Phenotypic Differences Research Articles

Differences in the autoantibody phenotypes and long-term outcomes between juvenile- and adult-onset systemic sclerosis.

[Objective] To investigate differences in autoantibodies, clinical features, and long-term outcomes between juvenile- and adult-onset systemic sclerosis (SSc). [Methods] Autoantibodies and survival rates over a maximum of 20 years were retrospectively analyzed in 504 Japanese patients with SSc (juvenile-onset SSc, n=17; adult-onset SSc, n=487) using data from Kyoto University Registry. [Results] The autoantibodies observed were anti-topoisomerase-I (71% vs. 26%), anti-centromere (24% vs. 54%), and anti-RNA-polymerase-III (0% vs. 12%). A diffuse type and multi-organ involvement were observed in patients with anti-topoisomerase-I in both juvenile- and adult-onset SSc. In patients with anti-centromere, a diffuse type (juvenile-onset SSc vs. adult-onset SSc, 75% vs. 28%) and pulmonary fibrosis (50% vs. 17%) were more frequently observed in juvenile-onset SSc than in adult-onset SSc. Cox-proportional hazard analyses showed that older onset (hazard ratio: 1.06, 95% confidence interval: 1.03-1.09) was associated with death, while autoantibodies were not significantly associated with death. Cumulative survival rates for 20 years were similar between juvenile- and adult-onset SSc when classified based on the presence of anti-centromere (100% vs. 89%, p=0.20) and anti-topoisomerase-I (90% vs. 90%, p=0.70). [Conclusions] Juvenile-onset SSc had more frequent diffuse-type and anti-topoisomerase-I. An older onset was slightly associated with mortality, whereas autoantibodies were not associated with mortality.

Exploiting Cancer Dormancy Signaling Mechanisms in Epithelial Ovarian Cancer Through Spheroid and Organoid Analysis

Epithelial ovarian cancer (EOC) exhibits a unique mode of metastasis, involving spheroid formation in the peritoneum. Our research on EOC spheroid cell biology has provided valuable insights into the signaling plasticity associated with metastasis. We speculate that EOC cells modify their biology between tumour and spheroid states during cancer dormancy, although the specific mechanisms underlying this transition remain unknown. Here, we present novel findings from direct comparisons between cultured EOC spheroids and organoids. Our results indicated that AMP-activated protein kinase (AMPK) activity was significantly upregulated and protein kinase B (Akt) was downregulated in EOC spheroids compared to organoids, suggesting a clear differential phenotype. Through RNA sequencing analysis, we further supported these phenotypic differences and highlighted the significance of cell cycle regulation in organoids. By inhibiting the G2/M checkpoint via kinase inhibitors, we confirmed that this pathway is essential for organoids. Interestingly, our results suggest that specifically targeting aurora kinase A (AURKA) may represent a promising therapeutic strategy since our cells were equally sensitive to Alisertib treatment as both spheroids and organoids. Our findings emphasize the importance of studying cellular adaptations of EOC cells, as there may be different therapeutic targets depending on the step of EOC disease progression.

Core microbe Bifidobacterium in the hindgut of calves improves the growth phenotype of young hosts by regulating microbial functions and host metabolism

