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1.
Article in English | MEDLINE | ID: mdl-39126384

ABSTRACT

Antimicrobial peptides (AMPs) are expected to be an alternative promising solution to the global public health problem of antibiotic resistance due to their unique antimicrobial mechanism. However, extensive efforts are still needed to improve the shortcomings of traditional AMPs, such as rapid proteolysis, hemolysis, slow response, toxicity, etc., by exploring AMP-based new antimicrobial strategies. Here, we develop cationic peptide bundles into novel antimicrobial architectures that can rapidly kill multiple types of bacteria including drug-resistant bacteria. Remarkably, cationic peptide bundles can be used as polymerization units to cross-link with other polymers through simple two-component polymerization to produce diverse antimicrobial materials. For the proof of concept, three materials were fabricated and investigated, including an antimicrobial hydrogel that can significantly accelerate the healing of infected wounds, a multifunctional antimicrobial bioadhesive that shows promise in antimicrobial coatings for medical devices, and a photo-cross-linked antimicrobial gelatin hydrogel with broad application potential. The integration of antimicrobial units into the materials' backbone endows their biocompatibility. Cationic peptide bundles not only represent a new antimicrobial strategy but also provide a versatile and promising processing method to create diversified, multifunctional, and biocompatible antimicrobial materials.

2.
MedComm (2020) ; 5(9): e661, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39156767

ABSTRACT

In the past, hydrogen sulfide (H2S) was recognized as a toxic and dangerous gas; in recent years, with increased research, we have discovered that H2S can act as an endogenous regulatory transmitter. In mammals, H2S-catalyzing enzymes, such as cystathionine-ß-synthase, cystathionine-γ-lyase, and 3-mercaptopyruvate sulfurtransferase, are differentially expressed in a variety of tissues and affect a variety of biological functions, such as transcriptional and posttranslational modification of genes, activation of signaling pathways in the cell, and metabolic processes in tissues, by producing H2S. Various preclinical studies have shown that H2S affects physiological and pathological processes in the body. However, a detailed systematic summary of these roles in health and disease is lacking. Therefore, this review provides a thorough overview of the physiological roles of H2S in different systems and the diseases associated with disorders of H2S metabolism, such as ischemia-reperfusion injury, hypertension, neurodegenerative diseases, inflammatory bowel disease, and cancer. Meanwhile, this paper also introduces H2S donors and novel release modes, as well as the latest preclinical experimental results, aiming to provide researchers with new ideas to discover new diagnostic targets and therapeutic options.

3.
Biochim Biophys Acta Mol Basis Dis ; : 167475, 2024 Aug 17.
Article in English | MEDLINE | ID: mdl-39159700

ABSTRACT

Acute lung injury (ALI) is a severe lung damage characterized by acute hypoxemia, increased pulmonary vascular permeability, and inflammatory reactions. Despite current treatments, mortality from ALI remains high. This study found that Sec13 is highly expressed in ALI and regulates it by glycolysis and epithelial-mesenchymal transition (EMT). In an ALI mouse model and cell model, Sec13 expression increased, accompanied by enhanced glycolysis, EMT, and inflammation. Sec13 knockdown suppressed these effects, alleviating ALI. Sec13 forms a protein complex with Pgm1, an enzyme regulating glucose-6-phosphate (G6P) production, and Ubqln1, an ubiquitin ligase. Sec13 inhibits Ubqln1-mediated Pgm1 ubiquitination, thereby stabilizing Pgm1. In ALI, Pgm1 binding to Sec13 increased but binding to Ubqln1 decreased. Sec13 knockdown decreased lactate, G6P, EMT markers, and inflammatory cytokines. Pgm1 knockdown produced similar effects. Ubqln1 overexpression suppressed inflammation but decreased Pgm1 expression. In conclusion, Sec13 plays a key role in ALI by inhibiting Ubqln1-mediated Pgm1 ubiquitination, affecting glycolysis and EMT. Sec13 and Pgm1 may be new targets for treating ALI.

