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2.
Front Bioeng Biotechnol ; 12: 1385986, 2024.
Article in English | MEDLINE | ID: mdl-38983600

ABSTRACT

Objective: 1. To assess the Inter-rater reliability and test-retest reliability of FPI-6 total score and individual scores in static foot posture evaluation among elderly female patients with knee osteoarthritis (KOA), aiming to establish the reliability of the FPI-6 scale. 2. To investigate the disparity between dominant and non-dominant quadriceps characteristics in elderly female KOA patients, as well as explore the correlation between quadriceps characteristics and abnormal foot posture, thereby offering novel insights for the prevention and treatment of KOA. Methods: The study enrolled a total of 80 lower legs of 40 participants (all female) with unilateral or bilateral KOA, who were assessed by two raters at three different time points. The inter-rater and test-retest reliability of the FPI-6 was evaluated using the intra-class correlation coefficient (ICC), while the absolute reliability of FPI-6 was examined using the standard error of measurement (SEM), minimum detectable change (MDC), and Bland-Altman analysis. The internal consistency of FPI-6 was assessed using Spearman's correlation coefficient. Additionally, MyotonPRO was employed to assess quadriceps muscle tone and stiffness in all participants, and the association between quadriceps muscle tone/stiffness and the total score of FPI-6 was analyzed. Result: Our study found excellent inter-rater and test-retest reliability (ICC values of 0.923 and 0.931, respectively) for the FPI-6 total score, as well as good to excellent reliability (ICC values ranging from 0.680 to 0.863 and 0.739-0.883) for individual items. The SEM and MDC values for the total score of FPI-6 among our study inter-rater were 0.78 and 2.15, respectively. and the SEM and MDC values for the test-retest total score of FPI-6 were found to be 0.76 and 2.11, respectively. Furthermore, the SEM and MDC values between inter-rater and test-retest across six individual items ranged from 0.30 to 0.56 and from 0.84 to 1.56. The Bland-Altman plots and respective 95% LOA showed no evidence of systematic bias. In terms of the mechanical properties of the quadriceps on both sides, the muscle tone and stiffness of rectus femoris (RF), vastus medialis (VM), and vastus lateralis (VL) were significantly higher in the non-dominant leg compared to the dominant leg. Additionally, in the non-dominant leg, there was a significant positive correlation between the muscle tone and stiffness of VM, VL, RF and the total score of FPI-6. However, in the dominant leg, only VM's muscle tone and stiffness showed a significant positive correlation with the total score of FPI-6. Conclusion: The reliability of the FPI-6 total score and its six individual items was good to excellent. Our findings offer a straightforward and dependable approach for researchers to assess foot posture in elderly female patients with KOA. Furthermore, we observed significantly greater quadriceps tension and stiffness in the non-dominant leg compared to the dominant leg. The FPI-6 total score exhibited a significant correlation with changes in quadriceps muscle performance among KOA patients. These observations regarding the relationship between changes in quadriceps muscle performance and foot posture in elderly female KOA patients may provide novel insights for disease prevention, treatment, and rehabilitation.

3.
bioRxiv ; 2024 May 24.
Article in English | MEDLINE | ID: mdl-38826271

ABSTRACT

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. The biased use of synonymous codons has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. The Saccharomycotina, the fungal subphylum containing the yeasts Saccharomyces cerevisiae and Candida albicans , has been a model system for studying codon usage. We characterized codon usage across 1,154 strains from 1,051 species to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns across the subphylum. We found evidence of a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is also distinct between the 12 orders within the subphylum to such a degree that yeasts can be classified into orders with an accuracy greater than 90% using a machine learning algorithm trained on codon usage. We also characterized the degree to which codon usage bias is impacted by translational selection. Interestingly, the degree of translational selection was influenced by a combination of genome features and assembly metrics that included the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs. The order contains 24 species, and 23 are computationally predicted to lack tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that extreme avoidance of the CGN codons is associated with a decline in arginine tRNA function. Codon usage bias within the Saccharomycotina is generally consistent with previous investigations in fungi, which show a role for both genomic features and GC bias in shaping codon usage. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

4.
Nat Aging ; 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38834883

ABSTRACT

Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.

5.
bioRxiv ; 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38895429

ABSTRACT

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

6.
Syst Biol ; 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38940001

ABSTRACT

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

7.
Science ; 384(6694): eadj4503, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38662846

ABSTRACT

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.


