Phytotoxicity and cytogenotoxicity of water and sediment of urban stream in bioassay with Lactuca sativa

The aim of this study was to evaluate the spatial and temporal influence of the phytotoxicity and cytogenotoxicity of water and sediment of urban stream on the germination and initial growth of Lactuca sativa. Samples were collected from water and sediment at five sites of the Pântano Stream (Alfenas, Minas Gerais) during the period from October 2010 to July 2011. The concentrations of the metals Cd, Pb and Zn were quantified. Moreover, phytotoxicity and cytogenotoxicity were tested with samples of water and aqueous extracts of sediments. The evaluated end points were the germination rate, root length, fresh and dry weight, mitotic index and frequency of chromosomal abnormalities. Higher levels of Cd and Pb were verified in water samples collected during the rainy months. Water and sediment showed phytotoxic effect on germination, fresh weight and dry weight of Lactuca sativa. Root length was stimulated and only samples of water reduced the mitotic index. Significant temporal variation related to rainfall was observed only for phytotoxicity tests.Objetivou-se, com este trabalho, avaliar a influência espacial e temporal da fitotoxicidade e da citogenotoxicidade da água e do sedimento de córrego urbano quanto às características germinativas e de crescimento inicial de Lactuca sativa. Amostras de água e de sedimento foram coletadas em 5 pontos do Córrego do Pântano (Alfenas, Minas Gerais), no período de outubro de 2010 a julho de 2011 e as concentrações dos metais Cd, Pb e Zn foram quantificadas. Os ensaios de fitotoxicidade e de citogenotoxicidade foram realizados com as amostras de água e extratos aquosos dos sedimentos. Os parâmetros avaliados foram taxa de germinação, comprimento de raízes, biomassa fresca e seca, índice mitótico e a frequência de anormalidades cromossômicas. Constataram-se maiores concentrações de Cd e Pb nas amostras de água coletadas nos meses com a ocorrência de precipitações pluviométricas. Água e sedimento apresentaram efeito fitotóxico sobre germinação, biomassa fresca e seca de Lactuca sativa. O comprimento de raízes foi estimulado e apenas as amostras de água reduziram o índice mitótico. Evidenciou-se, também, variação temporal significativa relacionada com o regime pluviométrico apenas para o teste de fitotoxicidade.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)UNIFAL Instituto de Ciências da NaturezaUNIFAL Instituto de Ciências ExatasUNIFESPUNIFESPSciEL

A multicomponent exercise intervention to improve physical functioning, cognition and psychosocial well-being in elderly nursing home residents: a study protocol of a randomized controlled trial in the PROCARE (prevention and occupational health in long-term care) project

Background Older adults, who are living in nursing homes that provide a high level of long-term nursing care, are characterized by multimorbidity and a high prevalence of dependency in activities of daily living. Results of recent studies indicate positive effects of structured exercise programs during long-term care for physical functioning, cognition, and psychosocial well-being. However, for frail elderly the evidence remains inconsistent. There are no evidence-based guidelines for exercises for nursing home residents that consider their individual deficits and capacities. Therefore, high-quality studies are required to examine the efficacy of exercise interventions for this multimorbid target group. The purpose of this study is to determine the feasibility and efficacy of a multicomponent exercise intervention for nursing home residents that aims to improve physical and cognitive functioning as well as quality of life. Methods A two-arm single-blinded multicenter randomized controlled trial will be conducted, including 48 nursing homes in eight regions of Germany with an estimated sample size of 1120 individuals. Participants will be randomly assigned to either a training or a waiting time control group. For a period of 16 weeks the training group will meet twice a week for group-based sessions (45–60 min each), which will contain exercises to improve physical functioning (strength, endurance, balance, flexibility) and cognitive-motor skills (dual-task). The intervention is organized as a progressive challenge which is successively adapted to the residents’ capacities. Physical functioning, cognitive performance, and quality of life will be assessed in both study groups at baseline (pre-test), after 16-weeks (post-treatment), and after 32-weeks (retention test, intervention group only). Discussion This study will provide information about the efficacy of a multicomponent exercise program in nursing homes (performance, recruitment). Results from this trial will contribute to the evidence of multicomponent exercises, which specifically focus on cognitive-motor approaches in the maintenance of mental and physical functioning. In addition, it will help to encourage older adults to actively engage in social life. Furthermore, the findings will lead to recommendations for health promotion interventions for frail nursing home residents. Trial registration The trial was prospectively registered at DRKS.de with the registration number DRKS00014957 on October 9, 2018

Public Deposits In Biological Resource Centres Is An Essential Part Of Fair Science