BackgroundThe growth and health of young ruminants are regulated by their gut microbiome, which can have lifelong consequences. Compared with subjective grouping, phenotypic clustering might be a more comprehensive approach to revealing the relationship between calf growth state and core gut microbes. However, the identification of beneficial gut bacteria and its internal mechanisms of shaping host phenotype differentiation remains unclear.ResultsIn this study, calves were divided into two clusters, cluster1 and cluster2, based on 29 phenotypic indicators using cluster analysis. Calves in cluster2 showed better growth performance, including higher body weight (BW), average daily gain (ADG), and dry matter intake (DMI), as well as better serum indicators with a high level of total superoxide dismutase (T-SOD), interleukin-6 (IL-6), and insulin-like growth factor-1 (IGF-1) compared to those in cluster1. Multi-omics was used to detect microbial features among calves in different phenotypic clusters. Distinct differences were observed between the two clustered gut microbiomes, including microbial diversity and composition. The close relationships between growth performance, blood metabolites, and microbiome were also confirmed. In cluster2, Bifidobacterium members were the dominant contributors to microbial metabolic functions with a higher abundance. Furthermore, pathways involved in carbohydrate degradation, glycolysis, and biosynthesis of propionate and proteins were active, while methane production was inhibited. In addition, the diversity and richness of hindgut resistome in cluster2 were lower than those in cluster1. The isolation and culture of Bifidobacterium strain, as well as the mice experiment, indicated that B. longum 1109 from calf feces in cluster2 could promote the growth of young hosts, enhance their blood immunity and antioxidation, and improve the development of hindgut.ConclusionsIn summary, cluster analysis has proved to be a feasible and reliable approach for identifying phenotypic subgroups of calves, prompting further exploration of host-microbiome interactions. Bifidobacterium as a core microbe in the hindgut of calves may play a crucial probiotic role in host phenotypic differentiation. This study enhances our comprehension of how gut core microbe shapes the host phenotype and provides new insights into the manipulation of beneficial gut colonizers to improve the growth performance and productivity of young ruminants.EbRLLe7F-yvVZ5Dd-FAxmeVideo

Friedreich ataxia: what can we learn from non-GAA repeat mutations?

Friedreich ataxia (FRDA) is a slowly progressive neurological disease resulting from decreased levels of the protein frataxin, a small mitochondrial protein that facilitates the synthesis of iron-sulfur clusters in the mitochondrion. It is caused by GAA (guanine-adenine-adenine) repeat expansions in the FXN gene in 96% of patients, with 4% of patients carrying other mutations (missense, nonsense, deletion) in the FXN gene. Compound heterozygote patients with one expanded GAA allele and a non-GAA repeat mutation can have subtle differences in phenotype from typical FRDA, including, in patients with selected missense mutations, both more severe features and less severe features in the same patient. In this review, we propose explanations for such phenotypes based on the potential for activities of frataxin other than enhancement of iron-sulfur cluster synthesis, as well as crucial future experiments for fully understanding the role of frataxin in cells.

Sleep and circadian rhythms in delayed sleep-wake phase disorder: Phenotypic differences between patients with and without comorbid depression.

Delayed sleep-wake phase disorder involves chronic difficulty going to bed and waking up at conventional times and often co-occurs with depression. This study compared sleep and circadian rhythms between patients with delayed sleep-wake phase disorder with depression(DSWPD-D) and without (DSWPD-ND) comorbid depression. Clinical records of 162 patients with delayed sleep-wake phase disorder (70 DSWPD-D, 92 DSWPD-ND) were analysed, including a subset of 76 patients with circadian phase determined by the dim light melatonin onset. Variables assessed included sleep behaviour on work and free days, weekly sleep duration, social jet lag, chronotype, and phase relationships between dim light melatonin onset and sleep/wake times. Mean (SD) or median [Q1-Q3] values were compared using t-tests or Mann-Whitney. Patients with DSWPD-D showed longer sleep on workdays (DSWPD-D = 7.63 hr [1.70] versus DSWPD-ND = 6.20 hr [1.59]; p < 0.001), but not on free days. DSWPD-D also showed later sleep onset (DSWPD-D = 03:30 14;hours [02:49 hours-04:23 hours], DSWPD-ND = 02:53 hours [02:00 hours-03:41 hours]; p = 0.02) and wake times (DSWPD-D = 11:30 hours [09:30 hours-13:00 hours], DSWPD-ND = 08:45 hours [07:20 hours-11:00 hours]; p < 0.01) on workdays. Furthermore, DSWPD-D showed less social jet lag (DSWPD-D = 0.38 [0.00-1.75] versus DSWPD-ND = 2.17 [1.25-3.03]; p < 0.01), and reported higher anxiety symptoms (DSWPD-D = 71.4% versus DSWPD-ND = 45.8%; p = 0.03) and medication use (DSWPD-D = 75.0% versus DSWPD-ND = 43.8%; p = 0.01). DSWPD-D also showed wider dim light melatonin onset phase relationships with dim light melatonin onset-mid-sleep (DSWPD-D = -5.77 [1.32] versus DSWPD-ND = -4.86 [1.53]; p = 0.01) and dim light melatonin onset-waketime (DSWPD-D = -9.46 [1.82]; DSWPD-ND = -8.13 [2.08]; p = 0.01). Multivariable Poisson regression, adjusted for age and sex, showed more medication use, less social jet lag, and longer weekly sleep duration as significantly associated with DSWPD-D. These findings suggest potential biopsychosocial protective factors linked to depression in delayed sleep-wake phase disorder. Further research is required to confirm these phenotypic differences and their relevance to delayed sleep-wake phase disorder aetiology and treatment.

