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1.
Phytomedicine ; 132: 155658, 2024 May 04.
Article in English | MEDLINE | ID: mdl-38981149

ABSTRACT

BACKGROUND: Alcohol-related liver damage is the most prevalent chronic liver disease, which creates a heavy public health burden worldwide. The leaves of Ampelopsis grossedentata have been considered a popular tea and traditional herbal medicine in China for more than one thousand years, and possess anti-inflammatory, antioxidative, hepatoprotective, and antiviral activities. PURPOSE: We explored the protective effects of Ampelopsis grossedentata extract (AGE) against chronic alcohol-induced hepatic injury (alcoholic liver disease, ALD), aiming to elucidate its underlying mechanisms. METHODS: Firstly, UPLC-Q/TOF-MS analysis and network pharmacology were used to identify the constituents and elucidate the potential mechanisms of AGE against ALD. Secondly, C57BL/6 mice were pair-fed the Lieber-DeCarli diet containing either isocaloric maltodextrin or ethanol, AGE (150 and 300 mg/kg/d) and silymarin (200 mg/kg) were administered to chronic ethanol-fed mice for 7 weeks to evaluate the hepatoprotective effects. Serum biochemical parameters were determined, hepatic and ileum sections were used for histologic examination, and levels of inflammatory cytokines and oxidative stress in the liver were examined. The potential molecular mechanisms of AGE in improving ALD were demonstrated by RNA-seq, Western blotting analysis, and immunofluorescence staining. RESULTS: Ten main constituents of AGE were identified using UPLC-Q/TOF-MS and 274 potential ALD-related targets were identified. The enriched KEGG pathways included Toll-like receptor signaling pathway, NF-κB signaling pathway, and necroptosis. Moreover, in vivo experimental studies demonstrated that AGE significantly reduced serum aminotransferase levels and improved pathological abnormalities after chronic ethanol intake. Meanwhile, AGE improved ALD in mice by down-regulating oxidative stress and inflammatory cytokines. Furthermore, AGE notably repaired damaged intestinal epithelial barrier and suppressed the production of gut-derived lipopolysaccharide by elevating intestinal tight junction protein expression. Subsequent RNA-seq and experimental validation indicated that AGE inhibited NF-κB nuclear translocation, suppressed IκB-α, RIPK3 and MLKL phosphorylation and alleviated hepatic necroptosis in mice. CONCLUSION: In this study, we have demonstrated for the first time that AGE protects against alcoholic liver disease by regulating the gut-liver axis and inhibiting the TLR4/NF-κB/MLKL-mediated necroptosis pathway. Therefore, our present work provides important experimental evidence for AGE as a promising candidate for protection against ALD.

2.
Int J Mol Sci ; 25(13)2024 Jun 30.
Article in English | MEDLINE | ID: mdl-39000358

ABSTRACT

The Chinese mitten crab (Eriocheir sinensis), an economically important crustacean that is endemic to China, has recently experienced high-temperature stress. The high thermal tolerance of E. sinensis points to its promise in being highly productive in an aquacultural context. However, the mechanisms underlying its high thermal tolerance remain unknown. In this study, female E. sinensis that were heat exposed for 24 h at 38.5 °C and 33 °C were identified as high-temperature-stressed (HS) and normal-temperature-stressed (NS) groups, respectively. The hepatopancreas of E. sinensis from the HS and NS groups were used for transcriptome and proteomic analyses. A total of 2350 upregulated and 1081 downregulated differentially expressed genes (DEGs) were identified between the HS and NS groups. In addition, 126 differentially expressed proteins (DEPs) were upregulated and 35 were downregulated in the two groups. An integrated analysis showed that 2641 identified genes were correlated with their corresponding proteins, including 25 genes that were significantly differentially expressed between the two omics levels. Ten Gene Ontology terms were enriched in the DEGs and DEPs. A functional analysis revealed three common pathways that were significantly enriched in both DEGs and DEPs: fluid shear stress and atherosclerosis, leukocyte transendothelial migration, and thyroid hormone synthesis. Further analysis of the common pathways showed that MGST1, Act5C, HSP90AB1, and mys were overlapping genes at the transcriptome and proteome levels. These results demonstrate the differences between the HS and NS groups at the two omics levels and will be helpful in clarifying the mechanisms underlying the thermal tolerance of E. sinensis.


