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While the viromes and immune systems of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores (order Eulipotyphla) despite their wide geographic distribution. Anthropogenic land use and outdoor recreational activities, as well as changes in the range of shrews, may lead to an expansion of the human-shrew interface with the risk of spillover infections, as reported for Borna disease virus 1. We investigated the virome of 45 individuals of 4 white-toothed shrew species present in Europe, using metagenomic RNA sequencing of tissue and intestine pools. Moderate to high abundances of sequences related to the families Paramyxoviridae, Nairoviridae, Hepeviridae and Bornaviridae were detected. Whole genomes were determined for novel orthoparamyxoviruses (n=3), orthonairoviruses (n=2) and an orthohepevirus. The novel paramyxovirus, tentatively named Hasua virus, was phylogenetically related to the zoonotic Langya virus and Mòjiang virus. The novel orthonairoviruses, along with the potentially zoonotic Erve virus, fall within the shrew-borne Thiafora virus genogroup. The highest viral RNA loads of orthoparamyxoviruses were detected in the kidneys, in well-perfused organs for orthonairoviruses and in the liver and intestine for orthohepevirus, indicating potential transmission routes. Notably, several shrews were found to be coinfected with viruses from different families. Our study highlights the virus diversity present in shrews, not only in biodiversity-rich regions but also in areas influenced by human activity. This study warrants further research to characterize and assess the clinical implications and risk of these viruses and the importance of shrews as reservoirs in European ecosystems.
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Filogenia , Musaranhos , Animais , Musaranhos/virologia , Genoma Viral , Europa (Continente) , Paramyxoviridae/genética , Paramyxoviridae/isolamento & purificação , Paramyxoviridae/classificação , Metagenômica , Viroma/genética , RNA Viral/genética , HumanosRESUMO
BACKGROUND: The mechanisms that regulate multi-annual population dynamics of rodent pest species of cereal crops is often unknown. Better knowledge of such aspects can aid pest management and in turn improve food security and human health. The patterns and processes of the population dynamics of Rattus argentiventer, in rice fields of Indonesia, and Rattus tanezumi, in rice fields of the Philippines were assessed in this article. RESULTS: The meta-analysis of trapping data over 20 years in Indonesia, and 16 years in the Philippines indicated that rodent populations in rice fields did not show a regular multi-annual pattern. Rattus argentiventer populations in Indonesia responded to less rainfall from the current year. Rattus tanezumi populations in the Philippines responded positively to both rainfall and rainfall anomaly with a 1-year time lag. CONCLUSIONS: Our study of long-term population data indicates that certain combinations of rainfall parameters could be useful to predict years when there is higher rodent abundance in rice fields. The key rodent pest species in rice fields in Indonesia (R. argentiventer) and the Philippines (R. tanezumi) differ, and the populations of each species respond differently to rainfall anomalies. Other factors such as crop cover and water availability may also be important and should be considered in future work. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Some rodent species cause significant damage to agriculture and forestry, and some can transmit pathogens to humans and livestock. The common vole (Microtus arvalis) is widespread in Europe, and its population outbreaks have resulted in massive crop loss. Bait-based fertility control could contribute to rodent pest management. Bait containing 4-vinylcyclohexene diepoxide (VCD) and triptolide (TP), registered as ContraPest®, was delivered to male common voles for 14 or 28 consecutive days. The effects on reproductive structures and residues in the liver and testes were assessed. There was no effect on testis weight, sperm viability, sperm motility and oxidative stress in sperm cells. Results regarding the mitochondrial membrane potential of sperm, DNA fragmentation and progressively motile sperm cells were inconclusive. However, there was an increase in morphological sperm defects in voles treated for 14/28 days and fewer normal sperm cells in voles treated for 28 days. There were no TP residues in the testes, few and low TP residues and no VCD residues in liver tissues, making considerable secondary exposure to non-target species unlikely. Treatments with VCD + TP seemed to have minor effects on the reproductive organs of males. Further studies should evaluate the effect of VCD + TP on females and on the reproductive success of common voles and other pest rodent species.
