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1.
Nature ; 625(7996): 822-831, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37783228

ABSTRACT

Argonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids1,2. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used by short pAgos remains elusive. Here we determined the cryo-electron microscopy structures of a short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA; a guide RNA-target DNA-loaded Crt-SPARTA; two Crt-SPARTA dimers with distinct TIR organization; and a Crt-SPARTA tetramer. These structures reveal that Crt-SPARTA is composed of a bilobal-fold Ago lobe that connects with a TIR lobe. Whereas the Crt-Ago contains a MID and a PIWI domain, Crt-TIR-APAZ has a TIR domain, an N-like domain, a linker domain and a trigger domain. The bound RNA-DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the trigger domain acts as a 'roadblock' that prevents the guide RNA 5' ends and the target DNA 3' ends from reaching their canonical pockets; this disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA-DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR domains assemble into two parallel head-to-tail-organized TIR dimers, indicating an NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short-pAgo-mediated defence against invading nucleic acids, and provide insights for optimizing the detection of SPARTA-based programmable DNA sequences.


Subject(s)
Argonaute Proteins , Cryoelectron Microscopy , NAD+ Nucleosidase , Nucleic Acids , Argonaute Proteins/chemistry , Argonaute Proteins/metabolism , Argonaute Proteins/ultrastructure , DNA/chemistry , DNA/genetics , DNA/metabolism , DNA/ultrastructure , Enzyme Activation , NAD+ Nucleosidase/chemistry , NAD+ Nucleosidase/genetics , NAD+ Nucleosidase/metabolism , NAD+ Nucleosidase/ultrastructure , Nucleic Acid Conformation , Nucleic Acids/metabolism , Protein Conformation , RNA, Guide, CRISPR-Cas Systems , Mutagenesis
2.
Mol Cell ; 81(6): 1200-1215.e9, 2021 03 18.
Article in English | MEDLINE | ID: mdl-33639093

ABSTRACT

Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.


Subject(s)
Escherichia coli Proteins , Evolution, Molecular , Genetic Loci , Hydro-Lyases , Monomeric GTP-Binding Proteins , Ribosome Subunits, Large, Bacterial , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Hydro-Lyases/chemistry , Hydro-Lyases/genetics , Hydro-Lyases/metabolism , Monomeric GTP-Binding Proteins/chemistry , Monomeric GTP-Binding Proteins/genetics , Monomeric GTP-Binding Proteins/metabolism , Ribosome Subunits, Large, Bacterial/chemistry , Ribosome Subunits, Large, Bacterial/genetics , Ribosome Subunits, Large, Bacterial/metabolism
3.
Cell ; 153(6): 1327-39, 2013 Jun 06.
Article in English | MEDLINE | ID: mdl-23746844

ABSTRACT

The transcription factor HIF1A is a key mediator of the cellular response to hypoxia. Despite the importance of HIF1A in homeostasis and various pathologies, little is known about how it regulates RNA polymerase II (RNAPII). We report here that HIF1A employs a specific variant of the Mediator complex to stimulate RNAPII elongation. The Mediator-associated kinase CDK8, but not the paralog CDK19, is required for induction of many HIF1A target genes. HIF1A induces binding of CDK8-Mediator and the super elongation complex (SEC), containing AFF4 and CDK9, to alleviate RNAPII pausing. CDK8 is dispensable for HIF1A chromatin binding and histone acetylation, but it is essential for binding of SEC and RNAPII elongation. Global analysis of active RNAPII reveals that hypoxia-inducible genes are paused and active prior to their induction. Our results provide a mechanistic link between HIF1A and CDK8, two potent oncogenes, in the cellular response to hypoxia.