Microbial succinate promotes the response to metformin by upregulating secretory immunoglobulin a in intestinal immunity

ABSTRACT Metformin is the first-line pharmacotherapy for type 2 diabetes mellitus; however, many patients respond poorly to this drug in clinical practice. The potential involvement of microbiota-mediated intestinal immunity and related signals in metformin responsiveness has not been previously investigated. In this study, we successfully constructed a humanized mouse model by fecal transplantation of the gut microbiota from clinical metformin-treated – responders and non-responders, and reproduced the difference in clinical phenotypes of responsiveness to metformin. The abundance of Bacteroides thetaiotaomicron, considered a representative differential bacterium of metformin responsiveness, and the level of secretory immunoglobulin A (SIgA) in intestinal immunity increased significantly in responder recipient mice following metformin treatment. In contrast, no significant alterations in B. thetaiotaomicron and SIgA were observed in non-responder recipient mice. The study of IgA˗/˗ mice confirmed that downregulated expression or deficiency of SIgA resulted in non-response to metformin, meaning that metformin was unable to improve dysfunctional glucose metabolism and reduce intestinal and adipose tissue inflammation, ultimately leading to systemic insulin resistance. Furthermore, supplementation with succinate, a microbial product of B. thetaiotaomicron, potentially reversed the non-response to metformin by inducing the production of SIgA. In conclusion, we demonstrated that upregulated SIgA, which could be regulated by succinate, was functionally involved in metformin response through its influence on immune cell-mediated inflammation and insulin resistance. Conversely, an inability to regulate SIgA may result in a lack of response to metformin.

The Haemagglutinin Gene of Bovine-Origin H5N1 Influenza Viruses Currently Retains Receptor-binding and pH-fusion Characteristics of Avian Host Phenotype.

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Over 891 dairy farms across 16 states have tested positive until 25th December 2024, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0 to 5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.

Angiographic Characterization and Sex-Related Anatomical Differences of Atrial Coronary Arteries Anatomy-A Proposal of Systematic Classification.

The coronary atrial circulation is the network of vessels that supply blood to the atria, originating from the left circumflex and right coronary arteries. Current descriptions of this arterial system are based on anatomical studies with a limited number of patients, predominantly male. In addition, there is a lack of consensus its angiographic nomenclature. This study aimed to evaluate the anatomical variations of coronary atrial branches (CAB) and investigate sex-related differences in their distribution. Consecutive patients with ST-elevation myocardial infarction who underwent primary PCI at a tertiary center between 2004 and 2013 were included. Angiographic anatomy of all visible CAB on index coronary angiography was systematically evaluated following a stepwise method, including type of branch; coronary artery of origin; segment of origin, branch course, and atrial dominancy. Specific differences between both sexes were analyzed. A total of 998 patients (age 61 ± 12, 79% male) were included. The sinus node artery was the dominant CAB in 916 (93%), originating in 37% from distal coronary segments. Different CAB anatomical patterns were identified in both sexes. Compared to females, males presented a higher prevalence of left-sided CAB (left circumflex CAB 459 [58%] vs. 96 [45%], p < 0.001; sigma-shaped CAB 267 [30%] vs. 39 [21%], p = 0.003) and of a left-balanced atrial circulation pattern-defined as the presence of at least two CAB originating from the LCx, with one of them being the dominant CAB-245 (31%) versus 45 (21%), p = 0.005. This study provides a systematic approach to the angiographic evaluation of CAB. Sex-related phenotypical differences of CAB distribution were found, with males presenting a higher presence of left-sided CAB and a left-balanced atrial circulation pattern.

