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1.
bioRxiv ; 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38948868

ABSTRACT

The Ca2+ sensor synaptotagmin-1 triggers neurotransmitter release together with the neuronal SNARE complex formed by syntaxin-1, SNAP25 and synaptobrevin. Moreover, synaptotagmin-1 increases synaptic vesicle priming and impairs spontaneous vesicle release. The synaptotagmin-1 C2B domain binds to the SNARE complex through a primary interface via two regions (I and II), but how exactly this interface mediates distinct functions of synaptotagmin-1, and the mechanism underlying Ca2+-triggering of release is unknown. Using mutagenesis and electrophysiological experiments, we show that region II is functionally and spatially subdivided: binding of C2B domain arginines to SNAP-25 acidic residues at one face of region II is crucial for Ca2+-evoked release but not for vesicle priming or clamping of spontaneous release, whereas other SNAP-25 and syntaxin-1 acidic residues at the other face mediate priming and clamping of spontaneous release but not evoked release. Mutations that disrupt region I impair the priming and clamping functions of synaptotagmin-1 while, strikingly, mutations that enhance binding through this region increase vesicle priming and clamping of spontaneous release, but strongly inhibit evoked release and vesicle fusogenicity. These results support previous findings that the primary interface mediates the functions of synaptotagmin-1 in vesicle priming and clamping of spontaneous release, and, importantly, show that Ca2+-triggering of release requires a rearrangement of the primary interface involving dissociation of region I, while region II remains bound. Together with modeling and biophysical studies presented in the accompanying paper, our data suggest a model whereby this rearrangement pulls the SNARE complex to facilitate fast synaptic vesicle fusion.

2.
Front Genet ; 15: 1389630, 2024.
Article in English | MEDLINE | ID: mdl-38894720

ABSTRACT

Introduction: Sepsis leads to multi-organ dysfunction due to disorders of the host response to infections, which makes diagnosis and prognosis challenging. Apoptosis, a classic programmed cell death, contributes to the pathogenesis of various diseases. However, there is much uncertainty about its mechanism in sepsis. Methods: Three sepsis gene expression profiles (GSE65682, GSE13904, and GSE26378) were downloaded from the Gene Expression Omnibus database. Apoptosis-related genes were obtained from the Kyoto Encyclopedia of Genes and Genomes Pathway database. We utilized LASSO regression and SVM-RFE algorithms to identify characteristic genes associated with sepsis. CIBERSORT and single cell sequencing analysis were employed to explore the potential relationship between hub genes and immune cell infiltration. The diagnostic capability of hub genes was validated across multiple external datasets. Subsequently, the animal sepsis model was established to assess the expression levels of hub genes in distinct target organs through RT-qPCR and Immunohistochemistry analysis. Results: We identified 11 apoptosis-related genes as characteristic diagnostic markers for sepsis: CASP8, VDAC2, CHMP1A, CHMP5, FASLG, IFNAR1, JAK1, JAK3, STAT4, IRF9, and BCL2. Subsequently, a prognostic model was constructed using LASSO regression with BCL2, FASLG, IRF9 and JAK3 identified as hub genes. Apoptosis-related genes were closely associated with the immune response during the sepsis process. Furthermore, in the validation datasets, aside from IRF9, other hub genes demonstrated similar expression patterns and diagnostic abilities as observed in GSE65682 dataset. In the mouse model, the expression differences of hub genes between sepsis and control group revealed the potential impacts on sepsis-induced organ injury. Conclusion: The current findings indicated the participant of apoptosis in sepsis, and apoptosis-related differentially expressed genes could be used for diagnosis biomarkers. BCL2, FASLG, IRF9 and JAK3 might be key regulatory genes affecting apoptosis in sepsis. Our findings provided a novel aspect for further exploration of the pathological mechanisms in sepsis.

