Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function.

Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-ß/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.

Isobavachalcone, a natural sirtuin 2 inhibitor, exhibits anti-triple-negative breast cancer efficacy in vitro and in vivo.

Triple-negative breast cancer (TNBC) is the most aggressive and lethal clinical subtype and lacks effective targeted therapies at present. Isobavachalcone (IBC), the main active component of Psoralea corylifolia L., has potential anticancer effects. Herein, we identified IBC as a natural sirtuin 2 (SIRT2) inhibitor and characterized the potential mechanisms underlying the inhibition of TNBC. Molecular dynamics analysis, enzyme activity assay, and cellular thermal shift assay were performed to evaluate the combination of IBC and SIRT2. The therapeutic effects, mechanism, and safety of IBC were analyzed in vitro and in vivo using cellular and xenograft models. IBC effectively inhibited SIRT2 enzyme activity with an IC50 value of 0.84 ± 0.22 µM by forming hydrogen bonds with VAL233 and ALA135 within its catalytic domain. In the cellular environment, IBC bound to and stabilized SIRT2, consequently inhibiting cellular proliferation and migration, and inducing apoptosis and cell cycle arrest by disrupting the SIRT2/α-tubulin interaction and inhibiting the downstream Snail/MMP and STAT3/c-Myc pathways. In the in vivo model, 30 mg/kg IBC markedly inhibited tumor growth by targeting the SIRT2/α-tubulin interaction. Furthermore, IBC exerted its effects by inducing apoptosis in tumor tissues and was well-tolerated. IBC alleviated TNBC by targeting SIRT2 and triggering the reactive oxygen species ROS/ß-catenin/CDK2 axis. It is a promising natural lead compound for future development of SIRT2-targeting drugs.

Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing.

Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.

Long- and short-read RNA sequencing from five reproductive organs of boar.

The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome.

Neoprzewaquinone A Inhibits Breast Cancer Cell Migration and Promotes Smooth Muscle Relaxation by Targeting PIM1 to Block ROCK2/STAT3 Pathway.

Salvia miltiorrhiza Bunge (Danshen) has been widely used to treat cancer and cardiovascular diseases in Chinese traditional medicine. Here, we found that Neoprzewaquinone A (NEO), an active component of S. miltiorrhiza, selectively inhibits PIM1. We showed that NEO potently inhibits PIM1 kinase at nanomolar concentrations and significantly suppresses the growth, migration, and Epithelial-Mesenchymal Transition (EMT) in the triple-negative breast cancer cell line, MDA-MB-231 in vitro. Molecular docking simulations revealed that NEO enters the PIM1 pocket, thereby triggering multiple interaction effects. Western blot analysis revealed that both NEO and SGI-1776 (a specific PIM1 inhibitor), inhibited ROCK2/STAT3 signaling in MDA-MB-231 cells, indicating that PIM1 kinase modulates cell migration and EMT via ROCK2 signaling. Recent studies indicated that ROCK2 plays a key role in smooth muscle contraction, and that ROCK2 inhibitors effectively control the symptoms of high intraocular pressure (IOP) in glaucoma patients. Here, we showed that NEO and SGI-1776 significantly reduce IOP in normal rabbits and relax pre-restrained thoracic aortic rings in rats. Taken together, our findings indicated that NEO inhibits TNBC cell migration and relaxes smooth muscles mainly by targeting PIM1 and inhibiting ROCK2/STAT3 signaling, and that PIM1 may be an effective target for IOP and other circulatory diseases.

Ibrutinib Prevents Acute Lung Injury via Multi-Targeting BTK, FLT3 and EGFR in Mice.

Ibrutinib has potential therapeutic or protective effects against viral- and bacterial-induced acute lung injury (ALI), likely by modulating the Bruton tyrosine kinase (BTK) signaling pathway. However, ibrutinib has multi-target effects. Moreover, immunity and inflammation targets in ALI treatment are poorly defined. We investigated whether the BTK-, FLT3-, and EGFR-related signaling pathways mediated the protective effects of ibrutinib on ALI. The intratracheal administration of poly I:C or LPS after ibrutinib administration in mice was performed by gavage. The pathological conditions of the lungs were assessed by micro-CT and HE staining. The levels of neutrophils, lymphocytes, and related inflammatory factors in the lungs were evaluated by ELISA, flow cytometry, immunohistochemistry, and immunofluorescence. Finally, the expression of proteins associated with the BTK-, FLT3-, and EGFR-related signaling pathways were evaluated by Western blotting. Ibrutinib (10 mg/kg) protected against poly I:C-induced (5 mg/kg) and LPS-induced (5 mg/kg) lung inflammation. The wet/dry weight ratio (W/D) and total proteins in the bronchoalveolar lavage fluid (BALF) were markedly reduced after ibrutinib (10 mg/kg) treatment, relative to the poly I:C- and LPS-treated groups. The levels of ALI indicators (NFκB, IL-1ß, IL-6, TNF-α, IFN-γ, neutrophils, and lymphocytes) were significantly reduced after treatment. Accordingly, ibrutinib inhibited the poly I:C- and LPS-induced BTK-, FLT3-, and EGFR-related pathway activations. Ibrutinib inhibited poly I:C- and LPS-induced acute lung injury, and this may be due to its ability to suppress the BTK-, FLT3-, and EGFR-related signaling pathways. Therefore, ibrutinib is a potential protective agent for regulating immunity and inflammation in poly I:C- and LPS-induced ALI.

