A near complete genome assembly of the East Friesian sheep genome.

Advancements in sequencing have enabled the assembly of numerous sheep genomes, significantly advancing our understanding of the link between genetic variation and phenotypic traits. However, the genome of East Friesian sheep (Ostfriesisches Milchschaf), a key high-yield milk breed, remains to be fully assembled. Here, we constructed a near-complete and gap-free East Friesian genome assembly using PacBio HiFi, ultra-long ONT and Hi-C sequencing. The resulting genome assembly spans approximately 2.96 Gb, with a contig N50 length of 104.1 Mb and only 164 unplaced sequences. Remarkably, our assembly has captured 41 telomeres and 24 centromeres. The assembled sequence is of high quality on completeness (BUSCO score: 97.1%) and correctness (QV: 69.1). In addition, a total of 24,580 protein-coding genes were predicted, of which 97.2% (23,891) carried at least one conserved functional domain. Collectively, this assembly provides not only a near T2T gap-free genome, but also provides a valuable genetic resource for comparative genome studies of sheep and will serve as an important tool for the sheep research community.

The nasal microbiota is a potential diagnostic biomarker for sepsis in critical care units.

This study aimed to characterize the composition of intestinal and nasal microbiota in septic patients and identify potential microbial biomarkers for diagnosis. A total of 157 subjects, including 89 with sepsis, were enrolled from the affiliated hospital. Nasal swabs and fecal specimens were collected from septic and non-septic patients in the intensive care unit (ICU) and Department of Respiratory and Critical Care Medicine. DNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced using Illumina technology. Bioinformatics analysis, statistical processing, and machine learning techniques were employed to differentiate between septic and non-septic patients. The nasal microbiota of septic patients exhibited significantly lower community richness (P = 0.002) and distinct compositions (P = 0.001) compared to non-septic patients. Corynebacterium, Staphylococcus, Acinetobacter, and Pseudomonas were identified as enriched genera in the nasal microbiota of septic patients. The constructed machine learning model achieved an area under the curve (AUC) of 89.08, indicating its efficacy in differentiating septic and non-septic patients. Importantly, model validation demonstrated the effectiveness of the nasal microecological diagnosis prediction model with an AUC of 84.79, while the gut microecological diagnosis prediction model had poor predictive performance (AUC = 49.24). The nasal microbiota of ICU patients effectively distinguishes sepsis from non-septic cases and outperforms the gut microbiota. These findings have implications for the development of diagnostic strategies and advancements in critical care medicine.IMPORTANCEThe important clinical significance of this study is that it compared the intestinal and nasal microbiota of sepsis with non-sepsis patients and determined that the nasal microbiota is more effective than the intestinal microbiota in distinguishing patients with sepsis from those without sepsis, based on the difference in the lines of nasal specimens collected.

Identification of a signature of histone modifiers in kidney renal clear cell carcinoma.

Kidney renal clear cell carcinoma (KIRC) is a cancer that is closely associated with epigenetic alterations, and histone modifiers (HMs) are closely related to epigenetic regulation. Therefore, this study aimed to comprehensively explore the function and prognostic value of HMs-based signature in KIRC. HMs were first obtained from top journal. Then, the mRNA expression profiles and clinical information in KIRC samples were downloaded from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. Cox regression analysis and least absolute shrinkage and selection operator (Lasso) analysis were implemented to find prognosis-related HMs and construct a risk model related to the prognosis in KIRC. Kaplan-Meier analysis was used to determine prognostic differences between high- and low-risk groups. Immune infiltration and drug sensitivity analysis were also performed between high- and low-risk groups. Eventually, 8 HMs were successfully identified for the construction of a risk model in KIRC. The results of the correlation analysis between risk signature and the prognosis showed HMs-based signature has good prognostic value in KIRC. Results of immune analysis of risk models showed there were significant differences in the level of immune cell infiltration and expression of immune checkpoints between high- and low-risk groups. The results of the drug sensitivity analysis showed that the high-risk group was more sensitive to several chemotherapeutic agents such as Sunitinib, Tipifarnib, Nilotinib and Bosutinib than the low-risk group. In conclusion, we successfully constructed HMs-based prognostic signature that can predict the prognosis of KIRC.