Subject(s)
Cell Hypoxia , Cyclin-Dependent Kinase 8/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Mediator Complex/metabolism , Neoplasms/metabolism , RNA Polymerase II/metabolism , Transcription Elongation, Genetic , Acetylation , Cell Line, Tumor , Cyclin-Dependent Kinase 8/chemistry , Cyclin-Dependent Kinases/metabolism , HeLa Cells , Histones/metabolism , Humans
4.
Mol Cell ; 79(5): 824-835.e5, 2020 09 03.
Article in English | MEDLINE | ID: mdl-32649882

ABSTRACT

DNA-protein crosslinks (DPCs) are highly toxic DNA lesions that threaten genomic integrity. Recent findings highlight that SPRTN, a specialized DNA-dependent metalloprotease, is a central player in proteolytic cleavage of DPCs. Previous studies suggest that SPRTN deubiquitination is important for its chromatin association and activation. However, the regulation and consequences of SPRTN deubiquitination remain unclear. Here we report that, in response to DPC induction, the deubiquitinase VCPIP1/VCIP135 is phosphorylated and activated by ATM/ATR. VCPIP1, in turn, deubiquitinates SPRTN and promotes its chromatin relocalization. Deubiquitination of SPRTN is required for its subsequent acetylation, which promotes SPRTN relocation to the site of chromatin damage. Furthermore, Vcpip1 knockout mice are prone to genomic instability and premature aging. We propose a model where two sequential post-translational modifications (PTMs) regulate SPRTN chromatin accessibility to repair DPCs and maintain genomic stability and a healthy lifespan.


Subject(s)
Aging/genetics , DNA Repair , DNA-Binding Proteins/metabolism , Acetylation , Aging/metabolism , Animals , Cell Line , DNA Damage , DNA-Binding Proteins/genetics , Deubiquitinating Enzymes/metabolism , Endopeptidases/metabolism , Female , Genomic Instability , HEK293 Cells , Humans , Male , Mice, Inbred C57BL , Mice, Knockout , Phosphorylation , Protein Domains , Protein Processing, Post-Translational , Ubiquitination
5.
Mol Cell ; 74(6): 1215-1226.e4, 2019 06 20.
Article in English | MEDLINE | ID: mdl-31053471

ABSTRACT

Programmed death ligand 1 (PD-L1, also called B7-H1) is an immune checkpoint protein that inhibits immune function through its binding of the programmed cell death protein 1 (PD-1) receptor. Clinically approved antibodies block extracellular PD-1 and PD-L1 binding, yet the role of intracellular PD-L1 in cancer remains poorly understood. Here, we discovered that intracellular PD-L1 acts as an RNA binding protein that regulates the mRNA stability of NBS1, BRCA1, and other DNA damage-related genes. Through competition with the RNA exosome, intracellular PD-L1 protects targeted RNAs from degradation, thereby increasing cellular resistance to DNA damage. RNA immunoprecipitation and RNA-seq experiments demonstrated that PD-L1 regulates RNA stability genome-wide. Furthermore, we developed a PD-L1 antibody, H1A, which abrogates the interaction of PD-L1 with CMTM6, thereby promoting PD-L1 degradation. Intracellular PD-L1 may be a potential therapeutic target to enhance the efficacy of radiotherapy and chemotherapy in cancer through the inhibition of DNA damage response and repair.


Subject(s)
B7-H1 Antigen/genetics , DNA Repair , DNA, Neoplasm/genetics , Exosome Multienzyme Ribonuclease Complex/genetics , Gene Expression Regulation, Neoplastic , Programmed Cell Death 1 Receptor/genetics , Animals , Antineoplastic Agents/pharmacology , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/metabolism , BRCA1 Protein/genetics , BRCA1 Protein/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Cisplatin/pharmacology , DNA Damage , DNA, Neoplasm/metabolism , Exosome Multienzyme Ribonuclease Complex/metabolism , Gamma Rays/therapeutic use , HCT116 Cells , HeLa Cells , Humans , MARVEL Domain-Containing Proteins , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice , Myelin Proteins , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Programmed Cell Death 1 Receptor/metabolism , Proteolysis/drug effects , Proteolysis/radiation effects , RNA Stability/drug effects , RNA Stability/radiation effects , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Xenograft Model Antitumor Assays
6.
Mol Cell ; 70(5): 881-893.e3, 2018 06 07.
Article in English | MEDLINE | ID: mdl-29883607

ABSTRACT

The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway.