Simultaneous Profiling of Multiple Phosphorylated Metabolites in Typical Biological Matrices via Ion-Pair Reversed-Phase Ultrahigh-Performance Liquid Chromatography and Mass Spectrometry.

Simultaneous analysis of multiple phosphorylated metabolites (phosphorylated metabolome) in biological samples is vital to reveal their physiological and pathophysiological functions, which is extremely challenging due to their low abundance in some biological matrices, high hydrophilicity, and poor chromatographic behavior. Here, we developed a new method with ion-pair reversed-phase ultrahigh-performance liquid chromatography and mass spectrometry using BEH C18 columns modified with hybrid surface technology. This method demonstrated good performances for various phosphorylated metabolites, including phosphorylated sugars and amino acids, nucleotides, NAD-based cofactors, and acyl-CoAs in a single run using standard LC systems. Specifically, the method showed good retention (capacity factor > 2) and reproducibility (ΔtR < 0.09 min, n = 6), peak symmetry (tailing factor < 2), and sensitivity (limit-of-detection < 238 fmol-on-column with QTOFMS) for all tested analytes especially for the medium- and/or long-chain acyl-CoAs. The method demonstrated reproducible applicability across numerous biological matrices, including tissue (liver), human biofluids (urine, plasma), cells, and feces, and revealed significant molecular phenotypic differences in phosphorylated metabolite composition.

New Brusatol Derivatives as Anti-Settlement Agents Against Barnacles, Targeting HSP90: Design, Synthesis, Biological Evaluation, and Molecular Docking Investigations

The increasing challenge of marine biofouling, mainly due to barnacle settlement, necessitates the development of effective antifoulants with minimal environmental toxicity. In this study, fifteen derivatives of brusatol were synthesized and characterized using 13C-NMR, 1H-NMR, and mass spectrometry. All the semi-synthesized compounds obtained using the Multi-Target-Directed Ligand (MTDL) strategy, when evaluated as anti-settlement agents against barnacles, showed promising activity. Compound 3 exhibited the highest anti-settlement capacity, with an EC50 value of 0.1475 μg/mL, an LC50/EC50 ratio of 42.2922 (&gt;15 indicating low toxicity), and a resuscitation rate of 71.11%, while it showed no significant phenotypic differences in the zebrafish embryos after treatment for 48 h. The toxicity screening of zebrafish also demonstrated the low ecotoxicity of the selected compounds. Furthermore, homology modeling of the HSP90 structure was performed based on related protein sequences in barnacles. Subsequently, molecular docking studies were conducted on HSP90 using these newly synthesized derivatives. Molecular docking analyses showed that most activated derivatives displayed low binding energies with HSP90, aligning well with the biological results. They were found to interact with key residues in the binding site, specifically ARG243, TYR101, and LEU73. These computational findings are anticipated to aid in predicting the enzyme targets of the tested inhibitors and their potential interactions, thus facilitating the design of novel antifoulants in future research endeavors.