Genome-wide scan for runs of homozygosity in Asian wild boars and Anqing six-end-white pigs.

Inbreeding and loss of genetic diversity are serious problems in local Chinese pig breeds. Runs of homozygosity (ROHs) are contiguous lengths of homozygous genotypes that can provide information on inbreeding levels, mating schemes, selection pressure, and genetic events. The Anqing six-end-white (AQ) pig, an important autochthonous pig breed bred in the Anhui province of China, plays a key role in the local pig industry. In recent decades, AQ pigs have become a closed breed with a small population size in conservation farms, raising the issue of inbreeding decline. In this study, we used 10× resequencing to detect the whole genome of 24 AQ pigs and six Asian wild boars (AWBs). We used the Plink software to analyze the homozygosity of the genome and the distribution of ROHs in the genome based on the resequencing data. We obtained 935.04 Gb of raw data from the resequencing results and more than 45 822 239 SNPs. Additionally, we identified 28 702 ROHs. Compared with AWB, AQ pigs had higher ROH numbers, longer ROH rates, and higher FROH values, which revealed that artificial selection influenced ROH distribution and genome inbreeding level. A total of 307 and 205 ROH islands were identified in the AQ pigs and AWBs respectively. The genes of ROH islands in AQ pigs were mainly enriched in immune biological processes. Our findings provide a useful reference for developing breeding programs to maintain genetic diversity and germplasm resources in AQ pigs.

The effect of in-hospital physiotherapy on handgrip strength and physical activity levels after cardiac valve surgery: a randomized controlled trial.

BACKGROUND: Patients who undergo cardiac valve surgery undertake routine physical therapy program. Despite its routine use, its influence on physical activity level post- surgery has not been illustrated. This study was to investigate whether 5 days of in-hospital physiotherapy could improve physical activity levels after cardiac valve surgery. METHODS: The study is a single-blind randomized controlled trial which performed in Cardiothoracic Surgery Department. Patients who underwent cardiac valve surgery (n=34) for confirmed cardiac valve disorders were assessed during hospitalization. The intervention group received a daily post-operative physiotherapy intervention, consisting of individualized mobilization, breathing exercises, ambulation with or without a walking aid. There was no physiotherapy treatment in the control group. Measurements: physical activity was assessed with the handgrip strength test and the timed up and go test. RESULTS: The treatment group showed significantly greater handgrip strength [20.58 (7.17) vs. 12.96 (4.65) kg] and less time on the timed up and go test [5.92 (2.91) vs. 6.53 (1.60) s] compared to the control group on the 5th post-operative day. Whilst there was no significant difference on the timed up and go test between the 2 groups, handgrip strength on the 5th post-operative day was significantly different between the 2 groups. CONCLUSIONS: Patients who received physiotherapy during hospitalization showed increased levels of handgrip strength and physical activity on the 5th day after cardiac valve surgery compared to the control group. The clinical value of increased levels of physical activity after in-hospital physiotherapy following cardiac valve surgery requires further investigation.

Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig.

Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (F ST ) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color ( MC1R ), salivary secretion ( STATH ), reproduction ( SPIRE2 , OSBP2 , LIMK2 , FANCA , and CABS1 ), olfactory transduction ( OR5K4 ), and growth ( NPY1R , NPY5R , and SELENOM ). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.

In Situ Observation of the Insulator-To-Metal Transition and Nonequilibrium Phase Transition for Li1-xCoO2 Films with Preferred (003) Orientation Nanorods.