Subject(s)
Escherichia coli/metabolism , RNA, Bacterial/metabolism , RNA, Ribosomal, 23S/metabolism , Ribosome Subunits, Large, Bacterial/metabolism , Cryoelectron Microscopy , Escherichia coli/genetics , Escherichia coli/ultrastructure , Models, Molecular , Nucleic Acid Conformation , Protein Conformation , RNA, Bacterial/genetics , RNA, Bacterial/ultrastructure , RNA, Ribosomal, 23S/genetics , RNA, Ribosomal, 23S/ultrastructure , Ribosome Subunits, Large, Bacterial/genetics , Ribosome Subunits, Large, Bacterial/ultrastructure , Structure-Activity Relationship
7.
Nucleic Acids Res ; 51(13): 7053-7070, 2023 07 21.
Article in English | MEDLINE | ID: mdl-37293979

ABSTRACT

Schlafen11 (SLFN11) is one of the most studied Schlafen proteins that plays vital roles in cancer therapy and virus-host interactions. Herein, we determined the crystal structure of the Sus scrofa SLFN11 N-terminal domain (NTD) to 2.69 Å resolution. sSLFN11-NTD is a pincer-shaped molecule that shares an overall fold with other SLFN-NTDs but exhibits distinct biochemical characteristics. sSLFN11-NTD is a potent RNase cleaving type I and II tRNAs and rRNAs, and with preference to type II tRNAs. Consistent with the codon usage-based translation suppression activity of SLFN11, sSLFN11-NTD cleaves synonymous serine and leucine tRNAs with different efficiencies in vitro. Mutational analysis revealed key determinates of sSLFN11-NTD nucleolytic activity, including the Connection-loop, active site, and key residues essential for substrate recognition, among which E42 constrains sSLFN11-NTD RNase activity, and all nonconservative mutations of E42 stimulated RNase activities. sSLFN11 inhibited the translation of proteins with a low codon adaptation index in cells, which mainly dependent on the RNase activity of the NTD because E42A enhanced the inhibitory effect, but E209A abolished inhibition. Our findings provide structural characterization of an important SLFN11 protein and expand our understanding of the Schlafen family.


Subject(s)
Nuclear Proteins , RNA, Transfer , Ribonucleases , Catalytic Domain , Mutation , Ribonucleases/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolism , Sus scrofa , Nuclear Proteins/metabolism , Animals
8.
Breast Cancer Res ; 26(1): 75, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38720366

ABSTRACT

BACKGROUND: Tumor-associated macrophages (TAMs) are a prominent immune subpopulation in the tumor microenvironment that could potentially serve as therapeutic targets for breast cancer. Thus, it is important to characterize this cell population across different tumor subtypes including patterns of association with demographic and prognostic factors, and breast cancer outcomes. METHODS: We investigated CD163+ macrophages in relation to clinicopathologic variables and breast cancer outcomes in the Women's Circle of Health Study and Women's Circle of Health Follow-up Study populations of predominantly Black women with breast cancer. We evaluated 611 invasive breast tumor samples (507 from Black women, 104 from White women) with immunohistochemical staining of tissue microarray slides followed by digital image analysis. Multivariable Cox proportional hazards models were used to estimate hazard ratios for overall survival (OS) and breast cancer-specific survival (BCSS) for 546 cases with available survival data (median follow-up time 9.68 years (IQR: 7.43-12.33). RESULTS: Women with triple-negative breast cancer showed significantly improved OS in relation to increased levels of tumor-infiltrating CD163+ macrophages in age-adjusted (Q3 vs. Q1: HR = 0.36; 95% CI 0.16-0.83) and fully adjusted models (Q3 vs. Q1: HR = 0.30; 95% CI 0.12-0.73). A similar, but non-statistically significant, association was observed for BCSS. Macrophage infiltration in luminal and HER2+ tumors was not associated with OS or BCSS. In a multivariate regression model that adjusted for age, subtype, grade, and tumor size, there was no significant difference in CD163+ macrophage density between Black and White women (RR = 0.88; 95% CI 0.71-1.10). CONCLUSIONS: In contrast to previous studies, we observed that higher densities of CD163+ macrophages are independently associated with improved OS and BCSS in women with invasive triple-negative breast cancer. Trial registration Not applicable.


