ResearchPad - birds https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Meta-analysis of the correlation between dietary copper supply and broiler performance]]> https://www.researchpad.co/article/elastic_article_15740 To conduct a meta-analysis assessing the correlation between dietary copper supply and broiler performanceMethodsStudies that were published prior to January 2019 and reported the dietary copper supply and broiler growth performance were identified using search functions in the Web of Science, Springer, Elsevier, Science Direct, and Taylor & Francis Online databases; the Journal of Dairy Research; and China National Knowledge Infrastructure (CNKI). We performed stratified analyses on the possible sources of bias, including differences in the study locations and years of publication. The publication bias was assessed with Egger’s test method.ResultsA total of 12 randomized controlled trial (RCT) studies were eligible for inclusion. The pooled WMDs of the ADG, ADFI and FCR were -0.166 (95% CI: -1.587 to 1.254), -0.844 (95% CI: -1.536 to -0.152) and -0.029 (95% CI: -0.057 to 0.000), respectively. In the Israeli and Indian studies, the ADG and ADFI data in the experimental group were higher than those in the control group; however, in America, a relatively high FCR value was found in the experimental group compared to that in the control group. The analysis of the study period showed that for the 1980s and 2010s, the ADG and ADFI of the experimental group were lower than those of the control group, while, in the 1990s and 2010s, the FCR of the experimental group were lower than those of the control group. The observed values were adjusted for study effects, and a model was used to obtain the copper supplementation under the optimal production performance. The results showed that the adjusted average daily gain (ADG), average daily feed intake (ADFI), and feed to gain ratio (FCR) presented a quadratic relationship with Cu supplementation (P<0.05). The maximum value of ADG (31.84 g/d) is reached when Cu is added at amount of 158 mg/kg, and the minimum value of FCR (1.53) is reached when Cu is added at amount of 217 mg/kg. No significant publication bias existed in the studies (Egger's test: P value were 0.81, 0.71 and 0.14).ConclusionFrom this study, it can be concluded that the traditional copper addition is no longer suitable for modern broiler breeding; the higher copper content may be beneficial for the production performance of broilers. ]]> <![CDATA[Development of plasma and whole blood taurine reference ranges and identification of dietary features associated with taurine deficiency and dilated cardiomyopathy in golden retrievers: A prospective, observational study]]> https://www.researchpad.co/article/elastic_article_14758 A surge in Food and Drug Administration (FDA) consumer complaints identified concerns that legume-rich, grain-free diets were associated with nutritionally-mediated dilated cardiomyopathy (DCM). Golden retrievers represent the most reported breed affected by this condition and previous studies documented the disease is responsive to dietary change and taurine supplementation. Although dietary findings across cases are compelling, prospective studies with control groups are lacking. The role of diet in developing taurine deficiency and echocardiographic changes consistent with DCM in healthy dogs is unknown.ObjectivesWe hypothesized that golden retrievers eating non-traditional diets are at a higher risk of having taurine deficiency and nutritionally-mediated DCM compared with those eating traditional commercial diets. We aimed to compare taurine concentrations and echocardiographic indices of systolic function between golden retrievers in each diet group and elucidate associations between diet and these variables. Additionally, we aimed to generate breed-specific reference intervals for whole blood and plasma taurine concentrations.Animals86 golden retrievers.MethodsGolden retrievers eating traditional or non-traditional diets were evaluated and diet history, taurine concentrations and echocardiographic data were collected. Dietary features, taurine concentrations and echocardiographic findings were compared between diet groups. Relative risks were calculated for the likelihood of echocardiographic abnormalities and taurine deficiency in each diet group. Breed-specific reference intervals were constructed for taurine concentrations in dogs from the traditional diet group.ResultsGolden retrievers eating non-traditional diets had significantly lower taurine concentrations and more frequent systolic dysfunction. Breed specific reference intervals are higher than previously reported across breeds.ConclusionsNon-traditional diets, which were typically grain-free and contained legumes in this study, were significantly associated with and have increased relative risk for the identification of taurine deficiency and echocardiographic abnormalities consistent with nutritionally-mediated DCM. These findings were identifiable in the absence of clinical signs and support the findings of multiple previous studies and the ongoing FDA investigation. ]]> <![CDATA[Development and evaluation of habitat suitability models for nesting white-headed woodpecker (<i>Dryobates albolarvatus</i>) in burned forest]]> https://www.researchpad.co/article/elastic_article_14713 Salvage logging in burned forests can negatively affect habitat for white-headed woodpeckers (Dryobates albolarvatus), a species of conservation concern, but also meets socioeconomic demands for timber and human safety. Habitat suitability index (HSI) models can inform forest management activities to help meet habitat conservation objectives. Informing post-fire forest management, however, involves model application at new locations as wildfires occur, requiring evaluation of predictive performance across locations. We developed HSI models for white-headed woodpeckers using nest sites from two burned-forest locations in Oregon, the Toolbox (2002) and Canyon Creek (2015) fires. We measured predictive performance by developing one model at each of the two locations and quantifying discrimination of nest from reference sites at two other wildfire locations where the model had not been developed (either Toolbox or Canyon Creek, and the Barry Point Fire [2011]). We developed and evaluated Maxent models based on remotely sensed environmental metrics to support habitat mapping, and weighted logistic regression (WLR) models that combined remotely sensed and field-collected metrics to inform management prescriptions. Both Maxent and WLR models developed either at Canyon Creek or Toolbox performed adequately to inform management when applied at the alternate Toolbox or Canyon Creek location, respectively (area under the receiver-operating-characteristic curve [AUC] range = 0.61–0.72) but poorly when applied at Barry Point (AUC = 0.53–0.57). The final HSI models fitted to Toolbox and Canyon Creek data quantified suitable nesting habitat as severely burned or open sites adjacent to lower severity and closed canopy sites, where foraging presumably occurs. We suggest these models are applicable at locations similar to development locations but not at locations resembling Barry Point, which were characterized by more (pre-fire) canopy openings, larger diameter trees, less ponderosa pine (Pinus ponderosa), and more juniper (Juniperus occidentalis). Considering our results, we recommend caution when applying HSI models developed at individual wildfire locations to inform post-fire management at new locations without first evaluating predictive performance.

