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Abstract Background There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity. Results A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks. Conclusions Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.

Yaks (Bos grunniens) exhibit exceptional adaptation to the challenging high-altitude environment of the Qinghai-Tibetan plateau, making them the sole bovine species capable of thriving in such exreme conditions. Investigating the cellular and molecular characteristics of yak ovaries across different reproductive states is crucial for gaining insight into their ovarian functions. Herein, the cellular atlases of yak ovaries in different reproductive states were depicted by single-cell RNA-sequencing (scRNA-seq). The cellular atlases of the ovaries were established by identifying specific gene expression patterns of various cell types, including granulosa cells, theca cells, stromal cells, smooth muscle cells, endothelial cells, glial cell, macrophages, natural killer cells, and proliferating cells. The cellular compositions of the ovaries vary among different reproductive states. Furthermore, the granulosa cells comprise six cell subtypes, while theca cells consist of eight cell subtypes. The granulosa cells and theca cells exhibit distinct biological functions throughout different reproductive states. The two cell types were aligned along their respective pseudotime trajectories. Moreover, a cell-to-cell communication network was constructed among distinct cell types within the ovary, spanning the three reproductive states. Notably, during the estrus period, the granulosa cells demonstrated more prominent interactions with other cell types compared to the remaining reproductive states.

Abstract Low‐dimensional hybrid halide perovskites represent a promising class of materials in optoelectronic applications because of strong broad self‐trapped exciton (STE) emissions. However, there exists a limitation in designing the ideal A‐site cation that makes the material satisfy the structure tolerance and exhibit STE emission raised by the appropriate electron–phonon coupling effect. To overcome this dilemma, we developed an inorganic metal‐organic dimethyl sulfoxide (DMSO) coordinating strategy to synthesize a series of zero‐dimensional (0D) Sb‐based halide perovskites including Na3SbBr6·DMSO6 (1), AlSbBr6·DMSO6 (2), AlSbCl6·DMSO6 (3), GaSbCl6·DMSO6 (4), Mn2Sb2Br10·DMSO13 (5) and MgSbBr5·DMSO7 (6), in which the distinctive coordinating A‐site cation [Am‐DMSO6]n+ efficiently separate the [SbXz] polyhedrons. Advantageously, these materials all exhibit broadband‐emissions with full widths at half maxima (FWHM) of 95–184 nm, and the highest photoluminescent quantum yield (PLQY) of 3 reaches 92%. Notably, compounds 2–4 are able to remain stable after storage of more than 120 d. First‐principles calculations indicate that the origin of the efficient STE emission can be attributed to the localized distortion in [SbXz] polyhedron upon optical excitation. Experimental and calculational results demonstrate that the proposed coordinating strategy provides a way to efficiently expand the variety of novel high‐performance STE emitters and continuously regulate their emission behaviors.

Milk lipids greatly affect the volatile flavor of milk, and the relationship between lipids and volatile flavor in yak milk was explored in this study. The volatile flavor compounds (VFCs), lipids profile, fatty acids in yak ordinary milk and colostrum were detected with HP/SPME-GC–MS, the semiquantitative lipidomics based on LC-MS/MS, GC–MS, respectively. The VFCs differences in yak milk were closely related to 1-((1 s,3ar,4r,7 s,7as)-4-hydroxy-7-isopropyl-4-methyloctahloctahydro-1h-inden-1-Yl)-ethanone,2,6,6-trimethyl-2,4-cycloheptadien-1-one, pentanal, 2-phenylethyl propionate, octanoic acid methyl ester, diphosphoric acid diisooctyl ester, (Z)-3,4,4-trimethyl-5-oxo-2-hexenoic acid and acetic acid. The volatile flavor in yak milk was well correlated with milk lipids, and TG(4:0_12:3_18:1), TG(6:0_8:0_18:1), TG(4:0_12:3_18:1), TG(12:0_18:2_18:3) and TG(16:0e_18:1_22:5) were the crucial lipid molecules affecting volatile flavor. The degeneration of above lipids by hydrolysis produced some fatty acids and alcohol, then these compounds were further derived into other VFCs especially above crucial 8 molecules. This study provided a theoretical basis for improving the volatile flavor by controlling lipids in yak milk.

Summary: Podocytopathies, such as focal segmental glomerulosclerosis (FSGS), are characterized by podocyte injury and can easily progress to end-stage kidney disease. However, the mechanisms underlying podocyte injury remain unclear. We observed podocyte injury along with pyroptosis in patients with FSGS. Bioinformatic analysis of public datasets revealed that transmembrane protein 30a (Tmem30a) might be associated with FSGS. The expression of Temem30a and the podocyte-related protein, nephrin, were significantly downregulated in patients with FSGS, adriamycin (ADR)-induced mice, and podocyte-specific Tmem30aloxP/loxP; NPHS2-Cre mice, whereas the expression of NLR family pyrin domain containing 3 (NLRP3) and ASC, two pyroptosis-related proteins, were significantly upregulated. Meanwhile, the pyroptosis inhibitor MCC950 and disulfiram (DSF) increased Tmem30a and podocyte-related proteins expression, and inhibited pyroptosis-related proteins expression in ADR-induced mouse podocytes and Tmem30a knockdown (KD) mouse podocytes. Therefore, Tmem30a might protect against podocyte injury by inhibiting pyroptosis, suggesting a potential therapeutic target for podocytopathies.

Abstract Background Patients with urosepsis associated with upper urinary tract stones require further stone management after emergency drainage. Objective To evaluate the safety and efficacy of elective flexible ureteroscopic lithotripsy (F-URSL) for upper urinary tract stones in patients with prior urosepsis who have undergone emergency drainage using retrograde ureteral stent(RUS) or percutaneous nephrostomy (PCN). Method Between January 2017 and December 2021, clinical data were collected for 102 patients who underwent elective F-URSL following emergency drainage for urosepsis caused by upper ureteral or renal stones. The patients were categorized into two groups based on the drainage method used: the RUS group and the PCN group. The collected data included patient demographics, stone parameters, infection recovery after emergency drainage, and clinical outcomes post F-URSL. Subsequently, the data underwent statistical analysis. Results A total of 102 patients were included in the statistical analysis, with 58 (56.86%) in the RUS group and 44 (43.14%) in the PCN group. Among the patients, 84 (82.35%) were female and 18 (17.65%) were male, with an average age of 59.36 years. Positive urine cultures were observed in 71 (69.61%) patients. Successful drainage was achieved in all patients in both groups, and there were no significant differences in the time required for normalization of white blood cell count (WBC) and body temperature following drainage. Additionally, all patients underwent F-URSL successfully, and no statistically significant differences were observed between the two groups in terms of operative time, stone-free rates, postoperative fever, and postoperative hospital stay. Conclusion Both RUS and PCN have been established as effective approaches for managing urosepsis caused by upper urinary tract stones. Furthermore, the impact of these two drainage methods on the subsequent management of stones through elective F-URSL has shown consistent outcomes.

Abstract Ferroelectricity, a spontaneous and reversible electric polarization, is found in certain classes of van der Waals (vdW) materials. The discovery of ferroelectricity in twisted vdW layers provides new opportunities to engineer spatially dependent electric and optical properties associated with the configuration of moiré superlattice domains and the network of domain walls. Here, we employ near-field infrared nano-imaging and nano-photocurrent measurements to study ferroelectricity in minimally twisted WSe2. The ferroelectric domains are visualized through the imaging of the plasmonic response in a graphene monolayer adjacent to the moiré WSe2 bilayers. Specifically, we find that the ferroelectric polarization in moiré domains is imprinted on the plasmonic response of the graphene. Complementary nano-photocurrent measurements demonstrate that the optoelectronic properties of graphene are also modulated by the proximal ferroelectric domains. Our approach represents an alternative strategy for studying moiré ferroelectricity at native length scales and opens promising prospects for (opto)electronic devices.

