Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

忘れられた作物「えどどころ」の起原 --ゲノム解析が明らかにする青森県三八上北地域に残る栽培イモの歴史--. 京都大学プレスリリース. 2022-08-10.A rhizomatous Dioscorea crop “Edo-dokoro” was described in old records of Japan, but its botanical identify has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of Aomori Prefecture, Japan. Rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, D. tokoro and D. tenuipes. Genome analysis revealed that Edo-dokoro is likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten from the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information

High-performance pipeline for MutMap and QTL-seq

[Summary] Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5–8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. [Availability] The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq)

SimSwap: An Efficient Framework For High Fidelity Face Swapping

We propose an efficient framework, called Simple Swap (SimSwap), aiming for generalized and high fidelity face swapping. In contrast to previous approaches that either lack the ability to generalize to arbitrary identity or fail to preserve attributes like facial expression and gaze direction, our framework is capable of transferring the identity of an arbitrary source face into an arbitrary target face while preserving the attributes of the target face. We overcome the above defects in the following two ways. First, we present the ID Injection Module (IIM) which transfers the identity information of the source face into the target face at feature level. By using this module, we extend the architecture of an identity-specific face swapping algorithm to a framework for arbitrary face swapping. Second, we propose the Weak Feature Matching Loss which efficiently helps our framework to preserve the facial attributes in an implicit way. Extensive experiments on wild faces demonstrate that our SimSwap is able to achieve competitive identity performance while preserving attributes better than previous state-of-the-art methods. The code is already available on github: https://github.com/neuralchen/SimSwap.Comment: Accepted by ACMMM 202

Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata)

西アフリカの主食作物ギニアヤムの起源を解明 --ギニアヤムはサバンナと熱帯雨林に生育する野生種の雑種起源--. 京都大学プレスリリース. 2020-12-11.White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding

Bone Morphogenetic Protein Signaling: Implications in Urology

The bone morphogenetic proteins (BMPs), as members of the transforming growth factor-β (TGF-β) superfamily, not only control bone formation, but also regulate multiple key steps during embryonic development and differentiation. Furthermore, BMPs play critical roles in maintaining the homeostasis of the cardiovascular, pulmonary, reproductive, urogenital, and nervous systems in adult life. Like all members of the TGF-β superfamily, BMP signaling is mediated through a heteromeric complex of type I and type II transmembrane serine/threonine kinase receptors. The subsequent signal transduction cascade includes either the canonical Smad-dependent or non-canonical Smad-independent pathways. Reflecting the critical function of BMPs, BMP signaling is tightly regulated at multiple steps by various mechanisms including extracellular endogenous antagonists, neutralizing antibodies/extracellular soluble receptor domains, small molecule inhibitors, cytoplasmic inhibitory Smads, and transcriptional co-repressors. Recently, dorsomorphin, the first small molecule inhibitor of BMP signaling, was identified and suggested as a useful tool for dissecting the mechanisms of signaling pathways and for developing novel therapeutics for diverse human diseases that are related to the BMP signaling pathways. In this article, we discuss various mechanisms involved in regulating BMP signaling pathways and their implications for urology

Copper (I) selenocyanate (CuSeCN) as a novel hole-transport layer for transistors, organic solar cells, and light-emitting diodes

The synthesis and characterization of copper (I) selenocyanate (CuSeCN) and its application as a solution-processable hole-transport layer (HTL) material in transistors, organic light-emitting diodes, and solar cells are reported. Density-functional theory calculations combined with X-ray photoelectron spectroscopy are used to elucidate the electronic band structure, density of states, and microstructure of CuSeCN. Solution-processed layers are found to be nanocrystalline and optically transparent ( > 94%), due to the large bandgap of ≥3.1 eV, with a valence band maximum located at -5.1 eV. Hole-transport analysis performed using field-effect measurements confirms the p-type character of CuSeCN yielding a hole mobility of 0.002 cm 2 V -1 s -1 . When CuSeCN is incorporated as the HTL material in organic light-emitting diodes and organic solar cells, the resulting devices exhibit comparable or improved performance to control devices based on commercially available poly(3,4-ethylenedioxythiophene):polystyrene sulfonate as the HTL. This is the first report on the semiconducting character of CuSeCN and it highlights the tremendous potential for further developments in the area of metal pseudohalides

A Single Acidic Residue Can Guide Binding Site Selection but Does Not Govern QacR Cationic-Drug Affinity

Structures of the multidrug-binding repressor protein QacR with monovalent and bivalent cationic drugs revealed that the carboxylate side-chains of E90 and E120 were proximal to the positively charged nitrogens of the ligands ethidium, malachite green and rhodamine 6G, and therefore may contribute to drug neutralization and binding affinity. Here, we report structural, biochemical and in vivo effects of substituting these glutamate residues. Unexpectedly, substitutions had little impact on ligand affinity or in vivo induction capabilities. Structures of QacR(E90Q) and QacR(E120Q) with ethidium or malachite green took similar global conformations that differed significantly from all previously described QacR-drug complexes but still prohibited binding to cognate DNA. Strikingly, the QacR(E90Q)-rhodamine 6G complex revealed two mutually exclusive rhodamine 6G binding sites. Despite multiple structural changes, all drug binding was essentially isoenergetic. Thus, these data strongly suggest that rather than contributing significantly to ligand binding affinity, the role of acidic residues lining the QacR multidrug-binding pocket is primarily to attract and guide cationic drugs to the “best available” positions within the pocket that elicit QacR induction

HMGB1 Mediates Endogenous TLR2 Activation and Brain Tumor Regression

Maria Castro and colleagues use cell line and transgenic mouse approaches to study the mechanisms underlying the immune response to glioblastoma multiforme

Chromosome Duplication in <i>Saccharomyces cerevisiae</i>

The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G 1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation. Keywords: DNA replication; cell cycle; chromatin; chromosome duplication; genome stability; YeastBookNational Institutes of Health (U.S.) (Grant GM-052339

Thermal adaptation of the elderly during summer in a hot humid area: Psychological, behavioral, and physiological responses

Elderly demand for thermal comfort and energy conservation in senior citizen centers is increasing in an aging society. To reveal the thermal responses of the elderly in a warm summer environment, a field study involving experimental measurements was conducted in Chongqing, China. The study included 333 subjects in 17 residential buildings and 119 subjects in 6 elderly nursing homes; it showed that elderly persons as passive users of air conditioners preferred cooling by natural ventilation. The mean thermal sensation vote was lower than estimates obtained from the PMV model in warm environments. The physiological responses of eight elderly subjects (65 ± 3) were measured in a climate chamber at 18 °C and 34 °C and compared with those from eight college students (22 ± 1) and eight middle-aged subjects (50 ± 5). In this chamber, oral temperature, blood pressure, and heart rate of elderly and middle-aged persons were determined to be almost constant as the air temperature was changed to a hot/cold environment for 30 min, a different result from that of the young subjects. However, the skin temperature for all age groups showed variation with air temperature, suggesting skin temperature as an optimal monitoring parameter for the entire population