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<![CDATA[Identification of potential vulnerable points and paths of contamination in the Dutch broiler meat trade network]]> https://www.researchpad.co/article/elastic_article_14703 The poultry meat supply chain is complex and therefore vulnerable to many potential contaminations that may occur. To ensure a safe product for the consumer, an efficient traceability system is required that enables a quick and efficient identification of the potential sources of contamination and proper implementation of mitigation actions. In this study, we explored the use of graph theory to construct a food supply chain network for the broiler meat supply chain in the Netherlands and tested it as a traceability system. To build the graph, we first identified the main actors in the supply chain such as broiler breeder farms, broiler farms, slaughterhouses, processors, and retailers. The capacity data of each supply chain actor, represented by its production or trade volumes, were gathered from various sources. The trade relationships between the supply chain actors were collected and the missing relationships were estimated using the gravity model. Once the network was modeled, we computed degree centrality and betweenness centrality to identify critical nodes in the network. In addition, we computed trade density to get insight into the complexity of sub-networks. We identified the critical nodes at each stage of the Dutch broiler meat supply chain and verified our results with a domain expert of the Dutch poultry industry and literature. The results showed that processors with own slaughtering facility were the most critical points in the broiler meat supply chain.

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<![CDATA[SPOP promotes ubiquitination and degradation of MyD88 to suppress the innate immune response]]> https://www.researchpad.co/article/elastic_article_14645 MyD88 is a central adaptor that mediates initiation of the innate immune response and production of the proinflammatory cytokines that restrain pathogens and activate adaptive immunity. Although MyD88 is crucial for a host to prevent pathogenic infection, misregulation of its abundance might lead to autoimmune diseases. Thus, degradation of MyD88 is a key canonical mechanism for terminating cytokine production. Here, we characterized a novel E3 ligase, SPOP, that targets MyD88 for degradation. ChSPOP attenuated IL-1β production through K48-linked polyubiquitination and degradation of chMyD88, and thus impaired immune responses. Spop deficient mice showed more susceptibility to infection by Salmonella typhimurium. These findings demonstrate that SPOP is a negative regulator of MyD88-dependent pathway activation triggered by LPS and Salmonella typhimurium, which helps the host to maintain immune homeostasis.

