A Solution for Universal Classification of Species Based on Genomic DNA

Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact

Manipulation of charge carrier flow in Bi₄NbO₈Cl nanoplate photocatalyst with metal loading

Separation of photoexcited charge carriers in semiconductors is important for efficient solar energy conversion and yet the control strategies and underlying mechanisms are not fully established. Although layered compounds have been widely studied as photocatalysts, spatial separation between oxidation and reduction reaction sites is a challenging issue due to the parallel flow of photoexcited carriers along the layers. Here we demonstrate orthogonal carrier flow in layered Bi₄NbO₈Cl by depositing a Rh cocatalyst at the edges of nanoplates, resulting in spatial charge separation and significant enhancement of the photocatalytic activity. Combined experimental and theoretical studies revealed that lighter photogenerated electrons, due to a greater in-plane dispersion of the conduction band (vs. valence band), can travel along the plane and are readily trapped by the cocatalyst, whereas the remaining holes hop perpendicular to the plane because of the anisotropic crystal geometry. Our results propose manipulating carrier flow via cocatalyst deposition to achieve desirable carrier dynamics for photocatalytic reactions in layered compounds

Genome Profiling (GP) Method Based Classification of Insects: Congruence with That of Classical Phenotype-Based One

Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in ambitious comparative biology studies. However, such technologies are still far from routine-use in species classification studies due to their high costs in terms of labor, equipment and consumables.Here, we describe a simple and powerful approach for species classification called genome profiling (GP). The GP method composed of random PCR, temperature gradient gel electrophoresis (TGGE) and computer-aided gel image processing is highly informative and less laborious. For demonstration, we classified 26 species of insects using GP and 18S rDNA-sequencing approaches. The GP method was found to give a better correspondence to the classical phenotype-based approach than did 18S rDNA sequencing employing a congruence value. To our surprise, use of a single probe in GP was sufficient to identify the relationships between the insect species, making this approach more straightforward.The data gathered here, together with those of previous studies show that GP is a simple and powerful method that can be applied for actually universally identifying and classifying species. The current success supported our previous proposal that GP-based web database can be constructible and effective for the global identification/classification of species

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

Numerical study on the structural color of blue birds by a disordered porous photonic crystal model

It has been observationally confirmed that the color of birds, such as kingfisher and red-flanked bluetail, is a structural color owing to the interference of the light within a sponge structure inside a barb. In this study, we consider the air rod photonic crystal to which disorder is introduced into the translation vectors and the radius as a model of the structural color of red-flanked bluetail; the optical property of the model is numerically analyzed and is compared with that of the structural color

Effects of the rigid and sterically bulky structure of non-fused nonfullerene acceptors on transient photon-to-current dynamics

Non-fused electron-accepting π-conjugated compounds have been investigated recently for application to nonfullerene acceptors (NFAs) in organic solar cells (OSCs). However, the establishment of rational molecular design for non-fused NFAs is still lagging because the influence of flexible non-fused structures on the dynamics of electron–hole pairs in OSCs is not entirely understood. In this study, we utilized cyclopentene-annelated thiophene with spiro-substituted 2,7-bis(2-ethylhexyl)fluorene (FT) as a rigid and sterically bulky linker unit and developed a non-fused NFA (TT–FT–DCI) containing FT units. Photophysical measurements indicated that the introduction of the FT unit leads to the formation of rigid molecular structure. OSCs based on donor polymer (PBDB-T) and TT–FT–DCI showed an improved power conversion efficiency of 7.13% due to the increase in the short-circuit current density and fill factor. Time-resolved optical and microwave spectroscopies showed that the FT unit contributes to the long lifetimes of excited state and charge-separated state in the PBDBT:TT–FT–DCI blend films. Time-resolved electron paramagnetic resonance measurements showed that the distant charge-separated states of the face-to-face PBDB-T:TT–FT–DCI structure, which is derived by avoiding over-crystallization by the steric bulkiness of TT–FT–DCI, can interact with the cathodes for preferential electron injection following charge generations. This study highlights that by using the rigid π-conjugated framework and suppressed self-aggregation of the non-fused acceptor, effective molecular design for the appropriate dynamics of photocurrent generation is possible