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The fluctuation of human infections by the Puumala orthohantavirus (PUUV) in Germany has been linked to weather and phenology parameters that drive the population growth of its host species. We quantified the annual PUUV-outbreaks at the district level by binarizing the reported infections in the period 2006-2021. With these labels we trained a model based on a support vector machine classifier for predicting local outbreaks and incidence well in advance. The feature selection for the optimal model was performed by a heuristic method and identified five monthly weather variables from the previous two years plus the beech flowering intensity of the previous year. The predictive power of the optimal model was assessed by a leave-one-out cross-validation in 16 years that led to an 82.8% accuracy for the outbreak and a 0.457 coefficient of determination for the incidence. Prediction risk maps for the entire endemic area in Germany will be annually available on a freely-accessible permanent online platform of the German Environment Agency. The model correctly identified 2022 as a year with low outbreak risk, whereas its prediction for large-scale high outbreak risk in 2023 was not confirmed.
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Surtos de Doenças , Febre Hemorrágica com Síndrome Renal , Virus Puumala , Alemanha/epidemiologia , Humanos , Febre Hemorrágica com Síndrome Renal/epidemiologia , Febre Hemorrágica com Síndrome Renal/virologia , Febre Hemorrágica com Síndrome Renal/transmissão , Incidência , Máquina de Vetores de Suporte , Tempo (Meteorologia)RESUMO
The effect of oxidative stress on the survival of various Brucella species has not been fully investigated yet. We here conducted a study in which we investigated the effect of different types of oxidative stress (Fe2+, H2O2, bleach) versus non-oxidative inhibitory effects (selenite, erythritol, and isopropanol) on the survival of B. abortus S19, B. abortus S19 ∆mglA 3.14, and B. neotomae 5K33. The work focuses on the appearance of ATP-CFU quotient imbalances indicating the existence of a viable but nonculturable (VBNC) form of B. abortus S19, as has previously been shown.
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Activity indices are used to determine the presence and activity of small mammals, such as the hair index derived from the use of hair tubes. In contrast to trapping animals, hair tubes are non-invasive and less labor-intensive, and appear to be a suitable alternative in appropriate settings. We developed a method to calculate hair density semi-automatically. In addition, hair tube data were validated with field data using wildlife cameras for the small mammal community in grassland, wheat crops, and hedges to assess how well data from hair tubes match data from wildlife cameras. Adhesive tape with hair from hair tubes was processed and scanned. The resulting images were analyzed using a newly developed computer program that enables background and adhesive tape to be automatically distinguished from hair, providing a quantitative measure of hair density. Based on validation with wildlife cameras, hair tubes seem to be a suitable tool to estimate small mammal activity at the community level in several habitats. There was a moderate-to-strong positive correlation of the hair tube index with the sum of voles and Apodemus individuals (activity index) recorded in grasslands (Spearman's correlation coefficient 0.43), hedges (0.79), and wheat (0.44). The newly developed computer program allows the automatic calculation of hair density, making it easier to assess the activity of small mammals.
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BACKGROUND: Worldwide, pest rodents can cause extensive damage to agriculture, forestry, food storage, and infrastructure and pose a risk to public health and livestock due to the spread of zoonotic pathogens. In Europe, the most common pest rodent species is the common vole (Microtus arvalis). Management during periodic outbreaks largely relies on rodenticidal bait with zinc phosphide. Efficient baiting with rodenticides or possibly anti-fertility products in the future require baiting methods that allow a sufficient proportion of the population to consume an effective dose of bait. We used a bait with the quantitative marker ethyl-iophenoxic acid (Et-IPA) to evaluate baiting strategies in enclosure experiments. This wheat-based bait with Et-IPA was placed in bait boxes or directly into the tunnel system entrances in different seasons and common vole abundances. Voles were live-trapped, individually marked and blood samples were collected to relate Et-IPA blood residues to bait uptake. RESULTS: The percentage of animals consuming bait was not heavily affected by the baiting strategy but voles had higher Et-IPA blood residues if tunnel baiting was used in autumn and if bait boxes were used in winter. Non-reproductive as well as lighter animals tended to have higher Et-IPA blood residues than reproductive individuals, whereas sex had no effect. Population density had a negative effect on the probability of residues present as well as on Et-IPA blood concentration. CONCLUSION: The results of this study might help to improve baiting techniques to manage overabundant rodent pest species regardless of the compounds to be delivered. © 2024 Julius Kühn-Institut. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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BACKGROUND: Snap traps and electronic traps are the main devices for nonchemical management of rodent pests. Traps should be efficient and should not cause unnecessary suffering of animals. Harmonized, systematic test methods are required to make sure that mechanical forces or electrical parameters are optimal to achieve swift unconsciousness and death. This study aimed to describe technical trap properties that can be used to facilitate future improvements in trap efficacy and humaneness. METHODS: We constructed a device to assess spring energy, triggering force, impulse and clamping force, and developed an arrangement to assess effective voltage, current, effective current and effective energy taking effect on rodent bodies in electronic traps - all without the use of animals. Descriptive data of trap characteristics were collated. RESULTS: All factors showed variability among snap trap models and trigger types, and there was considerable overlap between mouse and rat traps. For most trap models, there was no difference among new snap traps and traps that had been trigged 20 times. Effective current and effective energy decreased with lower voltage input, but the traps indicated weak battery by LED lights, and one model switched off automatically when voltage was insufficient. CONCLUSION: With the device and the electronic arrangement, the majority of snap trap models and electronic traps available on the market can be assessed in a standardized and repeatable way. Matching the data generated in this study with data on time for trapped target animals to reach irreversible unconsciousness, and experiences from pest control practitioners, should allow relating properties of traps to efficacy and animal welfare issues. This can support further development and optimization of traps for nonchemical rodent pest control. © 2024 Julius Kuehn-Institut and The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Fertility control is often heralded as a humane and effective technique for management of overabundant wildlife, including rodents. The intention is to reduce the use of lethal and inhumane methods, increase farm productivity and food security as well as reduce disease transmission, particularly of zoonoses. We developed a framework to guide researchers and stakeholders planning to assess the effectiveness of a potential contraceptive agent for a particular species. Our guidelines describe the overarching research questions which must be sequentially addressed to ensure adequate data are collected so that a contraceptive can be registered for use in broad-scale rodent management. The framework indicates that studies should be undertaken iteratively and, at times, in parallel, with initial research being conducted on (1) laboratory-based captive assessments of contraceptive effects in individuals; (2) simulation of contraceptive delivery using bait markers and/or surgical sterilization of different proportions of a field-based or enclosure population to determine how population dynamics are affected; (3) development of mathematical models which predict the outcomes of different fertility control scenarios; and (4) implementation of large-scale, replicated trials to validate contraceptive efficacy under various management-scale field situations. In some circumstances, fertility control may be most effective when integrated with other methods (e.g. some culling). Assessment of non-target effects, direct and indirect, and the environmental fate of the contraceptive must also be determined. Developing fertility control for a species is a resource-intensive commitment but will likely be less costly than the ongoing environmental and economic impacts by rodents and rodenticides in many contexts.
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Anticoncepção , Fertilidade , Animais , Anticoncepção/métodos , Anticoncepcionais , Dinâmica Populacional , Modelos Teóricos , Países em DesenvolvimentoRESUMO
Rodents are important reservoirs for zoonotic pathogens that cause diseases in humans. Biodiversity is hypothesized to be closely related to pathogen prevalence through multiple direct and indirect pathways. For example, the presence of non-host species can reduce contact rates of the main reservoir host and thus reduce the risk of transmission ("dilution effect"). In addition, an overlap in ecological niches between two species could lead to increased interspecific competition, potentially limiting host densities and reducing density-dependent pathogen transmission processes. In this study, we investigated the relative impact of population-level regulation of direct and indirect drivers of the prevalence of Puumala orthohantavirus (PUUV) in bank voles (Clethrionomys glareolus) during years with high abundance. We compiled data on small mammal community composition from four regions in Germany between 2010 and 2013. Structural equation modeling revealed a strong seasonality in PUUV control mechanisms in bank voles. The abundance of shrews tended to have a negative relationship with host abundance, and host abundance positively influenced PUUV seroprevalence, while at the same time increasing the abundance of competing non-hosts like the wood mouse (Apodemus sylvaticus) and the yellow-necked field mouse (Apodemus flavicollis) were associated with reduced PUUV seroprevalence in the host. These results indicate that for PUUV in bank voles, dilution is associated with increased interspecific competition. Anthropogenic pressures leading to the decline of Apodemus spp. in a specific habitat could lead to the amplification of mechanisms promoting PUUV transmission within the host populations.