The difference of affect improvement effect of music intervention in aerobic exercise at different time periods.

Objectives: A randomized controlled experimental design that combines exercise and music intervention was adopted in this study to verify whether this approach could help improve human affect. The differences in the effect of music listening on affective improvement were compared in four different periods: before, during, and after aerobic power cycling exercise and the whole exercise course. Method: A total of 140 subjects aged 19-30 years (average age: 23.6 years) were recruited and randomly divided into four music intervention groups, namely, the pre-exercise, during-exercise, post-exercise, and the whole-course groups. The subjects' demographic and sociological variables and daily physical activities were collected using questionnaires. Individual factors, such as the subjects' noise sensitivity, personality traits, and degree of learning burnout, were collected via scale scoring. A laboratory in Zhejiang Normal University was selected as the experimental site. The testing procedure can be summarized as follows. In a quiet environment, the subjects were asked to sit quietly for 5 min after completing a preparation work, and then they were informed to take a pre-test. The four subject groups wore headphones and completed 20 min of aerobic cycling (i.e., 7 min of moderate-intensity cycling [50%*HRR + RHR] + 6 min of low-intensity interval cycling [30%*HRR + RHR] + 7 min of moderate-intensity cycling [50%*HRR + RHR] after returning to a calm state (no less than 20 min) for post-testing. The affect improvement indicators (dependent variables) collected in the field included blood pressure (BP), positive/negative affect, and heart rate variability indicators (RMSSD, SDNN, and LF/HF). Results: 1) Significant differences were found in the participants' systolic BP (SBP) indices and the effect of improvement of the positive affect during the exercise-music intervention among the four groups at different durations for the same exercise intensity (F = 2.379, p = 0.030, ɳp 2 = 0.058; F = 2.451, p = 0.043, ɳp 2 = 0.091). 2) Music intervention for individuals during exercise contribute more to the reduction of SBP than the other three time periods (F = 3.170, p = 0.047, ɳp 2 = 0.068). Improvement in the participants' negativity affective score was also better during exercise, and it was significantly different than the other three time periods (F = 5.516, p = 0.006, ɳp 2 = 0.113). No significant differences were found in the improvement effects of the other effective indicators for the four periods. Conclusion: Exercise combined with music intervention has a facilitative effect on human affect improvement, and listening to music during exercise has a better impact on affective improvement than music interventions at the other periods. When people perform physical activities, listening to music during exercise positively affects the progress effect among them.

Analysis of microbial community evolution, autolysis phenomena, and energy metabolism pathways in Pholiota nameko endophytes.

Introduction: Pholiota nameko is a widely consumed edible fungus. This study focuses on two crucial developmental stages of Pholiota nameko, namely, mycelium and ascospores. The objectives of this research were to investigate changes in microbial diversity and community structure during the growth of Pholiota nameko and to analyze the adaptability of the dominant strains to their respective habitats through metabolic. Methods: Specifically, we conducted second-generation sequencing of the 16S rRNA gene (Illumina) on samples obtained from these stages. In addition, we isolated and characterized endophytes present in Pholiota nameko, focusing on examining the impact of dominant endophyte genera on autolysis. We also conducted a metabolic pathway analysis. Results and discussion: The results unveiled 578,414 valid sequences of Pholiota nameko endophytic fungi. At the phylum level, the dominant taxa were Basidiomycota, Ascomycota, Zoopagomycota, and Mucoromycota. At the genus level, the dominant taxa observed were Pholiota, Inocybe, Fusarium, and Hortiboletus. For endophytic bacteria, we obtained 458,475 valid sequences. The dominant phyla were Proteobacteria, TM6, Firmicutes, and Bacteroidetes, while the dominant genera were Edaphobacter, Xanthomonas, Burkholderia, and Pseudomonas. Moreover, we identified the isolated strains in Pholiota nameko using 16S rDNA, and most of them were found to belong to the genus Pseudomonas, with Pseudomonas putida being the most prevalent strain. The findings revealed that the Pseudomonas putida strain has the ability to slow down the breakdown of soluble proteins and partially suppress the metabolic processes that generate superoxide anion radicals in Pholiota nameko, thereby reducing autolysis. Additionally, our results demonstrated that molybdenum enzyme-mediated anaerobic oxidative phosphorylation reactions were the primary energy metabolism pathway in the Pseudomonas putida strain. This suggests that the molybdenum cofactor synthesis pathway might be the main mechanism through which Pholiota nameko adapts to its complex and diverse habitats.

