Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens.

BACKGROUND: Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. RESULTS: To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. CONCLUSION: Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.

Differential Resistance to Acetyl-CoA Carboxylase Inhibitors in Rice: Insights from Two Distinct Target-Site Mutations.

Weeds present a significant challenge to agricultural productivity, and acetyl-CoA carboxylase (ACCase)-inhibiting herbicides have proven to be effective in managing weed populations in rice fields. To develop ACCase-inhibiting herbicide-resistant rice, we generated mutants of rice ACCase (OsACC) featuring Ile-1792-Leu or Gly-2107-Ser substitutions through ethyl methyl sulfonate (EMS) mutagenesis. The Ile-1792-Leu mutant displayed cross-resistance to aryloxyphenoxypropionate (APP) and phenylpyrazoline (DEN) herbicides, whereas the Gly-2107-Ser mutants primarily exhibited cross-resistance to APP herbicides with diminished resistance to the DEN herbicide. In vitro assays of the OsACC activity revealed an increase in resistance to haloxyfop and quizalofop, ranging from 4.84- to 29-fold in the mutants compared to that in wild-type. Structural modeling revealed that both mutations likely reduce the binding affinity between OsACC and ACCase inhibitors, thereby imparting resistance. This study offers insights into two target-site mutations, contributing to the breeding of herbicide-resistant rice and presenting alternative weed management strategies in rice cultivation.

Discovery of Novel Aryl Triazolone Dihydropyridines (ATDPs) Targeting Highly Conserved Residue W229 as Promising HIV-1 NNRTIs.

NNRTI is an important component of the highly active antiretroviral therapy (HAART), but the rapid emergence of drug resistance and poor pharmacokinetics limited their clinical application. Herein, a series of novel aryl triazolone dihydropyridines (ATDPs) were designed by structure-guided design with the aim of improving drug resistance profiles and pharmacokinetic profiles. Compound 10n (EC50 = 0.009-17.7 µM) exhibited the most active potency, being superior to or comparable to that of doravirine (DOR) against the whole tested viral panel. Molecular docking was performed to clarify the reason for its higher resistance profiles. Moreover, 10n demonstrated excellent pharmacokinetic profile (T1/2 = 5.09 h, F = 108.96%) compared that of DOR (T1/2 = 4.4 h, F = 57%). Additionally, 10n was also verified to have no in vivo acute or subacute toxicity (LD50 > 2000 mg/kg), suggesting that 10n is worth further investigation as a novel oral NNRTIs for HIV-1 therapy.

Structure-Based Design of Novel G-Protein-Coupled Receptor TAAR1 Agonists as Potential Antipsychotic Drug Candidates.

The existing available antipsychotics have failed to manage the cognitive impairment of schizophrenia and induced a number of seriously undesirable effects. Trace amine-associated receptor 1 (TAAR1) has emerged as an ideal target for the design of antischizophrenia drugs, with the ability to mediate multiple psychological functions by sensing endogenous amine-containing metabolites without the side effects of catalepsy. In this work, a series of novel TAAR1 agonists were designed based on the structural analysis of the TAAR1 activation pocket. Among them, 6e displayed a potent TAAR1-Gs/Gq dual-pathway activation property, being different from that of the clinical drug candidate SEP-363856 with only TAAR1-Gs pathway activation. In rodent models, 6e significantly alleviated MK-801-induced schizophrenia-like cognitive phenotypes without inducing catalepsy. Furthermore, 6e·HCl exhibited favorable pharmacokinetic (T1/2 = 2.31 h, F = 39%) and safety properties. All these demonstrated that 6e·HCl may be used as a novel drug candidate for schizophrenia treatment.

Whole-genome variants dataset of 209 local chickens from China.