In order to investigate the composition and differences in volatile organic compounds (VOCs) in yak and cattle-yak meat and determine the key metabolites and metabolic pathways related to flavor formation. In this study, the VOCs and non-volatile metabolites in Longissimus dorsi muscle of two groups of samples were detected and analyzed by gas chromatography–ion migration spectrometry (GC-IMS) and gas chromatography–mass spectrometry (GC-MS). The results showed that 31 VOCs were identified by GC-IMS, including 5 alcohols, 5 ketones, 5 esters, 3 aldehydes, 2 furans, 2 hydrocarbons, 1 amine, 1 acid, 1 thiazole, 1 pyrazine, and 5 others. Most of them were alcohols, ketones, esters, and aldehydes. A total of 75 non-volatile metabolites with significant differences were obtained by GC-MS screening, among which amino acid contents such as serine, glycine, phenylalanine, and aspartic acid were significantly up-regulated in cattle-yak, and glutamic acid and tyrosine were significantly up-regulated in yak. The non-volatile differential metabolites in the two groups were significantly enriched in the metabolic pathways of arginine biosynthesis and oxidative phosphorylation. By combining GC-IMS and GC-MS, this study comprehensively and intuitively reflected the differences in VOCs between yak and cattle-yak meat, and clarified the metabolomic reasons for the differences in VOCs, so as to provide a theoretical basis for meat quality improvement.

Abstract Background Metformin is the most frequently prescribed medication for the treatment of type II diabetes mellitus and has played an anti-tumor potential in a variety of cancer types. Metformin can inhibit the growth of many cancer cells through various mechanisms, including ferroptosis. However, it is still unclear whether metformin can induce ferroptosis in lung cancer. Methods This study evaluated the anti-tumor effect of metformin by detecting the levels of oxidative stress factors, the levels of ferrous ions, and the expression of ferroptosis-related genes in A549 and H1299 lung cancer cell lines treated with or without metformin. Results The results showed that metformin treatment increased the levels of MDA, ROS and iron ions, while decreased the levels of GSH, T-SOD and CAT. Meanwhile, metformin treatment reduced the protein expression levels of Gpx4 and SLC7A11, Nrf2 and HO-1, while the addition of ferroptosis inhibitor ferrostatin-1 reversed the reduction. Conclusions These results demonstrated that metformin exerts anti-tumor effects by inducing ferroptosis through the Nrf2/HO-1 signaling pathway in lung cancer cells, providing a theoretical basis for drug therapy of lung cancer patients.

Abstract Background To study the influencing factors for coronary artery calcification (CAC) in maintenance hemodialysis (MHD) patients and the relationship between CAC and bone metabolism markers and to attempt to find a reliable marker linking vascular calcification and bone metabolism in MHD patients. Methods A total of 123 patients were enrolled. CAC was assessed by multislice spiral computed tomography (MSCT), and the CAC score (CACS) was evaluated using the Agaston method. Routine laboratory parameters, including triglycerides (TG), total cholesterol (TC), glucose (Glu), calcium (Ca), phosphorus (P), magnesium (Mg), etc., were measured. Serum markers of bone metabolism, such as alkaline phosphatase(ALP), calcitonin (CT), 25-hydroxy vitamin D [25-(OH)D], intact parathyroid hormone (iPTH), total type I procollagen amino-terminal peptide (tPINP), N-terminal mid-fragment of osteocalcin (N-MID OC), and β-type I collagen crosslinked carboxyl-terminal peptide (β-CTX), were also measured. Results Among 123 MHD patients, 37 patients (30.08%) did not have CAC, and 86 patients (69.92%) had CAC, including 41 patients (47.67%) with mild calcification and 45 patients (52.33%) with moderate to severe calcification. Age, Body Mass Index(BMI), the prevalence of hypertension and diabetes mellitus, TC, Glu, P, and Ca×P in the calcification group were higher than those in the noncalcification group, whereas Mg, iPTH, tPINP, N-MID OC, and β-CTX were lower than those in the noncalcified group (P 0.05). A logistic regression model was used to evaluate the influencing factors for CAC. The results showed that age, BMI, TC, Glu, P, and Ca×P were risk factors for CAC and its severity in MHD patients, whereas diabetes mellitus, Mg, and N-MID OC were protective factors for CAC in MHD patients. In addition, N-MID OC was a protective factor for the severity of CAC. After adjusting for the corresponding confounding factors, the results of the risk factors were consistent, and N-MID OC was still an independent protective factor for CAC and its severity. Conclusions Elevated serum P and Ca×P were independent risk factors for CAC in MHD patients, and serum Mg may be an independent protective factor for CAC. CAC was closely related to abnormal bone metabolism and bone metabolic markers in MHD patients. Relatively low bone turnover can promote the occurrence and development of CAC. N-MID OC may be a reliable bone metabolic marker linking vascular calcification and bone metabolism in MHD patients.

BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundation for the development of infection prevention and control strategies. This study aimed to determine the antimicrobial susceptibility profile, the molecular epidemiology and conduct homology analysis on CRAB strains isolated from ICUs.MethodsThe sensitivity to various antimicrobials was determined using the minimum inhibitory concentration (MIC) method, Kirby-Bauer disk diffusion (KBDD), and E-test assays. Resistance genes were identified by polymerase chain reaction (PCR). Molecular typing was performed using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA).ResultsAmong the 79 isolates collected, they exhibited high resistance to various antimicrobials but showed low resistance to levofloxacin, trimethoprim-sulfamethoxazole, and tetracyclines. Notably, all isolates of A. baumannii were identified as multidrug-resistant A. baumannii (MDR-AB). The blaOXA-51-like, adeJ, and adeG genes were all detected, while the detection rates of blaOXA-23-like (97.5%), adeB (93.67%), blaADC (93.67%), qacEΔ1-sul1 (84.81%) were higher; most of the Ambler class A and class B genes were not detected. MLST analysis on the 79 isolates identified five sequence types (STs), which belonged to group 3 clonal complexes 369. ST1145Ox was the most frequently observed ST with a count of 56 out of 79 isolates (70.89%). MLST analysis for non-sensitive tigecycline isolates, which were revealed ST1145Ox and ST1417Ox as well. By using the MLVA assay, the 79 isolates could be grouped into a total of 64 distinct MTs with eleven clusters identified in them. Minimum spanning tree analysis defined seven different MLVA complexes (MCs) labeled MC1 to MC6 along with twenty singletons. The locus MLVA-AB_2396 demonstrated the highest Simpson’s diversity index value at 0.829 among all loci tested in this study while also having one of the highest variety of tandem repeat species.ConclusionThe molecular diversity and clonal affinities within the genomes of the CRAB strains were clearly evident, with the identification of ST1144Ox, ST1658Ox, and ST1646Oxqaq representing novel findings.

AbstractObjective The pathogenesis of renal osteopathy and cardiovascular disease suggests the disordered bone–vessel axis in chronic kidney disease–mineral bone disorder (CKD–MBD). However, the mechanism of the bone–vessel axis in CKD–MBD remains unclear.Methods We established a CKD–MBD rat model to observe the pathophysiological phenotype of the bone–vessel axis and performed RNA sequencing of aortas to identify novel targets of the bone–vessel axis in CKD–MBD.Results The microarchitecture of the femoral trabecular bone deteriorated and alveolar bone loss was aggravated in CKD–MBD rats. The intact parathyroid hormone and alkaline phosphatase levels increased, 1,25-dihydroxyvitamin D3 levels decreased, and intact fibroblast growth factor-23 levels did not increase in CKD–MBD rats at 16 weeks; other bone metabolic parameters in the serum demonstrated dynamic characteristics. With calcium deposition in the abdominal aortas of CKD–MBD rats, RNA sequencing of the aortas revealed a significant decrease in inositol 1,4,5-trisphosphate receptor type 2 (ITPR2) gene levels in CKD–MBD rats. A similar trend was observed in rat aortic smooth muscle cells. As a secretory protein, ITPR2 serum levels decreased at 4 weeks and slightly increased without statistical differences at 16 weeks in CKD–MBD rats. ITPR2 serum levels were significantly increased in patients with vascular calcification, negatively correlated with blood urea nitrogen levels, and positively correlated with serum tartrate-resistant acid phosphatase 5b levels.Conclusion These findings provide preliminary insights into the role of ITPR2 in the bone–vessel axis in CKD–MBD. Thus, ITPR2 may be a potential target of the bone–vessel axis in CKD–MBD.