Subject(s)
Brachyura , Heat-Shock Response , Hepatopancreas , Proteome , Transcriptome , Animals , Female , Hepatopancreas/metabolism , Proteome/genetics , Proteome/metabolism , Brachyura/genetics , Brachyura/metabolism , Brachyura/physiology , Heat-Shock Response/genetics , Gene Expression Profiling , Proteomics/methods , Gene Ontology , Gene Expression Regulation
3.
Phenomics ; 4(2): 109-124, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38884056

ABSTRACT

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00121-1.

4.
ACS Appl Mater Interfaces ; 16(26): 34358-34366, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38913838

ABSTRACT

Work function of organometallic halide perovskite (OHP) films is one of the most crucial photoelectric properties, which dominates the carrier dynamics in OHP-based devices. Despite surface treatments by additives being widely used to promote crystallization and passivate defects in OHP films, these chemical strategies for modulation of work functions face two trade-offs: homogeneity on the surface versus along the thickness; the range versus the accuracy of modulation. Herein, by using ferroelectric substrates of uniform polarization and subnanometer roughness, homogeneous CH3NH3PbI3 films are fabricated with five states of work functions with large spanning (∼0.8 eV) and high precision (sd ∼ 0.01 eV). We reveal that the ferroelectric polarizations and the smooth surfaces regulate CH3NH3+ orientations and suppress distortions of PbI6 octahedrons. The wide-range and multistate work functions originate from the ordered CH3NH3+ orientations and PbI6 octahedrons, which result in intensity enhancements and wavelength shifts in photoluminescence with a 30-fold increase of photoexcited carrier lifetime.

5.
Front Biosci (Landmark Ed) ; 29(6): 211, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38940041

ABSTRACT

BACKGROUND: Dental pulp stem cells (DPSCs) have self-renewal and multidirectional differentiation potentials. As such, DPSCs have a wide range of clinical applications. Low-level laser therapy (LLLT) has positive photobiostimulatory effects on cell proliferation, angiogenesis, osteogenic differentiation, bone regeneration, and fracture healing. However, there have been few studies on the effect of low-energy lasers on DPSC proliferation. METHODS: DPSCs were obtained from dental pulp tissue. The effects of LLLT on the proliferation of DPSCs and the associated mechanisms were investigated by in vitro culture and laser irradiation. RESULTS: LLLT with energy densities of 3.5 J/cm2 and 14 J/cm2promoted the proliferation of DPSCs. Differential protein expression studies suggested the stimulation of DPSC proliferation by LLLT involved the PI3K-Akt and Rap1 signaling pathways, as well as the apoptosis-related pathway. CONCLUSION: This preliminary study demonstrated that low-energy lasers have a pro-proliferative effect on DPSCs, and identified possible associated mechanisms. Our findings provide a theoretical basis for the clinical application of DPSCs and suggest novel strategies for the treatment of related diseases.


Subject(s)
Cell Proliferation , Dental Pulp , Low-Level Light Therapy , Stem Cells , Dental Pulp/cytology , Dental Pulp/radiation effects , Cell Proliferation/radiation effects , Humans , Stem Cells/radiation effects , Stem Cells/cytology , Stem Cells/metabolism , Low-Level Light Therapy/methods , Cells, Cultured , Signal Transduction/radiation effects , Apoptosis/radiation effects , Cell Differentiation/radiation effects
6.
Microorganisms ; 12(6)2024 May 27.
Article in English | MEDLINE | ID: mdl-38930463

ABSTRACT

Lacticaseibacillus rhamnosus is applied as a probiotic to alleviate various metabolic, gastrointestinal, and psychological symptoms and diseases, and its probiotic effectiveness is strain-specific. In this study, we obtained 21 strains of Ls. rhamnosus, and their genomes were sequenced. We defined the pan- and core-genomes of Ls. rhamnosus. Phenotypes such as the assimilation of carbohydrates and antibiotic resistance were experimentally characterized and associated with genome annotations. Nine strains were selected and tested for growth rates, tolerance to acidity/alkalinity and bile acids, the production of short-chain fatty acids, and competition with pathogenic microbes. Strains WL11 and WL17 were targeted as potential probiotics and were applied in mouse model tests for the alleviation of chronic fatigue syndrome (CFS) and irritable bowel syndrome (IBS). The results showed that WL11 and WL17 effectively alleviated slow body weight gain, anxiety, poor memory, and cognitive impairment in CFS mouse models. They also reduced the expression of pro-inflammatory factors, such as TNF-α and IL-6, and alleviated intestinal peristalsis, visceral hypersensitivity, and anxiety-like behavior in IBS mouse models. This study reports new Ls. rhamnosus strain resources and their effect on alleviation of both IBS and CFS symptoms with mouse models; the probiotic functions of those strains in human patients remain to be further tested.