Subject(s)
Antigens, CD , Antigens, Differentiation, Myelomonocytic , Receptors, Cell Surface , Triple Negative Breast Neoplasms , Tumor Microenvironment , Humans , Female , Tumor Microenvironment/immunology , Antigens, Differentiation, Myelomonocytic/metabolism , Antigens, CD/metabolism , Middle Aged , Receptors, Cell Surface/metabolism , Triple Negative Breast Neoplasms/mortality , Triple Negative Breast Neoplasms/pathology , Triple Negative Breast Neoplasms/immunology , Triple Negative Breast Neoplasms/metabolism , Follow-Up Studies , Prognosis , Adult , Tumor-Associated Macrophages/metabolism , Tumor-Associated Macrophages/immunology , Macrophages/metabolism , Macrophages/immunology , Macrophages/pathology , Aged , Biomarkers, Tumor/metabolism , Proportional Hazards Models
9.
Am J Epidemiol ; 193(9): 1242-1252, 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-38775277

ABSTRACT

Limited estimates exist on risk factors for epithelial ovarian cancer (EOC) in Asian, Hispanic, and Native Hawaiian/Pacific Islander women. Participants in this study included 1734 Asian (n = 785 case and 949 control participants), 266 Native Hawaiian/Pacific Islander (n = 99 case and 167 control participants), 1149 Hispanic (n = 505 case and 644 control participants), and 24 189 White (n = 9981 case and 14 208 control participants) from 11 studies in the Ovarian Cancer Association Consortium. Logistic regression models estimated odds ratios (ORs) and 95% CIs for risk associations by race and ethnicity. Heterogeneity in EOC risk associations by race and ethnicity (P ≤ .02) was observed for oral contraceptive (OC) use, parity, tubal ligation, and smoking. We observed inverse associations with EOC risk for OC use and parity across all groups; associations were strongest in Native Hawaiian/Pacific Islander and Asian women. The inverse association for tubal ligation with risk was most pronounced for Native Hawaiian/Pacific Islander participants (odds ratio (OR) = 0.25; 95% CI, 0.13-0.48) compared with Asian and White participants (OR = 0.68 [95% CI, 0.51-0.90] and OR = 0.78 [95% CI, 0.73-0.85], respectively). Differences in EOC risk factor associations were observed across racial and ethnic groups, which could be due, in part, to varying prevalence of EOC histotypes. Inclusion of greater diversity in future studies is essential to inform prevention strategies. This article is part of a Special Collection on Gynecological Cancers.


Subject(s)
Carcinoma, Ovarian Epithelial , Ovarian Neoplasms , Adult , Aged , Female , Humans , Middle Aged , Asian , Carcinoma, Ovarian Epithelial/ethnology , Carcinoma, Ovarian Epithelial/epidemiology , Case-Control Studies , Contraceptives, Oral/adverse effects , Ethnicity , Hispanic or Latino , Logistic Models , Native Hawaiian or Other Pacific Islander , Odds Ratio , Ovarian Neoplasms/ethnology , Ovarian Neoplasms/epidemiology , Parity , Risk Factors , Smoking/ethnology , Smoking/epidemiology , Sterilization, Tubal/statistics & numerical data , United States/epidemiology , White
10.
Br J Cancer ; 131(6): 1043-1049, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39026080

ABSTRACT

BACKGROUND: Tea and coffee are the most frequently consumed beverages in the world. Green tea in particular contains compounds with potential anti-cancer effects, but its association with survival after ovarian cancer is uncertain. METHODS: We investigated the associations between tea and coffee consumption before diagnosis and survival using data from 10 studies in the Ovarian Cancer Association Consortium. Data on tea (green, black, herbal), coffee and caffeine intake were available for up to 5724 women. We used Cox proportional hazards regression to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CI). RESULTS: Compared with women who did not drink any green tea, consumption of one or more cups/day was associated with better overall survival (aHR = 0.84, 95% CI 0.71-1.00, p-trend = 0.04). A similar association was seen for ovarian cancer-specific survival in five studies with this information (aHR = 0.81, 0.66-0.99, p-trend = 0.045). There was no consistent variation between subgroups defined by clinical or lifestyle characteristics and adjustment for other aspects of lifestyle did not appreciably alter the estimates. We found no evidence of an association between coffee, black or herbal tea, or caffeine intake and survival. CONCLUSION: The observed association with green tea consumption before diagnosis raises the possibility that consumption after diagnosis might improve patient outcomes.