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Febre Hemorrágica com Síndrome Renal , Virus Puumala , Humanos , Animais , Camundongos , Febre Hemorrágica com Síndrome Renal/epidemiologia , Estudos Soroepidemiológicos , Murinae , Arvicolinae , Dinâmica PopulacionalRESUMO
Rickettsiae of the spotted fever group (SFG) are zoonotic tick-borne pathogens. Small mammals are important hosts for the immature life stages of two of the most common tick species in Europe, Ixodes ricinus and Dermacentor reticulatus. These hosts and vectors can be found in diverse habitats with different vegetation types like grasslands and forests. To investigate the influence of environmental and individual factors on Rickettsia prevalence, this study aimed to analyse the prevalence of SFG rickettsiae in ticks and small mammals in different small-scale habitats in central Germany for the first time. Small mammals of ten species and ticks of two species were collected from grasslands and forests in the Hainich-Dün region, central Germany. After species identification, DNA samples from 1098 ticks and ear snips of 1167 small mammals were screened for Rickettsia DNA by qPCR targeting the gltA gene. Positive samples were retested by conventional PCR targeting the ompB gene and sequencing. Rickettsia DNA was detected in eight out of ten small mammal species. Small mammal hosts from forests (14.0%) were significantly more often infected than those from grasslands (4.4%) (p < 0.001). The highest prevalence was found in the mostly forest-inhabiting genus Apodemus (14.8%) and the lowest in Microtus (6.6%), which inhabits grasslands. The prevalence was higher in D. reticulatus (46.3%) than in the I. ricinus complex (8.6%). Adult ticks were more often infected than nymphs (p = 0.0199). All sequenced rickettsiae in I. ricinus complex ticks were R. helvetica, and the ones in D. reticulatus were R. raoultii. Unlike adults, questing nymphs have had only one blood meal, which explains the higher prevalence in I. ricinus adults. Interestingly, habitat type did influence infection probability in small mammals, but did not in ticks. A possible explanation may be the high prevalence in Apodemus flavicollis and A. sylvaticus which were more abundant in the forest.
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Three species of white-toothed shrews of the order Eulipotyphla are present in central Europe: the bicolored (Crocidura leucodon), greater (Crocidura russula) and lesser (Crocidura suaveolens) white-toothed shrews. Their precise distribution in Germany is ill-defined and little is known about them as reservoirs for zoonotic pathogens (Leptospira spp., Coxiella burnetii, Brucella spp., Anaplasma phagocytophilum, Babesia spp., Neoehrlichia mikurensis and Bartonella spp.). We investigated 372 Crocidura spp. from Germany (n = 341), Austria (n = 18), Luxembourg (n = 2) and Slovakia (n = 11). West European hedgehogs (Erinaceus europaeus) were added to compare the presence of pathogens in co-occurring insectivores. Crocidura russula were distributed mainly in western and C. suaveolens mainly in north-eastern Germany. Crocidura leucodon occurred in overlapping ranges with the other shrews. Leptospira spp. DNA was detected in 28/227 C. russula and 2/78 C. leucodon samples. Further characterization revealed that Leptospira kirschneri had a sequence type (ST) 100. Neoehrlichia mikurensis DNA was detected in spleen tissue from 2/213 C. russula samples. Hedgehogs carried DNA from L. kirschneri (ST 100), L. interrogans (ST 24), A. phagocytophilum and two Bartonella species. This study improves the knowledge of the current distribution of Crocidura shrews and identifies C. russula as carrier of Leptospira kirschneri. However, shrews seem to play little-to-no role in the circulation of the arthropod-borne pathogens investigated.
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To prevent the non-acceptable effects of agrochemicals on arable fields, Environmental Risk Assessment (ERA) aims to assess and protect against a wide range of risks due to stressors to non-target species. While exposure to stress is a key factor in ERA models, exposure values are difficult to obtain and rely on laboratory studies with often debatable relevance to field situations. To improve intake estimates, data from realistic field-based scenarios are needed. We developed calibration curves relating known seed numbers of up to 20 onion and carrot seeds consumed by wild-caught wood mice (Apodemus sylvaticus) to the seed DNA content in the feces. Based on these inferred quantitative relationships, a field trial was run to determine seed intake in a natural setting using realistic levels of seed spillage. Onion DNA was detected in the fecal samples of the wood mice caught in the field, which resembled a seed intake of up to 1 onion seed. No intake of carrot seeds was detected. This is the first-ever study to quantify seed intake in a realistic field scenario using a DNA-based analysis, showing that accurate seed intake estimates can be obtained. Our approach can help to improve risk assessment models through its minimally-invasive and accurate assessment of seed intake by ERA representative and non-target species, which would otherwise be undetectable with traditional methods. Our novel approach and its results are highly relevant to studies of food intake and diet composition for basic and applied research alike.