Hypothalamic atrophy in primary lateral sclerosis, assessed by convolutional neural network-based automatic segmentation

Primary lateral sclerosis (PLS) is a motor neuron disease (MND) which mainly affects upper motor neurons. Within the MND spectrum, PLS is much more slowly progressive than amyotrophic laterals sclerosis (ALS). `Classical` ALS is characterized by catabolism and abnormal energy metabolism preceding onset of motor symptoms, and previous studies indicated that the disease progression of ALS involves hypothalamic atrophy. Very limited weight loss is observed in patients with PLS, which raises the question of whether there are also less hypothalamic alterations. The purpose of this study was to quantitatively investigate the hypothalamic volume in a group of PLS patients and to compare it with ALS and controls. Recently, we have introduced automatic hypothalamic quantification method based on the use of convolutional neural network (CNN) to reduce human variability and enhance analysis robustness. This CNN of U-Net architecture was applied for automatic segmentation of the hypothalamus and intracranial volume (ICV) to allow adjustments of the hypothalamic volume between subjects with different head sizes respectively. Automatic segmentation and volumetric analysis were performed in high resolution T1 weighted MRI volumes (acquired on a 1.5 T MRI scanner) of 46 PLS patients in comparison to 107 healthy controls and 411 `classical` ALS patients, respectively. Significant hypothalamic volume reduction was observed in PLS (818 ± 73 mm3) when compared to controls (852 ± 77 mm3); significant hypothalamic volume reduction was also confirmed in ALS (823 ± 84 mm3), in support of previous studies. No significant differences were found in normalized hypothalamic volumes between ALS patients and PLS patients at the group level. This unbiased CNN-based hypothalamus volume quantification study demonstrated similarly reduced hypothalamus volume in PLS and ALS patients, despite the clinical phenotypic differences.

Differences in Phenotypes, Treatments, and Outcomes of ANCA-associated Vasculitis across Europe, Japan, and the United States in 2020.

To clarify the differences in clinical phenotypes, therapeutic patterns, and outcomes of patients with granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA) across geographic regions using a multinational cohort. Data were collected from patients with newly diagnosed or relapsing GPA or MPA in Europe, Japan, and the United States (US) from January to July 2020. The composite outcome of kidney failure and/or death within 52 weeks after treatment was evaluated, and the hazard ratios across the regions were estimated using the Cox proportional hazard model. Heterogeneities of the effects were investigated via thorough subgroup analyses. Among the 254 eligible patients (Europe, 137; Japan, 73; the US, 44), those in Japan were older and had higher proportions of MPO-ANCA positivity and lung involvement compared with Europe and the US. The estimated glomerular filtration rate at diagnosis varied across regions, with the highest dialysis requirement in the US. Cyclophosphamide and rituximab use were 57% and 63% in Europe, 29% and 40% in Japan, and 34% and 86% in the US. Within 52 weeks, 8%, 10%, and 18% developed kidney failure, while 9%, 7%, and 7% died in Europe, Japan, and the US, respectively; and the composite outcome occurred in 15%, 14%, and 23% of patients. The hazard ratios for kidney failure and/or death were comparable across regions; however, they varied among certain subgroups. Although the kidney failure-free survival was comparable across continents, regional differences existed in clinical phenotypes and therapeutic patterns.

Molecular logic for cellular specializations that initiate the auditory parallel processing pathways

The cochlear nuclear complex (CN), the starting point for all central auditory processing, encompasses a suite of neuronal cell types highly specialized for neural coding of acoustic signals. However, the molecular logic governing these specializations remains unknown. By combining single-nucleus RNA sequencing and Patch-seq analysis, we reveal a set of transcriptionally distinct cell populations encompassing all previously observed types and discover multiple hitherto unknown subtypes with anatomical and physiological identity. The resulting comprehensive cell-type taxonomy reconciles anatomical position, morphological, physiological, and molecular criteria, enabling the determination of the molecular basis of the specialized cellular phenotypes in the CN. In particular, CN cell-type identity is encoded in a transcriptional architecture that orchestrates functionally congruent expression across a small set of gene families to customize projection patterns, input-output synaptic communication, and biophysical features required for encoding distinct aspects of acoustic signals. This high-resolution account of cellular heterogeneity from the molecular to the circuit level reveals the molecular logic driving cellular specializations, thus enabling the genetic dissection of auditory processing and hearing disorders with a high specificity.

Epigenetics and individuality: from concepts to causality across timescales.