7.
Dalton Trans ; 53(25): 10626-10636, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38859681

ABSTRACT

A photorechargeable supercapacitor was constructed using vanadium pentoxide (V2O5), reduced graphene oxide hydrogel (rGH), and zinc trifluoromethanesulfonate (Zn(CF3SO3)2) as the photoanode, cathode, and electrolyte, respectively. The phase composition, microstructure, chemical structure, light absorption, and specific surface area of the synthesized products and the electrochemical performance of the rGH/V2O5 supercapacitor were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), Raman spectroscopy, UV-Vis spectroscopy, the Brunauer-Emmett-Teller (BET) method, and an electrochemical workstation, respectively. The results show that the device has a specific capacity of 164 F g-1 at 0.5 A g-1 under illumination with 95 mW cm-2 light intensity, which is 20.5% higher than that under normal electrical charging. The supercapacitor has a 75% capacity retention rate and 100% coulombic efficiency, respectively, after 10 000 testing cycles under photoelectric synergistic charging and discharging. The as-constructed rGH/V2O5 photorechargeable supercapacitor exhibits promising application potential in electric vehicles and wearable electronics.

8.
Nano Lett ; 2024 Jun 02.
Article in English | MEDLINE | ID: mdl-38825790

ABSTRACT

The core task of neuromorphic devices is to effectively simulate the behavior of neurons and synapses. Based on the functionality of ferroelectric domains with the advantages of low power consumption and high-speed response, great progress has been made in realizing neuromimetic behaviors such as ferroelectric synaptic devices. However, the correlation between the ferroelectric domain dynamics and neuromimetic behavior remains unclear. Here, we reveal the correlation between domain/domain wall dynamics and neuromimetic behaviors from a microscopic perspective in real-time by using high temporal and spatial resolution in situ transmission electron microscopy. Furthermore, we propose utilizing ferroelectric microstructures for the simultaneous simulation of neuronal and synaptic plasticity, which is expected to improve the integration and performance of ferroelectric neuromorphic devices. We believe that this work to study neuromimetic behavior from the perspective of domain dynamics is instructive for the development of ferroelectric neuromorphic devices.

9.
Nano Lett ; 24(21): 6247-6254, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38709758

ABSTRACT

Two-dimensional (2D) semiconductors possess exceptional electronic, optical, and magnetic properties, making them highly desirable for widespread applications. However, conventional mechanical exfoliation and epitaxial growth methods are insufficient in meeting the demand for atomically thin films covering large areas while maintaining high quality. Herein, leveraging liquid metal oxidation reaction, we propose a motorized spin-coating exfoliation strategy to efficiently produce large-area 2D metal oxide (2DMO) semiconductors with high crystallinity, atomically thin thickness, and flat surfaces on diverse substrates. Moreover, we realized a 2D gallium oxide-based deep ultraviolet solar-blind photodetector featuring a metal-semiconductor-metal structure, showcasing high responsivity (8.24 A W-1) at 254 nm and excellent sensitivity (4.3 × 1012 cm Hz1/2 W-1). This novel liquid-metal-based spin-coating exfoliation strategy offers great potential for synthesizing atomically thin 2D semiconductors, opening new avenues for future functional electronic and optical applications.

10.
Elife ; 132024 May 30.
Article in English | MEDLINE | ID: mdl-38814174

ABSTRACT

Neurexins play diverse functions as presynaptic organizers in various glutamatergic and GABAergic synapses. However, it remains unknown whether and how neurexins are involved in shaping functional properties of the glycinergic synapses, which mediate prominent inhibition in the brainstem and spinal cord. To address these issues, we examined the role of neurexins in a model glycinergic synapse between the principal neuron in the medial nucleus of the trapezoid body (MNTB) and the principal neuron in the lateral superior olive (LSO) in the auditory brainstem. Combining RNAscope with stereotactic injection of AAV-Cre in the MNTB of neurexin1/2/3 conditional triple knockout mice, we showed that MNTB neurons highly express all isoforms of neurexins although their expression levels vary remarkably. Selective ablation of all neurexins in MNTB neurons not only reduced the amplitude but also altered the kinetics of the glycinergic synaptic transmission at LSO neurons. The synaptic dysfunctions primarily resulted from an impaired Ca2+ sensitivity of release and a loosened coupling between voltage-gated Ca2+ channels and synaptic vesicles. Together, our current findings demonstrate that neurexins are essential in controlling the strength and temporal precision of the glycinergic synapse, which therefore corroborates the role of neurexins as key presynaptic organizers in all major types of fast chemical synapses.


