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Background : Global food systems are essential to sustain life; however, unhealthy diets are the leading cause of poor health and death worldwide. Natural food environments are a critical source of healthful food such as fresh fruit and vegetables, lean meat and aquatic foods, particularly in low- and middle-income countries (LMICs) and Indigenous food systems. Understanding and monitoring natural food environments is critical to protecting the supply of healthy food, and the land and water it comes from, for current and future generations. Methods: A scoping review was applied to classify and summarise empirical methods and measures used for characterising natural food environments. The ways in which food environment characteristics are conceptualised and measured for natural (wild and cultivated) food environments were explored. Data were extracted from the included studies using the following fields: study country, aim/objective(s), type of natural food environment (wild vs. cultivated), method or measure used to measure the food environment, key food environment characteristic/s (up to four) measured and key findings in relation to the food environment measurement. Results: One hundred forty seven studies were found to be relevant in this review. Most studies investigated food environments in LMICs, with almost two-thirds of all studies focussing on middle-income countries (n = 89, 61%). There was a strong focus on food security and home-based agriculture from studies that measured the cultivated food environment in LMICs, while the majority of studies on the cultivated food environment from high-income countries focussed on urban and community gardening. In addition to the most common survey-based methodological approaches, our review yielded a broad range of both qualitative and quantitative methods for measuring natural food environments, such as geospatial analysis; biochemical analysis of food, soil and water; citizen science; photovoice and food availability calendars. Conclusions: Our review demonstrated that the concept and characteristics of the food environment are a promising conceptualization for measuring natural food environments, particularly in relation to food availability, healthiness and food security. Mapping the currently used methods and measures to assess natural food environments is important to help identify critical leverage points for strengthening policy interventions, and monitoring and evaluation of progress. [ABSTRACT FROM AUTHOR]

The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, various phenotypes are often present within the same vineyard due to the accumulation of somatic mutations. These mutations are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as a pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of domestication on methylation patterns in cultivated grapevines. Reduced-representation bisulfite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% were hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (consistently methylated in both wild and cultivated accessions) are associated with stress response and terpenoid/isoprenoid metabolic processes. Meanwhile, genes with differential methylation are linked to protein targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Collectively, our results highlight the significant roles that epialleles may have played throughout the domestication history of grapevines. [ABSTRACT FROM AUTHOR]

The marine migration of Atlantic salmon (Salmo salar) has been prioritised for research internationally as populations of S. salar have declined significantly throughout the species' range. The main objectives of this study were to use acoustic telemetry to partition survival during the early migration phase, investigate potential causes of mortality and establish diurnal and tidal influences on movements. In 2017 and 2018 wild (n = 49) and hatchery (n = 81) S. salar smolts were tagged with acoustic transmitters. Migration was monitored through a brackish tidal lake, which discharges through a short estuary into northeast Clew Bay in Ireland situated in the northeast Atlantic. Partitioned survival through each area was similar for both wild and hatchery smolts and both groups followed the same migration routes, travelling along the main current out of Clew Bay. Total survival was high within the brackish lake (wild = 98% ± 1.21 and hatchery = 100%) and estuary (wild = 98% ± 1.01 and hatchery = 89% ± 9.28) compared to the marine environment (wild = 67% ± 4.39 and hatchery = 66% ± 7.91). Leaving the brackish lake during an ebb tide and entering the marine environment during daylight increased the probability of survival through the early marine period. The majority of smolts transited through the study area during ebb tides. Migration of hatchery smolts occurred mainly during hours of daylight while wild smolt migration showed no diel patterns. High mortality rates during the initial stages of the marine migration have consequences for the persistence of salmon populations and should be addressed through regionally tailored management measures and conservation efforts aimed at increasing the resilience of salmon stocks. [ABSTRACT FROM AUTHOR]

Background: In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species. Results: We found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes. Conclusion: We found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes. [ABSTRACT FROM AUTHOR]

Background: Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. Results: Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. Conclusions: This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies. [ABSTRACT FROM AUTHOR]

Background: It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results: In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions: We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. [ABSTRACT FROM AUTHOR]

Background: The Encephalomyocarditis virus (EMCV) is a small, non enveloped, positive sense single-stranded RNA virus in the genus Cardiovirus, family Picornaviridae, with two known serotypes. It is spread worldwide and infects a huge range of vertebrate hosts with zoonotic potential for humans. The pig is the mammal most likely to be impacted on with the disease, but EMCV occurrence has also been reported in non-human primates and in a variety of domestic, captive and wild animals. Until now, human cases have been very rare and the risk appears to be almost negligible in spite of human susceptibility to the infection. Case presentation: Between September and November 2012 a fatal Encephalomyocarditis virus outbreak involving four Barbary macaques and 24 crested porcupines occurred at a rescue centre for wild and exotic animals in Central Italy. In this open-field zoo park located near Grosseto, Tuscany about 1000 animals belonging to different species, including various non-human primates were hosted at that time. Sudden deaths were generally observed without any evident symptoms or only with mild nonspecific clinical signs. The major gross change was characterised by grey-white necrotic foci in the myocardium and the same EMCV strain was isolated both in macaques and crested porcupines. Phylogenetic analysis has confirmed that only one EMCV strain is circulating in Italy, capable of infecting different animal species. Conclusions: This report confirms the susceptibility of non-human primates to the EMCV infection and describes the disease in porcupine, a common wild Italian and African species. No human cases were observed, but given the zoonotic potential of EMCV these findings are of importance in the context of animal-human interface. [ABSTRACT FROM AUTHOR]