Traditionally, differences among individuals have been divided into genetic and environmental causes. However, both types of variation can underlie regulatory changes in gene expression - that is, epigenetic changes - that persist across cell divisions (developmental differentiation) and even across generations (transgenerational inheritance). Increasingly, epigenetic variation among individuals is recognized as an important factor in human diseases and ageing. Moreover, non-genetic inheritance can lead to evolutionary changes within populations that differ from those expected by genetic inheritance alone. Despite its importance, causally linking epigenetic variation to phenotypic differences across individuals has proven difficult, particularly when epigenetic variation operates independently of genetic variation. New genomic approaches are providing unprecedented opportunity to measure and perturb epigenetic variation, helping to elucidate the role of epigenetic variation in mediating the genotype-phenotype map. Here, we review studies that have advanced our understanding of how epigenetic variation contributes to phenotypic differences between individuals within and across generations, and provide a unifying framework that allows historical and mechanistic perspectives to more fully inform one another.

Small RNA CjNC110 regulates the activated methyl cycle to enable optimal chicken colonization by Campylobacter jejuni.

Post-transcriptional gene regulation by non-coding small RNAs (sRNAs) is critical for colonization and survival of enteric pathogens, including the zoonotic pathogen Campylobacter jejuni. In this study, we utilized C. jejuni IA3902 (a representative isolate of the sheep abortion clone) and C. jejuni W7 (a highly motile variant of NCTC 11168, a human gastroenteritis strain) to further investigate regulation by sRNA CjNC110. Both motility and autoagglutination ability were confirmed to be phenotypes of conserved regulation by CjNC110. However, we demonstrated that W7∆CjNC110 does not change chicken colonization levels compared to W7 wild type, directly contrasting IA3902∆CjNC110, which had decreased colonization ability. Subsequently, we determined strain-specific phenotype variation between W7∆CjNC110 and IA3902∆CjNC110 when examining intracellular L-methionine (L-met) levels controlled by the activated methyl cycle (AMC). We hypothesized that the presence of a secondary system for L-met production conferred by MetAB in W7 but not IA3902 might explain the difference in both chicken colonization and L-met availability. Insertion of metAB within IA3902∆CjNC110 (naturally absent) restored intracellular L-met levels in IA3902∆CjNC110::metAB and overcame the colonization defect that resulted from mutagenesis of CjNC110 in IA3902. Deletion of metAB in W7∆CjNC110 (naturally present) led to a decrease in L-met in W7∆CjNC110∆metAB and a colonization defect which was otherwise masked in W7∆CjNC110. Our results indicate that regulation of the AMC leading to altered L-met availability is a conserved regulatory function of CjNC110 in C. jejuni and confirm that L-met generation via the AMC as activated by CjNC110 is critical for optimal host colonization.IMPORTANCEDuring this study, the regulatory action and conservation of function of CjNC110 between two different zoonotically important Campylobacter jejuni strains were examined. Critically, this work for the first time reveals regulation of L-methionine (L-met) production within the activated methyl cycle (AMC) by small RNA (sRNA) CjNC110 as a key factor driving C. jejuni optimal chicken colonization. As a growing body of evidence suggests that maintenance of L-met homeostasis appears to be critical for C. jejuni colonization, interventions targeting the AMC could provide a critical control point for therapeutic drug options to combat this zoonotic pathogen. Our results also indicate that even for conserved sRNAs such as CjNC110, strain-specific differences in phenotypes regulated by sRNAs may exist, independent of conserved regulatory action. Depending on the strain examined and accessory genomic content present, conserved regulatory actions might be masked, thus investigation in multiple strains may be warranted.

Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people.