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<![CDATA[Molecular epidemiology, genetic diversity and antimicrobial resistance of <i>Staphylococcus aureus</i> isolated from chicken and pig carcasses, and carcass handlers]]> https://www.researchpad.co/article/elastic_article_14574 The epidemiology of Staphylococcus aureus in food animals, associated products, and their zoonotic potential in Nigeria are poorly understood. This study aimed to provide data on the prevalence, genetic characteristics and antimicrobial resistance of S. aureus isolated from chicken and pig carcasses, and persons in contact with the carcasses at slaughterhouses in Nigeria. Surface swabs were collected randomly from 600 chicken and 600 pig carcasses. Nasal swabs were collected from 45 workers in chicken slaughterhouses and 45 pig slaughterhouse workers. S. aureus isolates were analyzed by spa typing. They were also examined for presence of the Panton-Valentine Leucocidin (PVL) and mecA genes, as well as for antimicrobial resistance phenotype. Overall, 53 S. aureus isolates were recovered (28 from chicken carcasses, 17 from pig carcasses, 5 from chicken carcass handlers and 3 from pig carcass handlers). Among the isolates, 19 (35.8%) were PVL-positive and 12 (22.6%) carried the mecA gene. The 53 isolates belonged to 19 spa types. The Based Upon Repeat Pattern (BURP) algorithm separated the isolates into 2 spa-clonal complexes (spa-CC) and 9 singletons including 2 novel spa types (t18345 and t18346). The clonal complexes (CC) detected were CC1, CC5, CC8, CC15, CC88 and CC152. CC15-related isolates represented by spa type t084 (32.1%) and CC5 represented by spa type t311 (35.3%) predominated among isolates from chicken carcasses/ handlers, and pig carcasses/ handlers, respectively. Multidrug resistance exhibited by all the CC except CC8, was observed among isolates from chicken carcasses (64.3%), pig carcasses (41.2%), handlers of chicken meat (40.0%) and handlers of pork (33.3%). All the CC showed varying degrees of resistance to tetracycline while CC15 and CC5 exhibited the highest resistance to sulphamethoxazole/trimethoprim and erythromycin, respectively. The predominant antimicrobial resistance pattern observed was penicillin-tetracycline-sulphamethoxazole/trimethoprim (PEN-TET-SXT). In conclusion, food animals processed in Enugu State in Southeast Nigeria are potential vehicles for transmission of PVL-positive multiple-drug resistant S. aureus and methicillin-resistant S. aureus from farm to slaughterhouse and potentially to the human population. Public health intervention programs at pre- and post-slaughter stages should be considered in Nigerian slaughterhouses.

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<![CDATA[Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen]]> https://www.researchpad.co/article/elastic_article_14547 Decades of work indicate that female birds can control their offspring sex ratios in response to environmental and social cues. In laying hens, hormones administered immediately prior to sex chromosome segregation can exert sex ratio skews, indicating that these hormones may act directly on the germinal disc to influence which sex chromosome is retained in the oocyte and which is discarded into an unfertilizable polar body. We aimed to uncover the gene pathways involved in this process by testing whether treatments with testosterone or corticosterone that were previously shown to influence sex ratios elicit changes in the expression of genes and/or gene pathways involved in the process of meiotic segregation. We injected laying hens with testosterone, corticosterone, or control oil 5h prior to ovulation and collected germinal discs from the F1 preovulatory follicle in each hen 1.5h after injection. We used RNA-sequencing (RNA-seq) followed by DESeq2 and gene set enrichment analyses to identify genes and gene pathways that were differentially expressed between germinal discs of control and hormone-treated hens. Corticosterone treatment triggered downregulation of 13 individual genes, as well as enrichment of gene sets related to meiotic spindle organization and chromosome segregation, and additional gene sets that function in ion transport. Testosterone treatment triggered upregulation of one gene, and enrichment of one gene set that functions in nuclear chromosome segregation. This work indicates that corticosterone can be a potent regulator of meiotic processes and provides potential gene targets on which corticosterone and/or testosterone may act to influence offspring sex ratios in birds.