Subject(s)
Coffee , Ovarian Neoplasms , Tea , Humans , Female , Ovarian Neoplasms/mortality , Ovarian Neoplasms/diagnosis , Middle Aged , Aged , Proportional Hazards Models , Adult , Caffeine/administration & dosage
11.
Hum Genet ; 143(3): 331-342, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38478153

ABSTRACT

Accurate discrimination of pathogenic and nonpathogenic variation remains an enormous challenge in clinical genetic testing of inherited retinal diseases (IRDs) patients. Computational methods for predicting variant pathogenicity are the main solutions for this dilemma. The majority of the state-of-the-art variant pathogenicity prediction tools disregard the differences in characteristics among different genes and treat all types of mutations equally. Since missense variants are the most common type of variation in the coding region of the human genome, we developed a novel missense mutation pathogenicity prediction tool, named Prediction of Deleterious Missense Mutation for IRDs (PdmIRD) in this study. PdmIRD was tailored for IRDs-related genes and constructed with the conditional random forest model. Population frequencies and a newly available prediction tool were incorporated into PdmIRD to improve the performance of the model. The evaluation of PdmIRD demonstrated its superior performance over nonspecific tools (areas under the curves, 0.984 and 0.910) and an existing eye abnormalities-specific tool (areas under the curves, 0.975 and 0.891). We also demonstrated the submodel that used a smaller gene panel further slightly improved performance. Our study provides evidence that a disease-specific model can enhance the prediction of missense mutation pathogenicity, especially when new and important features are considered. Additionally, this study provides guidance for exploring the characteristics and functions of the mutated proteins in a greater number of Mendelian disorders.


Subject(s)
Mutation, Missense , Retinal Diseases , Humans , Computational Biology/methods , Genetic Predisposition to Disease , Genetic Testing/methods , Retinal Diseases/diagnosis , Retinal Diseases/genetics
12.
Biochem Biophys Res Commun ; 734: 150732, 2024 11 19.
Article in English | MEDLINE | ID: mdl-39340924

ABSTRACT

This study aims to explore the regulating effect and mechanism of naringenin (NGN) on the hepatic stellate cells (HSCs) apoptosis and its preventive effects on MASH fibrosis. C57BL/6 mice were subjected to either high-fat diet (HFD) plus carbon tetrachloride (CCl4) injection (HFD + CCl4) for 8 weeks to induce a MASH fibrosis model or bile duct ligation (BDL) to establish a liver fibrosis model, NGN was administered by gavage. LX2 cells were stimulated by oleic acid (OA) and lipopolysaccharide (LPS) (OA + LPS) to study the effects of NGN on activated hepatic stellate cell (HSC). Additionally, LO2 cells stimulated with OA + LPS were used to assess the protective effects of NGN on lipotoxicity of hepatocytes. Our in vivo results showed that NGN administration effectively inhibited mouse liver fibrosis in both of the MASH model and BDL model. The in vitro results indicate that NGN directly inhibited HSCs activation and promoted apoptosis of the activated HSCs, while it suppressed the apoptosis of LO2 cells induced by OA + LPS. The underlying mechanisms were mainly elucidated through the reduction of TAK1 phosphorylation, leading to the downregulation of p-JNK and p-ERK expression. This in turn, inhibited the phosphorylation of FoxO3a and promoted the nuclear localization of FoxO3a. Consequently, this may enhance the transcription of apoptosis-related genes, resulting in the apoptosis of activated HSCs. In conclusion, NGN ameliorates MASH fibrosis by enhancing apoptosis of the activated HSCs. The inhibitory effects of NGN on the TAK1/MAPK/FoxO3a pathway were demonstrated as its preventive mechanisms against MASH fibrosis.