Compared to commercial chickens, local breeds exhibit better in meat quality and flavour, but the productivity (e.g., growth rate, body weight) of local chicken breeds is rather low. Genetic analysis based on whole-genome sequencing contributes to elucidating the genetic markers or putative candidate genes related to some economic traits, facilitating the improvement of production performance, the acceleration of breeding progress, and the conservation of genetic resources. Here, a total of 209 local chickens from 13 breeds were investigated, and the observation of approximately 91.4% high-quality sequences (Q30 > 90%) and a mapping rate over 99% for each individual indicated good results of this study, as confirmed by a genome coverage of 97.6%. Over 19 million single nucleotide polymorphisms (SNPs) and 1.98 million insertion-deletions (InDels) were identified using the reference genome (GRCg7b), further contributing to the public database. This dataset provides valuable resources for studying genetic diversity and adaptation and for the cultivation of new chicken breeds/lines.

Novel Insights into the Circadian Rhythms Based on Long Noncoding and Circular RNA Profiling.

Circadian rhythm disorders pose major risks to human health and animal production activity, and the hypothalamus is the center of circadian rhythm regulation. However, the epigenetic regulation of circadian rhythm based on farm animal models has been poorly investigated. We collected chicken hypothalamus samples at seven time points in one light/dark cycle and performed long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA sequencing to detect biomarkers associated with circadian rhythm. We enhanced the comprehensive expression profiling of ncRNAs and mRNAs in the hypothalamus and found two gene sets (circadian rhythm and retinal metabolism) associated with the light/dark cycle. Noncoding RNA networks with circadian expression patterns were identified by differential expression and circadian analysis was provided that included 38 lncRNAs, 15 circRNAs, and 200 candidate genes. Three lncRNAs (ENSGALT00000098661, ENSGALT00000100816, and MSTRG.16980.1) and one circRNA (novel_circ_010168) in the ncRNA-mRNA regulatory network were identified as key molecules influencing circadian rhythm by regulating AOX1 in retinal metabolism. These ncRNAs were predicted to be related to pernicious anemia, gonadal, eye disease and other disorders in humans. Together, the findings of this study provide insights into the epigenetic mechanisms of circadian rhythm and reveal AOX1 as a promising target of circadian rhythm regulation.

Harnessing 3D in vitro systems to model immune responses to solid tumours: a step towards improving and creating personalized immunotherapies.

In vitro 3D models are advanced biological tools that have been established to overcome the shortcomings of oversimplified 2D cultures and mouse models. Various in vitro 3D immuno-oncology models have been developed to mimic and recapitulate the cancer-immunity cycle, evaluate immunotherapy regimens, and explore options for optimizing current immunotherapies, including for individual patient tumours. Here, we review recent developments in this field. We focus, first, on the limitations of existing immunotherapies for solid tumours, secondly, on how in vitro 3D immuno-oncology models are established using various technologies - including scaffolds, organoids, microfluidics and 3D bioprinting - and thirdly, on the applications of these 3D models for comprehending the cancer-immunity cycle as well as for assessing and improving immunotherapies for solid tumours.

The Effect of Using Premedication of Simethicone/Pronase With or Without Postural Change on Visualization of the Mucosa Before Endoscopy: A Prospective, Double Blinded, Randomized Controlled Trial.

INTRODUCTION: To investigate the efficacy and safety of preprocedural simethicone (S) and pronase (P) for optimal mucosal visualization during esophagogastroduodenoscopy with sedation. The effect of postural change combined with premedication on mucosal visibility was also examined. METHODS: The study randomized 496 patients into 8 groups based on the type of premedication provided and whether a postural change occurred. The premedication in the control group was 100 mL of normal saline solution (NS). The remaining 3 intervention groups were administered 100 mL of simethicone alone (S), pronase solution alone (P), and simethicone plus pronase solution (S + P). Each group was classified into subgroups according to whether there was a postural change (PC). The mucosal visibility score (MVS), total mucosal visibility score (TVS), procedure time, water consumption for mucosal cleansing, and proportion of patients with diminutive lesions <5 mm were recorded. RESULTS: The P and S groups had a significantly better TVS than the NS group (11.86 ± 3.36 in group P vs 14.52 ± 2.57 in group NS, P < 0.001; 12.36 ± 2.93 in group S vs 14.52 ± 2.57 in group NS, P = 0.006). The TVS was better in the P group than in the S group (11.86 ± 3.36 vs 12.36 ± 2.93, P = 0.037). The MVS was significantly better in the esophagus and duodenum and worse in the upper and lower gastric body in the S group than in the P group. The P + S group had a significantly better TVS than the P and S groups (9.81 ± 2.90 in group P + S vs 11.86 ± 3.36 in group P and 12.36 ± 2.93 in group S, respectively, P < 0.001),\ and had a reduced amount of flushing water during the procedure (0 [interquartile range [IQR]: 0-33] mL in group P + S vs 40 [IQR: 0-70] mL in group P, P < 0.01; 0 [IQR: 0-33] mL in group P + S vs 50 [IQR: 20-98] mL in group S, P < 0.001). The TVS was significantly better in the P + S + PC group than in the P + S group (8.44 ± 2.10 vs 9.81 ± 2.90, P = 0.003). The MVS was significantly better in the gastric antrum, fundus, and upper and lower gastric body in the P + S + PC group than in the P + S group. There was no significant difference in the detection rate of diminutive lesions among the different groups during an endoscopic examination ( P > 0.05). DISCUSSION: The combination of preprocedural administration with simethicone and pronase achieved superior mucosal visualization compared with saline, simethicone, or pronase alone in patients receiving upper endoscopy. Postural change maneuvers performed before endoscopy further improved the mucosal visibility in most parts of the stomach when used with preprocedural simethicone and pronase.