Subject(s)
Glycine , Mice, Knockout , Trapezoid Body , Animals , Glycine/metabolism , Mice , Trapezoid Body/metabolism , Trapezoid Body/physiology , Synaptic Transmission/physiology , Neural Cell Adhesion Molecules/metabolism , Neural Cell Adhesion Molecules/genetics , Superior Olivary Complex/physiology , Superior Olivary Complex/metabolism , Brain Stem/physiology , Brain Stem/metabolism , Synapses/metabolism , Synapses/physiology , Neurons/metabolism , Neurons/physiology , Cell Adhesion Molecules, Neuronal/metabolism , Cell Adhesion Molecules, Neuronal/genetics , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Neurexins , Calcium-Binding Proteins
11.
Gut Microbes ; 16(1): 2347725, 2024.
Article in English | MEDLINE | ID: mdl-38722028

ABSTRACT

The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.


Subject(s)
Feces , Gastrointestinal Microbiome , Humans , Feces/microbiology , Clostridiales/genetics , Clostridiales/metabolism , Clostridiales/isolation & purification , Clostridiales/classification , Probiotics/metabolism , Metabolomics , Genomics , Male , Phylogeny , Female , Genome, Bacterial
12.
Sci China Life Sci ; 2024 Apr 07.
Article in English | MEDLINE | ID: mdl-38600293

ABSTRACT

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.

13.
Article in English | MEDLINE | ID: mdl-38687183

ABSTRACT

Three Gram-positive, obligately anaerobic bacterial strains, namely CSJ-1T, CSJ-3T, and CSJ-4T, were isolated from faeces of healthy persons. They were characterized through a combination of whole-genome sequencing, phenotypic traits, and metabolomic analysis. The genome sizes of CSJ-1T, CSJ-4T, and CSJ-3T were 3.3, 3.8, and 6.1 Mbp, with DNA G+C contents of 47.2, 48.3, and 48.8 mol%, respectively. Strain CSJ-3T was identified as representing a novel species, Diplocloster hominis (type strain CSJ-3T=CGMCC 1.18033T=JCM 36512T) of the genus Diplocloster. The 16S rRNA gene sequence similarity and whole genome average nucleotide identity (gANI) of CSJ-4T to its closest related species, Diplocloster modestus ASD 4241T, were 98.3 and 91.4 %, respectively. Comparative analysis of 16S rRNA gene sequences showed 91.6 % similarity between CSJ-1T and its closest phylogenetic neighbour, Catenibacillus scindens DSM 106146T, and 93.3 % similarity between CSJ-4T and its closest relative strain, Clostridium fessum SNUG30386T. Based on the polyphasic taxonomic results, we proposed two novel genera and three novel species. Strain CSJ-1T was identified as representing a novel species of novel genus, Anaerolentibacter hominis gen. nov. sp. nov. (type strain CSJ-1T=CGMCC 1.18046T=JCM 36511T) of the family Lachnospiraceae, and strain CSJ-4T was identified as representing a novel species of novel genus Pilosibacter fragilis gen. nov. sp. nov. (type strain CSJ-4T=CGMCC 1.18026T= JCM 36513T) of the family Clostridiaceae.


Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Feces , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Feces/microbiology , DNA, Bacterial/genetics , Humans , Fatty Acids/analysis , Genome, Bacterial , Whole Genome Sequencing
15.
BMC Ophthalmol ; 24(1): 104, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38443833

ABSTRACT

BACKGROUND: Myopia is the most prevalent refractive error and a growing global health concern that significantly affects visual function. Researchers have recently emphasized considerably on the influence of lifestyle on myopia incidence and development. This study investigates the relationship between leisure sedentary behaviors (LSB)/physical activity (PA)/sleep traits and myopia. METHODS: LSB, PA, and sleep trait-associated genetic variants were used as instrument variables in a Mendelian randomization (MR) study to examine their causal effects on myopia. Summary genome-wide association studies (GWASs) statistical data for LSB and PA were obtained from UK Biobank, and the data of sleep traits was obtained from UK Biobank, UK Biobank and 23andMe, and FinnGen. We used summary statistics data for myopia from MRC IEU. The MR analyses was performed using the inverse variance-weighted (IVW), MR-Egger, weighted median, and MR Pleiotropy RESidual Sum and Outlier methods. RESULTS: Computer use was genetically predicted to increase the myopia risk [IVW odds ratio (OR) = 1.057; 95% confidence interval (CI), 1.038-1.078; P = 7.04 × 10- 9]. The self-reported moderate-to-vigorous physical activity (MVPA) (IVW OR = 0.962; 95% CI, 0.932-0.993; P = 1.57 × 10- 2) and television watching (IVW OR = 0.973; 95% CI, 0.961-0.985, P = 1.93 × 10- 5) were significantly associated with a lower myopia risk. However, genetically predicted sleep traits or accelerometer-measured physical activity had no significant associations with myopia. CONCLUSION: Our results indicated that computer use is a risk factor for myopia, whereas television watching and MVPA may protect against myopia. These findings shed new light on possible strategies for reducing the prevalence of myopia.