The gut microbiome is amenable to dietary interventions, and polyphenol-rich diets have been shown to enhance abundances of bacteria associated with short-chain fatty acid (SCFA) production. We examined the effects of a strawberry-based intervention on the gut microbiome of 69 healthy elderly German adults. Participants in five groups consumed varying amounts of strawberries, freeze-dried strawberries, and capers in olive oil over 10 weeks as part of a randomized controlled trial. 16S rRNA sequencing was used to analyze differences in microbial composition, diversity, phenotypes, differential abundance, and functional pathways. The intervention group featuring the highest amounts of fresh and freeze-dried strawberries without capers in olive oil (group 4) showed changes in gut microbial diversity and differential abundance that could be linked to improved health. Beta diversity, based on weighted UniFrac distances, increased significantly (P = 0.0035), potentially pathogenic bacteria decreased (P = 0.04), and abundances of SCFA-producing genera Faecalibacterium and Prevotella increased significantly. Other findings included a significant reduction of CAG-352, Preveotellaceae_NK3B31-group, and Eubacterium coprostanoligenes (group 2), and a trend of lowered Firmicutes-to-Bacteroidetes ratio (P = 0.067) and a reduction in Ruminococcaceae (group 3). Our findings suggest that a dietary intervention based on strawberries can positively alter the gut microbiota of healthy elderly people as seen in an enrichment of SCFA-producing genera, increased diversity, and a reduction in potentially pathogenic bacteria.IMPORTANCEAging is often associated with changes in the gut microbiome, including a decline in beneficial bacteria and an increase in potentially pathogenic species. Addressing these changes through lifestyle interventions is of significant interest. Our study demonstrates that a 10-week dietary intervention with strawberries can beneficially modulate gut microbial composition and diversity in healthy elderly individuals. Notably, the group consuming the highest amount of strawberries (without capers in olive oil) initially had higher abundances of potentially pathogenic bacteria. Here, the intervention led to increased abundances of the beneficial genera Faecalibacterium and Prevotella, which are linked to health benefits including reduced inflammation and improved lipid metabolism. These findings suggest that strawberry consumption can positively influence gut microbial composition, thereby contributing to overall health and disease prevention in older adults.

Effect of exercise training on modulating the TH17/TREG imbalance in individuals with severe COPD: A randomized controlled trial.

Chronic obstructive pulmonary disease (COPD) induces an imbalance in T helper (Th) 17/regulatory T (Treg) cells that contributes to of the dysregulation of inflammation. Exercise training can modulate the immune response in healthy subjects. We aimed to evaluate the effects of exercise training on Th17/Treg responses and the differentiation of Treg phenotypes in individuals with COPD. This randomized controlled trial included 50 individuals with severe or very severe COPD who were allocated to the Exercise or Control groups. The Exercise group underwent eight weeks of aerobic and muscle strength training, whereas the Control group received usual care. The primary outcome was the change in the phenotypic characteristics of Tregs and Th17 profile differentiation in systemic inflammation. Exercise training increased the frequency of total and activated Tregs and decreased the frequency of Th17 cells in between-group comparisons. Additionally, Th17/Treg responses were moderately correlated with improvements in the six-minute walking test, muscle strength of the upper and lower limbs, and daily life physical activity levels. Exercise training improved functional exercise capacity, muscle strength, and physical fitness, which was associated with a decrease in the Th17 inflammatory response and an increase in Treg cell phenotypes immunosuppressive activity.

Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle.

Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal muscle, with phenotypic differences reflecting variations in cellular composition and transcriptional profiles. This study investigates the cellular-level transcriptional characteristics of LDM in large white pigs at two growth stages (170 days vs. 245 days) using single-nucleus RNA sequencing (snRNA-seq). We identified 56,072 cells across 12 clusters, including myofibers, fibro/adipogenic progenitor (FAP) cells, muscle satellite cells (MUSCs), and other resident cell types. The same cell types were present in the LDM at both growth stages, but their proportions and states differed. A higher proportion of FAPs was observed in the skeletal muscle of 245-day-old pigs. Additionally, these cells exhibited more active communication with other cell types compared to 170-day-old pigs. For instance, more interactions were found between FAPs and pericytes or endothelial cells in 245-day-old pigs, including collagen and integrin family signaling. Three subclasses of FAPs was identified, comprising FAPs_COL3A1+, FAPs_PDE4D+, and FAPs_EBF1+, while adipocytes were categorized into Ad_PDE4D+ and Ad_DGAT2+ subclasses. The proportions of these subclasses differed between the two age groups. We also constructed differentiation trajectories for FAPs and adipocytes, revealing that FAPs in 245-day-old pigs differentiated more toward fibrosis, a characteristic reminiscent of the high prevalence of skeletal muscle fibrosis in aging humans. Furthermore, the Ad_PDE4D+ adipocyte subclass, predominant in 245-day-old pigs, originated from FAPs_PDE4D+ expressing the same gene, while the Ad_DGAT2+ subclass stemmed from FAPs_EBF1+. In conclusion, our study elucidates transcriptional differences in skeletal muscle between two growth stages of pigs and provides insights into mechanisms relevant to pork meat quality and skeletal muscle diseases.