Subject(s)
Apoptosis , Flavanones , Forkhead Box Protein O3 , Hepatic Stellate Cells , Liver Cirrhosis , MAP Kinase Kinase Kinases , Animals , Humans , Male , Mice , Apoptosis/drug effects , Carbon Tetrachloride , Cell Line , Flavanones/pharmacology , Flavanones/therapeutic use , Forkhead Box Protein O3/metabolism , Hepatic Stellate Cells/drug effects , Hepatic Stellate Cells/metabolism , Hepatic Stellate Cells/pathology , Liver Cirrhosis/metabolism , Liver Cirrhosis/pathology , Liver Cirrhosis/drug therapy , Liver Cirrhosis/prevention & control , Liver Cirrhosis/chemically induced , MAP Kinase Kinase Kinases/metabolism , MAP Kinase Signaling System/drug effects , Mice, Inbred C57BL , Mitogen-Activated Protein Kinases/metabolism
13.
Small ; 20(1): e2304806, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37649194

ABSTRACT

The sluggish kinetics in Ni-rich cathodes at subzero temperatures causes decreased specific capacity and poor rate capability, resulting in slow and unstable charge storage. So far, the driving force of this phenomenon remains a mystery. Herein, with the help of in-situ X-ray diffraction and time of flight secondary ion mass spectrometry techniques, the continuous accumulation of both the cathode electrolyte interphase (CEI) film formation and the incomplete structure evolution during cycling under subzero temperature are proposed. It is presented that excessively uniform and thick CEI film generated at subzero temperatures would block the diffusion of Li+ -ions, resulting in incomplete phase evolution and clear charge potential delay. The incomplete phase evolution throughout the Li+ -ion intercalation/de-intercalation processes would further cause low depth of discharge and poor electrochemical reversibility with low initial Coulombic efficiency, as well. In addition, the formation of the thick and uniform CEI film would also consume Li+ -ions during the charging process. This discovery highlights the effects of the CEI film formation behavior and incomplete phase evolution in restricting electrochemical kinetics under subzero temperatures, which the authors believe would promote the further application of the Ni-rich cathodes.

14.
PLoS Pathog ; 18(2): e1009862, 2022 02.
Article in English | MEDLINE | ID: mdl-35134095

ABSTRACT

There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3', 5'-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.


Subject(s)
Adenylyl Cyclases/metabolism , Cholesterol/metabolism , Cyclic AMP/metabolism , Mycobacterium tuberculosis/genetics , Animals , Bacterial Proteins/metabolism , Mice, Inbred BALB C , Signal Transduction/physiology , Transcriptional Activation/physiology
15.
New Phytol ; 243(4): 1329-1346, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38898642

ABSTRACT

Drought-induced xylem embolism is a primary cause of plant mortality. Although c. 70% of cycads are threatened by extinction and extant cycads diversified during a period of increasing aridification, the vulnerability of cycads to embolism spread has been overlooked. We quantified the vulnerability to drought-induced embolism, pressure-volume curves, in situ water potentials, and a suite of xylem anatomical traits of leaf pinnae and rachises for 20 cycad species. We tested whether anatomical traits were linked to hydraulic safety in cycads. Compared with other major vascular plant clades, cycads exhibited similar embolism resistance to angiosperms and pteridophytes but were more vulnerable to embolism than noncycad gymnosperms. All 20 cycads had both tracheids and vessels, the proportions of which were unrelated to embolism resistance. Only vessel pit membrane fraction was positively correlated to embolism resistance, contrary to angiosperms. Water potential at turgor loss was significantly correlated to embolism resistance among cycads. Our results show that cycads exhibit low resistance to xylem embolism and that xylem anatomical traits - particularly vessels - may influence embolism resistance together with tracheids. This study highlights the importance of understanding the mechanisms of drought resistance in evolutionarily unique and threatened lineages like the cycads.