A multi-resolution physics-informed recurrent neural network: formulation and application to musculoskeletal systems.

This work presents a multi-resolution physics-informed recurrent neural network (MR PI-RNN), for simultaneous prediction of musculoskeletal (MSK) motion and parameter identification of the MSK systems. The MSK application was selected as the model problem due to its challenging nature in mapping the high-frequency surface electromyography (sEMG) signals to the low-frequency body joint motion controlled by the MSK and muscle contraction dynamics. The proposed method utilizes the fast wavelet transform to decompose the mixed frequency input sEMG and output joint motion signals into nested multi-resolution signals. The prediction model is subsequently trained on coarser-scale input-output signals using a gated recurrent unit (GRU), and then the trained parameters are transferred to the next level of training with finer-scale signals. These training processes are repeated recursively under a transfer-learning fashion until the full-scale training (i.e., with unfiltered signals) is achieved, while satisfying the underlying dynamic equilibrium. Numerical examples on recorded subject data demonstrate the effectiveness of the proposed framework in generating a physics-informed forward-dynamics surrogate, which yields higher accuracy in motion predictions of elbow flexion-extension of an MSK system compared to the case with single-scale training. The framework is also capable of identifying muscle parameters that are physiologically consistent with the subject's kinematics data.

Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering.

Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.

The Application of Bilayer Heterogeneous MOFs in pH and Heat-Triggered Systems for Controllable Fragrance Release.

To facilitate the integration of a fragrance encapsulation system into different products to achieve effective releases, a dual-responsive release system with pH and thermal trigger control is designed in this work. A series of ZIF-8 (M) and bilayer ZIF-8-on-ZIF-8 (MM) materials are synthesized by a solvent method at room temperature. The fragrance is encapsulated into the ZIFs by dynamic adsorption or in situ encapsulation combined dynamic adsorption. The fragrance loading contributed by dynamic adsorption was as high as 80%. The fragrance loaded in the double-layer MM host was almost twice that of the monolayer host M due to the stronger electrostatic interaction between MM and vanillin. In the pH and thermal trigger response release experiments, the second MOF layer in the MM host, as a controlled entity, greatly improved the load and kinetic equilibrium time of vanillin, and realized the controlled release of guest molecules. The developed dual-responsive release system in this work exhibits great potential in daily chemical products.

Screening of Litter-Size-Associated SNPs in NOX4, PDE11A and GHR Genes of Sheep.

In previous studies, NOX4, PDE11A and GHR genes have been screened as important candidate genes for litter size in sheep by using the GWAS method; however, neither their effects on litter size nor the loci associated with litter size have been identified. In this study, three candidate loci (c.1057-4C > T in NOX4, c.1983C > T in PDE11A and c.1618C > T in GHR) were first screened based on our previous resequencing data of 10 sheep breeds. After the three loci were genotyped using Sequenom MassARRAY technology, we carried out population genetics analysis on the three loci and performed association analysis between the polymorphism of the three loci and the litter size of sheep. The results of population genetics analysis suggested that c.1057-4C > T in NOX4 and c.1983C > T in PDE11A may be subject to natural or artificial selection. The results of association analysis indicated that litter size was significantly associated with c.1057-4C > T in NOX4 and c.1983C > T in PDE11A (p < 0.05) in Small Tail Han sheep, and there was no significant interaction effect between the two loci on the litter size. In summary, c.1057-4C > T in NOX4 and c.1983 C > T in PDE11A can be considered candidate molecular markers for improving litter size in sheep.