3.
Int J Ophthalmol ; 17(6): 1007-1017, 2024.
Article in English | MEDLINE | ID: mdl-38895685

ABSTRACT

AIM: To identify genetic defects in a Chinese family with congenital posterior polar cataracts and assess the pathogenicity. METHODS: A four-generation Chinese family affected with autosomal dominant congenital cataract was recruited. Nineteen individuals took part in this study including 5 affected and 14 unaffected individuals. Sanger sequencing targeted hot-spot regions of 27 congenital cataract-causing genes for variant discovery. The pathogenicity of the variant was evaluated by the guidelines of American College of Medical Genetics and InterVar software. Confocal microscopy was applied to detect the subcellular localization of fluorescence-labeled ephrin type-A receptor 2 (EPHA2). Co-immunoprecipitation assay was implemented to estimate the interaction between EphA2 and other lens membrane proteins. The mRNA and protein expression were analyzed by reverse transcription-polymerase chain reaction (qRT-PCR) and Western blotting assay, respectively. The cell migration was analyzed by wound healing assay. Zebrafish model was generated by ectopic expression of human EPHA2/p.R957P mutant to demonstrate whether the mutant could cause lens opacity in vivo. RESULTS: A novel missense and pathogenic variant c.2870G>C was identified in the sterile alpha motif (SAM) domain of EPHA2. Functional studies demonstrated the variant's impact: reduced EPHA2 protein expression, altered subcellular localization, and disrupted interactions with other lens membrane proteins. This mutant notably enhanced human lens epithelial cell migration, and induced a central cloudy region and roughness in zebrafish lenses with ectopic expression of human EPHA2/p.R957P mutant under differential interference contrast (DIC) optics. CONCLUSION: Novel pathogenic c.2870G>C variant of EPHA2 in a Chinese congenital cataract family contributes to disease pathogenesis.

4.
Sensors (Basel) ; 24(12)2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38931781

ABSTRACT

This study addresses the limitations of current tonometry techniques by exploring vibroacoustic properties for estimating intraocular pressure (IOP), a key diagnostic parameter for monitoring glaucoma-a significant risk factor for vision loss. Utilizing vivo porcine eyeballs, we investigated the relationship between IOP and the nonlinear vibration transfer function ratio (NVTFR). Through applying varying vibration levels and analyzing responses with transfer function analysis and univariate regression, we identified a strong negative correlation between NVTFR and IOP, evidenced by a Pearson correlation coefficient of -0.8111 and significant results from generalized linear model (GLM) regression (p-value < 0.001). These findings indicate the potential of NVTFR as a vital indicator of IOP changes. Our study highlights the feasibility of using vibroacoustic properties, specifically NVTFR, to measure IOP. While further refinement is necessary for in vivo application, this approach opens new possibilities for non-invasive and patient-friendly IOP monitoring, potentially enhancing ophthalmology diagnostic techniques and providing a foundation for future research and development in this critical area.


Subject(s)
Intraocular Pressure , Tonometry, Ocular , Vibration , Intraocular Pressure/physiology , Animals , Swine , Tonometry, Ocular/methods , Eye , Glaucoma/physiopathology , Glaucoma/diagnosis , Feasibility Studies , Humans
5.
Physiol Meas ; 45(6)2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38838702

ABSTRACT

Objective. Cerebral critical closing pressure (CrCP) represents the value of arterial blood pressure (BP) where cerebral blood flow (CBF) becomes zero. Its dynamic response to a step change in mean BP (MAP) has been shown to reflect CBF autoregulation, but robust methods for its estimation are lacking. We aim to improve the quality of estimates of the CrCP dynamic response.Approach. Retrospective analysis of 437 healthy subjects (aged 18-87 years, 218 males) baseline recordings with measurements of cerebral blood velocity in the middle cerebral artery (MCAv, transcranial Doppler), non-invasive arterial BP (Finometer) and end-tidal CO2(EtCO2, capnography). For each cardiac cycle CrCP was estimated from the instantaneous MCAv-BP relationship. Transfer function analysis of the MAP and MCAv (MAP-MCAv) and CrCP (MAP-CrCP) allowed estimation of the corresponding step responses (SR) to changes in MAP, with the output in MCAv (SRVMCAv) representing the autoregulation index (ARI), ranging from 0 to 9. Four main parameters were considered as potential determinants of the SRVCrCPtemporal pattern, including the coherence function, MAP spectral power and the reconstruction error for SRVMAP, from the other three separate SRs.Main results. The reconstruction error for SRVMAPwas the main determinant of SRVCrCPsignal quality, by removing the largest number of outliers (Grubbs test) compared to the other three parameters. SRVCrCPshowed highly significant (p< 0.001) changes with time, but its amplitude or temporal pattern was not influenced by sex or age. The main physiological determinants of SRVCrCPwere the ARI and the mean CrCP for the entire 5 min baseline period. The early phase (2-3 s) of SRVCrCPresponse was influenced by heart rate whereas the late phase (10-14 s) was influenced by diastolic BP.Significance. These results should allow better planning and quality of future research and clinical trials of novel metrics of CBF regulation.