Structural and signaling mechanisms of TAAR1 enabled preferential agonist design.

Trace amine-associated receptor 1 (TAAR1) senses a spectrum of endogenous amine-containing metabolites (EAMs) to mediate diverse psychological functions and is useful for schizophrenia treatment without the side effects of catalepsy. Here, we systematically profiled the signaling properties of TAAR1 activation and present nine structures of TAAR1-Gs/Gq in complex with EAMs, clinical drugs, and synthetic compounds. These structures not only revealed the primary amine recognition pocket (PARP) harboring the conserved acidic D3.32 for conserved amine recognition and "twin" toggle switch for receptor activation but also elucidated that targeting specific residues in the second binding pocket (SBP) allowed modulation of signaling preference. In addition to traditional drug-induced Gs signaling, Gq activation by EAM or synthetic compounds is beneficial to schizophrenia treatment. Our results provided a structural and signaling framework for molecular recognition by TAAR1, which afforded structural templates and signal clues for TAAR1-targeted candidate compounds design.

In situ click chemistry-based discovery of 1,2,3-triazole-derived diarylpyrimidines as novel HIV-1 NNRTIs by exploiting the tolerant region I in binding pocket.

HIV-1 reverse transcriptase (RT) is considered as one of the most significant targets for the anti-HIV-1 drug design due to their determined mechanism and well-decoded crystal structure. As a part of our continuous efforts towards the development of potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) by exploiting the tolerant region I of NNRTIs binding pocket (NNIBP), the miniaturized parallel synthesis via CuAAC click chemistry reaction followed by in situ biological screening have been performed in this work. The in situ enzyme inhibition screening results showed that 14 compounds exhibited higher or equivalent inhibitory activity compared to the lead K-5a2 and ETR. Anti-HIV-1 activity results indicated that C1N51 displayed the most potent activity (EC50 = 0.01-0.26 µM) against wild-type and a panel of NNRTIs-resistant strains. Moreover, the molecular simulation demonstrated that the newly introduced triazole ring could develop new hydrogen bonds with Lys103 and Pro236, which explained the feasibility of introducing triazole in the tolerant region I of the RT binding pocket.

Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation.

Small nuclear RNAs (snRNAs) are structural and functional cores of the spliceosome. In metazoan genomes, each snRNA has multiple copies/variants, up to hundreds in mammals. However, the expressions and functions of each copy/variant in one organism have not been systematically studied. Focus on U1 snRNA genes, we investigated all five copies in Drosophila melanogaster using two series of constructed strains. Analyses of transgenic flies that each have a U1 promoter-driven gfp revealed that U1:21D is the major and ubiquitously expressed copy, and the other four copies have specificities in developmental stages and tissues. Mutant strains that each have a precisely deleted copy of U1-gene exhibited various extents of defects in fly morphology or mobility, especially deletion of U1:82Eb. Interestingly, splicing was changed at limited levels in the deletion strains, while large amounts of differentially-expressed genes and alternative polyadenylation events were identified, showing preferences in the down-regulation of genes with 1-2 introns and selection of proximal sites for 3'-end polyadenylation. In vitro assays suggested that Drosophila U1 variants pulled down fewer SmD2 proteins compared to the canonical U1. This study demonstrates that all five U1-genes in Drosophila have physiological functions in development and play regulatory roles in transcription and 3'-end formation.