Subject(s)
Myopia , Sedentary Behavior , Humans , Genome-Wide Association Study , Mendelian Randomization Analysis , Myopia/epidemiology , Myopia/genetics , Exercise , Sleep , Leisure Activities
17.
Sci Rep ; 14(1): 7028, 2024 03 25.
Article in English | MEDLINE | ID: mdl-38528062

ABSTRACT

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.


Subject(s)
Benchmarking , High-Throughput Nucleotide Sequencing , Humans , Computational Biology , Quality Control , INDEL Mutation , Polymorphism, Single Nucleotide
18.
PLoS One ; 19(3): e0301290, 2024.
Article in English | MEDLINE | ID: mdl-38551985

ABSTRACT

Mating plugs in animals are ubiquitous and are commonly interpreted to be products of mating strategies. In spiders, however, mating plugs may also take on functions beyond female remating prevention. Due to the vagaries of female genital (spermathecal) anatomy, most spiders face the problem of having to secure additional, non-anatomical, protection for transferred sperm. Here, we test the hypothesis that mating plugs, rather than (or in addition to) being adaptations for mating strategies, may serve as sperm protection mechanism. Based on a comparative study on 411 epigyna sampled from 36 families, 187 genera, 330 species of entelegyne spiders, our results confirm the necessity of a sperm protection mechanism. We divided the entelegyne spermathecae into four types: SEG, SED, SCG and SCD. We also studied detailed morphology of epigynal tracts in the spider Diphya wulingensis having the SEG type spermathecae, using 3D-reconstruction based on semi thin histological series section. In this species, we hypothesize that two distinct types of mating plug, the sperm plug and the secretion plug, serve different functions. Morphological details support this: sperm plugs are formed on a modified spermathecal wall by the spilled sperm, and function as a temporary protection mechanism to prevent sperm from leaking and desiccating, while secretion plugs function in postcopulation both as a permanent protection mechanism, and to prevent additional mating. Furthermore, with the modified spermathecal wall of S2 stalk, the problem of shunt of sperm input and output, and the possibility of female multiple mating have been resolved. Variation in spermathecal morphology also suggests that the problem of sperm protection might be resolved in different ways in spiders. Considering mating plugs of varying shapes and origins in the vast morphospace of spiders, we conclude that mating plugs might serve different purposes that relate both to mating strategies, as well as to sperm protection.


Subject(s)
Sexual Behavior, Animal , Spiders , Humans , Animals , Male , Female , Spiders/anatomy & histology , Semen , Reproduction , Spermatozoa
19.
Front Microbiol ; 15: 1301073, 2024.
Article in English | MEDLINE | ID: mdl-38440147

ABSTRACT

Introduction: Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods: In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results: Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions: C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.

20.
Int J Health Plann Manage ; 39(4): 1131-1145, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38192193

ABSTRACT

OBJECTIVE: To integrate the qualitative research on the self-management experience of breast cancer patients and conduct a systematic review of their self-management experience. METHODS: Using a computer to search a series of databases such as CNKI, Wanfang, VIP, and China Biomedical Database, systematically collect and integrate qualitative research on the self-management experience of breast cancer patients, and the search time is limited to January 2010 to December 2022. The qualitative research quality evaluation standard of the Joanna Briggs Institute Centre for Evidence-Based Health Care in Australia was used as the evaluation standard of this project to complete the accurate evaluation of the literature; Meta-analysis was used to complete the effective integration of the results. RESULTS: 17 pieces of literature were included in this project, and 37 research results with strong integrity were extracted accordingly. On this basis, 7 different categories were summarised, and three integrated results were obtained: the experience of maintaining self-management, symptom recognition, and self-management. CONCLUSION: In the different stages of self-management of breast cancer patients, medical staff should give targeted guidance to help patients obtain a good prognosis.


Subject(s)
Breast Neoplasms , Qualitative Research , Self-Management , Female , Humans , Breast Neoplasms/therapy , Self-Management/methods
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