BackgroundA model to predict preoperative outcomes after percutaneous nephrolithotomy (PCNL) with renal staghorn stones is developed to be an essential preoperative consultation tool.ObjectiveIn this study, we constructed a predictive model for one-time stone clearance after PCNL for renal staghorn calculi, so as to predict the stone clearance rate of patients in one operation, and provide a reference direction for patients and clinicians.MethodsAccording to the 175 patients with renal staghorn stones undergoing PCNL at two centers, preoperative/postoperative variables were collected. After identifying characteristic variables using PCA analysis to avoid overfitting. A predictive model was developed for preoperative outcomes after PCNL in patients with renal staghorn stones. In addition, we repeatedly cross-validated their model’s predictive efficacy and clinical application using data from two different centers.ResultsThe study included 175 patients from two centers treated with PCNL. We used a training set and an external validation set. Radionics characteristics, deep migration learning, clinical characteristics, and DTL+Rad-signature were successfully constructed using machine learning based on patients’ pre/postoperative imaging characteristics and clinical variables using minimum absolute shrinkage and selection operator algorithms. In this study, DTL-Rad signal was found to be the outstanding predictor of stone clearance in patients with renal deer antler-like stones treated by PCNL. The DTL+Rad signature showed good discriminatory ability in both the training and external validation groups with AUC values of 0.871 (95% CI, 0.800-0.942) and 0.744 (95% CI, 0.617-0.871). The decision curve demonstrated the radiographic model’s clinical utility and illustrated specificities of 0.935 and 0.806, respectively.ConclusionWe found a prediction model combining imaging characteristics, neural networks, and clinical characteristics can be used as an effective preoperative prediction method.

Gas-containing renal stones (GCS) are rare urological entities. Current literature has suggested possible associations with premenopausal women, urinary tract infection, and metabolic diseases. We report the case of a 25-year-old young woman with no underlying co-morbidities who had multiple right GCS and suspected emphysematous pyelitis. Antibiotic therapy was initiated to control her urinary tract infection with E. coli. She then underwent elective right flexible ureteroscopy to relieve her ureteropelvic junction obstruction. Complete stone retrieval was achieved and she made an uneventful recovery with no stone recurrence during 1-year follow-up.

IntroductionVascular calcification (VC) is more likely to be detected in the chronic kidney disease (CKD) population. The mechanism of VC development from CKD is different from that for simple VC and has always been a major research area. The aim of this study was to detect alterations in the metabolome during development of VC in CKD and to identify the critical metabolic pathways and metabolites involved in its pathogenesis.MethodsRats in the model group were given an adenine gavage combined with a high-phosphorus diet to imitate VC in CKD. The aorta calcium content was measured and used to divide the model group into a VC group and non-vascular calcification group (non-VC group). The control group was fed a normal rat diet and given a saline gavage. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to determine the altered serum metabolome in the control, VC, and non-VC groups. The identified metabolites were mapped into the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (https://www.genome.jp/kegg/) for pathway and network analyses.ResultThere were 14 metabolites that changed significantly in the VC group, with three metabolic pathways playing critical roles in the pathogenesis of VC in CKD: steroid hormone biosynthesis; valine, leucine and isoleucine biosynthesis; and pantothenate and CoA biosynthesis.ConclusionOur results indicated changes in the expression of steroid sulfatase and estrogen sulfotransferase, and down-regulation of the in situ synthesis of estrogens in the VC group. In conclusion, the serum metabolome alters significantly during the pathogenesis of VC in CKD. The key pathways, metabolites, and enzymes we identified are worth further study and may become a promising therapeutic target for the treatment of VC in CKD.

Abstract Background High spontaneous miscarriage rate in yak, especially during late pregnancy, have caused a great economic loss to herdsmen living in the Qinghai-Tibet plateau. However, the mechanism underlying spontaneous miscarriage is still poorly understood. In the present study, placenta protein markers were identified to elucidate the pathological reasons for yak spontaneous miscarriage through isobaric tags for relative and absolute quantification (iTRAQ) proteomic technology and bioinformatic approaches. Results Subsequently, a total of 415 differentially expressed proteins (DEPs) were identified between aborted and normal placentas. The up-regulated DEPs in the aborted placentas were significantly associated with “spinocerebellar ataxia”, “sphingolipid signalling”, “relaxin signalling”, “protein export”, “protein digestion and absorption” and “aldosterone synthesis and secretion” pathway. While the down-regulated DEPs in the aborted placentas mainly participated in “valine, leucine and isoleucine degradation”, “PPAR signalling”, “peroxisome”, “oxidative phosphorylation”, “galactose metabolism”, “fatty acid degradation”, “cysteine and methionine metabolism” and “citrate cycle” pathway. Conclusions The results implied that the identified DEPs could be considered as placental protein markers for yak miscarriage during late pregnancy, and biomacromolecule metabolic abnormality and oxidative damage might be responsible for the high spontaneous miscarriage rate in yak. These findings provide an important theoretical basis for deciphering the pathologic mechanism of late spontaneous miscarriage in yak.

Abstract Background and aim Yak estrus is a seasonal phenomenon, probably involving epigenetic regulation of synthesis and secretion of sex hormones as well as growth and development of follicles. N6-methyladenosine (m6A) is the most common internal modification of the eukaryotic mRNA. However, there are no detailed reports on the m6A transcriptome map of yak ovary. Therefore, this study aimed to collected the yak ovarian tissues at three different states of anestrus (YO-A), estrus (YO-F), and pregnancy (YO-P), and obtained the full transcriptome m6A map in yak by MeRIP-seq. Results The HE staining revealed that the number of growing follicles and mature follicles in the ovary during the estrus period was relatively higher than those in the anestrus period and the pregnancy period. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries, which suggests that m6A may play a regulatory role in ovarian activity. Next, we identified 20,174, 19,747 and 13,523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3′untranslated region (3′UTR) as well as the conserved sequence of “RRACH.” The GO, KEGG and GSEA analysis revealed the involvement of m6A in many physiological activities of the yak’s ovary during reproductive cycle. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. Conclusions The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.