Multi-omics insights into the mechanism of the high-temperature tolerance in a thermotolerant Chlorella sorokiniana.

Improving high-temperature tolerance of microalgae is crucial to enhance the robustness and economy of microalgae industrial production. Herein, a continuous adaptive laboratory evolution (ALE) system was developed to generate the thermotolerant strain of Chlorella sorokiniana. The resulting thermotolerant strain TR42 exhibited excellent cell growth and biomass production at 42 °C, the temperature that the original strain (OS) could not survive. The high-temperature resistant mechanism of TR42 was investigated by integrating the physiology, transcriptome, proteome and metabolome analyses, which involved enhancing antioxidant capacity, maintaining protein homeostasis, remodeling photosynthetic metabolism, and regulating the synthesis of heat-stress related metabolites. The proof-of-concept high-temperature outdoor cultivation demonstrated that TR42 exhibited 1.15- to 5.72-fold increases in biomass production and 1.62- to 7.04-fold increases in lipid productivity compared to those of OS, respectively, which provided a promising platform for microalgae industrial production. Thus, the multi-system thermotolerant mechanism of TR42 offered potential targets for enhancing high-temperature tolerance of microalgae.

Crystal Field Engineering of Pr-Activated Gehlenite with Near Golden Ultraviolet C Emission for 100% Sterilization Efficiency.

Ultraviolet C (UVC) sterilization has the advantages of high efficiency, broad spectrum, and no secondary pollution. However, the emission wavelength of UVC phosphors still suffers from a large deviation from the golden sterilization wavelength of 265 nm and a low luminescence intensity. Herein, we report UVC emission near the golden sterilization wavelength as well as a long afterglow through crystal field engineering, which can lead to 100% sterilization efficiency. Combined with theoretical calculation and experimental studies, substitution of Ca2+ with large-sized Sr2+ could obtain slight expansion and distortion of cationic sites, resulting in a decrease in crystal field intensity and blue shift of Ca1.5Sr0.5Al2SiO7:1%Pr3+, and produce near golden UVC emission. Ca1.5Sr0.5Al2SiO7:1%Pr3+ phosphor can effectively inactivate Staphylococcus aureus within 10 min, showing more efficiency than the traditional mercury lamp. This work provides an effective solution for the design and preparation of UVC phosphors using crystal field engineering toward near golden UVC emission.

Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis.

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline-alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.

A Supported Catalyst that Enables the Synthesis of Colorless CO2 -Polyols with Ultra-Low Molecular Weight.

Ultra-low molecular weight (ULMW) CO2 -polyols with well-defined hydroxyl end groups represent useful soft segments for the preparation of high-performance polyurethane foams. However, owing to the poor proton tolerance of catalysts towards CO2 /epoxide telomerization, it remains challenging to synthesize ULMW yet colorless CO2 -polyols. Herein, we propose an immobilization strategy of constructing supported catalysts by chemical anchoring of aluminum porphyrin on Merrifield resin. The resulting supported catalyst displays both extremely high proton tolerance (≈8000 times the equivalents of metal centers) and independence of cocatalyst, affording CO2 -polyols with ULMW (580 g mol-1 ) and high polymer selectivity (>99 %). Moreover, the ULMW CO2 -polyols with various architectures (tri-, quadra-, and hexa-arm) can be obtained, suggesting the wide proton universality of supported catalysts. Notably, benefiting from the heterogeneous nature of the supported catalyst, colorless products can be facilely achieved by simple filtration. The present strategy provides a platform for the synthesis of colorless ULMW polyols derived from not only CO2 /epoxides, but also lactone, anhydrides etc. or their combinations.

Reconstruction of tumor microenvironment viain vitrothree-dimensional models.

