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1.
Mol Cell ; 83(7): 1180-1196.e8, 2023 04 06.
Article in English | MEDLINE | ID: mdl-37028415

ABSTRACT

Proper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here, we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in the controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independently of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular "shock absorbers" that converge on protecting cell homeostasis by dampening both toxic immune response and viral replication.


Subject(s)
DNA Helicases , RNA Helicases , Humans , DNA Helicases/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , Poly-ADP-Ribose Binding Proteins/metabolism , Stress Granules , RNA Recognition Motif Proteins/metabolism , Immunity, Innate , Inflammation/metabolism , Cytoplasmic Granules/metabolism , Carrier Proteins/metabolism
2.
Brief Bioinform ; 25(3)2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38770717

ABSTRACT

Drug therapy is vital in cancer treatment. Accurate analysis of drug sensitivity for specific cancers can guide healthcare professionals in prescribing drugs, leading to improved patient survival and quality of life. However, there is a lack of web-based tools that offer comprehensive visualization and analysis of pancancer drug sensitivity. We gathered cancer drug sensitivity data from publicly available databases (GEO, TCGA and GDSC) and developed a web tool called Comprehensive Pancancer Analysis of Drug Sensitivity (CPADS) using Shiny. CPADS currently includes transcriptomic data from over 29 000 samples, encompassing 44 types of cancer, 288 drugs and more than 9000 gene perturbations. It allows easy execution of various analyses related to cancer drug sensitivity. With its large sample size and diverse drug range, CPADS offers a range of analysis methods, such as differential gene expression, gene correlation, pathway analysis, drug analysis and gene perturbation analysis. Additionally, it provides several visualization approaches. CPADS significantly aids physicians and researchers in exploring primary and secondary drug resistance at both gene and pathway levels. The integration of drug resistance and gene perturbation data also presents novel perspectives for identifying pivotal genes influencing drug resistance. Access CPADS at https://smuonco.shinyapps.io/CPADS/ or https://robinl-lab.com/CPADS.


Subject(s)
Drug Resistance, Neoplasm , Internet , Neoplasms , Software , Humans , Neoplasms/drug therapy , Neoplasms/genetics , Drug Resistance, Neoplasm/genetics , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Computational Biology/methods , Databases, Genetic , Transcriptome , Gene Expression Profiling/methods
3.
Blood ; 143(18): 1825-1836, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38211332

ABSTRACT

ABSTRACT: Venetoclax, the first-generation inhibitor of the apoptosis regulator B-cell lymphoma 2 (BCL2), disrupts the interaction between BCL2 and proapoptotic proteins, promoting the apoptosis in malignant cells. Venetoclax is the mainstay of therapy for relapsed chronic lymphocytic leukemia and is under investigation in multiple clinical trials for the treatment of various cancers. Although venetoclax treatment can result in high rates of durable remission, relapse has been widely observed, indicating the emergence of drug resistance. The G101V mutation in BCL2 is frequently observed in patients who relapsed treated with venetoclax and sufficient to confer resistance to venetoclax by interfering with compound binding. Therefore, the development of next-generation BCL2 inhibitors to overcome drug resistance is urgently needed. In this study, we discovered that sonrotoclax, a potent and selective BCL2 inhibitor, demonstrates stronger cytotoxic activity in various hematologic cancer cells and more profound tumor growth inhibition in multiple hematologic tumor models than venetoclax. Notably, sonrotoclax effectively inhibits venetoclax-resistant BCL2 variants, such as G101V. The crystal structures of wild-type BCL2/BCL2 G101V in complex with sonrotoclax revealed that sonrotoclax adopts a novel binding mode within the P2 pocket of BCL2 and could explain why sonrotoclax maintains stronger potency than venetoclax against the G101V mutant. In summary, sonrotoclax emerges as a potential second-generation BCL2 inhibitor for the treatment of hematologic malignancies with the potential to overcome BCL2 mutation-induced venetoclax resistance. Sonrotoclax is currently under investigation in multiple clinical trials.