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<![CDATA[The fast and the frugal: Divergent locomotory strategies drive limb lengthening in theropod dinosaurs]]> https://www.researchpad.co/article/elastic_article_14509 Limb length, cursoriality and speed have long been areas of significant interest in theropod paleobiology, since locomotory capacity, especially running ability, is critical in the pursuit of prey and to avoid becoming prey. The impact of allometry on running ability, and the limiting effect of large body size, are aspects that are traditionally overlooked. Since several different non-avian theropod lineages have each independently evolved body sizes greater than any known terrestrial carnivorous mammal, ~1000kg or more, the effect that such large mass has on movement ability and energetics is an area with significant implications for Mesozoic paleoecology. Here, using expansive datasets that incorporate several different metrics to estimate body size, limb length and running speed, we calculate the effects of allometry on running ability. We test traditional metrics used to evaluate cursoriality in non-avian theropods such as distal limb length, relative hindlimb length, and compare the energetic cost savings of relative hindlimb elongation between members of the Tyrannosauridae and more basal megacarnivores such as Allosauroidea or Ceratosauridae. We find that once the limiting effects of body size increase is incorporated there is no significant correlation to top speed between any of the commonly used metrics, including the newly suggested distal limb index (Tibia + Metatarsus/ Femur length). The data also shows a significant split between large and small bodied theropods in terms of maximizing running potential suggesting two distinct strategies for promoting limb elongation based on the organisms’ size. For small and medium sized theropods increased leg length seems to correlate with a desire to increase top speed while amongst larger taxa it corresponds more closely to energetic efficiency and reducing foraging costs. We also find, using 3D volumetric mass estimates, that the Tyrannosauridae show significant cost of transport savings compared to more basal clades, indicating reduced energy expenditures during foraging and likely reduced need for hunting forays. This suggests that amongst theropods, hindlimb evolution was not dictated by one particular strategy. Amongst smaller bodied taxa the competing pressures of being both a predator and a prey item dominant while larger ones, freed from predation pressure, seek to maximize foraging ability. We also discuss the implications both for interactions amongst specific clades and Mesozoic paleobiology and paleoecological reconstructions as a whole.

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<![CDATA[Democratizing water monitoring: Implementation of a community-based qPCR monitoring program for recreational water hazards]]> https://www.researchpad.co/article/elastic_article_14486 Recreational water monitoring can be challenging due to the highly variable nature of pathogens and indicator concentrations, the myriad of potential biological hazards to measure for, and numerous access points, both official and unofficial, that are used for recreation. The aim of this study was to develop, deploy, and assess the effectiveness of a quantitative polymerase chain reaction (qPCR) community-based monitoring (CBM) program for the assessment of bacterial and parasitic hazards in recreational water. This study developed methodologies for performing qPCR ‘in the field,’ then engaged with water management and monitoring groups and tested the method in a real-world implementation study to evaluate the accuracy of CBM using qPCR both quantitatively and qualitatively. This study found high reproducibility between qPCR results performed by non-expert field users and expert laboratory results, suggesting that qPCR as a methodology could be amenable to a CBM program.

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<![CDATA[Assessment of the genomic prediction accuracy for feed efficiency traits in meat-type chickens]]> https://www.researchpad.co/article/5989db51ab0ee8fa60bdc4ab