4.
Article in English | MEDLINE | ID: mdl-39162411

ABSTRACT

BACKGROUND AND OBJECTIVES: Maximal and safe removal of insular gliomas by a transinsular cortex approach is challenging. In this article, a new transtemporal isthmus approach to resect insular gliomas is presented. METHODS: We retrospectively examined 53 patients with insular glioma who underwent resection through the temporal isthmus approach using magnetic resonance imaging and functional neuronavigation guidance and intraoperative electrophysiological monitoring. Extent of resection was determined using intraoperative magnetic resonance imaging. RESULTS: Fifty-three patients were included for analysis, 30 men and 23 women. The median (range) age was 45 (26-70) years. Tumor laterality was left in 22 patients and right in 31. All tumors involved at least zone III or IV (Berger-Sanai classification system), including zones I-IV were involved in 29 (54.7%) and zones III and IV in 17 (32.0%). Among the 37 low-grade gliomas, preoperative median (IQR) volume was 45.7 (31.8, 60.3) cm3, and gross total resection was achieved in 24 (64.9%). Among the 16 high-grade gliomas, preoperative median (IQR) volume was 45.3 (40.1, 54.0) cm3, and gross total resection was achieved in 14 (87.5%). The median (IQR) extent of resection of the whole group was 100% (89%-100%). The median (IQR) postoperative Karnofsky performance score 3 months after surgery was 90 (80-90). Mean temporal isthmus width was significantly higher in the affected side (involving tumor) than the contralateral one (21.6 vs 11.3 mm; 95% CI: 9.3 to 11.3, P < .01). Muscle strength was grade 4 or higher, and speech was nearly normal in all patients 3 months after surgery. CONCLUSION: Insular glioma surgery using the transtemporal isthmus approach can achieve safe and maximum resection. A widened temporal isthmus provides a surgical pathway for transisthmic resection of insular tumor.

5.
Nephrology (Carlton) ; 2024 Jul 29.
Article in English | MEDLINE | ID: mdl-39075751

ABSTRACT

AIM: Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury. Hydrogen sulphide (H2S) exerts a protective effect in renal IRI. The present study was carried out to investigate the effects of exogenous H2S on renal IRI by regulating autophagy in mice. METHODS: Mice were randomly assigned to control, IRI and NaHS (an H2S donor, 28, 56 and 100 µmol/kg) groups. Renal IRI was induced by clamping the bilateral renal pedicles with non-traumatic arterial clamp for 45 min and then reperfused for 24 h. Mice were administered intraperitoneally with NaHS 20 min prior to renal ischemia. Sham group mice underwent the same procedures without clamping. Serum and kidney tissues were harvested 24 h after reperfusion for functional, histological, oxidative stress, and autophagic determination. RESULTS: Compared with the control group, the concentrations of serum creatinine (Scr), blood urea nitrogen (BUN), and malondialdehyde (MDA), the protein levels of LC3II/I, Beclin-1 and P62, as well as the number of autophagosomes were significantly increased, but the activity of superoxide dismutase (SOD) was decreased after renal IRI. NaHS pre-treatment dramatically attenuated renal IRI-induced renal dysfunction, histological changes, MDA concentration and p62 expression in a dose-dependent manner. However, NaHS increased the SOD activity and the protein levels of LC3II/I and Beclin-1. CONCLUSION: These results indicate that exogenous H2S protects the kidney from IRI through enhancement of autophagy and reduction of oxidative stress. Novel H2S donors could be developed in the treatment of renal IRI.

6.
Integr Zool ; 2024 Jul 29.
Article in English | MEDLINE | ID: mdl-39075927

ABSTRACT

Our findings reveal that the western black crested gibbon (Nomascus concolor) did not divide into different subspecies, and the relatively low level of genetic diversity emphasizes the importance of monitoring this indicator for vulnerable wildlife. Meanwhile, phylogeographic analysis of the Nomascus genus shows a north-to-south trend of ancestral geographic distribution.

