Project description:Recently it was shown that individual differences in attention style in infants are associated with childhood effortful control, surgency, and hyperactivity-inattention. Here we investigated whether effortful control, surgency and behavioral problems in childhood can be predicted even earlier, from individual differences in newborns' average duration of gaze to stimuli. Eighty newborns participated in visual preference and habituation studies. Parents completed questionnaires at follow up (mean age = 7.5 years, SD = 1.0 year). Newborns' average dwell time was negatively associated with childhood surgency (β = -.25, R(2) = .04, p = .02) and total behavioral difficulties (β = -.28, R(2) = .05, p = .04) but not with effortful control (β = .03, R(2) = .001, p = .76). Individual differences in newborn visual attention significantly associated with individual variation in childhood surgency and behavioral problems, showing that some of the factors responsible for this variation are present at birth.
Project description:Japanese native chickens (JNCs) comprise approximately 50 breeds, making Japan a diversity hotspot for native chicken breeds. JNCs were established through the repeated introduction of chickens from foreign countries. Jidori, which is the generic name of JNC breeds whose ancestral morphology resembles that of their wild progenitor (red junglefowls), is generally thought to have propagated from north East Asia (Korea and north China) to ancient Japan. However, mitochondrial haplogroup D, which is abundant in Island Southeast Asia (ISEA) as well as the Pacific but relatively rare in other regions, can be observed in some Jidori breeds (e.g., Tosa-Jidori, Tokuji-Jidori) with high frequency, leading to speculation that chickens from ISEA or the Pacific also contributed genetically to JNCs. To test this hypothesis, we sequenced the mitochondrial genomes of Jidori breeds and conducted phylogeographic analysis. Our results indicate that the JNC Haplogroup D belongs to Sub-haplogroup D2, which is currently only observed in Xinjiang, northwest China, and not to Sub-haplogroup D1, which is widely distributed in the ISEA-Pacific region. The other mitochondrial haplogroups of Jidori examined in this study also showed affinity to those of chickens native to north East Asia. Therefore, our findings support the north East Asian origin hypothesis for Jidori.
Project description:Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. High-altitude associated with variant discovery highlighted the importance of COX3, a gene involved in cell respiration, in hypoxia adaptation. The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens.
Project description:Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation and breeding management of native Japanese chickens. In this study, genetic diversity, ROH, and selection signatures in 11 populations of seven native Japanese breeds and three foreign breeds with different genetic and behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited the highest genetic diversity. Six native Japanese breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), and Ukkokei (UK), showed intermediate levels of genetic diversity and ROH. Population analyses grouped the 11 populations into four distinct clusters: (1) five populations comprising three foreign breeds (the Fayoumi inbred line, closed-colony G line of White Leghorn, commercial T line of WL, and White Plymouth Rock) and the IG Japanese breed; (2) OSM and two old Jidori breeds (RYU and TJI); (3) TKU and UK; and (4) the meat-type Nagoya breed. ROH and Fst analyses identified seven SNPs on chromosomes 13, 17, 20, 24, and 26, five of which were candidate genetic variants for fear-related behavior. These findings provide insights into genetic diversity and conserved genomic segments valuable for breeding and conservation in Japanese chicken breeds.
Project description:Individual responses to physical restraint and temperament have been assessed in birds of several species; however, there is a paucity of research which investigates both aspects, especially in captive parrots. This lack of studies raises doubts about which temperament traits, if any, are evidenced during handling and if the intensity of responses to restraint is affected by behavioral training programs, a common practice used in ex situ conservation programs. To understand more about the subject, this study aimed to identify the main temperament dimensions of parrots and investigate their relationship with response to physical restraint for blood collection. A secondary aim was to evaluate whether parrots exhibited higher responsiveness to physical restraint after training to improve flight capacity and increase aversion to humans. The main dimensions identified were activity, neophilia, vigilance, and fearfulness. The more fearful parrots in temperament evaluations were more responsive to physical restraint, showing more vocalizations and struggle attempts than the less fearful ones. After training, the parrots showed higher responsiveness to physical restraint. We suggest that physical restraint for routine handling, such as blood collection, could be a feasible option for centers of rehabilitation to use to obtain data on individual behavioral differences in fear responses.
Project description:ObjectiveIn Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan.MethodsMaximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences.ResultsThis is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1.ConclusionThe sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.
Project description:Evidence from clinical research suggests that in the first two waves of COVID-19, the virus spread rapidly through a large number of undocumented asymptomatic infections. These 'silent' infections camouflaged the actual incidence of the disease, leading to downward biases in the rates of transmission, disease prevalence, and fatality. These, in turn, had implications for how people and policymakers responded to changing infection prevalence. This paper posits that in the early stages of the COVID-19 pandemic, a considerable number of SARS-CoV-2 infections spread through asymptomatic infected individuals who lacked economic incentives to test and isolate adequately. The decision to undertake testing and the subsequent possibility of isolation entails a calculus of benefits and costs for an individual. Given that the perceived net benefit of such actions is correlated with the observed risk of infection, the likelihood of an asymptomatic individual choosing to undergo testing increases with the existing infection prevalence rate. This behavior, in turn, influenced disease transmission and mortality dynamics. This study presents an analytical framework that integrates prevalence-dependent testing behavior into a traditional epidemiological model. The model's predictions provide critical policy insights. It reveals that failing to account for testing and isolation behavior results in underestimation of the infection propagation and fatality rates when reported disease prevalence is low, thereby, skewing the containment strategies in the initial and late stages of a pandemic. The findings underscore the necessity of enhancing testing capacity as a crucial countermeasure for future contagions like COVID-19.
Project description:Hyperuricemia, or elevated serum urate, causes urate kidney stones and gout and also increases the incidence of many other conditions including renal disease, cardiovascular disease, and metabolic syndrome. As we gain mechanistic insight into how urate contributes to human disease, a clear sex difference has emerged in the physiological regulation of urate homeostasis. This review summarizes our current understanding of urate as a disease risk factor and how being of the female sex appears protective. Further, we review the mechanisms of renal handling of urate and the significant contributions from powerful genome-wide association studies of serum urate. We also explore the role of sex in the regulation of specific renal urate transporters and the power of new animal models of hyperuricemia to inform on the role of sex and hyperuricemia in disease pathogenesis. Finally, we advocate the use of sex differences in urate handling as a potent tool in gaining a further understanding of physiological regulation of urate homeostasis and for presenting new avenues for treating the constellation of urate related pathologies.