Feed represents the major cost of chicken production. Selection for improving feed utilization is a feasible way to reduce feed cost and greenhouse gas emissions. The objectives of this study were to investigate the efficiency of genomic prediction for feed conversion ratio (FCR), residual feed intake (RFI), average daily gain (ADG) and average daily feed intake (ADFI) and to assess the impact of selection for feed efficiency traits FCR and RFI on eviscerating percentage (EP), breast muscle percentage (BMP) and leg muscle percentage (LMP) in meat-type chickens. Genomic prediction was assessed using a 4-fold cross-validation for two validation scenarios. The first scenario was a random family sampling validation (CVF), and the second scenario was a random individual sampling validation (CVR). Variance components were estimated based on the genomic relationship built with single nucleotide polymorphism markers. Genomic estimated breeding values (GEBV) were predicted using a genomic best linear unbiased prediction model. The accuracies of GEBV were evaluated in two ways: the correlation between GEBV and corrected phenotypic value divided by the square root of heritability, i.e., the correlation-based accuracy, and model-based theoretical accuracy. Breeding values were also predicted using a conventional pedigree-based best linear unbiased prediction model in order to compare accuracies of genomic and conventional predictions. The heritability estimates of FCR and RFI were 0.29 and 0.50, respectively. The heritability estimates of ADG, ADFI, EP, BMP and LMP ranged from 0.34 to 0.53. In the CVF scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR were slightly higher than those for RFI. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.360, 0.284, 0.574 and 0.520, respectively, and the model-based theoretical accuracies were 0.420, 0.414, 0.401 and 0.382, respectively. In the CVR scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR was lower than RFI, which was different from the CVF scenario. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.449, 0.593, 0.581 and 0.627, respectively, and the model-based theoretical accuracies were 0.577, 0.629, 0.631 and 0.638, respectively. The accuracies of genomic predictions were 0.371 and 0.322 higher than the conventional pedigree-based predictions for the CVF and CVR scenarios, respectively. The genetic correlations of FCR with EP, BMP and LMP were -0.427, -0.156 and -0.338, respectively. The correlations between RFI and the three carcass traits were -0.320, -0.404 and -0.353, respectively. These results indicate that RFI and FCR have a moderate accuracy of genomic prediction. Improving RFI and FCR could be favourable for EP, BMP and LMP. Compared with FCR, which can be improved by selection for ADG in typical meat-type chicken breeding programs, selection for RFI could lead to extra improvement in feed efficiency.

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<![CDATA[Daily and seasonal fluctuation in Tawny Owl vocalization timing]]> https://www.researchpad.co/article/N7177f503-3b7e-4d4b-a022-d9bd333d526e

A robust adaptation to environmental changes is vital for survival. Almost all living organisms have a circadian timing system that allows adjusting their physiology to cyclic variations in the surrounding environment. Among vertebrates, many birds are also seasonal species, adapting their physiology to annual changes in photoperiod (amplitude, length and duration). Tawny Owls (Strix aluco) are nocturnal birds of prey that use vocalization as their principal mechanism of communication. Diurnal and seasonal changes in vocalization have been described for several vocal species, including songbirds. Comparable studies are lacking for owls. In the present work, we show that male Tawny Owls present a periodic vocalization pattern in the seconds-to-minutes range that is subject to both daily (early vs. late night) and seasonal (spring vs. summer) rhythmicity. These novel theory-generating findings appear to extend the role of the circadian system in regulating temporal events in the seconds-to-minutes range to other species.

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<![CDATA[Do railway lines affect the distribution of woodland birds during autumn?]]> https://www.researchpad.co/article/N5f69b466-8155-4760-b7fb-9a995be0d1c7

Research results on the impact of railway noise on birds show a variety of bird responses. These behaviours are often different from those exhibited by birds occupying habitats along tarred roads. Knowledge of this subject is still incomplete. We attempted to define the influence of a heavily transited railway line on bird communities at stopover sites near the tracks during the autumn migration period. Birds were counted using the point method at 45 observation points located at three distances (30 m, 280 m, 530 m) from the tracks. At each point we determined the habitat parameters and the intensity of noise. A total of 614 individuals from 29 species were recorded on the study plot. The results of our observations indicate that the railway line does not adversely affect woodland birds during the autumn migration. The results showed that the abundance of birds and the species richness were actually the highest near the railway line. Species foraging on invertebrates preferred the neighbourhood of the tracks. The number of the most common species did not differ widely in relation to distance from the tracks. These data may be helpful in planning and managing the environment in the context of bird conservation, protection from railway noise and collisions with trains.

