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1.
Circ Res ; 135(2): 301-313, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38860363

ABSTRACT

BACKGROUND: The tumor suppressor and proapoptotic transcription factor P53 is induced (and activated) in several forms of heart failure, including cardiotoxicity and dilated cardiomyopathy; however, the precise mechanism that coordinates its induction with accessibility to its transcriptional promoter sites remains unresolved, especially in the setting of mature terminally differentiated (nonreplicative) cardiomyocytes. METHODS: Male and female control or TRIM35 (tripartite motif containing 35) overexpression adolescent (aged 1-3 months) and adult (aged 4-6 months) transgenic mice were used for all in vivo experiments. Primary adolescent or adult mouse cardiomyocytes were isolated from control or TRIM35 overexpression transgenic mice for all in vitro experiments. Adenovirus or small-interfering RNA was used for all molecular experiments to overexpress or knockdown, respectively, target genes in primary mouse cardiomyocytes. Patient dilated cardiomyopathy or nonfailing left ventricle samples were used for translational and mechanistic insight. Chromatin immunoprecipitation and DNA sequencing or quantitative real-time polymerase chain reaction (qPCR) was used to assess P53 binding to its transcriptional promoter targets, and RNA sequencing was used to identify disease-specific signaling pathways. RESULTS: Here, we show that E3-ubiquitin ligase TRIM35 can directly monoubiquitinate lysine-120 (K120) on histone 2B in postnatal mature cardiomyocytes. This epigenetic modification was sufficient to promote chromatin remodeling, accessibility of P53 to its transcriptional promoter targets, and elongation of its transcribed mRNA. We found that increased P53 transcriptional activity (in cardiomyocyte-specific Trim35 overexpression transgenic mice) was sufficient to initiate heart failure and these molecular findings were recapitulated in nonischemic human LV dilated cardiomyopathy samples. CONCLUSIONS: These findings suggest that TRIM35 and the K120Ub-histone 2B epigenetic modification are molecular features of cardiomyocytes that can collectively predict dilated cardiomyopathy pathogenesis.


Subject(s)
Heart Failure , Histones , Mice, Transgenic , Myocytes, Cardiac , Tumor Suppressor Protein p53 , Ubiquitination , Animals , Myocytes, Cardiac/metabolism , Heart Failure/metabolism , Heart Failure/genetics , Heart Failure/pathology , Humans , Male , Mice , Female , Histones/metabolism , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , Cells, Cultured , Cardiomyopathy, Dilated/metabolism , Cardiomyopathy, Dilated/genetics , Cardiomyopathy, Dilated/pathology , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Promoter Regions, Genetic , Mice, Inbred C57BL
2.
Nature ; 583(7818): 752-759, 2020 07.
Article in English | MEDLINE | ID: mdl-32728242

ABSTRACT

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.


Subject(s)
DNA Methylation , Epigenome , Fetus/embryology , Fetus/metabolism , Animals , Animals, Newborn , Chromatin/genetics , Chromatin/metabolism , Disease/genetics , Down-Regulation , Enhancer Elements, Genetic/genetics , Epigenetic Repression , Female , Gene Silencing , Humans , Mice , Mice, Inbred C57BL , Models, Animal , Molecular Sequence Annotation , Polymorphism, Single Nucleotide , Spatio-Temporal Analysis
3.
Nature ; 583(7818): 744-751, 2020 07.
Article in English | MEDLINE | ID: mdl-32728240

ABSTRACT

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.


Subject(s)
Chromatin/genetics , Chromatin/metabolism , Datasets as Topic , Fetal Development/genetics , Histones/metabolism , Molecular Sequence Annotation , Regulatory Sequences, Nucleic Acid/genetics , Animals , Chromatin/chemistry , Chromatin Immunoprecipitation Sequencing , Disease/genetics , Enhancer Elements, Genetic/genetics , Female , Gene Expression Regulation, Developmental/genetics , Genetic Variation , Histones/chemistry , Humans , Male , Mice , Mice, Inbred C57BL , Organ Specificity/genetics , Reproducibility of Results , Transposases/metabolism
4.
Nature ; 586(7830): 572-577, 2020 10.
Article in English | MEDLINE | ID: mdl-32726802