Recent advances in tumor microenvironment (TME) modeling as well as its applications to cancer therapy has brought various dramatical changes in multiple malignancies management. Understanding the mechanisms of response and resistance to cancer therapy requires a clear elucidation of the intricate interactions between TME cells, the surrounding stroma, and distant affected tissues or organs. To address this demand, various three-dimensional (3D) cell culture techniques have been developed in order to recapitulate and understand cancer biology over the past decade. This review summarizes some saliant progresses inin vitro3D TME modeling, including the cell-based, matrix-based, and vessel-based dynamic 3D modeling techniques and their applications in investigating tumor-stroma interactions and responses to cancer therapies. The review also discusses the limitations of current TME modeling approaches and proposes some new thoughts on the construction of more clinically relevant models.

Bismuth Vacancy-Induced Enhancement of Luminescence Intensity and Irradiation Resistance for Bi4Ge3O12.

Bi4Ge3O12 (BGO) is a traditional scintillator, widely used in high-energy physics and nuclear medicine. However, it not only suffers from low scintillation intensity but also tends to be damaged by high-energy rays. Herein, we prepare pure-phase BGO materials enriched with Bi vacancies by rationally reduced Bi content, showing significantly enhanced luminescence intensity and irradiation resistance ability. The optimized Bi3.6Ge3O12 shows 178% of luminescence intensity compared to BGO. After 50 h of ultraviolet irradiation, Bi3.6Ge3O12 possesses ∼80% of original luminescence intensity, much superior to the 60% for BGO. The existence of the Bi vacancy is identified by advanced experimental and theoretical studies. The mechanism studies show the Bi vacancies could cause the symmetry destruction of the local field around the Bi3+ ion. It enhances scintillation luminescence by increasing the probability of radiative transition while resisting nonradiative relaxation caused by irradiation damage. This study initiates vacancy-induced performance enhancement for inorganic scintillators.

Ethylidene-Tethered Chromene-Pyrone Hybrids as Potential Plant-Growth Regulators from an Endolichenic Phaeosphaeria Species.

Phaeosphaeria sp., a lichen-associated fungus, produced six skeletally new dimeric spiciferones (1-6) and four known metabolites (7-10). The new structures were elucidated by spectroscopic analysis, and their absolute configurations were determined by electronic circular dichroism calculations. Compounds 1 and 3-6 represent the first examples of ethylidene-bridged dimers from the building blocks 4H-chromene-4,7(8H)-dione and α-pyrone, and 2 is a unique homodimer of spiciferone. Compounds 1, 2, and 5-9 significantly inhibited the growth of weed-like dicot Arabidopsis thaliana at 100.0 µM. Notably, 8 showed the strongest inhibitory activity against the fresh weight and root elongation of A. thaliana with the IC50 values of 32.04 and 26.78 µM, respectively, whereas 1, 8, and 9 stimulated the growth of A. thaliana at lower concentrations. Meanwhile, compounds 2 and 6 exhibited weak inhibitory effects on the root elongation of monocot rice, while 1 and 8 exhibited growth-promoting effects on the shoot and root elongation of rice in a roughly dose-dependent manner.

Covalently Targeted Highly Conserved Tyr318 to Improve the Drug Resistance Profiles of HIV-1 NNRTIs: A Proof-of-Concept Study.

This study presents proof of concept for designing a novel HIV-1 covalent inhibitor targeting the highly conserved Tyr318 in the HIV-1 non-nucleoside reverse transcriptase inhibitors binding pocket to improve the drug resistance profiles. The target inhibitor ZA-2 with a fluorosulfate warhead in the structure was found to be a potent inhibitor (EC50 = 11-246 nM) against HIV-1 IIIB and a panel of NNRTIs-resistant strains, being far superior to those of NVP and EFV. Moreover, ZA-2 was demonstrated with lower cytotoxicity (CC50 = 125 µM). In the reverse transcriptase inhibitory assay, ZA-2 exhibited an IC50 value of 0.057 µM with the ELISA method, and the MALDI-TOF MS data demonstrated the covalent binding mode of ZA-2 with the enzyme. Additionally, the molecular simulations have also demonstrated that compounds can form covalent binding to the Tyr318.