Background: Thelazia callipaeda is a zoonotic nematode that affects the eyes of domestic and wild animals, including dogs, cats and red foxes. This parasitic eye worm is transmitted by Phortica variegata, which is a zoophilic fruit fly spread in Europe. Two wild European rabbits (Oryctolagus cuniculus) found dead in north-eastern Portugal were submitted to necropsy. Results: Both animals presented gross lesions compatible with haemorrhagic viral disease. Eye examination revealed the presence of six worms (three in each animal, on both eyes). Out of the six nematodes, five females and one male were morphologically and molecularly identified as T. callipaeda. Conclusions: This is the first report of T. callipaeda in wild rabbits from Portugal, which reveals a new host for this parasite in southern Europe and emphasizes the importance of including thelaziosis in the differential diagnosis of ocular alterations in both animals and humans from areas where the eye worm is endemic. [ABSTRACT FROM AUTHOR]

Background: Glucocorticoids are adrenal steroid hormones essential to homeostatic maintenance. Their daily variation at low concentrations regulates physiology and behavior to sustain proper immunological and metabolic function. Glucocorticoids rise well above these baseline levels during stress to elicit emergency-state responses that increase short-term survival. Despite this essence in managing life processes under both regular and adverse conditions, relationships of glucocorticoid release to environmental and intrinsic factors that vary at daily and seasonal scales are rarely studied in the wild. Methods: This study on 41 passerine species of the Ecuadorian Chocó applied a standardized capture-and-restraint protocol to examine diurnal variation in baseline and stress-related release of corticosterone, the primary avian glucocorticoid. Tests for relationships to relative body mass, hemoglobin concentration, molt status and date complemented this evaluation of the time of day effect on corticosterone secretion in free-living tropical rainforest birds. Analyses were also partitioned by sex as well as performed separately on two common species, the wedge-billed woodcreeper and olive-striped flycatcher. Results: Interspecific analyses indicated maximum baseline corticosterone levels at the onset of the active phase and reductions thereafter. Stress-related levels did not correspond to time of day but accompanied baseline reductions during molt and elevations in birds sampled later during the September - November study period. Baseline corticosterone related negatively to hemoglobin in the wedge-billed woodcreeper and stress-related levels increased with body mass in the olive-striped flycatcher. There were no substantial sex-related differences. Conclusions: The results of this study suggest a diurnal rhythmicity in baseline corticosterone release so robust as to emerge in pooled analyses across a highly variable dataset. While this detection in nature is singular, correspondent patterns have been demonstrated outside of the tropics in captive model species. Congruity in daily rhythms and links to physiological and life-history state across disparate taxa and environments may promote the yet unresolved utility of corticosterone release as a global metric for population health. However, certain results of this study also deviate from laboratory and field research at higher latitudes, cautioning generalization. Environmental distinctions such as high productivity and tempered seasonality may precipitate unique life-history strategies and underlying hormonal mechanisms in tropical rainforest birds. [ABSTRACT FROM AUTHOR]

Background: Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of different isolates of this bacterium could play an important role in the development of good management strategies. The aim of this study was to identify genetic markers for discrimination between isolates. A selection of eight VNTRs from 53 F. psychrophilum isolates from Norway, Chile, Denmark and Scotland were analyzed. The results were compared with previous work on the same pathogen using MLST for genetic differentiation. Results: The VNTR analysis gave a separation between the F. psychrophilum isolates supporting the results of previous MLST work. A higher diversity was found among the Chilean isolates compared to those from Norway, which suggests a more homogenous reservoir in Norway. Transgenerational transmission of F. psychrophilum from other countries, exporting salmon embryos to Chile, may explain the differences in diversity. The same transmission mechanisms could also explain the wide geographical distribution of identical isolates in Norway. But, this could also be a result of movement of smolts and embryos. The selected VNTRs are stable genetic markers and no variation was observed after several passages on agar plates at different temperatures. Conclusions: These VNTRs are important additions for genotyping of F. psychrophilum isolates. Future studies on VNTRs of F. psychrophilum should include isolates from more host species from a wider geographical area. To get a more robust genotyping the VNTRs should be used in concert with MLST. Future studies of isolates with high and low virulence should focus on identifying virulence markers using VTNRs and MLST. [ABSTRACT FROM AUTHOR]

This study was carried out on fatty acid composition in wild and cultured varieties of two fish species, Epinephelus coioides and Sparidentex hasta. Fresh fish samples were collected from Hormozgan, Iran. After lipid extraction, fatty acids composition was analysed by gas chromatography. Results showed DHA (C22:6n3), EPA (C20:5n3), palmitic acid (C16:0), stearic acid (C18:0), myristic acid (C14:0), oleic acid (C18:1n9c) and palmitoleic acid (C16:1) were important fatty acids in the fish samples. There was low concentrate of linolenic acid (ALA, C18:3n3) in all analysed samples. Cultured fishes were found to contain significantly higher values of SFA, while their wild relative contained higher levels of MUFA followed by PUFA. In the wild fish species among PUFA, DHA were the most abundant followed by EPA. Altogether, EPA was the most abundant followed by DHA in the cultured fish species. Also the ω3/ω6 ratio was significantly higher in wild fishes and it was highest (13.04) in wild E. coioides. [ABSTRACT FROM AUTHOR]