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<![CDATA[MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland]]> https://www.researchpad.co/article/N2eb0d267-f054-40f4-b445-0c8d9725ee43

Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C. jejuni from chicken sources (feces, carcasses, and meat) and from humans with diarrhea as well as to subtype the isolates to gain better insight into their population structure present in Poland. C. jejuni were genotyped using multilocus sequence typing (MLST) and sequence types (STs) were assigned in the MLST database. Among 602 isolates tested, a total of 121 different STs, including 70 (57.9%) unique to the isolates' origin, and 32 STs that were not present in the MLST database were identified. The most prevalent STs were ST464 and ST257, with 58 (9.6%) and 52 (8.6%) C. jejuni isolates, respectively. Isolates with some STs (464, 6411, 257, 50) were shown to be common in chickens, whereas others (e.g. ST21 and ST572) were more often identified among human C. jejuni. It was shown that of 47 human sequence types, 26 STs (106 isolates), 23 STs (102 isolates), and 29 STs (100 isolates) were also identified in chicken feces, meat, and carcasses, respectively. These results, together with the high and similar proportional similarity indexes (PSI) calculated for C. jejuni isolated from patients and chickens, may suggest that human campylobacteriosis was associated with contaminated chicken meat or meat products or other kinds of food cross-contaminated with campylobacters of chicken origin. The frequency of various sequence types identified in the present study generally reflects of the prevalence of STs in other countries which may suggest that C. jejuni with some STs have a global distribution, while other genotypes may be more restricted to certain countries.

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<![CDATA[New physiological bench test reproducing nocturnal breathing pattern of patients with sleep disordered breathing]]> https://www.researchpad.co/article/N13bd4ad3-60c6-4376-997d-f10f1c975c0e

Previous studies have shown that Automatic Positive Airway Pressure devices display different behaviors when connected to a bench using theoretical respiratory cycle scripts. However, these scripts are limited and do not simulate physiological behavior during the night. Our aim was to develop a physiological bench that is able to simulate patient breathing airflow by integrating polygraph data. We developed an algorithm analyzing polygraph data and transformed this information into digital inputs required by the bench hardware to reproduce a patient breathing profile on bench. The inputs are respectively the simulated respiratory muscular effort pressure input for an artificial lung and the sealed chamber pressure to regulate the Starling resistor. We did simulations on our bench for a total of 8 hours and 59 minutes for a breathing profile from the demonstration recording of a Nox T3 Sleep Monitor. The simulation performance results showed that in terms of relative peak-valley amplitude of each breathing cycle, simulated bench airflow was biased by only 1.48% ± 6.80% compared to estimated polygraph nasal airflow for a total of 6,479 breathing cycles. For total respiratory cycle time, the average bias ± one standard deviation was 0.000 ± 0.288 seconds. For patient apnea events, our bench simulation had a sensitivity of 84.7% and a positive predictive value equal to 90.3%, considering 149 apneas detected both in polygraph nasal simulated bench airflows. Our new physiological bench would allow personalizing APAP device selection to each patient by taking into account individual characteristics of a sleep breathing profile.

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<![CDATA[Diversity of A(H5N1) clade 2.3.2.1c avian influenza viruses with evidence of reassortment in Cambodia, 2014-2016]]> https://www.researchpad.co/article/Nf51e501a-7d3b-493b-bbd9-bf4dbc27c932

In Cambodia, highly pathogenic avian influenza A(H5N1) subtype viruses circulate endemically causing poultry outbreaks and zoonotic human cases. To investigate the genomic diversity and development of endemicity of the predominantly circulating clade 2.3.2.1c A(H5N1) viruses, we characterised 68 AIVs detected in poultry, the environment and from a single human A(H5N1) case from January 2014 to December 2016. Full genomes were generated for 42 A(H5N1) viruses. Phylogenetic analysis shows that five clade 2.3.2.1c genotypes, designated KH1 to KH5, were circulating in Cambodia during this period. The genotypes arose through multiple reassortment events with the neuraminidase (NA) and internal genes belonging to H5N1 clade 2.3.2.1a, clade 2.3.2.1b or A(H9N2) lineages. Phylogenies suggest that the Cambodian AIVs were derived from viruses circulating between Cambodian and Vietnamese poultry. Molecular analyses show that these viruses contained the hemagglutinin (HA) gene substitutions D94N, S133A, S155N, T156A, T188I and K189R known to increase binding to the human-type α2,6-linked sialic acid receptors. Two A(H5N1) viruses displayed the M2 gene S31N or A30T substitutions indicative of adamantane resistance, however, susceptibility testing towards neuraminidase inhibitors (oseltamivir, zanamivir, lananmivir and peramivir) of a subset of thirty clade 2.3.2.1c viruses showed susceptibility to all four drugs. This study shows that A(H5N1) viruses continue to reassort with other A(H5N1) and A(H9N2) viruses that are endemic in the region, highlighting the risk of introduction and emergence of novel A(H5N1) genotypes in Cambodia.