7.
Article in English | MEDLINE | ID: mdl-39041626

ABSTRACT

SIGNIFICANCE: Ferroptosis, a form of regulated cell death characterized by a large amount of lipid peroxidation-mediated membrane damage, joins the evolution of multisystem diseases. For instance, neurodegenerative diseases, chronic obstructive pulmonary disease and acute respiratory distress syndrome, osteoporosis and osteoarthritis, and so on. Since being identified as the third gasotransmitter in living organisms, the intricate role of hydrogen sulfide (H2S) in ferroptosis has emerged at the forefront of research. RECENT ADVANCES: The discovery of novel targets in the relevant metabolic pathways, including transferrin receptor 1, cystine/glutamate antiporter, and others, coupled with the exploration of new signaling pathways, particularly the p53 signaling pathway and the nitric oxide / nuclear factor erythroid 2-related factor 2 signaling pathway, and so on. Many diseases such as emphysema and airway inflammation, myocardial diseases, endothelial dysfunction in aging arteries, and traumatic brain injury have recently been found to be alleviated directly by H2S inhibition of ferroptosis. Safe, effective, and tolerable novel H2S donors have been developed and have shown promising results in phase I clinical trials. CRITICAL ISSUES: Complicated crosstalk between ferroptosis signaling pathway and oncogenic factors results in the risk of cancer when inhibiting ferroptosis. Notably, targeted delivery of H2S is still a challenging task. FUTURE DIRECTIONS: Discovering more reliable and stable novel H2S donors and achieving their targeted delivery will enable further clinical trials for diseases associated with ferroptosis inhibition by H2S, determining their safety, efficacy, and tolerance.

8.
ESC Heart Fail ; 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39030781

ABSTRACT

AIMS: Heritable dilated cardiomyopathy (DCM) or DCM associated with congenital or acquired left ventricular diseases carries a significant mortality risk. Pulmonary artery banding (PAB) has been proposed as an alternative to heart transplantation. This study aimed to delineate the clinical development, ventricular reverse remodelling, and functional regeneration of the dilated left ventricle, presenting as a pioneering approach in China. METHODS AND RESULTS: This prospective study was initiated in November 2021, involving paediatric patients with a significant dilated left ventricle and preserved right ventricle who underwent surgical PAB. The baseline characteristics and clinical information during follow-up were collected. Seven patients (five boys) with a median age of 240 (148, 1028) days have been included thus far. No procedural or follow-up mortality was observed. The modified Ross functional class improved from treatment to follow-up of 348 (200, 629) days, and the median left ventricular ejection fraction increased from 27.0 (15.0, 34.0) % before surgery to 61.0 (52.0, 68.0) % (P < 0.05); the median left ventricular end-diastolic diameter and corresponding Z-scores decreased from 43.0 (40.0, 55.0) mm [+9.4 (+7.7, +11.7)] to 33.0 (29.0, 39.0) mm [+1.8 (+1.3, +3.8)] (P < 0.05). Functional regeneration of the left ventricle was observed in five patients. Three of them underwent balloon dilation of the PAB to relieve excessively elevated right ventricular pressures. CONCLUSIONS: The application of PAB should adhere to strict criteria. Initial results are promising for infants and even toddlers with a dilated left ventricle and limited probability of spontaneous recovery. PAB can be an alternative when there is a shortage of donor transplants and assist devices, especially for low- and middle-income countries.

9.
Nitric Oxide ; 150: 18-26, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38971520

ABSTRACT

Hydrogen sulfide (H2S), together with carbon monoxide (CO) and nitric oxide (NO), is recognized as a vital gasotransmitter. H2S is biosynthesized by enzymatic pathways in the skin and exerts significant physiological effects on a variety of biological processes, such as apoptosis, modulation of inflammation, cellular proliferation, and regulation of vasodilation. As a major health problem, dermatological diseases affect a large proportion of the population every day. It is urgent to design and develop effective drugs to deal with dermatological diseases. Dermatological diseases can arise from a multitude of etiologies, including neoplastic growth, infectious agents, and inflammatory processes. The abnormal metabolism of H2S is associated with many dermatological diseases, such as melanoma, fibrotic diseases, and psoriasis, suggesting its therapeutic potential in the treatment of these diseases. In addition, therapies based on H2S donors are being developed to treat some of these conditions. In the review, we discuss recent advances in the function of H2S in normal skin, the role of altering H2S metabolism in dermatological diseases, and the therapeutic potential of diverse H2S donors for the treatment of dermatological diseases.

10.
Exp Cell Res ; 441(2): 114172, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39053869

ABSTRACT

In recent years, the impact of age-related diseases on human health has become increasingly severe, and developing effective drugs to deal with these diseases has become an urgent task. Considering the essential regulatory role of hydrogen sulfide (H2S) in these diseases, it is regarded as a promising target for treatment. H2S is a novel gaseous transmitter involved in many critical physiological activities, including anti-oxidation, anti-inflammation, and angiogenesis. H2S also regulates cell activities such as cell proliferation, migration, invasion, apoptosis, and autophagy. These regulatory effects of H2S contribute to relieving and treating age-related diseases. In this review, we mainly focus on the pathogenesis and treatment prospects of H2S in regulating age-related diseases.