Subject(s)
Antineoplastic Agents , Bridged Bicyclo Compounds, Heterocyclic , Drug Resistance, Neoplasm , Hematologic Neoplasms , Proto-Oncogene Proteins c-bcl-2 , Sulfonamides , Proto-Oncogene Proteins c-bcl-2/genetics , Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors , Proto-Oncogene Proteins c-bcl-2/metabolism , Sulfonamides/pharmacology , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Bridged Bicyclo Compounds, Heterocyclic/therapeutic use , Humans , Drug Resistance, Neoplasm/drug effects , Drug Resistance, Neoplasm/genetics , Animals , Hematologic Neoplasms/drug therapy , Hematologic Neoplasms/genetics , Hematologic Neoplasms/pathology , Mice , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Xenograft Model Antitumor Assays , Cell Line, Tumor , Mutation , Apoptosis/drug effects
4.
EMBO Rep ; 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38918502

ABSTRACT

Cellular senescence is a hallmark of advanced age and a major instigator of numerous inflammatory pathologies. While endothelial cell (EC) senescence is aligned with defective vascular functionality, its impact on fundamental inflammatory responses in vivo at single-cell level remain unclear. To directly investigate the role of EC senescence on dynamics of neutrophil-venular wall interactions, we applied high resolution confocal intravital microscopy to inflamed tissues of an EC-specific progeroid mouse model, characterized by profound indicators of EC senescence. Progerin-expressing ECs supported prolonged neutrophil adhesion and crawling in a cell autonomous manner that additionally mediated neutrophil-dependent microvascular leakage. Transcriptomic and immunofluorescence analysis of inflamed tissues identified elevated levels of EC CXCL1 on progerin-expressing ECs and functional blockade of CXCL1 suppressed the dysregulated neutrophil responses elicited by senescent ECs. Similarly, cultured progerin-expressing human ECs exhibited a senescent phenotype, were pro-inflammatory and prompted increased neutrophil attachment and activation. Collectively, our findings support the concept that senescent ECs drive excessive inflammation and provide new insights into the mode, dynamics, and mechanisms of this response at single-cell level.

5.
Mol Microbiol ; 121(4): 781-797, 2024 04.
Article in English | MEDLINE | ID: mdl-38242855

ABSTRACT

Invasive candidiasis caused by non-albicans species has been on the rise, with Candida glabrata emerging as the second most common etiological agent. Candida glabrata possesses an intrinsically lower susceptibility to azoles and an alarming propensity to rapidly develop high-level azole resistance during treatment. In this study, we have developed an efficient piggyBac (PB) transposon-mediated mutagenesis system in C. glabrata to conduct genome-wide genetic screens and applied it to profile genes that contribute to azole resistance. When challenged with the antifungal drug fluconazole, PB insertion into 270 genes led to significant resistance. A large subset of these genes has a role in the mitochondria, including almost all genes encoding the subunits of the F1F0 ATPase complex. We show that deleting ATP3 or ATP22 results in increased azole resistance but does not affect susceptibility to polyenes and echinocandins. The increased azole resistance is due to increased expression of PDR1 that encodes a transcription factor known to promote drug efflux pump expression. Deleting PDR1 in the atp3Δ or atp22Δ mutant resulted in hypersensitivity to fluconazole. Our results shed light on the mechanisms contributing to azole resistance in C. glabrata. This PB transposon-mediated mutagenesis system can significantly facilitate future genome-wide genetic screens.


Subject(s)
Candida glabrata , Fluconazole , Fluconazole/metabolism , Candida glabrata/genetics , Drug Resistance, Fungal/genetics , Antifungal Agents/pharmacology , Azoles , Proton-Translocating ATPases/metabolism , Microbial Sensitivity Tests
6.
Mol Cell ; 66(5): 581-596.e6, 2017 Jun 01.
Article in English | MEDLINE | ID: mdl-28552615

ABSTRACT

The action of DNA topoisomerase II (Top2) creates transient DNA breaks that are normally concealed inside Top2-DNA covalent complexes. Top2 poisons, including ubiquitously present natural compounds and clinically used anti-cancer drugs, trap Top2-DNA complexes. Here, we show that cells actively prevent Top2 degradation to avoid the exposure of concealed DNA breaks. A genome-wide screen revealed that fission yeast cells lacking Rrp2, an Snf2-family DNA translocase, are strongly sensitive to Top2 poisons. Loss of Rrp2 enhances SUMOylation-dependent ubiquitination and degradation of Top2, which in turn increases DNA damage at sites where Top2-DNA complexes are trapped. Rrp2 possesses SUMO-binding ability and prevents excessive Top2 degradation by competing against the SUMO-targeted ubiquitin ligase (STUbL) for SUMO chain binding and by displacing SUMOylated Top2 from DNA. The budding yeast homolog of Rrp2, Uls1, plays a similar role, indicating that this genome protection mechanism is widely employed, a finding with implications for cancer treatment.