Substrate-controlled [4+1] and [3+2] annulations of ninhydrin-derived Morita-Baylis-Hillman carbonates to access polysubstituted furans and cyclopentenes.

The effective and mild [4+1] annulation of ninhydrin-derived MBH carbonates with α,ß-unsaturated ketones has been developed, providing a wide range of multisubstituted furans in high yields (up to 90%) with excellent ß-regioselectivities. In contrast, the polysubstituted cyclopentenes bearing dispiro-bisindanedione motifs were obtained via classical [3+2] annulations by employing ninhydrin-derived MBH carbonates with 2-arylidene-1,3-indandiones under the same catalytic conditions. Furthermore, the structures of two kinds of cycloadducts were straightforwardly confirmed through X-ray diffraction analysis.

metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model.

Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model-based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains-derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae's potential marker. In different health-disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model-based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.

Massively Parallel CRISPR-Cas9 Knockout Screening in Sheep Granulosa Cells for FSH Response Genes.

Follicle-stimulating hormone (FSH) regulates ovarian follicle development through specific gene expression programs. Granulosa cells (GCs) are somatic cells surrounding the oocytes, secreting gonadotropins to regulate ovulation and promote follicular development. By analyzing the effects of different doses of FSH on the proliferation of GCs, we found that adding 10 ng/mL of FSH, as the optimal concentration, could promote the growth of GCs. Furthermore, we have successfully constructed the first CRISPR-Cas9 knockout library targeting the genes on chromosomes 2 and 3 and the X chromosomes of the sheep massively parallel coding gene, as well as an ovarian GCs knockout cell library. For the first time, we have exposed the knockout cell library to a concentration of 10 ng/mL FSH to explore the underlying mechanisms. Through this screening, we have identified 836 positive-negative screening genes that are responsive to FSH, thereby revealing the regulatory mechanisms and screening the functionality of candidate genes. Next, RNA-Seq of control (0 ng/mL), low (10 ng/mL), and high (100 ng/mL) doses of FSH revealed 1708 differentially expressed genes, and combined with 836 genes, we obtained 129 FSH dose-dependent genes with extremely significant differences. This enables us to delve deeper into investigating and identifying the mechanisms by which FSH regulates GCs. More generally, we have discovered new regulatory factors and identified reproductivity-associated major effectors. These findings provide novel research directions for further studies on sheep reproduction.

Identification and Structural Characterization of Twisted Atomically Thin Bilayer Materials by Deep Learning.

Two-dimensional materials are expected to play an important role in next-generation electronics and optoelectronic devices. Recently, twisted bilayer graphene and transition metal dichalcogenides have attracted significant attention due to their unique physical properties and potential applications. In this study, we describe the use of optical microscopy to collect the color space of chemical vapor deposition (CVD) of molybdenum disulfide (MoS2) and the application of a semantic segmentation convolutional neural network (CNN) to accurately and rapidly identify thicknesses of MoS2 flakes. A second CNN model is trained to provide precise predictions on the twist angle of CVD-grown bilayer flakes. This model harnessed a data set comprising over 10,000 synthetic images, encompassing geometries spanning from hexagonal to triangular shapes. Subsequent validation of the deep learning predictions on twist angles was executed through the second harmonic generation and Raman spectroscopy. Our results introduce a scalable methodology for automated inspection of twisted atomically thin CVD-grown bilayers.

Cavitation pit evolution process of epoxy and polyurea coatings on mortar substrates.

This study focuses on unraveling the failure mechanisms of three distinct polymer-coating structures applied to mortar substrates: an epoxy coating (MEP1), an epoxy coating with an intermediate epoxy mortar layer (MEP2), and a polyurea coating with an intermediate epoxy mortar layer (MPU). Ultrasonic cavitation experiments are conducted to investigate the initial stages of cavitation erosion. The damaged surfaces of these three coating structures are meticulously investigated and characterized. An in-depth analysis is performed on the distribution characteristics of cavitation pits and the evolutionary patterns of these pits. The results indicate that the introduction of epoxy mortar as an intermediate layer significantly enhances the material's cavitation resistance by improving its energy absorption capacity. This enhancement delays the formation of cavitation pits on the coating surface. Additionally, the superior adhesive properties of the intermediate epoxy mortar with the mortar substrate prevent direct cavitation erosion from forming on the substrate, even when brittleness failure occurs and coating erosion is observed on the surface epoxy polymer. The polyurea coatings demonstrate exceptional elastic-plastic deformation capabilities. When combined with the intermediate epoxy mortar layer, MPU can withstand prolonged and repetitive cavitation impacts, resulting in minimal coating erosion.