Subject(s)
Aging , Hydrogen Sulfide , Hydrogen Sulfide/metabolism , Hydrogen Sulfide/pharmacology , Humans , Aging/metabolism , Animals , Autophagy/drug effects , Apoptosis/drug effects , Cell Proliferation/drug effects
11.
Sci Rep ; 14(1): 12978, 2024 06 05.
Article in English | MEDLINE | ID: mdl-38839927

ABSTRACT

Diabetic cardiomyopathy is a specific type of cardiomyopathy. In DCM, glucose uptake and utilization are impaired due to insulin deficiency or resistance, and the heart relies more heavily on fatty acid oxidation for energy, resulting in myocardial lipid toxicity-related injury. MARK4 is a member of the AMPK-related kinase family, and improves ischaemic heart failure through microtubule detyrosination. However, the role of MARK4 in cardiac regulation of metabolism is unclear. In this study, after successful establishment of a diabetic cardiomyopathy model induced by streptozotocin and a high-fat diet, MARK4 expression was found to be significantly increased in STZ-induced DCM mice. After AAV9-shMARK4 was administered through the tail vein, decreased expression of MARK4 alleviated diabetic myocardial damage, reduced oxidative stress and apoptosis, and facilitated cardiomyocyte mitochondrial fusion, and promoted myocardial lipid oxidation metabolism. In addition, through the RNA-seq analysis of differentially expressed genes, we found that MARK4 deficiency promoted lipid decomposition and oxidative metabolism by downregulating the expression of ACSL4, thus reducing myocardial lipid accumulation in the STZ-induced DCM model.


Subject(s)
Coenzyme A Ligases , Diabetic Cardiomyopathies , Lipid Metabolism , Myocardium , Animals , Male , Mice , Apoptosis , Coenzyme A Ligases/metabolism , Coenzyme A Ligases/genetics , Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Experimental/complications , Diabetic Cardiomyopathies/metabolism , Diabetic Cardiomyopathies/pathology , Diabetic Cardiomyopathies/genetics , Diabetic Cardiomyopathies/etiology , Disease Models, Animal , Mice, Inbred C57BL , Myocardium/metabolism , Myocardium/pathology , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/pathology , Oxidative Stress , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Streptozocin
12.
Biol Pharm Bull ; 47(7): 1248-1254, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38866477

ABSTRACT

Ethanol (alcohol) is a risk factor that contributes to non-communicable diseases. Chronic abuse of ethanol is toxic to both the heart and overall health, and even results in death. Ethanol and its byproduct acetaldehyde can harm the cardiovascular system by impairing mitochondrial function, causing oxidative damage, and reducing contractile proteins. Endothelial cells are essential components of the cardiovascular system, are highly susceptible to ethanol, either through direct or indirect exposure. Thus, protection against endothelial injury is of great importance for persons who chronic abuse of ethanol. In this study, an in vitro model of endothelial injury was created using ethanol. The findings revealed that a concentration of 20.0 mM of ethanol reduced cell viability and Bcl-2 expression, while increasing cell apoptosis, intracellular reactive oxygen species (ROS) levels, mitochondrial depolarization, and the expression of Bax and cleaved-caspase-3 in endothelial cells. Further study showed that ethanol promoted nuclear translocation of nuclear factor kappa B (NF-κB), increased the secretion of tumor necrosis factor (TNF)-α, interleukin (IL)-1ß, IL-6 in the culture medium, and inhibited nuclear factor-erythroid 2-related factor 2 (Nrf2) signaling pathway. The aforementioned findings suggest that ethanol has a harmful impact on endothelial cells. Nevertheless, the application of epigallocatechin-3-gallate (EGCG) to the cells can effectively mitigate the detrimental effects of ethanol on endothelial cells. In conclusion, EGCG alleviates ethanol-induced endothelial injury partly through alteration of NF-κB translocation and activation of the Nrf2 signaling pathway. Therefore, EGCG holds great potential in safeguarding individuals who chronically abuse ethanol from endothelial dysfunction.