Subject(s)
Cycadopsida , Droughts , Plant Leaves , Water , Xylem , Xylem/physiology , Xylem/anatomy & histology , Plant Leaves/anatomy & histology , Plant Leaves/physiology , Cycadopsida/physiology , Cycadopsida/anatomy & histology , Species Specificity
16.
Cytotherapy ; 26(6): 616-631, 2024 06.
Article in English | MEDLINE | ID: mdl-38483361

ABSTRACT

BACKGROUND AIMS: Human pluripotent stem cells, including embryonic stem cells and induced pluripotent stem cells, offer groundbreaking therapeutic potential for degenerative diseases and cellular repair. Despite their significance, a comprehensive bibliometric analysis in this field, particularly in relation to age-related macular degeneration (AMD), is yet to be conducted. This study aims to map the foundational and emerging areas in stem cell and AMD research through bibliometric analysis. METHODS: This study analyzed articles and reviews on stem cells and AMD from 2000 to 2022, sourced from the Web of Science Core Collection. We used VOSviewer and CiteSpace for analysis and visualization of data pertaining to countries, institutions, authors, journals, references and key words. Statistical analyses were conducted using R language and Microsoft Excel 365. RESULTS: In total, 539 publications were included, indicating an increase in global literature on stem cells and AMD from 2000 to 2022. The USA was the leading contributor, with 239 papers and the highest H-index, also the USA had the highest average citation rate per article (59.82). Notably, 50% of the top 10 institutions were from the USA, with the University of California system being the most productive. Key authors included Masayo Takahashi, Michiko Mandai, Dennis Clegg, Pete J. Coffey, Boris Stanzel, and Budd A. Tucker. Investigative Ophthalmology & Visual Science published the majority of relevant papers (n = 27). Key words like "clinical trial," "stem cell therapy," "retinal organoid," and "retinal progenitor cells" were predominant. CONCLUSIONS: Research on stem cells and AMD has grown significantly, highlighting the need for increased global cooperation. Current research prioritizes the relationship between "ipsc," "induced pluripotent stem cell," "cell culture," and "human embryonic stem cell." As stem cell culture and safety have advanced, focus has shifted to prognosis and complications post-transplantation, signifying the movement of stem cell research from labs to clinical settings.


Subject(s)
Bibliometrics , Macular Degeneration , Stem Cell Transplantation , Humans , Embryonic Stem Cells/cytology , Embryonic Stem Cells/transplantation , Induced Pluripotent Stem Cells/cytology , Macular Degeneration/therapy , Stem Cell Transplantation/methods
17.
Pharmacol Res ; 208: 107349, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39151679

ABSTRACT

In future regenerative medicine, far-infrared radiation (FIR) may be an essential component of optical therapy. Many studies have confirmed or validated the efficacy and safety of FIR in various diseases, benefiting from new insights into FIR mechanisms and the excellent performance of many applications. However, the lack of consensus on the biological effects and therapeutic parameters of FIR limits its practical applications in the clinic. In this review, the definition, characteristics, and underlying principles of the FIR are systematically illustrated. We outline the therapeutic parameters of FIR, including the wavelength range, power density, irradiation time, and distance. In addition, the biological effects, potential molecular mechanisms, and preclinical and clinical applications of FIR are discussed. Furthermore, the future development and applications of FIR are described in this review. By applying optimal therapeutic parameters, FIR can influence various cells, animal models, and patients, eliciting diverse underlying mechanisms and offering therapeutic potential for many diseases. FIR could represent a superior alternative with broad prospects for application in future regenerative medicine.


Subject(s)
Infrared Rays , Regenerative Medicine , Regenerative Medicine/methods , Regenerative Medicine/trends , Humans , Animals , Infrared Rays/therapeutic use
18.
Bioorg Med Chem Lett ; 98: 129596, 2024 Jan 15.
Article in English | MEDLINE | ID: mdl-38142914

ABSTRACT

To identify new compounds that can effectively inhibit Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), we screened, synthesized, and evaluated a series of novel aryl fluorosulfate derivatives for their in vitro inhibitory activity against Mtb. Compound 21b exhibited an in vitro minimum inhibitory concentration (MIC) of 0.06 µM against Mtb, no cytotoxicity against both HEK293T and HepG2 mammalian cell lines, and had good in vivo mouse plasma exposure and lung concentration with a 20 mg/kg oral dose, which supports advanced development as a new chemical entity for TB treatment.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis , Animals , Humans , Mice , Antitubercular Agents , HEK293 Cells , Mammals , Microbial Sensitivity Tests , Structure-Activity Relationship , Tuberculosis/drug therapy , Sulfuric Acid Esters/chemistry , Sulfuric Acid Esters/pharmacology
19.
Mol Cell ; 61(4): 614-624, 2016 Feb 18.
Article in English | MEDLINE | ID: mdl-26876938