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a respiratory disease called coronavirus disease 2019 (COVID-19), the spread of which has led to a pandemic. An effective preventive vaccine against this virus is urgently needed. As an essential step during infection, SARS-CoV-2 uses the receptor-binding domain (RBD) of the spike protein to engage with the receptor angiotensin-converting enzyme 2 (ACE2) on host cells1,2. Here we show that a recombinant vaccine that comprises residues 319-545 of the RBD of the spike protein induces a potent functional antibody response in immunized mice, rabbits and non-human primates (Macaca mulatta) as early as 7 or 14 days after the injection of a single vaccine dose. The sera from the immunized animals blocked the binding of the RBD to ACE2, which is expressed on the cell surface, and neutralized infection with a SARS-CoV-2 pseudovirus and live SARS-CoV-2 in vitro. Notably, vaccination also provided protection in non-human primates to an in vivo challenge with SARS-CoV-2. We found increased levels of RBD-specific antibodies in the sera of patients with COVID-19. We show that several immune pathways and CD4 T lymphocytes are involved in the induction of the vaccine antibody response. Our findings highlight the importance of the RBD domain in the design of SARS-CoV-2 vaccines and provide a rationale for the development of a protective vaccine through the induction of antibodies against the RBD domain.


Subject(s)
Antibodies, Viral/immunology , Betacoronavirus/immunology , Coronavirus Infections/immunology , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/immunology , Pneumonia, Viral/prevention & control , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Viral Vaccines/immunology , Animals , Antibodies, Neutralizing/immunology , COVID-19 , COVID-19 Vaccines , Humans , Macaca mulatta/immunology , Macaca mulatta/virology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Models, Animal , Models, Molecular , Protein Domains , SARS-CoV-2 , Serum/immunology , Spleen/cytology , Spleen/immunology , T-Lymphocytes/immunology , Vaccination
6.
Proc Natl Acad Sci U S A ; 120(24): e2301312120, 2023 06 13.
Article in English | MEDLINE | ID: mdl-37279269

ABSTRACT

Glycan alterations are associated with aging, neuropsychiatric, and neurodegenerative diseases, although the contributions of specific glycan structures to emotion and cognitive functions remain largely unknown. Here, we used a combination of chemistry and neurobiology to show that 4-O-sulfated chondroitin sulfate (CS) polysaccharides are critical regulators of perineuronal nets (PNNs) and synapse development in the mouse hippocampus, thereby affecting anxiety and cognitive abilities such as social memory. Brain-specific deletion of CS 4-O-sulfation in mice increased PNN densities in the area CA2 (cornu ammonis 2), leading to imbalanced excitatory-to-inhibitory synaptic ratios, reduced CREB activation, elevated anxiety, and social memory dysfunction. The impairments in PNN densities, CREB activity, and social memory were recapitulated by selective ablation of CS 4-O-sulfation in the CA2 region during adulthood. Notably, enzymatic pruning of the excess PNNs reduced anxiety levels and restored social memory, while chemical manipulation of CS 4-O-sulfation levels reversibly modulated PNN densities surrounding hippocampal neurons and the balance of excitatory and inhibitory synapses. These findings reveal key roles for CS 4-O-sulfation in adult brain plasticity, social memory, and anxiety regulation, and they suggest that targeting CS 4-O-sulfation may represent a strategy to address neuropsychiatric and neurodegenerative diseases associated with social cognitive dysfunction.


Subject(s)
Extracellular Matrix , Neurodegenerative Diseases , Mice , Animals , Extracellular Matrix/chemistry , Neurons/physiology , Hippocampus , Chondroitin Sulfates/chemistry
7.
PLoS Pathog ; 19(8): e1011594, 2023 08.
Article in English | MEDLINE | ID: mdl-37611054