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Mamíferos , Murinae , Animais , Camundongos , Fezes/química , DNA , Medição de Risco , SementesRESUMO
Environmental risks from plant protection products (PPPs) need to be assessed to ensure safe use. The risk assessments are generally carried out using the common vole as a focal species with conservative theoretical estimates of external exposure. These are then compared to dose-related toxicity endpoints established in toxicity studies, often with laboratory species. The aim of the present study was to determine the actual internal dosimetry of PPPs' active ingredients (AIs) in a population of common voles to provide the basis for informed higher tier risk assessment. As a proof of concept, two fungicidal AIs (fludioxonil and cyprodinil) were investigated using a range of application methodologies. Individuals were treated using oral gavage application (AI dose: 100/200 mg/kg) and fed treated grass (AI sprayed at 2 kg/ha) under laboratory, semi-natural, and natural conditions. Our results show that demographic factors play a significant role in the individual residue profile and that age structure is a key aspect that determines the overall exposure risk of a population. These results are consistent from laboratory to field conditions. Future approaches could establish dose-residue relationships that are reflective of natural food intake rates in wild common vole populations in the risk assessment of PPPs.
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Arvicolinae , Humanos , Animais , DemografiaRESUMO
Second-generation anticoagulant rodenticides potentially build persistent residues in animals and accordingly pose a risk of secondary poisoning. We examined the effect of a low concentration of cholecalciferol in brodifacoum bait on bait consumption by Norway rats (Rattus norvegicus Berkenhout 1769) and on the control success in a laboratory study and in field trials. Additionally, the efficacy of both baits was determined against resistant Y139C rats. Cholecalciferol caused a strong stop-feed effect after two days in the laboratory study. On two field study sites each, bait containing either 25 mg kg-1 brodifacoum or 25 mg kg-1 brodifacoum and 100 mg kg-1 cholecalciferol was applied to treat infestations of Norway rats. Infestations were assessed pre- and post-treatment. Rats were radio-tagged, and carcasses were searched for during the treatment period. DNA of each rat was genotyped to determine the resistance status conferred by the VKORC1 gene. On all farms, control success exceeded 90%. On farms treated with brodifacoum only, the ratio of total bait consumption to pre-treatment census was significantly higher (6.6 and 4.8 times) than on farms treated with the combination (2.7 and 2.9 times). 78.8% of 183 rats were confirmed Y139C resistant. Bait ingestion was reduced by almost fifty per-cent when cholecalciferol was added to the bait with no impact on control success. All treatments resulted in control levels exceeding 90%, despite a high proportion of anticoagulant-resistant rats. When the use of highly toxic compounds is required in resistance management, addition of cholecalciferol to these baits may reduce the transfer of residues to the environment.
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Human Puumala virus (PUUV) infections in Germany fluctuate multi-annually, following fluctuations of the bank vole population size. We applied a transformation to the annual incidence values and established a heuristic method to develop a straightforward robust model for the binary human infection risk at the district level. The classification model was powered by a machine-learning algorithm and achieved 85% sensitivity and 71% precision, despite using only three weather parameters from the previous years as inputs, namely the soil temperature in April of two years before and in September of the previous year, and the sunshine duration in September of two years before. Moreover, we introduced the PUUV Outbreak Index that quantifies the spatial synchrony of local PUUV-outbreaks, and applied it to the seven reported outbreaks in the period 2006-2021. Finally, we used the classification model to estimate the PUUV Outbreak Index, achieving 20% maximum uncertainty.