Abstract Background Ovarian follicle fluid (FF) as a microenvironment surrounding oocyte plays critical roles in physio-biochemical processes of follicle development and oocyte maturation. It is hypothesized that proteins in yak FF participate in the physio-biochemical pathways. The primary aims of this study were to find differentially expressed proteins (DEPs) between mature and immature FF, and to elucidating functions of the mature and immature FF in yak. Results The mature and immature FF samples were obtained from three healthy yaks that were nonpregnant, aged from four to five years, and free from any anatomical reproductive disorders. The FF samples were subjected to mass spectrometry with the isobaric tags for relative and absolute quantification (iTRAQ). The FF samples went through correlation analysis, principle component analysis, and expression pattern analysis based on quantification of the identified proteins. Four hundred sixty-three DEPs between mature and immature FF were identified. The DEPs between the mature and immature FF samples underwent gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and protein-protein interaction (PPI) analysis. The DEPs highly expressed in the mature FF mainly took parts in the complement and coagulation cascades, defense response, acute-phase response, response to other organism pathways to avoid invasion of exogenous microorganisms. The complement activation pathway contains eight DEPs, namely C2, C5, C6, C7, C9, C4BPA, CFH, and MBL2. The three DEPs, CATHL4, CHGA, and PGLYRP1, take parts in defense response pathway to prevent invasion of exogenetic microorganism. The coagulation cascades pathway involves many coagulation factors, such as F7, F13A1, FGA, FGB, FGG, KLKB1, KNG1, MASP1, SERPINA1, and SERPIND1. While the DEPs highly expressed in the immature FF participated in protein translation, peptide biosynthetic process, DNA conformation change, and DNA geometric change pathways to facilitate follicle development. The translation pathway contains many ribosomal proteins, such as RPL3, RPL5, RPS3, RPS6, and other translation factors, such as EIF3J, EIF4G2, ETF1, MOV10, and NARS. The DNA conformation change and DNA geometric change involve nine DEPs, DDX1, G3BP1, HMGB1, HMGB2, HMGB3, MCM3, MCM5, MCM6, and RUVBL2. Furthermore, the expressed levels of the main DEPs, C2 and SERPIND1, were confirmed by western blot. Conclusions The differential proteomics revealed the up-regulated DEPs in mature FF take parts in immunoreaction to prevent invasion of microorganisms and the up-regulated DEPs in immature FF participate in protein synthesis, which may improve our knowledge of the follicular microenvironment and its biological roles for reproductive processes in yak. The DEPs, C2 and SERPIND1, can be considered as protein markers for mature yak follicle.

Excitons play an important role in the optical properties of 2D semiconductors, but their spatial characterization is usually constrained by the diffraction limit. Here, the authors report near-field optical spectroscopy of 2D transition metal dichalcogenides with 20 nm resolution, revealing their spatially dependent excitonic spectra and complex dielectric function.

Studying the mechanism of spermatogenesis is key to exploring the reproductive characteristics of male yaks. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from juvenile and adult yaks and found that the m6A level significantly increased after sexual maturity in yaks. In MeRIP-seq, 1702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during the sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study indexed the m6A characteristics of yak testicles at different developmental stages, providing basic data for further research of m6A modification regulating yak testicular development.

Background: Qaidam cattle are local breeds that habitats in northwest China. It has many excellent characteristics, such as high cold and roughage tolerance, low oxygen adaptability, and tender meat quality. Copy number variation (CNV) can induce phenotypic changes in animals by a variety of effects, and thus affects the biological functions of the animals. To explore the molecular mechanism of its adaptation to extreme cold weather and muscle fat development, the CNV variations in the genome of three Qaidam cattle were detected by whole-genome sequencing, in this study. Results: A total of 16,743 CNVs and 9498 copy number variable regions (CNVRs) were obtained after the screening, which accounts for 2.18% of the bovine genome. The CNVR length detected ranged from 0.3 KB to 10.77 KB, with a total length of 58.17 MB and an average length of 6.12 KB/ CNVR. Through functional enrichment of CNVR related genes, LDHB, and ME1 genes were screened as the key genes for Qaidam cattle to adapt to the cold and low oxygen environments, whereas KIT and FGF18 genes might be related to the coat color and growth. In the CNVR overlapped with QTLs, variation in CAPN1 and CAST genes might be closely related to the tender meat quality of Qaidam cattle. Conclusions: Therefore, this study provides new genetic insights on the environmental adaptability and important economic traits of Qaidam cattle.How to cite: Guo S, Wu X, Pei J, et al. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.006

Hurricane Irma caused significant damages to mangrove forested wetlands in south Florida, including defoliation, tree snapping, and uprooting. Previous studies have used optical satellite imagery to estimate large-scale forest disturbance and resilience patterns. However, satellite images alone cannot provide measurements of vertical mangrove structure. In this study, we used dense point cloud data collected by NASA Goddard’s LiDAR, Hyperspectral, and Thermal (G-LiHT) airborne imager before (March 2017) and after (December 2017 and March 2020) Hurricane Irma to quantify the recovery, or lack thereof, of the three-dimensional (3D) mangrove forest structure. Recent resilience and vulnerability models developed from Landsat time series following the storm were used to group the lidar data into distinct disturbance-recovery classes. We then analyzed lidar-based forest canopy within each of the recovery classes to test a suite of forest structural characteristics. Our results indicate that 77.0 % of the survey area experienced canopy height loss three months after Hurricane Irma, whereby the majority of canopy height loss occurred in areas with the tallest mangrove forests (i.e., 15–25 m tall). Our analysis shows that the mangrove canopy height in South Florida increased by an average 0.26 m from December 2017 to March 2020, with most of the forest (84.7 % of the survey area) experiencing canopy height regrowth. However, only 38.1 % of the survey area has recovered to pre-storm canopy height. The distribution of canopy height was significantly altered by Hurricane Irma in the low and intermediate resilience classes, but were not significantly different 2.5 years later. Indeed, in areas of low resilience, little to no vertical change has occurred suggesting the absence of canopy regrowth and natural regeneration. Conversely, mangroves in high resilience class, which are dominated by shorter canopies (

N6-methyladenosine (m6A) is the most common form of eukaryotic mRNA modification, and it has been shown to exhibit broad regulatory activity in yeast, plants, and mammals. The specific role of m6A methylation as a regulator of spermatogenesis, however, has yet to be established. In this experiment, through a series of preliminary studies and methylated RNA immunoprecipitation sequencing, the m6A map of cattle-yak testicular tissue was established as a means of exploring how m6A modification affects cattle-yak male infertility. Cattle-yak testis tissues used in this study were found to contain sertoli cells and spermatogonia. Relative to sexually mature yak samples, those isolated from cattle-yak testis exhibited slightly reduced levels of overall methylation, although these levels were significantly higher than those in samples from pre-sexually mature yaks. Annotation analyses revealed that differentially methylated peaks were most concentrated in exonic regions, with progressively lower levels of concentration in the 3'-untranslated region (UTR) and 5'-UTR regions. To further explore the role of such m6A modification, enrichment analyses were performed on differentially methylated and differentially expressed genes in these samples. For the cattle-yaks vs. 18-months-old yaks group comparisons, differentially methylated genes were found to be associated with spermatogenesis-related GO terms related to the cytoskeleton and actin-binding, as well as with KEGG terms related to the regulation of the actin cytoskeleton and the MAPK signaling pathway. Similarly, enrichment analyses performed for the cattle-yaks vs. 5-years-old yaks comparison revealed differentially methylated genes to be associated with GO terms related to protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism, and endocytotic activity, as well as with KEGG terms related to apoptosis and the Fanconi anemia pathway. Overall, enrichment analyses for the cattle-yaks vs. 18-months-old yaks comparison were primarily associated with spermatogenesis, whereas those for the cattle-yaks vs. 5-years-old yaks comparison were primarily associated with apoptosis.

Spermatogenesis is a complex process that involves proliferation and differentiation of diploid male germ cells into haploid flagellated sperm and requires intricate interactions between testicular somatic cells and germ cells. The cellular heterogeneity of this process presents a challenge in analyzing the different cell types at various developmental stages. Single-cell RNA sequencing (scRNA-seq) provides a useful tool for exploring cellular heterogeneity. In this study, we performed a comprehensive and unbiased single-cell transcriptomic study of spermatogenesis in sexually mature 4-year-old yak using 10× Genomics scRNA-seq. Our scRNA-seq analysis identified six somatic cell types and various germ cells, including spermatogonial stem cells, spermatogonia, early-spermatocytes, late-spermatocytes, and spermatids in yak testis. Pseudo-timing analysis showed that Leydig and myoid cells originated from common progenitor cells in yaks. Moreover, functional enrichment analysis demonstrated that the top expressed genes in yak testicular somatic cells were significantly enriched in the cAMP signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, and ECM receptor interactions. Throughout the spermatogenesis process, genes related to spermatogenesis, cell differentiation, DNA binding, and ATP binding were expressed. Using immunohistochemical techniques, we identified candidate marker genes for spermatogonial stem cells and Sertoli cells. Our research provides new insights into yak spermatogenesis and the development of various types of cells in the testis, and presents more reliable marker proteins for in vitro culture and identification of yak spermatogonial stem cells in the later stage.