ABSTRACT

Treponema pallidum (Tp) has a well-known ability to evade the immune system and can cause neurosyphilis by invading the central nervous system (CNS). Microglia are resident macrophages of the CNS that are essential for host defense against pathogens, this study aims to investigate the interaction between Tp and microglia and the potential mechanism. Here, we found that Tp can exert significant toxic effects on microglia in vivo in Tg (mpeg1: EGFP) transgenic zebrafish embryos. Single-cell RNA sequencing results showed that Tp downregulated autophagy-related genes in human HMC3 microglial cells, which is negatively associated with apoptotic gene expression. Biochemical and cell biology assays further established that Tp inhibits microglial autophagy by interfering with the autophagosome-lysosome fusion process. Transcription factor EB (TFEB) is a master regulator of lysosome biogenesis, Tp activates the mechanistic target of rapamycin complex 1 (mTORC1) signaling to inhibit the nuclear translocation of TFEB, leading to decreased lysosomal biogenesis and accumulated autophagosome. Importantly, the inhibition of autophagosome formation reversed Tp-induced apoptosis and promoted microglial clearance of Tp. Taken together, these findings show that Tp blocks autophagic flux by inhibiting TFEB-mediated lysosomal biosynthesis in human microglia. Autophagosome accumulation was demonstrated to be a key mechanism underlying the effects of Tp in promoting apoptosis and preventing itself from clearing by human microglia. This study offers novel perspectives on the potential mechanism of immune evasion employed by Tp within CNS. The results not only establish the pivotal role of autophagy dysregulation in the detrimental effects of Tp on microglial cells but also bear considerable implications for the development of therapeutic strategies against Tp, specifically involving mTORC1 inhibitors and autophagosome formation inhibitors, in the context of neurosyphilis patients.


Subject(s)
Microglia , Neurosyphilis , Humans , Animals , Treponema pallidum/genetics , Zebrafish , Autophagy , Apoptosis
8.
Nature ; 568(7750): 93-97, 2019 04.
Article in English | MEDLINE | ID: mdl-30918407

ABSTRACT

Sodium is the main cation in the extracellular fluid and it regulates various physiological functions. Depletion of sodium in the body increases the hedonic value of sodium taste, which drives animals towards sodium consumption1,2. By contrast, oral sodium detection rapidly quenches sodium appetite3,4, suggesting that taste signals have a central role in sodium appetite and its satiation. Nevertheless, the neural mechanisms of chemosensory-based appetite regulation remain poorly understood. Here we identify genetically defined neural circuits in mice that control sodium intake by integrating chemosensory and internal depletion signals. We show that a subset of excitatory neurons in the pre-locus coeruleus express prodynorphin, and that these neurons are a critical neural substrate for sodium-intake behaviour. Acute stimulation of this population triggered robust ingestion of sodium even from rock salt, while evoking aversive signals. Inhibition of the same neurons reduced sodium consumption selectively. We further demonstrate that the oral detection of sodium rapidly suppresses these sodium-appetite neurons. Simultaneous in vivo optical recording and gastric infusion revealed that sodium taste-but not sodium ingestion per se-is required for the acute modulation of neurons in the pre-locus coeruleus that express prodynorphin, and for satiation of sodium appetite. Moreover, retrograde-virus tracing showed that sensory modulation is in part mediated by specific GABA (γ-aminobutyric acid)-producing neurons in the bed nucleus of the stria terminalis. This inhibitory neural population is activated by sodium ingestion, and sends rapid inhibitory signals to sodium-appetite neurons. Together, this study reveals a neural architecture that integrates chemosensory signals and the internal need to maintain sodium balance.


Subject(s)
Appetite Regulation/drug effects , Appetite Regulation/physiology , Eating/drug effects , Neural Pathways/drug effects , Sodium/pharmacology , Taste/drug effects , Taste/physiology , Administration, Oral , Animals , Appetite Regulation/genetics , Avoidance Learning/drug effects , Avoidance Learning/physiology , Eating/genetics , Eating/physiology , Enkephalins/metabolism , Female , GABAergic Neurons/drug effects , GABAergic Neurons/metabolism , Homeostasis/drug effects , Homeostasis/genetics , Homeostasis/physiology , Locus Coeruleus/cytology , Locus Coeruleus/drug effects , Locus Coeruleus/physiology , Male , Mice , Motivation/drug effects , Neural Pathways/cytology , Neural Pathways/physiology , Neurons/drug effects , Neurons/physiology , Protein Precursors/metabolism , Satiety Response/drug effects , Satiety Response/physiology , Sodium/administration & dosage , Taste/genetics
9.
J Neurosci ; 43(12): 2090-2103, 2023 03 22.
Article in English | MEDLINE | ID: mdl-36781221