F A I R s c i e n c e a i m s a t s h a r i n g s c i e n t i f i c o u t p u t i n s u c h a w a y a s t o m a x i m i z e t h e a c c e s s , r e u s e a n d i m p a c t o f r e s e a r c h . T h i s a l l o w s t r a n s p a r e n c y o f r e s u l t s , r e p r o d u c i b i l i t y o f e x p e r i m e n t s , c u m u l a t i v e r e s e a r c h , a n d a v o i d s a w a s t e o f r e s s o u r c e s ( 1 ) . A l t h o u g h t h e F A I R d a t a p r i n c i p l e i s b e c o m i n g a w e l l - k n o w n c o n c e p t , l e s s a t t e n t i o n i s g i v e n t o i t s a p p l i c a t i o n t o b i o l o g i c a l r e s o u r c e s . I n l i f e s c i e n c e s , p u b l i c m i c r o b i a l - a n d p l a s m i d c o l l e c t i o n s r e p r e s e n t a h i s t o r i c a l e x a m p l e o f F A I R s c i e n c e , t h a n k s t o t h e i r l o n g s t a n d i n g e x p e r i e n c e i n t h e p r e s e r v a t i o n a n d d i s t r i b u t i o n o f l i v i n g m i c r o b i a l s t r a i n s a n d ( g ) D N A f o r f u r t h e r s c i e n t i f i c i n v e s t i g a t i o n s o r d e v e l o p m e n t , w h i l e r e s p e c t i n g ( i n t e r ) n a t i o n a l l e g i s l a t i o n s a n d c a s e - s p e c i f i c r e s t r i c t i o n s a s d e f i n e d b y t h e c l i e n t s . T h e s e b i o l o g i c a l r e s o u r c e c e n t r e s ( B R C ) p r o v i d e w e l l - c h a r a c t e r i z e d , q u a l i t y - c o n t r o l l e d a n d a u t h e n t i c a t e d s t r a i n s , p l a s m i d s a n d a s s o c i a t e d d a t a ( 2 ) . T h e y a l s o s u p p o r t t h e b i o - i n d u s t r y , f o r w h i c h t h e d i v e r s i t y o f n a t u r a l l y o c c u r r i n g o r g e n e t i c a l l y e n g i n e e r e d m i c r o o r g a n i s m s a r e a n i n v a l u a b l e s o u r c e o f a p p l i c a t i o n s . T h e r e s p o n s i b i l i t y t o d e p o s i t t h e m i c r o o r g a n i s m s a n d g e n e t i c r e s o u r c e s i n p u b l i c B R C s i s s h a r e d b y r e s e a r c h e r s , f u n d i n g a g e n c i e s a n d p u b l i s h e r s ( 2 ) . L i f e s c i e n t i s t s n e e d t o b e c o m e m o r e a w a r e o f t h e i m p o r t a n c e o f s t r a i n a n d p l a s m i d c o n s e r v a t i o n a n d g r o w a c c u s t o m e d t o d e p o s i t t h e m d u r i n g t h e p u b l i c a t i o n p r o c e s s o r a t t h e e n d o f p r o j e c t s . G o v e r n m e n t a l f u n d i n g p o l i c i e s s h o u l d r e q u e s t i n t h e i r c o n t r a c t s t h e d e p o s i t o f b i o l o g i c a l m a t e r i a l s i s o l a t e d o r c o n s t r u c t e d d u r i n g f i n a n c e d p r o j e c t s . R e g a r d i n g p u b l i s h e r s , m o s t j o u r n a l s e n c o u r a g e a u t h o r s t o d e p o s i t t h e i r d a t a s e t s ( c o d e s , s e q u e n c e s , e t c ) i n p u b l i c r e p o s i t o r i e s b u t v e r y f e w s p e c i f i c a l l y r e q u i r e d e p o s i t o f b i o l o g i c a l m a t e r i a l a n d c u l t i v a t e d s t r a i n s i n p u b l i c c o l l e c t i o n s . E d i t o r s s h o u l d t h e r e f o r e i m p l e m e n t m e c h a n i s m s f o r a c t i v e a g r e e m e n t b y a u t h o r s t o d e p o s i t s t r a i n s a n d o t h e r g e n e t i c r e s o u r c e s w h e n s u b m i t t i n g a n a r t i c l e , o r t o j u s t i f y w h y i t w o u l d n o t b e p o s s i b l e . S u c h m e c h a n i s m s c o u l d f o l l o w T r a n s p a r e n c y a n d O p e n n e s s P r o m o t i o n g u i d e l i n e s ( 3 ) f o r j o u r n a l s t h a t i n c l u d e s t a n d a r d s f o r research materials.Belgian Consortium of Collections of Microorganism

Physical activity and health promotion for nursing staff in elderly care: a study protocol for a randomised controlled trial