Subject(s)
Arterial Pressure , Cerebrovascular Circulation , Humans , Male , Middle Aged , Adult , Aged , Female , Adolescent , Aged, 80 and over , Young Adult , Arterial Pressure/physiology , Cerebrovascular Circulation/physiology , Retrospective Studies , Middle Cerebral Artery/physiology , Middle Cerebral Artery/diagnostic imaging , Homeostasis
6.
Cureus ; 16(5): e59895, 2024 May.
Article in English | MEDLINE | ID: mdl-38854351

ABSTRACT

INTRODUCTION: Gender determination of deceased individuals may become necessary in scenarios involving sudden and unforeseen fatalities like explosions, fires, transportation accidents, or instances of mutilation or decomposition, which frequently require medicolegal expertise. Forensic radiology is instrumental in identifying gender. The shape of the frontal sinus is considered distinct for every person, differing even among identical twins, much like individual fingerprints and establishing personal identity. AIMS AND OBJECTIVES: This study was designed to validate and determine gender identification by evaluating frontal sinus measurements using digital posteroanterior cephalograms with reference to Yoshino's classification and to determine gender based on measurements of frontal sinus size, bilateral asymmetry, the outline of the upper border of the frontal sinus, partial septa, and supraorbital cells of the frontal sinus. MATERIALS AND METHODS: A total of 300 digital posteroanterior cephalograms (150 males and 150 females) of age groups ranging from 18 to 30 years were collected from the records of the Department of Oral Medicine and Radiology, Panineeya Institute of Dental Sciences & Research Centre, Hyderabad. The parameters that were assessed in a digital radiograph are Yoshino's frontal sinus pattern of the individual, which includes frontal sinus size, bilateral asymmetry, superiority of the side, outline of the upper border, partial septa, and supraorbital cells. The measurements were taken, tabulated, and compared with the standard values of the gender measurement. The values were subjected to statistical analysis. RESULTS: Results showed a statistically significant difference in the mean height (p=0.000), width (p=0.000), area (p=0.000), partial septa (p=0.002), and outline of the upper border on the right side (p=0.011) of the frontal sinus for both males and females. The mean values for length, width, and area of the frontal sinus were higher in males than females. No statistical difference is found on the outline of the upper border on the left side, superiority of the side, and supraorbital cells. The application of discriminative analysis to the data accurately identified gender in 65.3% of the cases. CONCLUSION: Thus, from the above study, the forensic application of frontal sinus morphology can be recommended as an adjunctive tool for gender determination.