It is notoriously difficult to distinguish the stoichiometric LiCoO2 (LCO) with a O3-I structure from its lithium defective O3-II phase because of their similar crystal symmetry. Interestingly, moreover, the O3-II phase shows metallic conductivity, whereas the O3-I phase is an electronic insulator. How to effectively reveal the intrinsic mechanism of the conductivity difference and nonequilibrium phase transition induced by the lithium deintercalation is of vital importance for its practical application and development. Based on the developed technology of in situ peak force tunneling atomic force microscopy (PF-TUNA) in liquids, the phase transition from O3-I to O3-II and consequent insulator-to-metal transition of LCO thin-film electrodes with preferred (003) orientation nanorods designed and prepared via magnetron sputtering were observed under an organic electrolyte for the first time in this work. Then, studying the post-mortem LCO thin-film electrode by using ex situ time-dependent XRD and conductive atomic force microscopy, we find the phase relaxation of LCO electrodes after the nonequilibrium deintercalation, further proving the differences of the electronic conductivity and work function between the O3-I and O3-II phases. Moreover, X-ray absorption spectroscopy results indicate that the oxidation of Co ions and the increasing of O 2p-Co 3d hybridization in the O3-II phase lead to electrical conductivity improvement in Li1-xCoO2. Simultaneously, it is found that the nonequilibrium deintercalation at a high charging rate can result in phase-transition hysteresis and the O3-I/O3-II coexistence at the charging end, which is explained well by an ionic blockade model with an antiphase boundary. At last, this work strongly suggests that PF-TUNA can be used to reveal the unconventional phenomena on the solid/liquid interfaces.

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs. Comparison of the breeds from different altitudes reveals strong signals of population differentiation at the locus of hypoxia-related genes including endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) and beta hemoglobin cluster. Notably, four novel nonsynonymous mutations specific to high-altitude dogs are identified at EPAS1, one of which occurred at a quite conserved site in the PAS domain. The association testing between EPAS1 genotypes and blood-related phenotypes on additional high-altitude dogs reveals that the homozygous mutation is associated with decreased blood flow resistance, which may help to improve hemorheologic fitness. Interestingly, EPAS1 was also identified as a selective target in Tibetan highlanders, though no amino acid changes were found. Thus, our results not only indicate parallel evolution of humans and dogs in adaptation to high-altitude hypoxia, but also provide a new opportunity to study the role of EPAS1 in the adaptive processes.

Inhibition of freshwater algal species by co-culture with two fungi.

Microorganisms have attracted worldwide attention as possible agents for the inhibition of water blooms. Algae can usually be inhibited and degraded directly by fungi. In this study, the effects of Trichaptum abietinum 1302BG and Lopharia spadicea on different freshwater algal species, namely, Microcystis aeruginosa, Chlorella vulgaris, Glenodinium sp., Navicula sp., Cryptomonas ovata, and Euglena gracilis, were detected. After 24h, there was a significant inhibitory effect in all algal cultures with T. abietinum 1302BG, except E. gracilis, and all algal cultures with L. spadicea, except Navicula sp. and E. gracilis. The dried masses of two fungi increased while majority of the algal cells disappeared after 72 h of co-incubation with M. aeruginosa, C. vulgaris, Glenodinium sp., and C. ovata. Thus, the two fungi might inhibit the growth of different freshwater algal species and utilize the algal cells for their growth.

A fungus capable of degrading microcystin-lr in the algal culture of Microcystis aeruginosa PCC7806.

Microcystins (MCs) are a family of natural toxins produced by cyanobacteria (blue-green algae). Microbial degradation is considered an efficient method for eliminating cyanobacteria and MCs in environmental conditions. This study examines the ability of Trichaptum abietinum 1302BG, a white rot fungus, to degrade microcystin-LR in the harmful algal culture of Microcystis aeruginosa PCC7806. Results showed that microcystin-LR could not be detected by high-performance liquid chromatography after 12 h in algal culture incubated with the fungus. There were also high activities of catalase and peroxidase in algal culture incubated with the fungus. However, similar to the control, they decreased to normal levels after 72 h. Meanwhile, the micronucleus test in the toxicity studies revealed that the degraded algal culture had low toxicity.

The local origin of the Tibetan pig and additional insights into the origin of Asian pigs.

BACKGROUND: The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig. METHODS AND FINDINGS: We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively. CONCLUSIONS: We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.

[Study on the growth, development and artificial propagation of Hypericum ascyron].

OBJECTIVE: To explore the morphological changes, growth conditions and artificial propagation of Hypericum ascyron. METHODS: The morphological changes were observed and recorded in the scene, the height and diameter of the plants were measured; the growth Verhaulst model was set up with the SPSS 17.0 software; the sexual reproduction and asexual reproduction were carried out in artificial cultivation. RESULTS: Hypericum ascyron started germinating in late April each year, branching in late May, flowering in late June, the period of full bearing was in early August, seeds were mature in early October. The Verhaulst models of the increase in the height (H), the quantity of leaf pairs (L) and the branching (B) were, H = 127.109/(1 + 23.744 x e(-0.062t)), L = 23.343/(1 + 11.303 x e(-0.062t)), B = 22.037/(1 + 73.068 x e(-0.068t)). The survival rate of whole graft and segmentation plant were 100% and 67.2% respectively on asexual reproduction; on the sexual reproduction, the seed germination rate was 15.2%, the survival rate of transplant seedlings was 36%. CONCLUSIONS: The period of growth and development of Hypericum ascyron is from April to October and it can be carried out artificial propagation.