Subject(s)
Ascomycota , Carbon , Gene-Environment Interaction , Nitrogen , Ascomycota/classification , Ascomycota/genetics , Ascomycota/metabolism , Carbon/metabolism , Genome, Fungal , Metabolic Networks and Pathways/genetics , Nitrogen/metabolism , Phylogeny
8.
J Am Chem Soc ; 146(17): 11978-11990, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38626322

ABSTRACT

Tethered nonplanar aromatics (TNAs) make up an important class of nonplanar aromatic compounds showing unique features. However, the knowledge on the synthesis, structures, and properties of TNAs remains insufficient. In this work, a new type of TNAs, the tethered aromatic lactams, is synthesized via Pd-catalyzed consecutive intramolecular direct arylations. These molecules possess a helical ladder-type conjugated system of up to 13 fused rings. The overall yields ranged from 3.4 to 4.3%. The largest of the tethered aromatic lactams, 6L-Bu-C14, demonstrates a guest-adaptive hosting capability of TNAs for the first time. When binding fullerene guests, the cavity of 6L-Bu-C14 became more circular to better accommodate spherical fullerene molecules. The host-guest interaction is thoroughly studied by X-ray crystallography, theoretical calculations, fluorescence titration, and nuclear magnetic resonance (NMR) titration experiments. 6L-Bu-C14 shows stronger binding with C70 than with C60 due to the better convex-concave π-π interaction. P and M enantiomers of all tethered aromatic lactams show distinct and persistent chiroptical properties and demonstrate the potential of chiral TNAs as circularly polarized luminescence (CPL) emitters.

9.
Proc Natl Acad Sci U S A ; 121(18): e2315314121, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38669185

ABSTRACT

How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype-phenotype map, and their application will uncover novel biology, even in well-studied traits.


Subject(s)
Galactose , Machine Learning , Galactose/metabolism , Genome, Fungal , Metabolic Networks and Pathways/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics
10.
Dev Cell ; 59(11): 1363-1378.e4, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38579719

ABSTRACT

The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.


Subject(s)
Germination , Oryza , Peroxisomes , Plant Growth Regulators , Plant Proteins , Oryza/metabolism , Oryza/growth & development , Germination/physiology , Peroxisomes/metabolism , Plant Growth Regulators/metabolism , Plant Proteins/metabolism , Gene Expression Regulation, Plant , Coenzyme A Ligases/metabolism , Indoleacetic Acids/metabolism , Seeds/metabolism , Seeds/growth & development , Salicylic Acid/metabolism , Cinnamates/metabolism
11.
Proc Natl Acad Sci U S A ; 121(10): e2316031121, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38412132

ABSTRACT

The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.


Subject(s)
Biodiversity , Ecosystem , Climate , Forests , Carbon , Yeasts
12.
New Phytol ; 242(1): 192-210, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38332398

ABSTRACT

Eukaryotes have evolved sophisticated post-translational modifications to regulate protein function and numerous biological processes, including ubiquitination controlled by the coordinated action of ubiquitin-conjugating enzymes and deubiquitinating enzymes (Dubs). However, the function of deubiquitination in pathogenic fungi is largely unknown. Here, the distribution of Dubs in the fungal kingdom was surveyed and their functions were systematically characterized using the phytopathogen Fusarium graminearum as the model species, which causes devastating diseases of all cereal species world-wide. Our findings demonstrate that Dubs are critical for fungal development and virulence, especially the ubiquitin-specific protease 15 (Ubp15). Global ubiquitome analysis and subsequent experiments identified three important substrates of Ubp15, including the autophagy-related protein Atg8, the mitogen-activated protein kinase Gpmk1, and the mycotoxin deoxynivalenol (DON) biosynthetic protein Tri4. Ubp15 regulates the deubiquitination of the Atg8, thereby impacting its subcellular localization and the autophagy process. Moreover, Ubp15 also modulates the deubiquitination of Gpmk1 and Tri4. This modulation subsequently influences their protein stabilities and further affects the formation of penetration structures and the biosynthetic process of DON, respectively. Collectively, our findings reveal a previously unknown regulatory pathway of a deubiquitinating enzyme for fungal virulence and highlight the potential of Ubp15 as a target for combating fungal diseases.


Subject(s)
Fusarium , Mycotoxins , Virulence , Fungal Proteins/metabolism , Mycotoxins/metabolism , Deubiquitinating Enzymes/metabolism , Plant Diseases/microbiology
13.
Mol Biol Evol ; 41(4)2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38415839

ABSTRACT

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.


Subject(s)
Enterobactin , Evolution, Molecular , Operon , Phylogeny , Enterobactin/metabolism , Enterobactin/genetics , Siderophores/metabolism , Siderophores/genetics , Genes, Fungal , Saccharomycetales/genetics , Saccharomycetales/metabolism , Gene Transfer, Horizontal
14.
Angew Chem Int Ed Engl ; 63(8): e202316227, 2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38179837

ABSTRACT

The limited exciton lifetime (τ, generally <1 ns) leads to short exciton diffusion length (LD ) of organic semiconductors, which is the bottleneck issue impeding the further improvement of power conversion efficiencies (PCEs) for organic solar cells (OSCs). However, efficient strategies to prolong intrinsic τ are rare and vague. Herein, we propose a facile method to efficiently reduce vibrational frequency of molecular skeleton and suppress exciton-vibration coupling to decrease non-radiative decay rate and thus prolong τ via deuterating nonfullerene acceptors. The τ remarkably increases from 0.90 ns (non-deuterated L8-BO) to 1.35 ns (deuterated L8-BO-D), which is the record for organic photovoltaic materials. Besides, the inhibited molecular vibration improves molecular planarity of L8-BO-D for enhanced exciton diffusion coefficient. Consequently, the LD increases from 7.9 nm (L8-BO) to 10.7 nm (L8-BO-D). The prolonged LD of L8-BO-D enables PM6 : L8-BO-D-based bulk heterojunction OSCs to acquire higher PCEs of 18.5 % with more efficient exciton dissociation and weaker charge carrier recombination than PM6 : L8-BO-based counterparts. Moreover, benefiting from the prolonged LD , D18/L8-BO-D-based pseudo-planar heterojunction OSCs achieve an impressive PCE of 19.3 %, which is among the highest values. This work provides an efficient strategy to increase the τ and thus LD of organic semiconductors, boosting PCEs of OSCs.