ABSTRACT

The macaque middle temporal (MT) area is well known for its visual motion selectivity and relevance to motion perception, but the possibility of it also reflecting higher-level cognitive functions has largely been ignored. We tested for effects of task performance distinct from sensory encoding by manipulating subjects' temporal evidence-weighting strategy during a direction discrimination task while performing electrophysiological recordings from groups of MT neurons in rhesus macaques (one male, one female). This revealed multiple components of MT responses that were, surprisingly, not interpretable as behaviorally relevant modulations of motion encoding, or as bottom-up consequences of the readout of motion direction from MT. The time-varying motion-driven responses of MT were strongly affected by our strategic manipulation-but with time courses opposite the subjects' temporal weighting strategies. Furthermore, large choice-correlated signals were represented in population activity distinct from its motion responses, with multiple phases that lagged psychophysical readout and even continued after the stimulus (but which preceded motor responses). In summary, a novel experimental manipulation of strategy allowed us to control the time course of readout to challenge the correlation between sensory responses and choices, and population-level analyses of simultaneously recorded ensembles allowed us to identify strong signals that were so distinct from direction encoding that conventional, single-neuron-centric analyses could not have revealed or properly characterized them. Together, these approaches revealed multiple cognitive contributions to MT responses that are task related but not functionally relevant to encoding or decoding of motion for psychophysical direction discrimination, providing a new perspective on the assumed status of MT as a simple sensory area.SIGNIFICANCE STATEMENT This study extends understanding of the middle temporal (MT) area beyond its representation of visual motion. Combining multineuron recordings, population-level analyses, and controlled manipulation of task strategy, we exposed signals that depended on changes in temporal weighting strategy, but did not manifest as feedforward effects on behavior. This was demonstrated by (1) an inverse relationship between temporal dynamics of behavioral readout and sensory encoding, (2) a choice-correlated signal that always lagged the stimulus time points most correlated with decisions, and (3) a distinct choice-correlated signal after the stimulus. These findings invite re-evaluation of MT for functions outside of its established sensory role and highlight the power of experimenter-controlled changes in temporal strategy, coupled with recording and analysis approaches that transcend the single-neuron perspective.


Subject(s)
Motion Perception , Animals , Male , Female , Macaca mulatta , Motion Perception/physiology , Choice Behavior/physiology , Temporal Lobe/physiology , Photic Stimulation
10.
J Cell Physiol ; 239(1): 152-165, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37991435

ABSTRACT

Polycomb repressive complexes (PRCs) play critical roles in cell fate decisions during normal development as well as disease progression through mediating histone modifications such as H3K27me3 and H2AK119ub. How exactly PRCs recruited to chromatin remains to be fully illuminated. Here, we report that YTHDF1, the N6-methyladenine (m6 A) RNA reader that was previously known to be mainly cytoplasmic, associates with RNF2, a PRC1 protein that mediates H2AK119ub in human embryonic stem cells (hESCs). A portion of YTHDF1 localizes in the nuclei and associates with RNF2/H2AK119ub on a subset of gene loci related to neural development functions. Knock-down YTHDF1 attenuates H2AK119ub modification on these genes and promotes neural differentiation in hESCs. Our findings provide a noncanonical mechanism that YTHDF1 participates in PRC1 functions in hESCs.


Subject(s)
Cell Cycle Proteins , Human Embryonic Stem Cells , RNA-Binding Proteins , Humans , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Chromatin , Human Embryonic Stem Cells/metabolism , Polycomb Repressive Complex 1/genetics , Polycomb Repressive Complex 1/metabolism , Polycomb-Group Proteins/genetics , Polycomb-Group Proteins/metabolism , Protein Processing, Post-Translational , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Histones/genetics , Histones/metabolism
11.
BMC Genomics ; 25(1): 639, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38926642

ABSTRACT

BACKGROUND: Aging is a prominent risk factor for diverse diseases; therefore, an in-depth understanding of its physiological mechanisms is required. Nonhuman primates, which share the closest genetic relationship with humans, serve as an ideal model for exploring the complex aging process. However, the potential of the nonhuman primate animal model in the screening of human aging markers is still not fully exploited. Multiomics analysis of nonhuman primate peripheral blood offers a promising approach to evaluate new therapies and biomarkers. This study explores aging-related biomarker through multilayer omics, including transcriptomics (mRNA, lncRNA, and circRNA) and proteomics (serum and serum-derived exosomes) in rhesus monkeys (Macaca mulatta). RESULTS: Our findings reveal that, unlike mRNAs and circRNAs, highly expressed lncRNAs are abundant during the key aging period and are associated with cancer pathways. Comparative analysis highlighted exosomal proteins contain more types of proteins than serum proteins, indicating that serum-derived exosomes primarily regulate aging through metabolic pathways. Finally, eight candidate aging biomarkers were identified, which may serve as blood-based indicators for detecting age-related brain changes. CONCLUSIONS: Our results provide a comprehensive understanding of nonhuman primate blood transcriptomes and proteomes, offering novel insights into the aging mechanisms for preventing or treating age-related diseases.