Epididymis development is the basis of male reproduction and is a crucial site where sperm maturation occurs. In order to further understand the epididymal development of yak and how to regulate sperm maturation, we conducted a multi-omics analysis. We detected 2274 differential genes, 222 differential proteins and 117 co-expression genes in the cauda epididymis of yak before and after sexual maturity by RNA-seq and proteomics techniques, which included TGFBI, COL1A1, COL1A2, COL3A1, COL12A1, SULT2B1, KRT19, and NPC2. These high abundance genes are mainly related to cell growth, differentiation, adhesion and sperm maturation, and are mainly enriched via extracellular matrix receptor interaction, protein differentiation and absorption, and lysosome and estrogen signaling pathways. The abnormal expression of these genes may lead to the retardation of epididymal cauda development and abnormal sperm function in yak. In conclusion, through single and combined analysis, we provided a theoretical basis for the development of the yak epididymal cauda, sperm maturation, and screening of key genes involved in the regulation of male yak reproduction.

The utilization of yak milk is still in a primary stage, and the nutrition composition of yak colostrum is not systematically characterized at present. In this study, the lipids, fatty acids, amino acids and their derivatives, metabolites in yak colostrum, and mature milk were detected by the non−targeted lipidomics based on (ultra high performance liquid chromatography tandem quadrupole mass spectrometer) UHPLC−MS, the targeted metabolome based on gas chromatography−mass spectrometer (GC−MS), the targeted metabolome analysis based on UHPLC−MS, and the non-targeted metabolome based on ultra high performance liquid chromatography tandem quadrupole time of flight mass spectrometer (UHPLC−TOF−MS), respectively. Meanwhile, the nutrition composition of yak colostrum was compared with the data of cow mature milk in the literatures. The results showed that the nutritive value of yak colostrum was higher by contrast with yak and cow mature milk from the perspective of the fatty acid composition and the content of Σpolyunsaturated fatty acids (PUFAs), Σn−3PUFAs; the content of essential amino acid (EAA) and the ratio of EAA/total amino acid (TAA) in yak colostrum were higher than the value in yak mature milk; and the content of functional active lipids including phosphatidylcholines (PC), phosphatidylglycerol (PG), phosphatidylserine (PS), lyso-phosphatidylcholine (LPC), lyso-phosphatidylglycerol (LPG), lyso-phosphatidylinositol (LPI), sphingomyelin (SM), ganglioside M3 (GM3), ganglioside T3 (GT3), and hexaglycosylceramide (Hex1Cer) in yak colostrum, was higher than the value of yak mature milk. Moreover, the differences of nutritive value between yak colostrum and mature milk were generated by the fat, amino acids and carbohydrate metabolism that were regulated by the ovarian hormone and referencesrenin-angiotensin-aldosterone system in yaks. These research results can provide a theoretical basis for the commercial product development of yak colostrum.

Fat deposition is very important to the growth and reproduction of yaks. In this study, the effect of the feeding system on fat deposition in yaks was explored by transcriptomics and lipidomics. The thickness of the subcutaneous fat in yaks under stall (SF) and graze feeding (GF) was evaluated. The transcriptomes and lipidomes of the subcutaneous fat in yaks under different feeding systems were detected by RNA-sequencing (RNA-Seq) and non-targeted lipidomics based on ultrahigh-phase liquid chromatography tandem mass spectrometry (UHPLC-MS), respectively. The differences in lipid metabolism were explored, and the function of differentially expressed genes (DEGs) was evaluated by gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) analysis. Compared with GF yaks, SF yaks possessed stronger fat deposition capacity. The abundance of 12 triglycerides (TGs), 3 phosphatidylethanolamines (PEs), 3 diglycerides (DGs), 2 sphingomyelins (SMs) and 1 phosphatidylcholine (PC) in the subcutaneous fat of SF and GF yaks was significantly different. Under the mediation of the cGMP–PKG signaling pathway, the blood volume of SF and GF yaks may be different, which resulted in the different concentrations of precursors for fat deposition, including non-esterified fatty acid (NEFA), glucose (GLU), TG and cholesterol (CH). The metabolism of C16:0, C16:1, C17:0, C18:0, C18:1, C18:2 and C18:3 in yak subcutaneous fat was mainly realized under the regulation of the INSIG1, ACACA, FASN, ELOVL6 and SCD genes, and TG synthesis was regulated by the AGPAT2 and DGAT2 genes. This study will provide a theoretical basis for yak genetic breeding and healthy feeding.

Background: Transmembrane protein 95 (TMEM95) plays a role in male fertility. Previous studies showed that genes with a significant impact on reproductive traits can also affect the growth traits of livestock. Thus, we speculated that the genetic variation of TMEM95 gene may have effects on growth traits of cattle. Results: Two SNPs were genotyped. The rs136174626 and rs41904693 were in the intron 4 and 3′-untranslated region, respectively. The linkage disequilibrium analysis illustrated that these two loci were not linked. The rs136174626 was associated with six growth traits of Nanyang cattle, four traits of Luxi cattle, and three traits of Ji’an cattle. For rs41904693 locus, the GG individuals had greater body height and abdominal girth in Ji’ an cattle than TT and TG individuals. In Jinnan cattle, GG and TT individuals had greater body height, height at hip cross, body length, and heart girth than TG individuals. The potential splice site prediction results suggest that the rs136174626 may influence the splicing efficiency of TMEM95, and the miRNA binding site prediction results showed that the rs41904693 may influence the expression of TMEM95 by affecting the binding efficiency of Bta-miR-1584 and TMEM95 3′-UTR. Conclusions: The findings of the study suggested that the two SNPs in TMEM95 could be a reliable basis for molecular breeding in cattle.How to cite: Guo X, Zhang S, Yang H, et al. Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.03.004

Skeletal muscle growth and development is a complicated process that is regulated at multiple steps and by numerous myogenesis genes. RNA editing represents one of the events at the post-transcriptional level, which contributes to the diversity of transcriptome and proteome by altering the nucleotides of RNAs. However, RNA editing events in the skeletal muscle of yaks are still not well defined. This study conducted whole-genome RNA-editing identification in skeletal muscle of yaks at embryonic stage (ES) and adult stage (AS). We found a total of 11,168 unique RNA editing sites, most of which were detected in the intergenic region. After annotation, we totally identified 2,718 editing sites within coding regions, among which 858 were missense changes. Moreover, totally 322 editing sites in the 3′ untranslated regions (UTR) were also predicted to alter the set of miRNA target sites, indicating that RNA editing may be involved in translational repression or mRNA degradation. We found 838 RNA editing sites (involving 244 common genes) that are edited differentially in ES as compared to AS. According to the KEGG enrichment analysis, these differentially edited genes were mainly involved in pathways highly related to skeletal muscle development and myogenesis, including MAPK, AMPK, Wnt, and PI3K-Akt signaling pathways. Altogether, our work presents the first characterization of RNA editing sites within yak skeletal muscles on a genome-wide scale and enhances our understanding of the mechanism of skeletal muscle development and myogenesis.