7.
BMC Plant Biol ; 24(1): 590, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38902595

ABSTRACT

BACKGROUND: The Prunus sibirica seeds with rich oils has great utilization, but contain amygdalin that can be hydrolyzed to release toxic HCN. Thus, how to effectively reduce seed amygdalin content of P. sibirica is an interesting question. Mandelonitrile is known as one key intermediate of amygdalin metabolism, but which mandelonitrile lyase (MDL) family member essential for its dissociation destined to low amygdalin accumulation in P. sibirica seeds still remains enigmatic. An integration of our recent 454 RNA-seq data, amygdalin and mandelonitrile content detection, qRT-PCR analysis and function determination is described as a critical attempt to determine key MDL and to highlight its function in governing mandelonitrile catabolism with low amygdalin accumulation in Prunus sibirica seeds for better developing edible oil and biodiesel in China. RESULTS: To identify key MDL and to unravel its function in governing seed mandelonitrile catabolism with low amygdalin accumulation in P. sibirica. Global identification of mandelonitrile catabolism-associated MDLs, integrated with the across-accessions/developing stages association of accumulative amount of amygdalin and mandelonitrile with transcriptional level of MDLs was performed on P. sibirica seeds of 5 accessions to determine crucial MDL2 for seed mandelonitrile catabolism of P. sibirica. MDL2 gene was cloned from the seeds of P. sibirica, and yeast eukaryotic expression revealed an ability of MDL2 to specifically catalyze the dissociation of mandelonitrile with the ideal values of Km (0.22 mM) and Vmax (178.57 U/mg). A combination of overexpression and mutation was conducted in Arabidopsis. Overexpression of PsMDL2 decreased seed mandelonitrile content with an increase of oil accumulation, upregulated transcript of mandelonitrile metabolic enzymes and oil synthesis enzymes (involving FA biosynthesis and TAG assembly), but exhibited an opposite situation in mdl2 mutant, revealing a role of PsMDL2-mediated regulation in seed amygdalin and oil biosynthesis. The PsMDL2 gene has shown as key molecular target for bioengineering high seed oil production with low amygdalin in oilseed plants. CONCLUSIONS: This work presents the first integrated assay of genome-wide identification of mandelonitrile catabolism-related MDLs and the comparative association of transcriptional level of MDLs with accumulative amount of amygdalin and mandelonitrile in the seeds across different germplasms and developmental periods of P. sibirica to determine MDL2 for mandelonitrile dissociation, and an effective combination of PsMDL2 expression and mutation, oil and mandelonitrile content detection and qRT-PCR assay was performed to unravel a mechanism of PsMDL2 for controlling amygdalin and oil production in P. sibirica seeds. These findings could offer new bioengineering strategy for high oil production with low amygdalin in oil plants.


Subject(s)
Amygdalin , Prunus , Seeds , Amygdalin/metabolism , Prunus/genetics , Prunus/metabolism , Prunus/enzymology , Seeds/metabolism , Seeds/genetics , Plant Proteins/metabolism , Plant Proteins/genetics , Plant Oils/metabolism , Aldehyde-Lyases/metabolism , Aldehyde-Lyases/genetics , Gene Expression Regulation, Plant
9.
J Forensic Leg Med ; 104: 102688, 2024 May.
Article in English | MEDLINE | ID: mdl-38703465

ABSTRACT

Analyzing skeletal remains is crucial for identifying individuals, and forensic anthropologists use this analysis to determine biological characteristics, particularly sex, aiding criminal investigations. Among thoracic vertebrae, the twelfth thoracic vertebra (T12) is highly sexually dimorphic in various populations. This study aims to establish a discriminant function equation (DFE) for sex determination based on T12 in the Central Thai population. A total of 15 parameters of T12 were examined in 69 bone samples (43 males and 26 females). Among the 15 parameters, 14 were significantly different between males and females. The discriminant function equation (DFE) was generated as DFE = -19.578 + 0.376(i) BDsm + 0.254(l) PW + 0.081TDm, with a cutoff value of -0.296 for males and females, showing 92.8 % accuracy. The evaluation of the DFE using 10 blind samples showed 90 % accuracy. These findings may offer an additional method for sex determination through T12, complementing the examination of other skeletal elements.


Subject(s)
Forensic Anthropology , Sex Determination by Skeleton , Thoracic Vertebrae , Humans , Sex Determination by Skeleton/methods , Male , Female , Thoracic Vertebrae/anatomy & histology , Thailand , Discriminant Analysis , Adult , Middle Aged , Aged , Asian People , Young Adult , Aged, 80 and over , Southeast Asian People
10.
Molecules ; 29(10)2024 May 08.
Article in English | MEDLINE | ID: mdl-38792058

ABSTRACT

The 1092 bp F3H gene from Trapa bispinosa Roxb., which was named TbF3H, was cloned and it encodes 363 amino acids. Bioinformatic and phylogenetic tree analyses revealed the high homology of TbF3H with flavanone 3-hydroxylase from other plants. A functional analysis showed that TbF3H of Trapa bispinosa Roxb. encoded a functional flavanone 3-hydroxylase; it catalyzed the formation of dihydrokaempferol (DHK) from naringenin in S. cerevisiae. The promoter strengths were compared by fluorescence microscopy and flow cytometry detection of the fluorescence intensity of the reporter genes initiated by each constitutive promoter (FITC), and DHK production reached 216.7 mg/L by the promoter adjustment strategy and the optimization of fermentation conditions. The results presented in this study will contribute to elucidating DHK biosynthesis in Trapa bispinosa Roxb.