Subject(s)
DNA Damage , DNA Topoisomerases, Type II/metabolism , DNA, Fungal/metabolism , DNA-Binding Proteins/metabolism , Genome, Fungal , Genomic Instability , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/enzymology , Sumoylation , DNA Damage/drug effects , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Topoisomerases, Type II/genetics , DNA, Fungal/drug effects , DNA, Fungal/genetics , DNA-Binding Proteins/genetics , Drug Resistance , Etoposide/pharmacology , Genome, Fungal/drug effects , Genomic Instability/drug effects , Mutation , Protein Binding , Protein Interaction Domains and Motifs , Proteolysis , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Schizosaccharomyces/drug effects , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/genetics , Topoisomerase II Inhibitors/pharmacology , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
7.
Proc Natl Acad Sci U S A ; 119(24): e2103615119, 2022 06 14.
Article in English | MEDLINE | ID: mdl-35671424

ABSTRACT

Skeletal muscle atrophy is commonly associated with aging, immobilization, muscle unloading, and congenital myopathies. Generation of mature muscle cells from skeletal muscle satellite cells (SCs) is pivotal in repairing muscle tissue. Exercise therapy promotes muscle hypertrophy and strength. Primary cilium is implicated as the mechanical sensor in some mammalian cells, but its role in skeletal muscle cells remains vague. To determine mechanical sensors for exercise-induced muscle hypertrophy, we established three SC-specific cilium dysfunctional mouse models-Myogenic factor 5 (Myf5)-Arf-like Protein 3 (Arl3)-/-, Paired box protein Pax-7 (Pax7)-Intraflagellar transport protein 88 homolog (Ift88)-/-, and Pax7-Arl3-/--by specifically deleting a ciliary protein ARL3 in MYF5-expressing SCs, or IFT88 in PAX7-expressing SCs, or ARL3 in PAX7-expressing SCs, respectively. We show that the Myf5-Arl3-/- mice develop grossly the same as WT mice. Intriguingly, mechanical stimulation-induced muscle hypertrophy or myoblast differentiation is abrogated in Myf5-Arl3-/- and Pax7-Arl3-/- mice or primary isolated Myf5-Arl3-/- and Pax7-Ift88-/- myoblasts, likely due to defective cilia-mediated Hedgehog (Hh) signaling. Collectively, we demonstrate SC cilia serve as mechanical sensors and promote exercise-induced muscle hypertrophy via Hh signaling pathway.


Subject(s)
Cilia , Muscle Strength , Physical Conditioning, Animal , Satellite Cells, Skeletal Muscle , Animals , Cell Differentiation , Cilia/physiology , Exercise Therapy , Hedgehog Proteins/genetics , Hedgehog Proteins/metabolism , Mice , Muscle Fibers, Skeletal/cytology , Muscle Fibers, Skeletal/physiology , PAX7 Transcription Factor/genetics , PAX7 Transcription Factor/metabolism , Satellite Cells, Skeletal Muscle/cytology , Satellite Cells, Skeletal Muscle/physiology
8.
Proc Natl Acad Sci U S A ; 119(8)2022 Feb 22.
Article in English | MEDLINE | ID: mdl-35165186

ABSTRACT

Solar water splitting is regarded as holding great potential for clean fuels production. However, the efficiency of charge separation/transfer of photocatalysts is still too low for industrial application. This paper describes the synthesis of a Pt-Au binary single-site loaded g-C3N4 nanosheet photocatalyst inspired by the concept of the dipole. The existent larger charge imbalance greatly enhanced the localized molecular dipoles over adjacent Pt-Au sites in contrast to the unary counterparts. The superposition of molecular dipoles then further strengthened the internal electric field and thus promoted the charge transportation dynamics. In the modeling photocatalytic hydrogen evolution, the optimal Pt-Au binary site photocatalysts (0.25% loading) showed 4.9- and 2.3-fold enhancement of performance compared with their Pt and Au single-site counterparts, respectively. In addition, the reaction barrier over the Pt-Au binary sites was lowered, promoting the hydrogen evolution process. This work offers a valuable strategy for improving photocatalytic charge transportation dynamics by constructing polynary single sites.

