infections had a higher increased risk of school-age asthma than those with upper respiratory tract infections (OR (95%CI): ranging from 2.10 (1.98, 2.22) to 6.30 (5.64, 7.04)), and from 1.25 (1.18, 1.32) to 1.55 (1.47, 1.65)), respectively). Adjustment for preceding respiratory tract infections slightly decreased the strength of the effects. Observed associations were similar for those with and without early-life wheezing as proxy for early-life asthma. CONCLUSION: Our findings suggest that early-life respiratory tract infections affect development of chronic obstructive respiratory diseases in later life, with the strongest effects for lower upper respiratory tract infections