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Virus Puumala , Humanos , Animais , Algoritmos , Arvicolinae , Surtos de Doenças , Aprendizado de MáquinaRESUMO
Trapping small mammals is frequently used to study the dynamics, demography, behavior and presence of pathogens. When only particular small mammal species are in the focus of interest, all other species are unnecessary bycatch. We analyzed data from extensive live trapping campaigns conducted over the last decade in Germany, following a consistent standard trapping protocol that resulted in about 18,500 captures of small mammals. Animals were trapped with Ugglan multiple capture traps in grassland, forest and margin habitat. Trap success and the proportion of bycatch were about 30% when target species were common voles (Microtus arvalis) in grassland and common voles and bank voles (Clethrionomys glareolus) in margins and forests. This was more pronounced in spring and along margins. Species mentioned in the early warning list according to the Red List Germany were higher in numbers and proportion in spring and in grassland. The results will help to avoid periods with enhanced presence of bycatch, including endangered species (if the purpose of the study allows) or to pay particular attention in certain seasons and habitats when the occurrence of bycatch is most likely.
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Rodentia is the most speciose mammalian order, found across the globe, with some species occurring in close proximity to humans. Furthermore, rodents are known hosts for a variety of zoonotic pathogens. Among other animal species, rodents came into focus when the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) spread through human populations across the globe, initially as laboratory animals to study the viral pathogenesis and to test countermeasures. Under experimental conditions, some rodent species including several cricetid species are susceptible to SARS-CoV-2 infection and a few of them can transmit the virus to conspecifics. To investigate whether SARS-CoV-2 is also spreading in wild rodent populations in Germany, we serologically tested samples of free-ranging bank voles (Myodes glareolus, n = 694), common voles (Microtus arvalis, n = 2), house mice (Mus musculus, n = 27), brown or Norway rats (Rattus norvegicus, n = 97) and Apodemus species (n = 8) for antibodies against the virus. The samples were collected from 2020 to 2022 in seven German federal states. All but one sample tested negative by a multispecies ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The remaining sample, from a common vole collected in 2021, was within the inconclusive range of the RBD-ELISA, but this result could not be confirmed by a surrogate virus neutralization test as the sample gave a negative result in this test. These results indicate that SARS-CoV-2 has not become highly prevalent in wild rodent populations in Germany.
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BACKGROUND: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. RESULTS: We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. CONCLUSION: Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms.
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Domesticação , Genoma , Animais , Camundongos , Nucleotídeos , Fenótipo , Seleção Genética , Sequenciamento Completo do GenomaRESUMO
Leptospirosis is a neglected zoonotic disease and one of the leading causes of zoonotic morbidity and mortality, particularly in resource-poor settings. Sri Lanka has one of the highest disease burdens worldwide, with occasional endemic leptospirosis outbreaks (2008, 2011). Rodents are considered the main wildlife reservoir, but due to a scarcity of studies it is unclear which particular species contributes to bacterial transmission and reservoir maintenance in this multi-host multi-parasite system. Several rodent species act as agricultural pests both in rice fields and in food storage facilities. To unravel the interactions among the small mammal communities, pathogenic Leptospira spp. and human transmission pathways, we collected animals from smallholder food storage facilities, where contact between humans and small mammals is most likely, and screened kidney tissue samples for Leptospira spp. using PCR. Samples were collected in three climatic zones along a rainfall gradient. Pathogenic Leptospira spp. were detected in small mammal communities in 37 (74%) out of 50 sampled farms and 61 (12%) out of 500 collected individuals were infected. The small mammal community was comprised of Rattus rattus (87.6%), Suncus shrews (8.8%), Bandicota spp. (2.8%) and Mus booduga (0.8%). Three pathogenic Leptospira spp. were identified, L. borgpetersenii (n = 34), L. interrogans (n = 15), and L. kirschneri (n = 1). Suncus shrews were commonly infected (32%), followed by B. indica (23%) and R. rattus (10%). L. borgpetersenii strains similar to strains previously extracted from human clinal samples in Sri Lanka were detected in R. rattus and Suncus shrews. L. interrogans was observed in R. rattus only. A single L. kirschneri infection was found in M. booduga. The presence of human pathogenic Leptospira species in an agricultural pest rodent (R. rattus) and in commensal shrews (Suncus) calls for management of these species in commensal settings. Further investigation of the interplay between pathogen and reservoir population dynamics, overlap in geographic range and the extent of spill-over to humans in and around rural settlements is required to identify optimal management approaches.