Subject(s)
Flavanones , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Flavanones/biosynthesis , Flavanones/metabolism , Phylogeny , Promoter Regions, Genetic , Cloning, Molecular/methods , Flavonoids/biosynthesis , Plant Proteins/genetics , Plant Proteins/metabolism , Fermentation
11.
BMC Plant Biol ; 24(1): 376, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38714947

ABSTRACT

BACKGROUND: Casuarina equisetifolia (C. equisetifolia) is a woody species with many excellent features. It has natural resistance against drought, salt and saline-alkali stresses. WRKY transcription factors (TFs) play significant roles in plant response to abiotic stresses, therefore, molecular characterization of WRKY gene family under abiotic stresses holds great significance for improvement of forest trees through molecular biological tools. At present, WRKY TFs from C. equisetifolia have not been thoroughly studied with respect to their role in salt and saline-alkali stresses response. The current study was conducted to bridge the same knowledge gap. RESULTS: A total of 64 WRKYs were identified in C. equisetifolia and divided into three major groups i.e. group I, II and III, consisting of 10, 42 and 12 WRKY members, respectively. The WRKY members in group II were further divided into 5 subgroups according to their homology with Arabidopsis counterparts. WRKYs belonging to the same group exhibited higher similarities in gene structure and the presence of conserved motifs. Promoter analysis data showed the presence of various response elements, especially those related to hormone signaling and abiotic stresses, such as ABRE (ABA), TGACG (MeJA), W-box ((C/T) TGAC (T/C)) and TC-rich motif. Tissue specific expression data showed that CeqWRKYs were mainly expressed in root under normal growth conditions. Furthermore, most of the CeqWRKYs were up-regulated by NaCl and NaHCO3 stresses with few of WRKYs showing early responsiveness to both stresses while few others exhibiting late response. Although the expressions of CeqWRKYs were also induced by cold stress, the response was delayed compared with other stresses. Transgenic C. equisetifolia plants overexpressing CeqWRKY11 displayed lower electrolyte leakage, higher chlorophyll content, and enhanced tolerance to both stresses. The higher expression of abiotic stress related genes, especially CeqHKT1 and CeqPOD7, in overexpression lines points to the maintenance of optimum Na+/K+ ratio, and ROS scavenging as possible key molecular mechanisms underlying salt stress tolerance. CONCLUSIONS: Our results show that CeqWRKYs might be key regulators of NaCl and NaHCO3 stresses response in C. equisetifolia. In addition, positive correlation of CeqWRKY11 expression with increased stress tolerance in C. equisetifolia encourages further research on other WRKY family members through functional genomic tools. The best candidates could be incorporated in other woody plant species for improving stress tolerance.


Subject(s)
Plant Proteins , Transcription Factors , Transcription Factors/genetics , Transcription Factors/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Gene Expression Regulation, Plant , Sodium Chloride/pharmacology , Phylogeny , Sodium Bicarbonate/pharmacology , Salt Stress/genetics , Stress, Physiological/genetics , Genome, Plant
12.
Environ Res ; 252(Pt 4): 119127, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38750998

ABSTRACT

With the ability to generate in situ real-time electric signals, electrochemically active biofilm (EAB) sensors have attracted wide attention as a promising water biotoxicity early-warning device. Organic matters serving as the electron donors potentially affect the electric signal's output and the sensitivity of the EAB sensor. To explore the influence of organic matters on EAB sensor's performance, this study tested six different organic matters during the sensor's inoculation. Besides the acetate, a conventional and widely used organic matter, propionate and lactate were also found capable of starting up the sensor. Moreover, the propionate-fed (PF) sensor delivered the highest sensitivity, which are respectively 1.4 times and 2.8 times of acetate-fed (AF) sensor and lactate-fed (LF) sensor. Further analysis revealed that EAB of PF sensor had more vulnerable intracellular metabolism than the others, which manifested as the most severe energy metabolic suppression and reactive oxygen species attack. Regarding the microbial function, a two-component system that was deemed as an environment awareness system was found in the EAB of PF, which also contributed to its high sensitivity. Finally, PF sensor was tested in real water environment to deliver early-warning signals.