Subject(s)
Catechin , Ethanol , NF-E2-Related Factor 2 , NF-kappa B , Signal Transduction , Ethanol/toxicity , NF-E2-Related Factor 2/metabolism , Catechin/analogs & derivatives , Catechin/pharmacology , Catechin/therapeutic use , NF-kappa B/metabolism , Humans , Signal Transduction/drug effects , Apoptosis/drug effects , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/metabolism , Reactive Oxygen Species/metabolism , Cell Survival/drug effects , Endothelial Cells/drug effects , Endothelial Cells/metabolism , Proto-Oncogene Proteins c-bcl-2/metabolism
13.
Sci Rep ; 14(1): 13863, 2024 06 15.
Article in English | MEDLINE | ID: mdl-38879652

ABSTRACT

Heart rate (HR) and respiration rate (RR) play an important role in the study of complex behaviors and their physiological correlations in non-human primates (NHPs). However, collecting HR and RR information is often challenging, involving either invasive implants or tedious behavioral training, and there are currently few established simple and non-invasive techniques for HR and RR measurement in NHPs owing to their stress response or indocility. In this study, we employed a frequency-modulated continuous wave (FMCW) radar to design a novel contactless HR and RR monitoring system. The designed system can estimate HR and RR in real time by placing the FMCW radar on the cage and facing the chest of both awake and anesthetized macaques, the NHP investigated in this study. Experimental results show that the proposed method outperforms existing methods, with averaged absolute errors between the reference monitor and radar estimates of 0.77 beats per minute (bpm) and 1.29 respirations per minute (rpm) for HR and RR, respectively. In summary, we believe that the proposed non-invasive and contactless estimation method could be generalized as a HR and RR monitoring tool for NHPs. Furthermore, after modifying the radar signal-processing algorithms, it also shows promise for applications in other experimental animals for animal welfare, behavioral, neurological, and ethological research.


Subject(s)
Heart Rate , Radar , Respiratory Rate , Animals , Heart Rate/physiology , Respiratory Rate/physiology , Monitoring, Physiologic/methods , Macaca , Vital Signs , Male
14.
Angew Chem Int Ed Engl ; 63(30): e202405765, 2024 07 22.
Article in English | MEDLINE | ID: mdl-38721653

ABSTRACT

In this study, peptide-based self-assembled nanosheets with a thickness of approximately 1 nm were prepared using a hierarchical covalent physical fabrication strategy. The covalent alternating polymerization of helical peptide E3 with an azobenzene (AZO) structure yielded copolymers CoP(E3-AZO), which physically self-assembled into ultrathin nanosheets in an unanticipated two-dimensional horizontal monolayer arrangement. This special monolayer arrangement enabled the thickness of the nanosheets to be equal to the cross-sectional diameter of a single linear copolymer, which is a rare phenomenon. Molecular dynamics simulations suggested that the synergistic effect of multiple molecular interactions drives the self-assembly of CoP(E3-AZO) into nanosheets and that various methods, including phototreatment, pH adjustment, the addition of additives, and introduction of cosolvents, can alter the molecular interactions and modulate the self-assembly of CoP(E3-AZO), yielding diverse nanostructures. Remarkably, the ultrathin nanosheets selectively inhibited cancer cells at certain concentrations.


Subject(s)
Nanostructures , Peptides , Nanostructures/chemistry , Peptides/chemistry , Humans , Molecular Dynamics Simulation , Azo Compounds/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry
15.
J Med Internet Res ; 26: e49848, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38728685