Retrograde intrarenal surgery with intelligent control of renal pelvic pressure for staghorn calculi: a case report.

Percutaneous nephrolithotomy is the gold standard treatment for staghorn calculi. However, this study reviews a case of an almost complete removal of staghorn calculi following one session of retrograde intrarenal surgery with intelligent control of renal pelvic pressure (RIRS-ICP). A 45 years-old female patient with an 8.3 × 4.5 cm complete staghorn stone was infected with Proteus mirabilis. Two sensitive antibiotics, piperacillin tazobactam and etimicin, were administered for 3 days. Semirigid 7/8.4 Fr ureteroscope was used to treat the renal pelvis and upper calyceal calculi for 57 min. A 550 µm holmium laser fiber with 2.0 J × 30 Hz was set. Next, a disposable flexible ureteroscope of 8.4 Fr was used to address residual middle and lower calyx stones for 94 min. A 200 µm holmium laser fiber with 1.0 J × 30 Hz was set. The renal pelvis pressure was controlled within 15 mmHg. A 2 mm CT scan on the first postoperative day showed inferior caliceal residue of approximately 1.0 × 0.6 cm. No complications occurred. This suggests that RIRS-ICP is a safe and effective treatment for staghorn calculi.

Running Gait and Control of Quadruped Robot Based on SLIP Model.

Legged robots have shown great adaptability to various environments. However, conventional walking gaits are insufficient to meet the motion requirements of robots. Therefore, achieving high-speed running for legged robots has become a significant research topic. In this paper, based on the Spring-Loaded Inverted Pendulum (SLIP) model and the optimized Double leg-Spring-Loaded Inverted Pendulum (D-SLIP) model, the running control strategies for the double flying phase Bound gait and the Rotatory gallop gait of quadruped robots are designed. First, the dynamics of the double flying phase Bound gait and Rotatory gallop gait are analyzed. Then, based on the "three-way" control idea of the SLIP model, the running control strategy for the double flying phase Bound gait is designed. Subsequently, the SLIP model is optimized to derive the D-SLIP model with two touchdown legs, and its dynamic characteristics are analyzed. And the D-SLIP model is applied to the running control strategy of the Rotatory gallop gait. Furthermore, joint simulation verification is conducted using Adams virtual prototyping and MATLAB/Simulink control systems for the designed control strategies. Finally, experimental verification is performed for the double flying phase Bound gait running control strategy. The experimental results demonstrate that the quadruped robot can achieve high-speed and stable running.

Ureteroscopic lithotripsy with pressure-measuring ureteral access sheath for large ureteral stones.

INTRODUCTION: To evaluate the safety and efficacy of ureteroscopic lithotripsy with pressure-measuring ureteral access sheath (PM-UAS) for large ureteral stones. MATERIAL AND METHODS: A total of 258 consecutive patients with large ureteral stones ≥15 mm was enrolled. They were treated by ureteroscopic lithotripsy with PM-UAS in the oblique supine lithotomy position. The technology can precisely monitor and automatically control cavity pressure. The cavity pressure control value was set at -15 mmHg∼-5 mmHg. The cavity pressure limit value was set at 30 mmHg. Infusion flow rate was set at 100-200 ml/min. Postoperative data such as stone-free rate and complications were analyzed. RESULTS: PM-UAS was successfully implanted in 225 patients at one stage. Eighteen cases of patients who had failed the first surgery were successfully treated with a second operation. Fifty-one cases with stones migrating up to the kidney were converted to flexible lithotripsy. The other 15 cases were converted to percutaneous nephrolithotomy due to significant ureteral stenosis. The operative time was 49.5 ± 11.2 min. The stone-free rates after one month and three months were 87.2% (212/243) and 94.2% (229/243), respectively. Complications from grade I to II were observed in 25(10.3%) patients. No other complications from grade III to V were noted. CONCLUSION: The ureteroscopic lithotripsy with PM-UAS is safe and efficacious for large ureteral stones.

Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material.

A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan'an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.

Kaistella yananensis sp. nov., a Novel Indoleacetic Acid-Producing Bacterium Isolated from the Root Nodules of Sophora davidii (Franch.) Skeels.

A novel endophytic bacterium, designated strain BT6-1-3T, was isolated from the root nodules of a leguminous shrub named Sophora davidii (Franch.) Skeels, found growing wild in Yan'an, Shaanxi Province, China. Cells were Gram-staining-negative, non-motile, catalase-positive, oxidase-positive, and did not produce H2S. Strain BT6-1-3T grew at 15-40 °C (optimum 30 °C), at pH 6.0-10.0 (optimum pH 9.0), and with 0-1% (w/v) NaCl (optimum 0.5%). The quinone system was menaquinone 6. The major fatty acids present in BT6-1-3T were iso-C11:0, iso-C15:0, and C16:0. The G+C content of genomic DNA was 39.4 mol% by whole genome sequencing. According to the analysis of 16S rRNA gene sequence, the closest relative was Kaistella montana WG4 (nucleotide identity was 97.6%). The genome of strain BT6-1-3T was sequenced, and the genome similarity was calculated using average nucleotide identity and genome-to-genome distance analysis with the genomes of other strains of Kaistella. Both strongly supported that the strain BT6-1-3T belonged to the genus Kaistella as a representative of a new species. Based on phylogenetic analysis, chemotaxonomic data, and physiological and biochemical characteristics, strain BT6-1-3T represents a new species of the genus Kaistella and is named as Kaistella yananensis sp. nov. Type strain is BT6-1-3T (= NBRC 115452T = CGMCC 1.60032T).

Effects of resveratrol on DLD and NDUFB9 decrease in frozen semen of Mongolian sheep.

Mongolian sheep are a breed of sheep in China known for their excellent cold and drought resistance. Sperm from Mongolian sheep are often cryopreserved to improve breeding outcomes. However, cryopreservation of sperm often results in issues such as reduced vitality and altered morphology. Therefore, the objective of this study was to investigate the impact of the cryoprotectant resveratrol on frozen sperm from Mongolian sheep, specifically examining its effects on key proteins during cryopreservation. In this study, sperm samples were obtained from three adult Mongolian rams and processed through semen centrifugation. The sperm motility parameters of Fresh Sperm Group (FR), Resveratrol added before freezing group (FF-Res), Resveratrol-free frozen sperm group (FT), and Resveratrol added after freeze-thawing group (FA-Res) were determined. The tandem mass tags (TMT) peptide labeling combined with LC-MS/MS was used for proteomic analysis of the total proteins in FR and FT groups. A total of 2651 proteins were identified, among which 41 proteins were upregulated and 48 proteins were downregulated after freezing. In-depth bioinformatics analysis of differentially abundant proteins (DAPs) revealed their close association with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation pathway. The energy-related protein dihydrolipoamide dehydrogenase (DLD) and the reactive oxygen species (ROS)-related protein NADH dehydrogenase 1 beta subcomplex subunit 9 (NDUFB9) exhibited significant decreases, indicating their potential role as key proteins contributing to reduced sperm vitality. The study demonstrated that the addition of resveratrol (RES) to semen could elevate the expression levels of DLD and NDUFB9 proteins. This study represents the pioneering proteomic analysis of Mongolian ram sperm before and after cryopreservation, establishing the significance of DLD and NDUFB9 as key proteins influencing the decline in vitality following cryopreservation of Mongolian ram sperm. These findings clarify that resveratrol can enhance the levels of DLD and NDUFB9 proteins in cryopreserved Mongolian ram sperm, consequently enhancing their vitality.