Subject(s)
Acetates , Biofilms , Electrochemical Techniques , Propionates , Biofilms/drug effects , Biofilms/growth & development , Electrochemical Techniques/instrumentation , Electrochemical Techniques/methods , Water Pollutants, Chemical/analysis , Water Pollutants, Chemical/toxicity , Biosensing Techniques/instrumentation , Biosensing Techniques/methods
13.
Heliyon ; 10(10): e31331, 2024 May 30.
Article in English | MEDLINE | ID: mdl-38813169

ABSTRACT

The current study was carried out at Nuclear Institute of Agriculture, Tandojam to assess ten mungbean mutants together with one check cultivar in two separate cropping seasons. The findings revealed that all mutants, with the exception of the branches per plant, had significantly different examined traits. By characterizing ten variables, including plant height (cm), number of branches/plant, number of seeds per pod, grain yield per plot (g/plot), grain weight per plant, pod length (cm), pods per plant, days to flowering, above ground biological weight per plot (g/plot) and days to maturity, the results could considerably differentiate between low and high producing mutants. Discriminant analysis was used to choose high-yielding genotypes. The discriminant score demonstrated a significant canonical correlation of 0.994** and could account for 98.8 % of differences in mungbean production. According to the results of discriminant function analysis, the most significant features are pod length, days to flowering, plant height and above ground biological weight. The highest discriminant scores were displayed by the genotypes AEM66, AEM27, AEM25 and AEM14, identified as high yielding mutants. The low yielding mungbean mutants, designated Viz, AEM20, AEM30, AEM35, AEM-96, AEM29, AEM40 and AEM32 are those that exhibit the lowest values of the discriminant score. Mungbean cultivation is more successful in the summer than it is in the spring.

14.
IUCrJ ; 11(Pt 3): 423-433, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38700232

ABSTRACT

Appreciating that the role of the solute-solvent and other outer-sphere interactions is essential for understanding chemistry and chemical dynamics in solution, experimental approaches are needed to address the structural consequences of these interactions, complementing condensed-matter simulations and coarse-grained theories. High-energy X-ray scattering (HEXS) combined with pair distribution function analysis presents the opportunity to probe these structures directly and to develop quantitative, atomistic models of molecular systems in situ in the solution phase. However, at concentrations relevant to solution-phase chemistry, the total scattering signal is dominated by the bulk solvent, prompting researchers to adopt a differential approach to eliminate this unwanted background. Though similar approaches are well established in quantitative structural studies of macromolecules in solution by small- and wide-angle X-ray scattering (SAXS/WAXS), analogous studies in the HEXS regime-where sub-ångström spatial resolution is achieved-remain underdeveloped, in part due to the lack of a rigorous theoretical description of the experiment. To address this, herein we develop a framework for differential solution scattering experiments conducted at high energies, which includes concepts of the solvent-excluded volume introduced to describe SAXS/WAXS data, as well as concepts from the time-resolved X-ray scattering community. Our theory is supported by numerical simulations and experiment and paves the way for establishing quantitative methods to determine the atomic structures of small molecules in solution with resolution approaching that of crystallography.

