Agro-climate tools for a new climate-smart agriculture

The way we produce food must adapt to a variable and changing climate. And key to achieving this is to improve the link between climate information and agricultural practices, especially those of smallholder farmers in developing countries. ‘Agro-climate tools’ do just that and some are introduced here

Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays

Abstract Background The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro. Results We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The chY1, chY3 and chY5 genes were highly conserved with their vertebrate counterparts, whilst the chY4 gene showed a relatively high degree of diversification from the other vertebrate Y4 genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four Y RNA genes present in the hamster genome, we found that only the chY1 and chY3 RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the chY4 and chY5 RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system. Conclusions These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat

A gene co-association network regulating gut microbial communities in a Duroc pig population

Background: Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results: In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance

Association between physical activity levels and polypharmacy in hypertensive patients

Background: exercise reduces medication usage in hypertensive people. However, different domains of physical activity (PA) have not been studied in order to analyze their relationship with the use of multiple medications, known as polypharmacy. Purpose: To examine the association between PA in different domains (leisure-time, locomotion and occupational) and polypharmacy in hypertensive patients. Methods: This is a cross-sectional study carried out with 190 hypertensive patients. Polypharmacy was defined as simultaneous use of three or more drugs. The PA domains were the independent variables: Locomotion PA (LPA), Leisure Time PA (LTPA) and Occupational PA (OPA). The multiple logistic regression was performed to analyze the associations. The Mann Whitney test determined whether medications usage differ according to each domain of PA. Results: The total number of drugs used ranged from 0 to 7, which represents an average of 2.35 (±1.6) drugs per person. Scores of LTPA (OR: 3.25; CI95%:1.61-6.54) and LPA (OR: 2.15; CI95%:1.09-4.25) were inversely associated with polypharmacy in hypertensive patients, in the multiple logistic regression analysis (controlled by BMI, chronic diseases, smoking, alcohol consumption and skin color). Conclusions: lower PA in leisure time and locomotion were associated with polypharmacy in hypertensive peopleIntrodução: o exercício reduz o uso de medicamentos em indivíduos hipertensos. Contudo, diferentes domínios de atividade física (AF) não têm sido estudados no intuito de analisar suas relações com o uso de múltiplos medicamentos, conhecido como polifarmácia. Objetivo: analisar a associação entre AF em diferentes domínios (tempo livre, locomoção e ocupação) e polifarmácia em indivíduos hipertensos. Métodos: trata-se de um estudo transversal realizado com 190 hipertensos. Polifarmácia foi definida como o uso simultâneo de três ou mais drogas. As variáveis independentes foram os domínios de AF: Locomoção (AFL); Tempo Livre (AFTL) e Ocupacional (AFO). A regressão logística múltipla foi empregada para analisar as associações. O teste de Mann Whitney foi empregado para comparar se a média de medicamentos usados diferia entre domínios de AF. Resultados: o número total de drogas usadas variou de 0 a 7, com média de 2.35 (±1.6) por pessoa. Escores de AFTL (OR: 3.25; IC95%: 1.61-6.54) e AFL (OR: 2.15; IC95%: 1.09-4.25) foram inversamente associadas à polifarmácia em hipertensos (controlado por IMC, número de doenças crônicas, fumo, consumo de álcool e cor da pele). Conclusão: menor AF no tempo livre e de locomoção foi associada à polifarmácia em indivíduos hipertenso

High doses of zinc and copper alter neither cerebral metal levels nor acetylcholinesterase activity of suckling rats

This research investigated the in vivo (ZnCl2 27 mg/kg; CuSO4 10.2 mg/kg) and in vitro effects of zinc and copper on acetylcholinesterase activity of different cerebral areas, Zn and Cu levels in cerebrum, and body weight gain of young Wistar rats. Three-day-old rats were injected (s.c.) with 5 doses (saline, Zn, Cu or Zn+Cu) for 5 consecutive days and were killed 24 h after the last dose. In the other experiment, 7-day-old rats received only 1 dose (saline, Zn or Cu) and were killed at 1, 6 or 24 h after. For the in vitro experiments, the acetylcholinesterase activity from cerebrum of 8-day-old rats was analyzed in presence of Zn or Cu (0.01 to 1 mM). Regarding the in vivo experiments, only body weight gain was decreased by 5 simultaneous administrations of Zn and Cu. The acetylcholinesterase activity from cerebrum and cerebellum and cerebral zinc and copper contents were not altered by the treatments. In vitro, Cu 0.1 and 1 mM, but not Zn, inhibited the enzyme of both cerebrum and cerebellum. The enzymatic activity from cerebrum and cerebellum homogenate was more sensitive to Cu than the enzymatic activity from S2 and S1 fractions, respectively, since less metal was necessary to inhibit the enzyme

Neutron activation analysis and X-ray Rayleigh and Raman scattering of hair and nail clippings as noninvasive bioindicators for Cu liver status in Labrador Retrievers

The heritability of chronic hepatitis in the Labrador Retriever is studied with the aim of identifying the related gene mutation. Identification of cases and controls is largely based on instrumental neutron activation analysis (INAA) Cu determination in liver biopsies. The burden for these companion animals may be reduced if nail clippings and hair (fur) could serve as a noninvasive indicator for the hepatic Cu concentrations. No correlation was found between hepatic Cu concentrations and Cu concentrations in hair and nail samples. However, hair and nail samples were also analyzed by X-ray tube excitation, taking advantage of the X-ray Compton, Rayleigh, and Raman scattering which reflects the organic components such as the type of melanin. Principal component analysis provided first indications that some differentiation between healthy and sick dogs could indeed be obtained from hair and nail analysis

Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h 2 ; proportion of phenotypic variance explained by the host genetics) and microbiability (m 2 ; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m 2 (0.275) compared to h 2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs. The online version contains supplementary material available at 10.1186/s42523-021-00138-9