Introduction Nursing staff is burdened by high workload and stress. Furthermore, heavy lifting, as well as transferring nursing home residents, cause lumbar tissue damage and back pain. Exercise intervention studies to reduce work-related problems are rare and the evidence for efficacy of studies among nurses is limited. Studies including targeted analysis of requirements are necessary to generate effective recommendations and tailored interventions for health promotion programmes. The purpose of this multicentred intervention study is to identify work-related problems, to implement health promotion programmes and to evaluate their effectiveness. Methods and analysis A randomised controlled trial will be conducted, including a total of 48 nursing home facilities in eight regions of Germany with an estimated sample size of 700 nurses. Standardised ergonomics and posture training (10 weeks, once a week for 20–30 min) and subsequently, back-fitness training (12 weeks, once a week for 45–60 min) will be administered. Following the implementation of standardised health promotion programmes, further demand-oriented interventions can be implemented. The perceived exposure to work-related demands, work-related pain in different parts of the body, health-related quality of life, perceived stress, work-related patterns of behaviour and experience, presentism behaviour, work environment as well as general needs and barriers to health promotion, will be assessed at baseline (pre-test), at 10 weeks (post-test, after ergonomics training), at 22 weeks (post-test, after back-fitness training) and at 34 weeks of the programme (follow-up). Ethics and dissemination The study was reviewed and approved by the local ethics committee of the University of Hamburg (AZ: 2018_168). The results of the study will be published in open-access and international journals. Furthermore, the results will be presented in the participating nursing homes and at national and international conferences

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

peer reviewed[en] BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox, a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). This public toolbox is designed for researchers without a specific training in bioinformatics (launched by a single command line). Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. All the workflows are based on Singularity containers and Nextflow to increase reproducibility. The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales (Cyanobacteria). This study is published at https://doi.org/10.1093/gigascience/giad022GENER

Taxonomic annotation of public fungal ITS sequences from the built environment - A report from an April 10-11, 2017 workshop (Aberdeen, UK)

The UNITE database community gratefully acknowledges support from the Alfred P. Sloan Foundation. HN and CW gratefully acknowledges financial support from Stiftelsen Olle Engkvist Byggmästare, Stiftelsen Lars Hiertas Minne, Kapten Carl Stenholms Donationsfond, and Birgit och Birger Wålhströms Minnesfond. CW gratefully acknowledges a Marie Skłodowska-Curie post doctoral grant from the ERC. Leho Tedersoo is gratefully acknowledged for providing helpful feedback on an earlier draft of this manuscript.Peer reviewedPublisher PD

Rapid Etiological Classification of Meningitis by NMR Spectroscopy Based on Metabolite Profiles and Host Response

Bacterial meningitis is an acute disease with high mortality that is reduced by early treatment. Identification of the causative microorganism by culture is sensitive but slow. Large volumes of cerebrospinal fluid (CSF) are required to maximise sensitivity and establish a provisional diagnosis. We have utilised nuclear magnetic resonance (NMR) spectroscopy to rapidly characterise the biochemical profile of CSF from normal rats and animals with pneumococcal or cryptococcal meningitis. Use of a miniaturised capillary NMR system overcame limitations caused by small CSF volumes and low metabolite concentrations. The analysis of the complex NMR spectroscopic data by a supervised statistical classification strategy included major, minor and unidentified metabolites. Reproducible spectral profiles were generated within less than three minutes, and revealed differences in the relative amounts of glucose, lactate, citrate, amino acid residues, acetate and polyols in the three groups. Contributions from microbial metabolism and inflammatory cells were evident. The computerised statistical classification strategy is based on both major metabolites and minor, partially unidentified metabolites. This data analysis proved highly specific for diagnosis (100% specificity in the final validation set), provided those with visible blood contamination were excluded from analysis; 6-8% of samples were classified as indeterminate. This proof of principle study suggests that a rapid etiologic diagnosis of meningitis is possible without prior culture. The method can be fully automated and avoids delays due to processing and selective identification of specific pathogens that are inherent in DNA-based techniques

The Amsterdam Declaration on Fungal Nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented

Joint Observation of the Galactic Center with MAGIC and CTA-LST-1

MAGIC is a system of two Imaging Atmospheric Cherenkov Telescopes (IACTs), designed to detect very-high-energy gamma rays, and is operating in stereoscopic mode since 2009 at the Observatorio del Roque de Los Muchachos in La Palma, Spain. In 2018, the prototype IACT of the Large-Sized Telescope (LST-1) for the Cherenkov Telescope Array, a next-generation ground-based gamma-ray observatory, was inaugurated at the same site, at a distance of approximately 100 meters from the MAGIC telescopes. Using joint observations between MAGIC and LST-1, we developed a dedicated analysis pipeline and established the threefold telescope system via software, achieving the highest sensitivity in the northern hemisphere. Based on this enhanced performance, MAGIC and LST-1 have been jointly and regularly observing the Galactic Center, a region of paramount importance and complexity for IACTs. In particular, the gamma-ray emission from the dynamical center of the Milky Way is under debate. Although previous measurements suggested that a supermassive black hole Sagittarius A* plays a primary role, its radiation mechanism remains unclear, mainly due to limited angular resolution and sensitivity. The enhanced sensitivity in our novel approach is thus expected to provide new insights into the question. We here present the current status of the data analysis for the Galactic Center joint MAGIC and LST-1 observations