9.
Glia ; 2024 May 24.
Article in English | MEDLINE | ID: mdl-38785370

ABSTRACT

We have previously shown that phosphodiesterase 4 (PDE4) inhibition protects against neuronal injury in rats following middle cerebral artery occlusion/reperfusion (MCAO/R). However, the effects of PDE4 on brain edema and astrocyte swelling are unknown. In this study, we showed that inhibition of PDE4 by Roflumilast (Roflu) reduced brain edema and brain water content in rats subjected to MCAO/R. Roflu decreased the expression of aquaporin 4 (AQP4), while the levels of phosphorylated protein kinase B (Akt) and forkhead box O3a (FoxO3a) were increased. In addition, Roflu reduced cell volume and the expression of AQP4 in primary astrocytes undergoing oxygen and glucose deprivation/reoxygenation (OGD/R). Consistently, PDE4B knockdown showed similar effects as PDE4 inhibition; and PDE4B overexpression rescued the inhibitory role of PDE4B knockdown on AQP4 expression. We then found that the effects of Roflu on the expression of AQP4 and cell volume were blocked by the Akt inhibitor MK2206. Since neuroinflammation and astrocyte activation are the common events that are observed in stroke, we treated primary astrocytes with interleukin-1ß (IL-1ß). Astrocytes treated with IL-1ß showed decreased AQP4 and phosphorylated Akt and FoxO3a. Roflu significantly reduced AQP4 expression, which was accompanied by increased phosphorylation of Akt and FoxO3a. Furthermore, overexpression of FoxO3a partly reversed the effect of Roflu on AQP4 expression. Our findings suggest that PDE4 inhibition limits ischemia-induced brain edema and astrocyte swelling via the Akt/FoxO3a/AQP4 pathway. PDE4 is a promising target for the intervention of brain edema after cerebral ischemia.

10.
Neurobiol Dis ; 193: 106440, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38369213

ABSTRACT

Limited treatment options have been shown to alter the natural course of constipation-predominant irritable bowel syndrome (IBS-C). Therefore, safer and more effective approaches are urgently needed. We investigated the effects of transcutaneous auricular vagus nerve stimulation (taVNS) in a mouse model of IBS-C. In the current study, C57BL/6 mice were randomly divided into normal control, IBS-C model control, sham-electrostimulation (sham-ES), taVNS, and drug treatment groups. The effects of taVNS on fecal pellet number, fecal water content, and gastrointestinal transit were evaluated in IBS-C model mice. We assessed the effect of taVNS on visceral hypersensitivity using the colorectal distention test. 16S rRNA sequencing was used to analyze the fecal microbiota of the experimental groups. First, we found that taVNS increased fecal pellet number, fecal water content, and gastrointestinal transit in IBS-C model mice compared with the sham-ES group. Second, taVNS significantly decreased the abdominal withdrawal reflex (AWR) score compared with the sham-ES group, thus relieving visceral hyperalgesia. Third, the gut microbiota outcomes showed that taVNS restored Lactobacillus abundance while increasing Bifidobacterium probiotic abundance at the genus level. Notably, taVNS increased the number of c-kit-positive interstitial cells of Cajal (ICC) in the myenteric plexus region in IBS-C mice compared with the sham-ES group. Therefore, our study indicated that taVNS effectively ameliorated IBS-C in the gut microbiota and ICC.


Subject(s)
Irritable Bowel Syndrome , Vagus Nerve Stimulation , Mice , Animals , Irritable Bowel Syndrome/therapy , Irritable Bowel Syndrome/microbiology , RNA, Ribosomal, 16S , Mice, Inbred C57BL , Disease Models, Animal , Constipation/etiology , Constipation/therapy , Water , Vagus Nerve
11.
Crit Rev Eukaryot Gene Expr ; 34(4): 13-23, 2024.
Article in English | MEDLINE | ID: mdl-38505869