Subject(s)
Aging , Biomarkers , Exosomes , Macaca mulatta , Proteomics , Animals , Aging/genetics , Biomarkers/blood , Exosomes/metabolism , Exosomes/genetics , Proteomics/methods , Transcriptome , Gene Expression Profiling , RNA, Long Noncoding/genetics , RNA, Long Noncoding/blood , RNA, Long Noncoding/metabolism , Models, Animal , RNA, Messenger/genetics , RNA, Messenger/metabolism , Proteome/metabolism , Genomics/methods
12.
J Am Chem Soc ; 146(4): 2465-2473, 2024 Jan 31.
Article in English | MEDLINE | ID: mdl-38232304

ABSTRACT

Photocatalytic oxidative coupling of methane (OCM) into value-added industrial chemicals offers an appealing green technique for achieving sustainable development, whereas it encounters double bottlenecks in relatively low methane conversion rate and severe overoxidation. Herein, we engineer a continuous gas flow system to achieve efficient photocatalytic OCM while suppressing overoxidation by synergizing the moderate active oxygen species, surface plasmon-mediated polarization, and multipoint gas intake flow reactor. Particularly, a remarkable CH4 conversion rate of 218.2 µmol h-1 with an excellent selectivity of ∼90% toward C2+ hydrocarbons and a remarkable stability over 240 h is achieved over a designed Au/TiO2 photocatalyst in our continuous gas flow system with a homemade three-dimensional (3D) printed flow reactor. This work provides an informative concept to engineer a high-performance flow system for photocatalytic OCM by synergizing the design of the reactor and photocatalyst to synchronously regulate the mass transfer, activation of reactants, and inhibition of overoxidation.

13.
Anal Chem ; 96(19): 7411-7420, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38652893

ABSTRACT

Accurate analysis of microRNAs (miRNAs) at the single-cell level is extremely important for deeply understanding their multiple and intricate biological functions. Despite some advancements in analyzing single-cell miRNAs, challenges such as intracellular interferences and insufficient detection limits still remain. In this work, an ultrasensitive nanopore sensor for quantitative single-cell miRNA-155 detection is constructed based on ionic current rectification (ICR) coupled with enzyme-free catalytic hairpin assembly (CHA). Benefiting from the enzyme-free CHA amplification strategy, the detection limit of the nanopore sensor for miRNA-155 reaches 10 fM and the nanopore sensor is more adaptable to complex intracellular environments. With the nanopore sensor, the concentration of miRNA-155 in living single cells is quantified to realize the early diagnosis of triple-negative breast cancer (TNBC). Furthermore, the nanopore sensor can be applied in screening anticancer drugs by tracking the expression level of miRNA-155. This work provides an adaptive and universal method for quantitatively analyzing intracellular miRNAs, which will greatly improve our understanding of cell heterogeneity and provide a more reliable scientific basis for exploring major diseases at the single-cell level.


Subject(s)
MicroRNAs , Nanopores , Single-Cell Analysis , Triple Negative Breast Neoplasms , MicroRNAs/analysis , Triple Negative Breast Neoplasms/diagnosis , Triple Negative Breast Neoplasms/genetics , Triple Negative Breast Neoplasms/pathology , Humans , Female , Cell Line, Tumor , Limit of Detection
14.
Biochem Biophys Res Commun ; 720: 150079, 2024 Aug 06.
Article in English | MEDLINE | ID: mdl-38759300