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<![CDATA[The evolution and genetic diversity of avian influenza A(H9N2) viruses in Cambodia, 2015 – 2016]]> https://www.researchpad.co/article/Ncf402c92-86f9-4684-b431-03c7c64bd7da

Low pathogenic A(H9N2) subtype avian influenza viruses (AIVs) were originally detected in Cambodian poultry in 2013, and now circulate endemically. We sequenced and characterised 64 A(H9N2) AIVs detected in Cambodian poultry (chickens and ducks) from January 2015 to May 2016. All A(H9) viruses collected in 2015 and 2016 belonged to a new BJ/94-like h9-4.2.5 sub-lineage that emerged in the region during or after 2013, and was distinct to previously detected Cambodian viruses. Overall, there was a reduction of genetic diversity of H9N2 since 2013, however two genotypes were detected in circulation, P and V, with extensive reassortment between the viruses. Phylogenetic analysis showed a close relationship between A(H9N2) AIVs detected in Cambodian and Vietnamese poultry, highlighting cross-border trade/movement of live, domestic poultry between the countries. Wild birds may also play a role in A(H9N2) transmission in the region. Some genes of the Cambodian isolates frequently clustered with zoonotic A(H7N9), A(H9N2) and A(H10N8) viruses, suggesting a common ecology. Molecular analysis showed 100% of viruses contained the hemagglutinin (HA) Q226L substitution, which favours mammalian receptor type binding. All viruses were susceptible to the neuraminidase inhibitor antivirals; however, 41% contained the matrix (M2) S31N substitution associated with resistance to adamantanes. Overall, Cambodian A(H9N2) viruses possessed factors known to increase zoonotic potential, and therefore their evolution should be continually monitored.

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<![CDATA[Scrutinizing assortative mating in birds]]> https://www.researchpad.co/article/5c784fead5eed0c4840078f1

It is often claimed that pair bonds preferentially form between individuals that resemble one another. Such assortative mating appears to be widespread throughout the animal kingdom. Yet it is unclear whether the apparent ubiquity of assortative mating arises primarily from mate choice (“like attracts like”), which can be constrained by same-sex competition for mates; from spatial or temporal separation; or from observer, reporting, publication, or search bias. Here, based on a conventional literature search, we find compelling meta-analytical evidence for size-assortative mating in birds (r = 0.178, 95% CI 0.142–0.215, 83 species, 35,591 pairs). However, our analyses reveal that this effect vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased by 42% when we used previously unpublished data from nine long-term field studies, i.e., data free of reporting and publication bias (r = 0.103, 95% CI 0.074–0.132, eight species, 16,611 pairs). Moreover, in those data, assortative mating effectively disappeared when both partners were measured by independent observers or separately in space and time (mean r = 0.018, 95% CI −0.016–0.057). Likewise, we also found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of Zebra finches (r = −0.020, 95% CI −0.148–0.107, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may not be driven by mate choice or mating competition for preferred mates.

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<![CDATA[Host-parasite interaction explains variation in the prevalence of avian haemosporidians at the community level]]> https://www.researchpad.co/article/5c897744d5eed0c4847d2876