ABSTRACT

The AMP-activated protein kinase (AMPK) is the master regulator of metabolic homeostasis by sensing cellular energy status. When intracellular ATP levels decrease during energy stress, AMPK is initially activated through AMP or ADP binding and phosphorylation of a threonine residue (Thr-172) within the activation loop of its kinase domain. Here we report a key molecular mechanism by which AMPK activation is amplified under energy stress. We found that ubiquitination on AMPKα blocks AMPKα phosphorylation by LKB1. The deubiquitinase USP10 specifically removes ubiquitination on AMPKα to facilitate AMPKα phosphorylation by LKB1. Under energy stress, USP10 activity in turn is enhanced through AMPK-mediated phosphorylation of Ser76 of USP10. Thus, USP10 and AMPK form a key feedforward loop ensuring amplification of AMPK activation in response to fluctuation of cellular energy status. Disruption of this feedforward loop leads to improper AMPK activation and multiple metabolic defects.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Ubiquitin Thiolesterase/chemistry , Ubiquitin Thiolesterase/metabolism , Animals , Energy Metabolism , Enzyme Activation , HCT116 Cells , HEK293 Cells , Humans , Mice , Phosphorylation , Protein Serine-Threonine Kinases/metabolism , Serine/metabolism , Ubiquitination
20.
Lipids Health Dis ; 23(1): 323, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39350087

ABSTRACT

BACKGROUND: Glaucoma is a leading cause of vision impairment and permanent blindness. Primary open-angle glaucoma (POAG) is a prominent type of primary glaucoma; however, its cause is difficult to determine. This study aimed to analyze the serum lipid profile of Chinese POAG patients and assess its correlation with intraocular pressure (IOP). METHODS: The study included 1,139, 1,248, and 356 Chinese individuals with POAG, primary angle closure glaucoma (PACG), and controls, respectively. Peripheral whole blood samples were collected at the time of diagnosis. Enzymatic colorimetry was used to determine serum levels of different lipids: high-density lipoproteins (HDL), low-density lipoproteins (LDL), triglycerides, cholesterol, and very low-density lipoproteins (VLDL). Additionally, immunoturbidimetry was used to quantify serum levels of apolipoproteins A (APOA), B (APOB), E (APOE), and lipoprotein A [Lp(a)], while intraocular pressure (IOP) was measured in all patients with POAG. RESULTS: After adjusting for age and sex, patients with POAG exhibited elevated serum levels of VLDL, APOA, and APOE but mitigated cholesterol levels compared with the control participants. Significantly lower serum triglyceride, VLDL, and Lp(a) levels were found in patients with PACG than in control participants. Serum cholesterol (P = 0.019; ß = -0.75, 95% confidence interval [CI]: -1.38 - -0.12) and HDL levels (P < 0.001; ß = -2.91, 95% CI: -4.58 - -1.25) were inversely linked to IOP in patients with POAG, after adjusting for age, sex, and ocular metrics. In addition, serum Lp(a) levels were correlated with the average IOP (P = 0.023; ß = -0.0039, 95% CI: -0.0073 - -0.006) and night peak (P = 0.027; ß = -0.0061, 95% CI: -0.0113 - -0.0008) in patients with POAG. CONCLUSIONS: Significantly different serum lipid and lipoprotein profiles were observed in POAG and PACG patients. This study highlighted the differences in serum lipid and lipoprotein levels among Chinese POAG patients and their relationship with IOP and IOP fluctuation. Serum lipid and lipoprotein profiles should be considered while evaluating glaucoma risk.


Subject(s)
Glaucoma, Open-Angle , Intraocular Pressure , Humans , Glaucoma, Open-Angle/blood , Glaucoma, Open-Angle/physiopathology , Male , Female , Middle Aged , Cross-Sectional Studies , Aged , Triglycerides/blood , Lipids/blood , China , Lipoproteins/blood , Glaucoma, Angle-Closure/blood , Glaucoma, Angle-Closure/physiopathology , Apolipoproteins E/blood , Apolipoproteins E/genetics , Adult , Cholesterol/blood , Apolipoproteins A/blood , East Asian People
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