Abstract—A novel double-layer transmitarray element is presented at 60 GHz with linearly- and circularly-polarized characteristics. A planar frequency-selective structure using the complementary design is adopted to augment the element performance for millimeter-wave applications. By integrating two different types of structure, i.e. cross and slot type, the compensation phase range is extended effectively with a satisfactory transmission magnitude. A transmitarray prototype is fabricated and tested to verify this double-layer complementary design. The measured gain at 60.5 GHz is 33.1 dBi with an aperture efficiency of 42.15%. Low side-lobe and cross-polarization levels are obtained. The proposed double-layer complementary design can reduce the structure complexity effectively and offer a high aperture efficiency at a low cost, which can be a potential candidate for the millimeter-wave transmitarray.

Abstract The current study aimed to investigate the damage of long-term high concentrate diet feeding pattern on Yak jejunal structure, physiological function and protein composition during cold season. Twelve Datong male Yak (Bos grunniens) with the same age from cold season were randomly selected and slaughtered to determine Yak jejunal digestive enzyme activity, morphology and protein composition on different feeding patterns in Tibetan Plateau. The results showed that Yak jejunum digestive enzyme activity and morphology of grazing reared group were better than those in the intensively reared group. A total of 96 differentially expressed proteins were identified by label-free Mass Spectrometry (MS), which could be concluded to two predominant themes: protein structure and inflammatory response. Nine differentially expressed proteins were correlated in Yak jejunum damage in different feeding patterns. According to this research, we found that feeding pattern resulted the differences in Yak jejunum physiological function, morphology and protein composition. This fact was confirmed long-term high dietary concentrate feeding could damage the jejunum epithelial morphology and function.

Abstract Aims To explore the clinical characteristics and placental pathological changes of pregnant women with 2019 novel coronavirus (CoV) disease (COVID-19) in the third trimester, and to assess the possibility of vertical transmission. Methods and results The placenta tissues were evaluated by using immunohistochemistry for inflammatory cells and Hofbauer cells, and using severe acute respiratory syndrome (SARS) CoV-2 RNA Fluorescence In-Situ Hybridization (FISH) and SARS-CoV-2 spike protein immunofluorescence (IF) double staining. All eight placentas from the third trimester pregnancy women were studied. All patients were cured, no clinical or serological evidence pointed to vertical transmission of SARS-CoV-2. Features of maternal vascular malperfusion (MVM) such as increased syncytial knots were present in all 8 cases (8/8), and increased focal perivillous fibrin depositions were presented in 7 cases (7/8). No significate chronic histiocytic intervillositis was noted in the placenta. The number of macrophages and inflammatory cells such as T cells, B cells and plasma cells in the placental villous was not significantly increased in all cases. Moreover, all of eight cases demonstrated negative results by FISH using a SARS-CoV-2 virus RNA probe and by IF using a monoclonal antibody against SARS-CoV-2 spike protein. Conclusions We found no evidence of vertical transmission and adverse maternal-fetal outcomes in the placentas of third trimester COVID-19 pregnancy women, which provided further information for the clinical management of those women in the third trimester. However, further studies are still needed for patients with infections in different stage of gestation, especially in first and second trimester.

Although the tumor-stroma ratio (TSR) has prognostic value in many cancers, the traditional semi-quantitative visual assessment method has inter-observer variability, making it impossible for clinical practice. We aimed to develop a machine learning (ML) algorithm for accurately quantifying TSR in hematoxylin-and-eosin (H&E)-stained whole slide images (WSI) and further investigate its prognostic effect in patients with muscle-invasive bladder cancer (MIBC). We used an optimal cell classifier previously built based on QuPath open-source software and ML algorithm for quantitative calculation of TSR. We retrospectively analyzed data from two independent cohorts to verify the prognostic significance of ML-based TSR in MIBC patients. WSIs from 133 MIBC patients were used as the discovery set to identify the optimal association of TSR with patient survival outcomes. Furthermore, we performed validation in an independent external cohort consisting of 261 MIBC patients. We demonstrated a significant prognostic association of ML-based TSR with survival outcomes in MIBC patients (p < 0.001 for all comparisons), with higher TSR associated with better prognosis. Uni- and multivariate Cox regression analyses showed that TSR was independently associated with overall survival (p < 0.001 for all analyses) after adjusting for clinicopathological factors including age, gender, and pathologic stage. TSR was found to be a strong prognostic factor that was not redundant with the existing staging system in different subgroup analyses (p < 0.05 for all analyses). Finally, the expression of six genes (DACH1, DEEND2A, NOTCH4, DTWD1, TAF6L, and MARCHF5) were significantly associated with TSR, revealing possible potential biological relevance. In conclusion, we developed an ML algorithm based on WSIs of MIBC patients to accurately quantify TSR and demonstrated its prognostic validity for MIBC patients in two independent cohorts. This objective quantitative method allows application in clinical practice while reducing the workload of pathologists. Thus, it might be of significant aid in promoting precise pathology services in MIBC.

The BlueFlux field campaign, supported by NASA’s Carbon Monitoring System, will develop prototype blue carbon products to inform coastal carbon management. While blue carbon has been suggested as a nature-based climate solution (NBS) to remove carbon dioxide (CO _2 ) from the atmosphere, these ecosystems also release additional greenhouse gases (GHGs) such as methane (CH _4 ) and are sensitive to disturbances including hurricanes and sea-level rise. To understand blue carbon as an NBS, BlueFlux is conducting multi-scale measurements of CO _2 and CH _4 fluxes across coastal landscapes, combined with long-term carbon burial, in Southern Florida using chambers, flux towers, and aircraft combined with remote-sensing observations for regional upscaling. During the first deployment in April 2022, CO _2 uptake and CH _4 emissions across the Everglades National Park averaged −4.9 ± 4.7 μ mol CO _2 m ^−2 s ^−1 and 19.8 ± 41.1 nmol CH _4 m ^−2 s ^−1 , respectively. When scaled to the region, mangrove CH _4 emissions offset the mangrove CO _2 uptake by about 5% (assuming a 100 year CH _4 global warming potential of 28), leading to total net uptake of 31.8 Tg CO _2 -eq y ^−1 . Subsequent field campaigns will measure diurnal and seasonal changes in emissions and integrate measurements of long-term carbon burial to develop comprehensive annual and long-term GHG budgets to inform blue carbon as a climate solution.

Yaks (Bos grunniens) are the only bovine species that adapt well to the harsh high-altitude environment in the Qinghai-Tibetan plateau. However, the reproductive adaptation to the climate of the high elevation remains to be elucidated. Cell composition and molecular characteristics are the foundation of normal ovary function which determines reproductive performance. So, delineating ovarian characteristics at a cellular molecular level is conducive to elucidating the mechanism underlying the reproductive adaption of yaks. Here, the single-cell RNA-sequencing (scRNA-seq) was employed to depict an atlas containing different cell types with specific molecular signatures in the yak ovary. The cell types were identified on the basis of their specifically expressed genes and biological functions. As a result, a cellular atlas of yak ovary was established successfully containing theca cells, stromal cells, endothelial cells, smooth muscle cells, natural killer cells, macrophages, and proliferating cells. A cell-to-cell communication network between the distinct cell types was constructed. The theca cells were clustered into five subtypes based on their biological functions. Further, CYP11A1 was confirmed as a marker gene for the theca cells by immunofluorescence staining. Our work reveals an ovarian atlas at the cellular molecular level and contributes to providing insights into reproductive adaption in yaks.