15.
Ecol Evol ; 14(5): e11342, 2024 May.
Article in English | MEDLINE | ID: mdl-38799395

ABSTRACT

The morphological variation in Schizothorax oconnori, Schizothorax waltoni, and their natural hybrids was examined using conventional and image-based analysis approaches. In total, 38 specimens of S. oconnori, 35 of S. waltoni, and 37 natural hybrids were collected from the Shigatse to the Lhasa section of the Yarlung Zangbo River during June and July 2021. A total of 21 morphometric, 4 meristic, and 27 truss variables were employed for the classification of S. oconnori, S. waltoni, and natural hybrids. Principal component analysis (PCA) and factor analysis (FA), as well as discriminant function analysis (DFA) and cluster analysis (CA), were conducted to identify differences based on traditional and truss measurements. Four principal components explained 75.92% of the variation among the morphometric characters, while five principal components accounted for 79.69% of the variation among the truss distances. FA results showed that factor 1 was associated with head shape, and factor 2 was associated with fins based on morphometric characters. Among the truss characters, factor 1 was related to head shape, and factor 2 was related to chest shape. In DFA, morphometric measurements achieved higher accuracy (100%) compared to truss distances (94.55%). The head morphology of hybrids exhibited intermediate traits between S. oconnori and S. waltoni. Both morphometry-based and truss-based clustering indicated that the morphology of natural hybrids leaned toward S. oconnori. In conclusion, the combination of morphometric and truss analysis is beneficial for classifying S. oconnori, S. waltoni, and their natural hybrids. The presence of natural hybrids could be considered an evolutionary response to the differentiation of nutritional and spatial niches in the middle Yarlung Zangbo River.

16.
Methods Mol Biol ; 2788: 227-241, 2024.
Article in English | MEDLINE | ID: mdl-38656517

ABSTRACT

The Coffea spp. plant is a significant crop in Latin America, Africa, and Asia, and recent advances in genomics and transcriptomics have opened possibilities for studying candidate genes and introducing new desirable traits through genetic engineering. While stable transformation of coffee plants has been reported using various techniques, it is a time-consuming and laborious process. To overcome this, transient transformation methods have been developed, which avoid the limitations of stable transformation. This chapter describes an ex vitro protocol for transient expression using A. tumefaciens-mediated infiltration of coffee leaves, which could be used to produce coffee plants expressing desirable traits against biotic and abiotic stresses, genes controlling biochemical and physiological traits, as well as for gene editing through CRISPR/Cas9.


Subject(s)
Agrobacterium tumefaciens , Coffea , Gene Editing , Plant Leaves , Plants, Genetically Modified , Transgenes , Coffea/genetics , Plant Leaves/genetics , Plant Leaves/metabolism , Plants, Genetically Modified/genetics , Agrobacterium tumefaciens/genetics , Gene Editing/methods , Transformation, Genetic , CRISPR-Cas Systems , Gene Expression Regulation, Plant
18.
BMC Genomics ; 25(1): 342, 2024 Apr 04.
Article in English | MEDLINE | ID: mdl-38575876

ABSTRACT

BACKGROUND: Dendrobium huoshanense, a traditional medicinal and food plant, has a rich history of use. Recently, its genome was decoded, offering valuable insights into gene function. However, there is no comprehensive gene functional analysis platform for D. huoshanense. RESULT: To address this, we created a platform for gene function analysis and comparison in D. huoshanense (DhuFAP). Using 69 RNA-seq samples, we constructed a gene co-expression network and annotated D. huoshanense genes by aligning sequences with public protein databases. Our platform contained tools like Blast, gene set enrichment analysis, heatmap analysis, sequence extraction, and JBrowse. Analysis revealed co-expression of transcription factors (C2H2, GRAS, NAC) with genes encoding key enzymes in alkaloid biosynthesis. We also showcased the reliability and applicability of our platform using Chalcone synthases (CHS). CONCLUSION: DhuFAP ( www.gzybioinformatics.cn/DhuFAP ) and its suite of tools represent an accessible and invaluable resource for researchers, enabling the exploration of functional information pertaining to D. huoshanense genes. This platform stands poised to facilitate significant biological discoveries in this domain.


Subject(s)
Dendrobium , Dendrobium/genetics , Dendrobium/metabolism , Reproducibility of Results
19.
J Cereb Blood Flow Metab ; : 271678X241235878, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38635887