ABSTRACT

Stroke and major depression disorder are common neurological diseases, and a large number of clinical studies have shown that there is a close relationship between the two diseases, but whether the two diseases are linked at the genetic level needs to be further explored. The purpose of this study was to explore the comorbidity mechanism of stroke and major depression by using bioinformatics technology and animal experiments. From the GEO database, we gathered transcriptome data of stroke and depression mice (GSE104036, GSE131712, GSE81672, and GSE146845) and identified comorbid gene set through edgR and WGCNA analyses. Further analysis revealed that these genes were enriched in pathways associated with cell death. Programmed cell death gene sets (PCDGs) are generated from genes related to apoptosis, necroptosis, pyroptosis and autophagy. The intersection of PCDGs and comorbid gene set resulted in two hub genes, Mlkl and Nlrp3. Single-cell sequencing analysis indicated that Mlkl and Nlrp3 are mainly influential on endothelial cells and microglia, suggesting that the impairment of these two cell types may be a factor in the relationship between stroke and major depression. This was experimentally confirmed by RT-PCR and immunofluorescence staining. Our research revealed that two specific genes, namely, Mlkl and Nlrp3, play crucial roles in the complex mechanism that links stroke and major depression. Additionally, we have predicted six possible therapeutic agents and the outcomes of docking simulations of target proteins and drug molecules.


Subject(s)
Depressive Disorder, Major , Stroke , Animals , Depressive Disorder, Major/genetics , Depressive Disorder, Major/metabolism , Stroke/genetics , Stroke/metabolism , Mice , Mice, Inbred C57BL , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/genetics , Male , Transcriptome , Computational Biology/methods , Apoptosis/genetics
15.
Breast Cancer Res Treat ; 203(3): 543-551, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37897648

ABSTRACT

PURPOSE: Secretory breast carcinoma is a rare histological subtype of invasive breast cancer and considered with an indolent clinical behavior. This study was conducted to analyze the clinicopathological features of patients with secretory breast carcinoma (SBC), explore the outcome, and compare the prognostic difference with invasive ductal breast carcinoma (IDC). METHODS AND MATERIALS: Patients with SBC diagnosed between 2006 and 2017 from Fudan University Shanghai Cancer Center were included in the study, excluding patients with previous malignant tumor history and incomplete clinical data or follow-up records. Peculiar clinicopathological and immunohistochemical features of the cases were fully described. Clinical data of 4979 cases of IDC were also evaluated during this period. After propensity score matching, prognostic analysis of SBCs and IDCs was calculated by Kaplan-Meier method and landmark analysis method. RESULTS: The data of 52 patients diagnosed with SBC were identified from the pathological files. Among them, 47 patients were women, and 5 were men. The median age of the 52 SBCs was 46 years (mean, 48.1 years; range, 10-80 years). The tumor sizes ranged from 0.3 to 6.8 cm, with a mean of 3.5 cm. Eight patients (15.4%) had positive axillary lymph node involvement. The molecular classification was mostly triple-negative breast cancer (65.4%). Fluorescence in situ hybridization confirmed the presence of ETV6::NTRK3 rearrangement in 16 of 18 cases (88.9%). Furthermore, Kaplan-Meier survival analysis and landmark analysis demonstrated that there were no statistically significant differences in DFS and OS between SBC and IDC patients. CONCLUSION: Although SBCs are generally associated with a favorable prognosis, our work exhibited that the clinicopathological features of SBC were partly different from former understandings, indicating that therapeutic procedure should be prudent. Further studies are necessary to fully identify the clinical behavior and predictive markers to improve diagnosis and management in this unique subtype of breast cancer.


Subject(s)
Breast Neoplasms , Carcinoma, Ductal, Breast , Carcinoma , Triple Negative Breast Neoplasms , Male , Humans , Female , Middle Aged , Breast Neoplasms/diagnosis , Breast Neoplasms/genetics , Breast Neoplasms/therapy , Carcinoma, Ductal, Breast/pathology , In Situ Hybridization, Fluorescence , China , Prognosis , Triple Negative Breast Neoplasms/pathology
16.
Small ; 20(7): e2305658, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37798674

