Evolutionary adaptation of visual pigments in geckos for their photic environment

家の守り神「ヤモリ」が夜でも色を見分けられるのはなぜ --ヤモリが持つ特殊な色覚能力の分子メカニズムを解明--. 京都大学プレスリリース. 2021-10-04.Vertebrates generally have a single type of rod for scotopic vision and multiple types of cones for photopic vision. Noteworthily, nocturnal geckos transmuted ancestral photoreceptor cells into rods containing not rhodopsin but cone pigments, and, subsequently, diurnal geckos retransmuted these rods into cones containing cone pigments. High sensitivity of scotopic vision is underlain by the rod’s low background noise, which originated from a much lower spontaneous activation rate of rhodopsin than of cone pigments. Here, we revealed that nocturnal gecko cone pigments decreased their spontaneous activation rates to mimic rhodopsin, whereas diurnal gecko cone pigments recovered high rates similar to those of typical cone pigments. We also identified amino acid residues responsible for the alterations of the spontaneous activation rates. Therefore, we concluded that the switch between diurnality and nocturnality in geckos required not only morphological transmutation of photoreceptors but also adjustment of the spontaneous activation rates of visual pigments

Risk and Time Preference on Schooling: Experimental Evidence from a Low-Income Country

経済学 / EconomicsEducational investment involves risks and long-term commitment, and the degree of risk aversion or patience of parents could play a vital role in the schooling decision. Yet, there are few studies analyzing the impact of such preferences on educational investment. This paper utilizes a unique dataset with a large-scale field experiment of preferences and estimates the impacts of the patience and risk aversion of the parents on school attendance, delayed enrollment, and the education expenditure of their children in Uganda. Our results show that the risk aversion of the parent delays enrollment of young children, especially boys. This could be explained by parents’security concerns for their young children. Girls of impatient parents have high attendance rates when they are young (6 – 9 years old) but have low attendance rates when they are older (10 – 13 years old). Boys aged 10 to 13 have low attendance rates if their parents have a high present bias. Finally, the patience of the parents increases the education expenditure

Haki Yetu (It’s Our Right): Determinants of Post-Election Violence in Kenya

経済学 / EconomicsDuring the violence following the 2007 presidential election in Kenya, it has been reported that around 1,000 people were killed and over 500,000 people were displaced. In this paper, we investigate the root causes of the violence by using a panel survey of 295 rural households living Rift Valley and Nyanza Provinces, where the violence took place. Among our sample households, 11 percent of male members and 9 percent of female members were victims of the violence, 11 percent of households were displaced, and 23 percent of households hosted at least one internally displaced person. The results show that certain ethnic groups had higher probabilities of being victims of the violence. In addition, we find that members of households without land titles were victimized more than those with land titles, but they were less likely to leave their homes. They could be victimized because the mobs wanted to chase them away, but they hesitated to leave their homes, knowing that it would be difficult for them to retain their land without land titles. The land issue was clearly one of the root causes of the violence, and the issue should be solved or at least addressed to prevent similar conflicts in the future

Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates

脊椎動物の視覚進化モデルを修正 --暗所視と色覚はどっちが先か--. 京都大学プレスリリース. 2018-10-02.Pinopsin is the opsin most closely related to vertebrate visual pigments on the phylogenetic tree. This opsin has been discovered among many vertebrates, except mammals and teleosts, and was thought to exclusively function in their brain for extraocular photoreception. Here, we show the possibility that pinopsin also contributes to scotopic vision in some vertebrate species. Pinopsin is distributed in the retina of non-teleost fishes and frogs, especially in their rod photoreceptor cells, in addition to their brain. Moreover, the retinal chromophore of pinopsin exhibits a thermal isomerization rate considerably lower than those of cone visual pigments, but comparable to that of rhodopsin. Therefore, pinopsin can function as a rhodopsin-like visual pigment in the retinas of these lower vertebrates. Since pinopsin diversified before the branching of rhodopsin on the phylogenetic tree, two-step adaptation to scotopic vision would have occurred through the independent acquisition of pinopsin and rhodopsin by the vertebrate lineage

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Realization of a Human-like Gait for a Bipedal Robot Based on Gait Analysis

There are many studies analyzing human motion. However, we do not yet fully understand the mechanisms of our own bodies. We believe that mimicking human motion and function using a robot will help us to deepen our understanding of humans. Therefore, we focus on the characteristics of the human gait, and the goal is to realize a human-like bipedal gait that lands on its heels and takes off from its toes. In this study, we focus on kinematic synergy (planar covariation) in the lower limbs as a characteristic gait seen in humans. Planar covariation is that elevation angles at the thigh, shank, and foot in the sagittal plane are plotted on one plane when the angular data are plotted on the three axes. We propose this feature as a reward for reinforcement learning. By introducing this reward, the bipedal robot achieved a human-like bipedal gait in which the robot lands on its heels and takes off from its toes. We also compared the learning results with those obtained when this feature was not used. The results suggest that planar covariation is one factor that characterizes a human-like gait