Parasites are a selective force that shape host community structure and dynamics, but host communities can also influence parasitism. Understanding the dual nature from host-parasite interactions can be facilitated by quantifying the variation in parasite prevalence among host species and then comparing that variation to other ecological factors that are known to also shape host communities. Avian haemosporidian parasites (e.g. Plasmodium and Haemoproteus) are abundant and widespread representing an excellent model for the study of host-parasite interactions. Several geographic and environmental factors have been suggested to determine prevalence of avian haemosporidians in bird communities. However, it remains unknown whether host and parasite traits, represented by phylogenetic distances among species and degree of specialization in host-parasite relationships, can influence infection status. The aims of this study were to analyze factors affecting infection status in a bird community and to test whether the degree of parasite specialization on their hosts is determined by host traits. Our statistical analyses suggest that infection status is mainly determined by the interaction between host species and parasite lineages where tolerance and/or susceptibility to parasites plays an essential role. Additionally, we found that although some of the parasite lineages infected a low number of bird individuals, the species they infected were distantly related and therefore the parasites themselves should not be considered typical host specialists. Infection status was higher for generalist than for specialist parasites in some, but not all, host species. These results suggest that detected prevalence in a species mainly results from the interaction between host immune defences and parasite exploitation strategies wherein the result of an association between particular parasite lineages and particular host species is idiosyncratic.

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<![CDATA[It’s a trap: Optimizing detection of rare small mammals]]> https://www.researchpad.co/article/5c8823a9d5eed0c484638d89

Improving detection probabilities for rare species is critical when assessing presence or habitat associations. Our goal was to create a new small mammal trapping protocol that improved detection of rare species, such as the olive-backed pocket mouse (Perognathus fasciatus). We used three trap and bait types and trapped an area 4.4 times larger than the standard grid. We also assessed the effect of captures of non-target species on detection probability of pocket mice. Regardless of species, trap success was higher for Havaharts. We found that bait and trap type selection varied significantly by species, with pocket mice showing strongest selection for Havahart traps baited with bird seed. Increasing grid size, while maintaining a similar trapping effort, resulted in higher detection probability, although our analyses showed that effective grids can be about three-quarters of the size we use to achieve similar results. We were also able to demonstrate that by deploying a combination of different traps and baits it is possible to overcome the potential effect of non-target species (e.g., deer mice, Peromyscus maniculatus) on the detection probability of pocket mice. Our results show that simple changes to standard small-mammal trapping methods can dramatically increase the detectability of rare and elusive small mammals. Increasing detection probability of rare components of a community can improve the results and understanding of future studies.

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<![CDATA[PDIP38/PolDIP2 controls the DNA damage tolerance pathways by increasing the relative usage of translesion DNA synthesis over template switching]]> https://www.researchpad.co/article/5c897795d5eed0c4847d30a7

Replicative DNA polymerases are frequently stalled at damaged template strands. Stalled replication forks are restored by the DNA damage tolerance (DDT) pathways, error-prone translesion DNA synthesis (TLS) to cope with excessive DNA damage, and error-free template switching (TS) by homologous DNA recombination. PDIP38 (Pol-delta interacting protein of 38 kDa), also called Pol δ-interacting protein 2 (PolDIP2), physically associates with TLS DNA polymerases, polymerase η (Polη), Polλ, and PrimPol, and activates them in vitro. It remains unclear whether PDIP38 promotes TLS in vivo, since no method allows for measuring individual TLS events in mammalian cells. We disrupted the PDIP38 gene, generating PDIP38-/- cells from the chicken DT40 and human TK6 B cell lines. These PDIP38-/- cells did not show a significant sensitivity to either UV or H2O2, a phenotype not seen in any TLS-polymerase-deficient DT40 or TK6 mutants. DT40 provides a unique opportunity of examining individual TLS and TS events by the nucleotide sequence analysis of the immunoglobulin variable (Ig V) gene as the cells continuously diversify Ig V by TLS (non-templated Ig V hypermutation) and TS (Ig gene conversion) during in vitro culture. PDIP38-/- cells showed a shift in Ig V diversification from TLS to TS. We measured the relative usage of TLS and TS in TK6 cells at a chemically synthesized UV damage (CPD) integrated into genomic DNA. The loss of PDIP38 also caused an increase in the relative usage of TS. The number of UV-induced sister chromatid exchanges, TS events associated with crossover, was increased a few times in PDIP38-/- human and chicken cells. Collectively, the loss of PDIP38 consistently causes a shift in DDT from TLS to TS without enhancing cellular sensitivity to DNA damage. We propose that PDIP38 controls the relative usage of TLS and TS increasing usage of TLS without changing the overall capability of DDT.

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