ABSTRACT

Defect engineering is promising to tailor the physical properties of 2D semiconductors for function-oriented electronics and optoelectronics. Compared with the extensively studied 2D binary materials, the origin of defects and their influence on physical properties of 2D ternary semiconductors are not clarified. Here, the effect of defects on the electronic structure and optical properties of few-layer hexagonal Znln2 S4 is thoroughly studied via versatile spectroscopic tools in combination with theoretical calculations. It is demonstrated that the Zn-In antistructural defects induce the formation of a series of donor and acceptor energy levels and sulfur vacancies induce donor energy levels, leading to rich recombination paths for defect emission and extrinsic absorption. Impressively, the emission of donor-acceptor pair in Znln2 S4 can be significantly tailored by electrostatic gating due to efficient tunability of Fermi level (Ef ). Furthermore, the layer-dependent dipole orientation of defect emission in Znln2 S4 is directly revealed by back focal plane imagining, where it presents obviously in-plane dipole orientation within a dozen-layer thickness of Znln2 S4 . These unique features of defects in Znln2 S4 including extrinsic absorption, rich recombination paths, gate tunability, and in-plane dipole orientation are definitely a benefit to the advanced orientation-functional optoelectronic applications.

17.
Plant Physiol ; 193(2): 1244-1262, 2023 09 22.
Article in English | MEDLINE | ID: mdl-37427874

ABSTRACT

Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are 2 primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoid divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contributes to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.


Subject(s)
Alkyl and Aryl Transferases , Terpenes , Humans , Terpenes/metabolism , Diphosphates , Plant Breeding , Fruit/genetics , Fruit/metabolism , Plants/metabolism , Alkyl and Aryl Transferases/genetics
18.
Opt Express ; 32(5): 6800-6813, 2024 Feb 26.
Article in English | MEDLINE | ID: mdl-38439377

ABSTRACT

Digital mask projection lithography (DMPL) technology is gaining significant attention due to its characteristics of free-mask, flexibility, and low cost. However, when dealing with target layouts featuring sizes smaller than the wavelength scale, accurately producing resist patterns that closely match the target layout using conventional methods to design the modulation coefficients of digital masks produced by spatial light modulators (SLM) becomes challenging. Here, we present digital inversion lithography technology (DILT), which offers what we believe to be a novel approach to reverse engineer the modulation coefficients of digital masks. In the case of binary amplitude modulation, DILT achieves a remarkable reduction in pattern errors (PE), reaching the original 0.26. At the same time, in the case of the gray amplitude modulation, the PE can be reduced to the original 0.05, which greatly improves the high-fidelity transfer of the target layout. This significant improvement enhances the accuracy of target design transfer. By leveraging the capabilities of DILT, DMPL can now attain higher precision and reliability, paving the way for more advanced applications in the field of micro-nano device manufacturing.

19.
Opt Express ; 32(7): 11613-11628, 2024 Mar 25.
Article in English | MEDLINE | ID: mdl-38571004

ABSTRACT

The increasing use of transparent ceramics in laser systems presents a challenge; their low damage threshold has become a significant impediment to the development of powerful laser systems. Consequently, it is imperative to undertake research into the damage sustained by these materials. Micropores, the most common structural defects in transparent ceramics, inevitably remain within the material during its preparation process. However, the relationship between the density and size of these micropores and their impact on nanosecond laser damage threshold and damage evolution remains unclear. In this study, we utilize the annealing process to effectively manage the density and size of micropores, establishing a correlation between micropores in relation to damage thresholds. This study confirms for the first time that micropores significantly contribute to laser damage, comparing and analyzing the damage morphology characteristics of both front and rear surfaces of transparent ceramics. It also presents, potential mechanisms that may contribute to these differences in damage. This paper offers guidance for controlling micropores during the preparation and processing of transparent ceramics with high laser damage thresholds. The findings are expected to further improve the anti-nanosecond laser damage capabilities of transparent ceramics.

20.
Opt Express ; 32(2): 2015-2028, 2024 Jan 15.
Article in English | MEDLINE | ID: mdl-38297740

ABSTRACT

Quantum communication satellites have potential for applications in future quantum networks. Photonics integrated chips, due to their compact and lightweight nature, are well-suited for satellite deployment. However, the harsh radiation environment of space can cause permanent damage to these chips, resulting in degraded performance or complete loss of functionality. In this work, we conducted a series of radiation experiments to evaluate the effects of γ rays and high energy protons on quantum key distribution transmitter chips. The results suggest that the insertion loss of the chip is slightly reduced by about 1.5 dB after 100 krad (Si) γ ray irradiation, and further reduced by about 0.5 to 1 dB after 2.39 × 1011/cm2 proton radiation. The half-wave voltages, extinction ratios, and polarization angles are not changed significantly within the measurement error range. Our work proves the feasibility of deploying quantum constellations utilizing terminals based on photonics chips.

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