15.
Curr Protoc ; 4(1): e969, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38265166

ABSTRACT

PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Constructing a phylogenomic dataset Basic Protocol 2: Performing phylogenomic analyses Support Protocol 1: Installing PhyloFisher Support Protocol 2: Creating a custom phylogenomic database.


Subject(s)
Amino Acids , Biological Evolution , Phylogeny , Amino Acid Sequence , Culture
16.
Plant Cell ; 36(5): 1637-1654, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38114096

ABSTRACT

MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.


Subject(s)
Actinidia , Arabidopsis , Gene Expression Regulation, Plant , MicroRNAs , RNA, Plant , MicroRNAs/genetics , MicroRNAs/metabolism , Actinidia/genetics , Actinidia/metabolism , Arabidopsis/genetics , RNA, Plant/genetics , RNA, Plant/metabolism , Seeds/genetics , Seeds/metabolism , Base Sequence
17.
bioRxiv ; 2023 Nov 21.
Article in English | MEDLINE | ID: mdl-38045280

ABSTRACT

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.

18.
Front Physiol ; 14: 1269338, 2023.
Article in English | MEDLINE | ID: mdl-38046948

ABSTRACT

Background: Cellular senescence is associated with age-related pathological changes, senescent cells promote the development of knee osteoarthritis. A better understanding between knee osteoarthritis and cellular senescence may enhance the effectiveness of therapies that aim to slow or stop the progression of this disease. Purpose: This study aimed to systematically analyze and visualize the publication trends, research frontiers and current research hotspots of knee osteoarthritis and cellular senescence by using bibliometrics. Methods: The publication search was performed on the Web of Science Core Collection database for documents published from 1992 to 2023. VOSviewer, Citespace, R package Bibliometrix and Microsoft Office Excel were used to study the characteristics of the publications. The publication number, countries, institutions, authors, journals, citations and co-citations, keywords were analyzed. Results: A total of 1,074 publications were analyzed, with an average annual growth rate of 29.89%. United States accounted for the biggest contributor, ranked first in publications and citations. Publications of this field were published in 420 journals, OSTEOARTHRITIS and CARTILAGE was the most influential. A total of 5,657 authors contributed to this research. The most productive author was Lotz, MK (n = 31, H-index = 22, Total citation = 2,619), followed by Loeser, R.F (n = 16, H-index = 14, Total citation = 2,825). However, the collaboration between authors was relatively weak. Out of the 1,556 institutions involved, 60% were from the United States. Scripps Research ranked first with 25 papers and a total of 2,538 citations. The hotspots of this field had focused on the pathomechanisms (e.g., expression, inflammation, apoptosis, autophagy, oxidative stress) and therapeutics (e.g., stem cell, platelet-rich plasma, transplantation, autologous chondrocytes, repair), and the exploration of Senolytics might be the important direction of future research. Conclusion: Research on the cross field of knee osteoarthritis and cellular senescence is flourishing. Age-related pathomechanism maps of various cells in the joint and the targeted medicines for the senescent cells may be the future trends. This bibliometric study provides a comprehensive analysis of this cross field and new insights into future research.

19.
Math Biosci Eng ; 20(9): 16033-16044, 2023 08 07.
Article in English | MEDLINE | ID: mdl-37920001

ABSTRACT

The purpose of this study was to examine the effect of neuromuscular electrical stimulation (NMES) immediate intervention training on the countermovement jump (CMJ) height and to explore kinematic differences in the CMJ at each instant. A total of 15 male students who had never received electrical stimulation were randomly selected as the research participants. In the first test, the CMJ performance was completed with an all-out effort. The second experiment was best performed immediately to complete the CMJ operation after NMES for 30 min. Both experiments used a high-speed camera optical capture system to collect kinematic data. The results of this experiment revealed that after im-mediate NMES training, neuromuscular activation causes post-activation potentiation, which increases the height of the center of gravity of the CMJ and affects the angular velocity of the hip joint, the velocity and acceleration of the thigh and the shank and the velocity of the soles of the feet. The use of NMES interventional training based on the improvement of technical movements and physical exercises is recommended in the future.


Subject(s)
Exercise , Foot , Humans , Male , Biomechanical Phenomena , Movement
20.
bioRxiv ; 2023 Aug 31.
Article in English | MEDLINE | ID: mdl-37693602

ABSTRACT

The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth1; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild2. Here, we trained machine learning models on 12,221 occurrence records and 96 environmental variables to infer global distribution maps for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversification. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many longstanding macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and latitude-dependent range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.

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