Abstract Background Lactoferricin (Lfcin) is an antimicrobial activity center of lactoferrin, produced by hydrolysis from the N-terminal of lactoferrin. It was hypothesized that the intramolecular disulfide bond in Lfcin could affect its antibacterial function through influencing its molecular structure. To prove this hypothesis, bovine Lfcin (bLfcin) and its two derivatives, bLfcin with an intramolecular disulfate bond (bLfcin DB) and bLfcin with a mutation C36G (bLfcin C36G), were synthesized, purified, and identified. The circular dichroism spectra of the peptides were detected in solutions with different ionic and hydrophobic strength. The antibacterial activity of the peptides against Trueperella pyogenes, separated from cow milk with mastitis, were determined. Results The secondary structure of bLfcin DB showed more β-turn and less random coil than the other peptides in H2O, similar ratios of secondary structures with bLfcin and bLfcin C36G under ionic conditions, and close percentages of secondary structure with bLfcin under hydrophobic conditions. The synthetic peptides exhibited strong antimicrobial activity against T. pyogenes isolates, T. pyogenes ATCC 19,411, and E. coli ATCC 25,922. The antimicrobial activities of the three peptides were greater against T. pyogenes than against E. coli, and bLfcin DB exhibited higher antibacterial activity compared with its derivatives. Conclusions The intramolecular disulfide bond could change the molecular structure of bLfcin under alternative ionic strengths and hydrophobic effects, and the formation of the disulfide bond is beneficial to executing the antibacterial function of bLfcin.

Objectives: Radiotherapy improves the survival rate of cancer patients, yet it also involves some inevitable complications. Radiation-induced heart disease (RIHD) is one of the most serious complications, especially the radiotherapy of thoracic tumors, which is characterized by cardiac oxidative stress disorder and programmed cell death. At present, there is no effective treatment strategy for RIHD; in addition, it cannot be reversed when it progresses. This study aims to explore the role and potential mechanism of microRNA-223-3p (miR-223-3p) in RIHD.Methods: Mice were injected with miR-223-3p mimic, inhibitor, or their respective controls in the tail vein and received a single dose of 20 Gy whole-heart irradiation (WHI) for 16 weeks after 3 days to construct a RIHD mouse model. To inhibit adenosine monophosphate activated protein kinase (AMPK) or phosphodiesterase 4D (PDE4D), compound C (CompC) and AAV9-shPDE4D were used.Results: WHI treatment significantly inhibited the expression of miR-223-3p in the hearts; furthermore, the levels of miR-223-3p decreased in a radiation time-dependent manner. miR-223-3p mimic significantly relieved, while miR-223-3p inhibitor aggravated apoptosis, oxidative damage, and cardiac dysfunction in RIHD mice. In addition, we found that miR-223-3p mimic improves WHI-induced myocardial injury by activating AMPK and that the inhibition of AMPK by CompC completely blocks these protective effects of miR-223-3p mimic. Further studies found that miR-223-3p lowers the protein levels of PDE4D and inhibiting PDE4D by AAV9-shPDE4D blocks the WHI-induced myocardial injury mediated by miR-223-3p inhibitor.Conclusion: miR-223-3p ameliorates WHI-induced RIHD through anti-oxidant and anti-programmed cell death mechanisms via activating AMPK by PDE4D regulation. miR-223-3p mimic exhibits potential value in the treatment of RIHD.

The authors use time-resolved scanning near-field optical microscopy to probe the ultrafast excitonic processes and their impact on waveguide operation in transition metal dichalcogenide crystals. They observe significant modulation of the complex index by monitoring waveguide modes on the fs time scale, and identify both coherent and incoherent manipulations of WSe2 excitonic resonances.

The potential regulatory role of N6-methyladenosine (m6A), the most prominent mRNA modification in eukaryotes, has recently been identified in mammals, plants, and yeast. However, whether and how m6A methylation is involved in sexual maturation in mammals remains largely unexplored. In this study, testicular tissue was obtained from yaks before and after sexual maturation, and m6A maps were generated via preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonial cells and a few primary spermatocytes were observed in the testicular tissue of yaks before sexual maturation, while spermatogenic cells at different stages of maturity could observed after sexual maturation. Experiments examining the expression of methylation-related enzymes and overall methylation levels showed that the methylation levels in yak testes increased after sexual maturation. Overall, 1,438 methylation peaks were differentially expressed before and after sexual maturation; 1,226 showed significant up-regulation and 212 showed significant down-regulation after sexual maturation. Annotation analysis showed that the differential methylation peaks were most commonly concentrated in the exon region, followed by the 3′UTR and finally the 5′UTR region. KEGG pathway analysis demonstrated that homologous recombination, the Notch signaling pathway, growth hormone synthesis, and other signaling pathways may be involved in testicular development and maturation in yaks. Levels of most m6A modifications were positively correlated with mRNA abundance, suggesting that m6A plays a regulatory role in mammalian sexual maturation. To our knowledge, this is the first report of an m6A transcriptional map of the yak testes, and our study lays the foundation for elucidating the function of m6A in the development of yak testes.

MAX dimerization protein 3 (MXD3), a transcriptional regulator of the MXD3 superfamily, is a part of the MYC–MAX–MXD network. However, its role in tumors has been reported in several cancers, such as B-cell acute lymphoblastic leukemia, medulloblastoma, neuroblastoma, and glioblastoma. Based on TCGA and GEO data, our first pancancer study of MXD3 confirmed the high expression of MXD3 in cancer tissues. Our results revealed that patients suffering from cancers with higher MXD3 expression had poor OS, DSS, DFI, and PFI. We further explored the methylation status of the MXD3 gene body and gene promoter in cancer. Patients with a higher MXD3 gene body have better OS, while the prognosis of patients with a high MXD3 promoter is more complex. We also verified the differential expression of three clinical phenotypes of MXD3: age, sex, and tumor stage, in a variety of tumors, suggesting a correlation between MXD3 and clinical characteristics. We explored the negative relationship between MXD3 and TMB and MSI in most types of cancer, indicating the poor prognosis of patients with high MXD3 expression. We further investigated the relationship between MXD3 and immune infiltrating cells and identified the relationship between MXD3 and immune genes, immunosuppressive genes, and antigen-presenting genes. All of the above findings established a solid relationship between MXD3 and the immune environment and immune cells. These results demonstrated that MXD3 might also be a potential immune factor. We also found a higher expression of MXD3 and promoter according to the increasing glioma WHO grade or histologic types. Glioma patients with high MXD3 or MXD3 promoter expression had poor survival. Finally, we used IHC to verify the higher expression of MXD3 in glioma samples compared to normal samples. Our study shows that MXD3, as a poor prognostic factor, plays a significant role in many cancers, especially glioma. Although more clinical evidence for MXD3 as a clinical therapeutic target and an immunotherapy site is needed, MXD3 can play an important guiding role in multiple clinical treatments, including immunotherapy and demethylation therapy.

Chemoresistance remains as a major hindrance in the treatment of hepatocellular carcinoma (HCC). High mobility group box protein 1 (HMGB1) enhances autophagic flux and protects tumor cells from apoptosis, which results in acquired drug resistance. However, the exact mechanisms underlying HMGB1-modulated autophagy in HCC chemoresistance remain to be defined. In the present study, we found that administration of doxorubicin (DOX) significantly promoted HMGB1 expression and induced HMGB1 cytoplasmic translocation in human HCC cell lines BEL7402 and SMMC7721, which enhanced autophagy that contributes to protecting HCC cells from apoptosis and increasing drug resistance. Moreover, we observed HMGB1 translocation and elevation of autophagy in DOX-resistant BEL7402 and SMMC7721 cells. Additionally, inhibition of HMGB1 and autophagy increased the sensitivities of BEL-7402 and SMMC-7721 cells to DOX and re-sensitized their DOX-resistant cells. Subsequently, we confirmed with HMGB1 regulated autophagy by activating the 5ʹ adenosine monophosphate-activated protein kinase (AMPK)/mTOR pathway. In summary, our results indicate that HMGB1 promotes acquired DOX resistance in DOX-treated BEL7402 and SMMC7721 cells by enhancing autophagy through the AMPK/mTOR signaling pathway. These findings provide the proof-of-concept that HMGB1 inhibitors might be an important targeted treatment strategy for HCC.

Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produce sperm, which adversely restricted the fixation of heterosis. Many prior attempts have been made to decipher the mechanism underlying the spermatogenesis stagnation of cattle-yak. However, the open chromatin region (OCR) map of yak and cattle-yak testes has not been generated yet. Here, we have analyzed the OCRs landscape of testicular tissues of cattle-yak and yaks by performing ATAC-seq technology. The OCRs of cattle-yak and yak testes displayed similar genome distribution and showed priority in intergenic regions, introns and promoters. The pathway enrichment analysis indicated that the differential OCRs-related genes were involved in spermatogenesis, involving the cell cycle, as well as Hippo, mTOR, MAPK, Notch, and Wnt signaling pathways. The integration of ATAC-seq and mRNA-seq indicated that the majority of the gene expression levels were positively correlated with chromatin openness. At the same time, we have identified a number of transcription factors (TFs) related to spermatogenesis and the differential expression of these TFs may contribute to the spermatogenesis stagnation of the cattle-yak. Overall, the findings of this study provide valuable information for advancing the research related to yak crossbreeding improvement and sperm production stagnation of cattle-yak.

(1) Purpose: Although assessment of tumor-infiltrating lymphocytes (TILs) has been acknowledged to have important predictive prognostic value in muscle-invasive bladder cancer (MIBC), it is limited by inter- and intra-observer variability, hampering widespread clinical application. We aimed to evaluate the prognostic value of quantitative TILs score based on a machine learning (ML) algorithm to identify MIBC patients who might benefit from immunotherapy or the de-escalation of therapy. (2) Methods: We constructed an artificial neural network classifier for tumor cells, lymphocytes, stromal cells, and “ignore” cells from hematoxylin-and-eosin-stained slide images using the QuPath open source software. We defined four unique TILs variables based on ML to analyze TILs measurements. Pathological slide images from 133 MIBC patients were retrospectively collected as the discovery set to determine the optimal association of ML-read TILs variables with patient survival outcomes. For validation, we evaluated an independent external validation set consisting of 247 MIBC patients. (3) Results: We found that all four TILs variables had significant prognostic associations with survival outcomes in MIBC patients (p < 0.001 for all comparisons), with higher TILs score being associated with better prognosis. Univariate and multivariate Cox regression analyses demonstrated that electronic TILs (eTILs) variables were independently associated with overall survival after adjustment for clinicopathological factors including age, sex, and pathological stage (p < 0.001 for all analyses). Results analyzed in different subgroups showed that the eTILs variable was a strong prognostic factor that was not redundant with pre-existing clinicopathological features (p < 0.05 for all analyses). (4) Conclusion: ML-driven cell classifier-defined TILs variables were robust and independent prognostic factors in two independent cohorts of MIBC patients. eTILs have the potential to identify a subset of high-risk stage II or stage III-IV MIBC patients who might benefit from adjuvant immunotherapy.

(1) Background: Early diagnosis and treatment are essential to reduce the mortality rate of bladder cancer (BLCA). We aimed to develop deep learning (DL)-based weakly supervised models for the diagnosis of BLCA and prediction of overall survival (OS) in muscle-invasive bladder cancer (MIBC) patients using whole slide digitized histological images (WSIs). (2) Methods: Diagnostic and prognostic models were developed using 926 WSIs of 412 BLCA patients from The Cancer Genome Atlas cohort. We collected 250 WSIs of 150 BLCA patients from the Renmin Hospital of Wuhan University cohort for external validation of the models. Two DL models were developed: a BLCA diagnostic model (named BlcaMIL) and an MIBC prognostic model (named MibcMLP). (3) Results: The BlcaMIL model identified BLCA with accuracy 0.987 in the external validation set, comparable to that of expert uropathologists and outperforming a junior pathologist. The C-index values for the MibcMLP model on the internal and external validation sets were 0.631 and 0.622, respectively. The risk score predicted by MibcMLP was a strong predictor independent of existing clinical or histopathologic indicators, as demonstrated by univariate Cox (HR = 2.390, p < 0.0001) and multivariate Cox (HR = 2.414, p < 0.0001) analyses. The interpretability of DL models can help in the analysis of critical regions associated with tumors to enrich the information obtained from WSIs. Furthermore, the expression of six genes (ANAPC7, MAPKAPK5, COX19, LINC01106, AL161431.1 and MYO16-AS1) was significantly associated with MibcMLP-predicted risk scores, revealing possible potential biological correlations. (4) Conclusions: Our study developed DL models for accurately diagnosing BLCA and predicting OS in MIBC patients, which will help promote the precise pathological diagnosis of BLCA and risk stratification of MIBC to improve clinical treatment decisions.

Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.

The effect of lipids on yak meat quality and volatile flavor compounds in yak meat under graze feeding (GF) and stall feeding (SF) was explored using untargeted lipidomics based on liquid chromatography–mass spectrometry (LC-MS) in this study. First, the volatile flavor compounds in longissimus dorsi (LD) of SF and GF yaks were detected by gas chromatography–mass spectrometry (GC-MS). In total 49 and 39 volatile flavor substances were detected in the LD of GF and SF yaks, respectively. The contents of pelargonic aldehyde, 3-hydroxy-2-butanone and 1-octen-3-ol in the LD of both GF and SF yaks were the highest among all detected volatile flavor compounds, and the leading volatile flavor substances in yak LD were aldehydes, alcohols and ketones. In total, 596 lipids were simultaneously identified in the LD of SF and GF yaks, and the leading lipids in the LD of both GF and SF yaks were sphingolipids (SPs), glycerolipids (GLs) and glycerophospholipids (GPs). Seventy-five significantly different lipids (SDLs) between GF and SF yaks were identified in the LD. The high content of TG(16:1/18:1/18:1), TG(16:0/17:1/18:1) and TG(16:0/16:1/18:1), PE(18:0/22:4) and PC(18:2/18:0) can improve the a* (redness) and tenderness of yak muscle. The changes in volatile flavor compounds in yak muscle were mainly caused by TG(18:1/18:1/18:2), TG(18:0/18:1/18:1), TG(16:0/17:1/18:1), TG(16:0/16:1/18:1), PC(18:2/18:0), TG(16:1/18:1/18:1), PI(18:0/20:4), TG(16:1/16:1-/18:1) and TG(17:0/18:1/18:1). The above results provide a theoretical basis for improving yak meat quality from the perspective of intramuscular lipids.

Fat deposition in yaks plays an important part in survival, multiplication, and meat quality. In this work, the characteristic of fat deposition in male yaks (MYs) and female yaks (FYs) and the regulations of gender to yak fat deposition were explored by mRNA-Seq and non-targeted metabolomics analyses. FYs possessed a higher body fat rate (BFR) of visceral fat, fat content in longissimus dorsi (LD) and liver, and subcutaneous fat thickness (p < 0.05). The fat and cholesterol synthesis in liver and the fat transport in FY blood increased. The fat metabolism in yaks is the combined effect of carbohydrate, fatty acid, and amino acid metabolism by tricarboxylic acid (TCA) cycle, and an increase of triglyceride (TG) synthesis was accompanied by an increase of steroid synthesis. The high levels of myo-inositol and cortisol (COR) (p < 0.01) activated the calcium signaling in FY subcutaneous fat, followed by the increase of adipocyte secretion, and resulted in more leptin (LEP) secretion (p < 0.01). Then peroxisome proliferator-activated receptor (PPAR) signaling was activated by the focal adhesions and ECM–receptor interaction. Finally, the TG and steroid synthesis increased by the expression regulation of ME1, SCD, ELOVL6, DGAT2, DBI, LPL, CPT1, PLIN1, LIPA, DHCR24, and SQLE gene. The above genes can be considered as the candidate genes for yak with higher fat amount in molecular breeding in the future. This study can provide a theoretical basis for improving the meat quality and breeding of yaks.