ABSTRACT

Lung adenocarcinoma (LUAD) severely affects human health, and cisplatin (DDP) resistance is the main obstacle in LUAD treatment, the mechanism of which is unknown. Bioinformatics methods were utilized to predict expression and related pathways of AURKB in LUAD tissues, as well as the upstream regulated microRNAs. qRT-PCR assayed expression of AURKB and microRNA-486-5p. RIP and dual-luciferase experiments verified the binding and interaction between the two genes. CCK-8 was used to detect cell proliferation ability and IC50 values. Flow cytometry was utilized to assess the cell cycle. Comet assay and western blot tested DNA damage and γ-H2AX protein expression, respectively. In LUAD, AURKB was upregulated, but microRNA-486-5p was downregulated. The targeted relationship between the two was confirmed by RIP and dual-luciferase experiments. Cell experiments showed that AURKB knock-down inhibited cell proliferation, reduced IC50 values, induced cell cycle arrest, and caused DNA damage. The rescue experiment presented that high expression of microRNA-486-5p could weaken the impact of AURKB overexpression on LUAD cell behavior and DDP resistance. microRNA-486-5p regulated DNA damage to inhibit DDP resistance in LUAD by targeting AURKB, implying that microRNA-486-5p/AURKB axis may be a possible therapeutic target for DDP resistance in LUAD patients.


Subject(s)
Adenocarcinoma of Lung , Lung Neoplasms , MicroRNAs , Humans , Cisplatin/pharmacology , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/genetics , DNA Damage , MicroRNAs/genetics , Cell Proliferation , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Luciferases , Cell Line, Tumor , Aurora Kinase B
12.
Biochem Biophys Res Commun ; 711: 149888, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38603833

ABSTRACT

OBJECTIVE: To investigate the effect of intermittent parathyroid hormone (iPTH) administration on pathological new bone formation during treatment of ankylosing spondylitis-related osteoporosis. METHODS: Animal models with pathological bone formation caused by hypothetical AS pathogenesis received treatment with iPTH. We determined the effects of iPTH on bone loss and the formation of pathological new bone with micro-computed tomography (micro-CT) and histological examination. In addition, the tamoxifen-inducible conditional knockout mice (CAGGCre-ERTM; PTHflox/flox, PTH-/-) was established to delete PTH and investigate the effect of endogenous PTH on pathological new bone formation. RESULTS: iPTH treatment significantly improved trabecular bone mass in the modified collagen-induced arthritis (m-CIA) model and unbalanced mechanical loading models. Meanwhile, iPTH treatment did not enhance pathological new bone formation in all types of animal models. Endogenous PTH deficiency had no effects on pathological new bone formation in unbalanced mechanical loading models. CONCLUSION: Experimental animal models of AS treated with iPTH show improvement in trabecular bone density, but not entheseal pathological bone formation,indicating it may be a potential treatment for inflammatory bone loss does in AS.


Subject(s)
Osteogenesis , Parathyroid Hormone , Animals , Parathyroid Hormone/administration & dosage , Parathyroid Hormone/pharmacology , Parathyroid Hormone/therapeutic use , Osteogenesis/drug effects , Mice , Osteoporosis/drug therapy , Osteoporosis/pathology , Mice, Knockout , Male , X-Ray Microtomography , Spondylitis, Ankylosing/drug therapy , Spondylitis, Ankylosing/pathology , Mice, Inbred C57BL , Disease Models, Animal , Arthritis, Experimental/drug therapy , Arthritis, Experimental/pathology , Bone Density/drug effects
13.
Small ; : e2400487, 2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38537118

ABSTRACT

Hierarchical polyimides (PIs) not only show outstanding thermal stability and high mechanical strength but also have great advantages in terms of microstructure and surface area, which makes them highly valuable in various fields such as aerospace, microelectronics, adsorption, catalysis, and energy storage. However, great challenges still remain in the synthesis of hierarchical PIs with well-defined microstructure. Herein, polyamide acid salts (PAAS) with tunable ionization degree are synthesized first via the polymerization of dianhydride and diamine monomers in deionized water with 1,2-dimethylimidazole (DMIZ). Then cationic cetyltrimethylammonium chloride (CTAC) is added to the PAAS aqueous solution to induce the formation of polyelectrolyte-surfactant complexes based on electrostatic interaction. After a typical hydrothermal reaction (HTR) procedure, hierarchical PIs with different microstructures such as urchin-like PI microparticles, flower-like PI microparticles, and lamellar PI petals can be fabricated simply by changing the additive amount of DMIZ and CTAC. The nanostructure self-assemblies of PAAS are dominated by the charges on macromolecular chains and the formation of hierarchical structures of polymers is ascribed to a geometrical selection process during crystal growth. This work provides valuable insights into the self-assembly behaviors of polyelectrolyte systems for synthesizing well-defined hierarchical polymers.