ABSTRACT

BACKGROUND: Acute myocardial infarction (AMI) is one of the most severe cardiovascular diseases and is associated with a high risk of in-hospital mortality. However, the current deep learning models for in-hospital mortality prediction lack interpretability. OBJECTIVE: This study aims to establish an explainable deep learning model to provide individualized in-hospital mortality prediction and risk factor assessment for patients with AMI. METHODS: In this retrospective multicenter study, we used data for consecutive patients hospitalized with AMI from the Chongqing University Central Hospital between July 2016 and December 2022 and the Electronic Intensive Care Unit Collaborative Research Database. These patients were randomly divided into training (7668/10,955, 70%) and internal test (3287/10,955, 30%) data sets. In addition, data of patients with AMI from the Medical Information Mart for Intensive Care database were used for external validation. Deep learning models were used to predict in-hospital mortality in patients with AMI, and they were compared with linear and tree-based models. The Shapley Additive Explanations method was used to explain the model with the highest area under the receiver operating characteristic curve in both the internal test and external validation data sets to quantify and visualize the features that drive predictions. RESULTS: A total of 10,955 patients with AMI who were admitted to Chongqing University Central Hospital or included in the Electronic Intensive Care Unit Collaborative Research Database were randomly divided into a training data set of 7668 (70%) patients and an internal test data set of 3287 (30%) patients. A total of 9355 patients from the Medical Information Mart for Intensive Care database were included for independent external validation. In-hospital mortality occurred in 8.74% (670/7668), 8.73% (287/3287), and 9.12% (853/9355) of the patients in the training, internal test, and external validation cohorts, respectively. The Self-Attention and Intersample Attention Transformer model performed best in both the internal test data set and the external validation data set among the 9 prediction models, with the highest area under the receiver operating characteristic curve of 0.86 (95% CI 0.84-0.88) and 0.85 (95% CI 0.84-0.87), respectively. Older age, high heart rate, and low body temperature were the 3 most important predictors of increased mortality, according to the explanations of the Self-Attention and Intersample Attention Transformer model. CONCLUSIONS: The explainable deep learning model that we developed could provide estimates of mortality and visual contribution of the features to the prediction for a patient with AMI. The explanations suggested that older age, unstable vital signs, and metabolic disorders may increase the risk of mortality in patients with AMI.


Subject(s)
Deep Learning , Hospital Mortality , Myocardial Infarction , Humans , Myocardial Infarction/mortality , Female , Male , Retrospective Studies , Middle Aged , Aged , Algorithms , Risk Factors , ROC Curve
16.
Cell Signal ; 120: 111236, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38810860

ABSTRACT

Hydrogen sulfide (H2S) is one of the three most crucial gaseous messengers in the body. The discovery of H2S donors, coupled with its endogenous synthesis capability, has sparked hope for the treatment of hematologic malignancies. In the last decade, the investigation into the impact of H2S has expanded, particularly within the fields of cardiovascular function, inflammation, infection, and neuromodulation. Hematologic malignancies refer to a diverse group of cancers originating from abnormal proliferation and differentiation of blood-forming cells, including leukemia, lymphoma, and myeloma. In this review, we delve deeply into the complex interrelation between H2S and hematologic malignancies. In addition, we comprehensively elucidate the intricate molecular mechanisms by which both H2S and its donors intricately modulate the progression of tumor growth. Furthermore, we systematically examine their impact on pivotal aspects, encompassing the proliferation, invasion, and migration capacities of hematologic malignancies. Therefore, this review may contribute novel insights to our understanding of the prospective therapeutic significance of H2S and its donors within the realm of hematologic malignancies.


Subject(s)
Hematologic Neoplasms , Hydrogen Sulfide , Hydrogen Sulfide/metabolism , Hydrogen Sulfide/pharmacology , Humans , Hematologic Neoplasms/drug therapy , Hematologic Neoplasms/metabolism , Hematologic Neoplasms/pathology , Animals , Cell Proliferation/drug effects
17.
BMC Genomics ; 25(1): 430, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38693501

ABSTRACT

BACKGROUND: Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. RESULTS: We identified varying numbers (17,497-17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 "missing" genes in birds in general, and 36 of the 174 "missing" genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. CONCLUSION: The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.


Subject(s)
Chickens , Genome , Molecular Sequence Annotation , Animals , Chickens/genetics , Base Composition , Telomere/genetics , Chromosomes/genetics , Genomics/methods
18.
Genome Biol ; 25(1): 107, 2024 04 26.
Article in English | MEDLINE | ID: mdl-38671502

ABSTRACT

Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly tool for noisy long reads, which achieves a high level of accuracy in genome assembly. We apply NextDenovo to assemble 35 diverse human genomes from around the world using Nanopore long-read data. These genomes allow us to identify the landscape of segmental duplication and gene copy number variation in modern human populations. The use of NextDenovo should pave the way for population-scale long-read assembly using Nanopore long-read data.