ABSTRACT

Numerous driven techniques have been utilized to assess dynamic cerebral autoregulation (dCA) in healthy and clinical populations. The current review aimed to amalgamate this literature and provide recommendations to create greater standardization for future research. The PubMed database was searched with inclusion criteria consisting of original research articles using driven dCA assessments in humans. Risk of bias were completed using Scottish Intercollegiate Guidelines Network and Methodological Index for Non-Randomized Studies. Meta-analyses were conducted for coherence, phase, and gain metrics at 0.05 and 0.10 Hz using deep-breathing, oscillatory lower body negative pressure (OLBNP), sit-to-stand maneuvers, and squat-stand maneuvers. A total of 113 studies were included, with 40 of these incorporating clinical populations. A total of 4126 participants were identified, with younger adults (18-40 years) being the most studied population. The most common techniques were squat-stands (n = 43), deep-breathing (n = 25), OLBNP (n = 20), and sit-to-stands (n = 16). Pooled coherence point estimates were: OLBNP 0.70 (95%CI:0.59-0.82), sit-to-stands 0.87 (95%CI:0.79-0.95), and squat-stands 0.98 (95%CI:0.98-0.99) at 0.05 Hz; and deep-breathing 0.90 (95%CI:0.81-0.99); OLBNP 0.67 (95%CI:0.44-0.90); and squat-stands 0.99 (95%CI:0.99-0.99) at 0.10 Hz. This review summarizes clinical findings, discusses the pros/cons of the 11 unique driven techniques included, and provides recommendations for future investigations into the unique physiological intricacies of dCA.

20.
Huan Jing Ke Xue ; 45(2): 1161-1172, 2024 Feb 08.
Article in Chinese | MEDLINE | ID: mdl-38471953

ABSTRACT

With the vigorous development of agriculture in China, plastic mulch film and pesticides are widely used in agricultural production. However, the accumulation of microplastics (formed by the degradation of plastic mulch film) and pesticides in soil has also caused many environmental problems. At present, the environmental biological effects of microplastics or pesticides have been reported, but there are few studies on the combined effects on crop growth and the rhizosphere soil bacterial community. Therefore, in this study, the high density polyethylene microplastics (HDPE, 500 mesh) were designed to be co-treated with sulfonylurea herbicide chlorimuron-ethyl to study their effects on soybean growth. In addition, the effects of the combined stress of HDPE and chlorimuron-ethyl on soybean rhizosphere soil bacterial community diversity, structure composition, microbial community network, and soil function were investigated using high-throughput sequencing technology, interaction network, and PICRUSt2 function analysis to clarify the combined toxicity of HDPE and chlorimuron-ethyl to soybean. The results showed that the half-life of chlorimuron-ethyl in soil was prolonged by the 1% HDPE treatment (from 11.5 d to 14.3 d), and the combined stress of HDPE and chlorimuron-ethyl had more obvious inhibition effects on soybean growth than that of the single pollutant or control. The HiSeq 2 500 sequencing showed that the rhizosphere bacterial community of soybean was composed of 20 phyla and 312 genera under combined stress, the number of phyla and genera was significantly less than that of the control and single pollutant treatment, and the relative abundances of bacteria with potential biological control and plant growth-promoting characteristics (such as Nocardioides and Sphingomonas) were reduced. Alpha diversity analysis showed that the combined stress significantly reduced the richness and diversity of the soybean rhizosphere bacterial community, and Beta diversity analysis showed that the combined stress significantly changed the structure of the bacterial community. The dominant flora of the rhizosphere bacterial community were regulated, and the abundances of secondary functional layers such as amino acid metabolism, energy metabolism, and lipid metabolism were reduced under combined stress by the analysis of LEfSe and PICRUSt2. It was inferred from the network analysis that the combined stress of HDPE and chlorimuron-ethyl reduced the total number of connections and network density of soil bacteria, simplified the network structure, and changed the important flora species to maintain the stability of the network. The results above indicated that the combined stress of HDPE and chlorimuron-ethyl significantly affected the growth of soybean and changed the rhizosphere bacterial community structure, soil function, and network structure. Compared with that of the single pollutant treatment, the potential risk of combined stress was greater. The results of this study can provide guidance for evaluating the ecological risks of polyethylene microplastics and chlorimuron-ethyl and for the remediation of contaminated soil.


Subject(s)
Environmental Pollutants , Herbicides , Pyrimidines , Sulfonylurea Compounds , Polyethylene/metabolism , Polyethylene/pharmacology , Rhizosphere , Glycine max , Microplastics , Plastics , Bacteria , Soil , Soil Microbiology
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