14.
Theor Appl Genet ; 137(3): 59, 2024 Feb 26.
Article in English | MEDLINE | ID: mdl-38407588

ABSTRACT

KEY MESSAGE: GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.


Subject(s)
Aspartic Acid Proteases , Gossypium/genetics , Cotton Fiber , Phenotype
15.
Syst Biol ; 2023 Dec 29.
Article in English | MEDLINE | ID: mdl-38157277

ABSTRACT

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which - in combination - support the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

16.
Arch Microbiol ; 206(5): 237, 2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38678508

ABSTRACT

Invasive fungal infections (IFIs) are common and life-threatening complications in post-hematopoietic stem cell transplantation (post-HSCT) recipients, Severe IFIs can lead to systemic infection and organ damage, which results in high mortality in HSCT recipients. With the development of the field of fungal infection diagnosis, more and more advanced non-culture diagnostic tools have been developed, such as glip biosensors, metagenomic next-generation sequencing, Magnetic Nanoparticles and Identified Using SERS via AgNPs+ , and artificial intelligence-assisted diagnosis. The advanced diagnostic approaches contribute to the success of HSCT and improve the overall survival of post-HSCT leukemia patients by supporting therapeutical decisions. This review provides an overview of the characteristics of two high-incidence IFIs in post-HSCT recipients and discusses some of the recently developed IFI detection technologies. Additionally, it explores the potential application of cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) technology for IFI detection. The aim is to offer insights into selecting appropriate IFI detection methods and gaining an understanding of novel fungal diagnostic approaches in laboratory settings.


Subject(s)
Hematopoietic Stem Cell Transplantation , Invasive Fungal Infections , Humans , Hematopoietic Stem Cell Transplantation/adverse effects , Invasive Fungal Infections/diagnosis , Fluorescence Resonance Energy Transfer , High-Throughput Nucleotide Sequencing , Biosensing Techniques/methods
17.
Anim Cogn ; 27(1): 8, 2024 Mar 02.
Article in English | MEDLINE | ID: mdl-38429588

ABSTRACT

Predation risk may affect the foraging behavior of birds. However, there has been little research on the ability of domestic birds to perceive predation risk and thus adjust their feeding behavior. In this study, we tested whether domestic budgerigars (Melopsittacus undulatus) perceived predation risk after the presentation of specimens and sounds of sparrowhawks (Accipiter nisus), domestic cats (Felis catus), and humans, and whether this in turn influenced their feeding behavior. When exposed to visual or acoustic stimuli, budgerigars showed significantly longer latency to feed under sparrowhawk, domestic cat, and human treatments than with controls. Budgerigars responded more strongly to acoustic stimuli than visual stimuli, and they showed the longest latency to feed and the least number of feeding times in response to sparrowhawk calls. Moreover, budgerigars showed shorter latency to feed and greater numbers of feeding times in response to human voices than to sparrowhawk or domestic cat calls. Our results suggest that domestic budgerigars may identify predation risk through visual or acoustic signals and adjust their feeding behavior accordingly.


Subject(s)
Auditory Perception , Melopsittacus , Humans , Animals , Cats , Auditory Perception/physiology , Melopsittacus/physiology , Predatory Behavior , Acoustics , Sound
18.
World J Urol ; 42(1): 360, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38811391

ABSTRACT

PURPOSE: To estimate the incidences of left renal vein (LRV) entrapment by right renal artery (RRA), a phenomenon primarily reported as case reports. METHODS: The cross-sectional study consecutively screened renal vessel CT data of 38 (Renal) patients with nephropathy and 305 (Non-renal) patients with peripheral arterial diseases in a teaching hospital in northeast China between November 2018 and March 2023. The LRV compression by adjacent anatomical structures, including but not limited to RRA and multiple compression-related parameters, were investigated through multiplanar analysis of the CT data. RESULTS: The overall LRV entrapment rates by adjacent structures were 41.93% (12/31) and 24.00% (6/25), the rates of RRA-sourced LRV compression 22.58% (7/31) and 20.00% (5/25), and the rates of compression by superior mesenteric artery (SMA) 16.13% (5/31) and 4.00% (1/25) in the Renal and Non-renal groups, respectively, with no significance. The venous segments distal to the RRA-compressed site had a significantly larger transectional lumen area than those of the non-compressed veins in both groups (3.09 ± 1.29 vs. 1.82 ± 0.23, p < 0.001 and 4.30 ± 2.65 vs. 2.12 ± 0.55, p = 0.006; maximum-to-minimum area ratios in Renal and Non-renal groups, respectively). Nearly 80% of RRAs were found arising anteriorly rightwards instead of passing straight to the right. CONCLUSION: RRA-sourced LRV compression was not rare, and its incidence was higher than that of the compression by SMA in both patient cohorts. RRA could be a more common compression source than SMA concerning LRV entrapment. Further investigations involving different populations, including healthy individuals, are needed.