Subject(s)
DNA Copy Number Variations , Genome, Human , Humans , High-Throughput Nucleotide Sequencing/methods , Software , Nanopore Sequencing/methods , Sequence Analysis, DNA/methods , Genomics/methods
19.
Biochim Biophys Acta Gen Subj ; 1868(7): 130612, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38626830

ABSTRACT

Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are characterized by rapid onset and widespread inflammation in the lungs, often leading to respiratory failure. These conditions can be triggered by various factors, resulting in a severe inflammatory response within the lungs. Resveratrol, a polyphenolic compound found in grapes and peanuts, is renowned for its potent antioxidative and anti-inflammatory properties. In this study, we investigated how resveratrol protects against lipopolysaccharide (LPS)-induced ALI in mice. We established mouse models of LPS-induced ALI and inflammation in bronchoalveolar lavage fluid (BALF) macrophages. Through histopathological examination, immunofluorescence, western blot, enzyme-linked immunosorbent assay (ELISA), and transmission electron microscopy (TEM), we assessed the impact of resveratrol on the activation of NOD-like receptor thermal protein domain-associated protein 3 (NLRP3) inflammasomes and the process of mitophagy. Our findings indicate that resveratrol significantly mitigated the lung injury and inflammation caused by LPS. This was achieved by inhibiting the oligomerization of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and the activation of NLRP3 inflammasomes. Resveratrol also reduced the levels of IL-1ß and IL-18 in serum and BALF, decreased caspase-1 expression, and diminished macrophage pyroptosis. Furthermore, it upregulated Pink1, Parkin, Beclin-1, Autophagy-Related 5 (Atg5), and Microtubule-Associated Proteins 1 A/1B Light Chain 3B (LC3B-II), thereby enhancing mitophagy. Conversely, mitophagy was inhibited by Pink1 siRNA. In conclusion, resveratrol ameliorated ALI in mice, potentially by inhibiting the activation of NLRP3 inflammasomes, activating the Pink1/Parkin pathway, and promoting mitophagy.


Subject(s)
Acute Lung Injury , Inflammasomes , Mitophagy , NLR Family, Pyrin Domain-Containing 3 Protein , Protein Kinases , Resveratrol , Ubiquitin-Protein Ligases , Animals , Acute Lung Injury/drug therapy , Acute Lung Injury/metabolism , Acute Lung Injury/pathology , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Mitophagy/drug effects , Mice , Resveratrol/pharmacology , Inflammasomes/metabolism , Inflammasomes/drug effects , Ubiquitin-Protein Ligases/metabolism , Protein Kinases/metabolism , Male , Mice, Inbred C57BL , Lipopolysaccharides , Bronchoalveolar Lavage Fluid/chemistry
20.
BMC Vet Res ; 20(1): 134, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38570774

ABSTRACT

BACKGROUND: Porcine acute diarrhea syndrome coronavirus (SADS-CoV) is one of the novel pathogens responsible for piglet diarrhea, contributing to substantial economic losses in the farming sector. The broad host range of SADS-CoV raises concerns regarding its potential for cross-species transmission. Currently, there are no effective means of preventing or treating SADS-CoV infection, underscoring the urgent need for identifying efficient antiviral drugs. This study focuses on evaluating quercetin as an antiviral agent against SADS-CoV. RESULTS: In vitro experiments showed that quercetin inhibited SADS-CoV proliferation in a concentration-dependent manner, targeting the adsorption and replication stages of the viral life cycle. Furthermore, quercetin disrupts the regulation of the P53 gene by the virus and inhibits host cell cycle progression induced by SADS-CoV infection. In vivo experiments revealed that quercetin effectively alleviated the clinical symptoms and intestinal pathological damage caused by SADS-CoV-infected piglets, leading to reduced expression levels of inflammatory factors such as TLR3, IL-6, IL-8, and TNF-α. CONCLUSIONS: Therefore, this study provides compelling evidence that quercetin has great potential and promising applications for anti- SADS-CoV action.


Subject(s)
Alphacoronavirus , Coronavirus Infections , Coronavirus , Swine Diseases , Swine , Animals , Coronavirus/genetics , Quercetin/pharmacology , Quercetin/therapeutic use , Coronavirus Infections/drug therapy , Coronavirus Infections/veterinary , Diarrhea/veterinary , Swine Diseases/drug therapy
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