Influence of wildfire ash concentration on development, survival, and skin and gut microbiota of Rana dybowskii

Climate changes can increase wildfires and thereby endanger the habitats and survival of amphibians, but relevant research is limited. The gut and skin microbiota plays a critical role in amphibian protection. Wildfire ash may negatively impact amphibians, causing inflammation and microbiota disruption, but the impact on microbial communities is still uncertain. In this study, the impact of wildfire ash on the cutaneous and gut microbiota of Rana dybowskii was investigated over a 28-day period using five groups with aqueous extracts of ash. Polycyclic aromatic hydrocarbons in the ash were analyzed. Body mass, development, survival rates, and microbiota diversity were tested. Significant differences in body mass, development rates, and survival rates among the treatment groups were observed. The survival and development rates at lower concentrations of ash (T0 and T0_75) were more similar to those under control conditions. Analyses of alpha and beta diversity revealed significant changes in microbiota composition across ash concentrations, with specific phyla and genera affected. Linear discriminant analysis effect analysis identified distinct microbiota associated with each treatment group, demonstrating the specific influence of ash concentrations on the microbiota composition of tadpoles. BugBase analysis revealed significant differences in the same phenotypes in gut microbiota, but not in nine skin microbiota phenotypes across groups. This research underscores the sensitivity of amphibian microbiota to environmental changes and provides insights into the ecological consequences of wildfires on aquatic ecosystems.

Hepatitis B virus genotypes A1 and A2 have distinct replication phenotypes due to polymorphisms in the HBx gene.

HBV genotype A has two major subtypes, A1 (commonly in Africa) and A2 (commonly in Europe) with only 4% nucleotide differences. Individuals infected with these two subtypes appear to have different clinical manifestations and virologic features. Whether such a difference results from the virus or host has not been established. Using HBV generated from molecule clones of subtypes A1 and A2 in cell culture (HBVcc), we demonstrate that HBVcc of subtypes A1 and A2 can be passaged in vitro and in vivo and respond equally well to human IFN-α treatment. HBVcc passaged in human liver chimeric mice (HBVmp) infected human hepatocytes more efficiently than that of the original HBVcc. Subtype A2 showed a much higher viral replication level than that of subtype A1. Mechanistic investigations using constructs with chimeric A1/A2 sequences and specific mutations indicated that subtype A2 has an inherently higher replication phenotype due to specific polymorphisms in the HBx gene resulting in amino acid variations. Studies of HBx expression demonstrated that A1 HBx is expressed at a much lower level than that of A2 HBx. Mutagenesis studies identified two HBx amino acid variations responsible for the observed phenotypic difference. Using AlphaFold2, we generated structural models of HBx proteins of A1 and A2. Superposition of the two models reveal that the overall structural motifs are similarly aligned, except for the C-terminal peptides diverging between the A1 and A2 models, possibly explaining their functional difference. In conclusion, using various in vitro and in vivo models, here we show that subtype A2 has an inherently higher replication phenotype due to polymorphisms in HBx that result in possible differences in structure and expression level of the two subtype HBx proteins. This genotypic difference potentially explains the reported clinical differences between the two subtypes as well as providing a previously unrecognized association between viral sequence variations and clinical manifestations of HBV infection in humans.