Subject(s)
Renal Artery , Renal Veins , Humans , Cross-Sectional Studies , Middle Aged , Male , Female , Renal Veins/diagnostic imaging , Renal Veins/abnormalities , Aged , Renal Artery/diagnostic imaging , Adult , Tomography, X-Ray Computed , Renal Nutcracker Syndrome/complications , Renal Nutcracker Syndrome/diagnostic imaging , Incidence
19.
EMBO Rep ; 23(6): e54275, 2022 06 07.
Article in English | MEDLINE | ID: mdl-35437924

ABSTRACT

Our understanding of human hepatocellular carcinoma (HCC) development and progression has been hampered by the lack of in vivo models. We performed a genetic screen of 10 oncogenes and genetic mutations in Fah-ablated immunodeficient mice in which primary human hepatocytes (PHHs) are used to reconstitute a functional human liver. We identified that MYC, TP53R249S , and KRASG12D are highly expressed in induced HCC (iHCC) samples. The overexpression of MYC and TP53R249S transform PHHs into iHCC in situ, though the addition of KRASG12D significantly increases the tumorigenic efficiency. iHCC, which recapitulate the histological architecture and gene expression characteristics of clinical HCC samples, reconstituted HCC after serial transplantations. Transcriptomic analysis of iHCC and PHHs showed that MUC1 and FAP are expressed in iHCC but not in normal livers. Chimeric antigen receptor (CAR) T cells against these two surface markers efficiently lyse iHCC cells. The properties of iHCC model provide a biological basis for several clinical hallmarks of HCC, and iHCC may serve as a model to study HCC initiation and to identify diagnostic biomarkers and targets for cellular immunotherapy.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Animals , Carcinoma, Hepatocellular/genetics , Hepatocytes , Humans , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Mice , Proto-Oncogene Proteins p21(ras)
20.
Int Arch Occup Environ Health ; 97(2): 189-197, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38156995

ABSTRACT

PURPOSE: The air health index (AHI) captures the combined effects of air pollution and non-optimal temperatures and helps assess the atmospheric environment's overall health risk. Shandong Province is a crucial industrial base in China, and the health effects of air pollution and non-optimal temperature cannot be ignored. To construct an AHI for Shandong Province and assess the district-level mortality burden due to AHI in the study area. METHODS: Daily district-specific mortality, meteorological, and air pollution data over 2013-2018 were collected in Shandong Province, China. The AHI construction eventually incorporated PM2.5 and NO2, O3, and non-optimal temperatures. Attributable fraction (AF) and attributable number (AN) were used to estimate the district-specific mortality burden attributable to AHI. RESULTS: The average AHI value observed in Shandong Province was 6. Our research revealed a positive association between the total AHI and total mortality, with an overall trend of a slow increase followed by a rapid increase. The exposure-response curves, when stratified by gender, age, and cause of death, were approximately consistent with the overall trend. The provincial attributable fraction (AF) was 5.31% (95% CI 4.58%, 5.91%), and the attributable number (AN) was 188,246 (95% CI 162,396, 209,533). Overall, higher ANs mainly appeared in the southwestern area, while higher values of AF were observed in the central-eastern and central-northern areas. CONCLUSIONS: The air health index performs well in predicting death burden and can convey health risks related to exposure to the ambient environment to the public.


Subject(s)
Air Pollutants , Air Pollution , Humans , Air Pollutants/adverse effects , Air Pollutants/analysis , Temperature , Particulate Matter/analysis , Air Pollution/adverse effects , Air Pollution/analysis , China/epidemiology , Environmental Exposure/adverse effects , Environmental Exposure/analysis
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