Genomic prediction of pig growth traits based on machine learning.

This study aimed to assess and compare the performance of different machine learning models in predicting selected pig growth traits and genomic estimated breeding values (GEBV) using automated machine learning, with the goal of optimizing whole-genome evaluation methods in pig breeding. The research employed genomic information, pedigree matrices, fixed effects, and phenotype data from 9968 pigs across multiple companies to derive four optimal machine learning models: deep learning (DL), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGB). Through 10-fold cross-validation, predictions were made for GEBV and phenotypes of pigs reaching weight milestones (100 kg and 115 kg) with adjustments for backfat and days to weight. The findings indicated that machine learning models exhibited higher accuracy in predicting GEBV compared to phenotypic traits. Notably, GBM demonstrated superior GEBV prediction accuracy, with values of 0.683, 0.710, 0.866, and 0.871 for B100, B115, D100, and D115, respectively, slightly outperforming other methods. In phenotype prediction, GBM emerged as the best-performing model for pigs with B100, B115, D100, and D115 traits, achieving prediction accuracies of 0.547, followed by DL at 0.547, and then XGB with accuracies of 0.672 and 0.670. In terms of model training time, RF required the most time, while GBM and DL fell in between, and XGB demonstrated the shortest training time. In summary, machine learning models obtained through automated techniques exhibited higher GEBV prediction accuracy compared to phenotypic traits. GBM emerged as the overall top performer in terms of prediction accuracy and training time efficiency, while XGB demonstrated the ability to train accurate prediction models within a short timeframe. RF, on the other hand, had longer training times and insufficient accuracy, rendering it unsuitable for predicting pig growth traits and GEBV.

Bergapten inhibits NLRP3 inflammasome activation and pyroptosis via promoting mitophagy.

Inhibition of NLRP3 inflammasome activation produces potent therapeutic effects in a wide array of inflammatory diseases. Bergapten (BeG), a furocoumarin phytohormone present in many herbal medicines and fruits, exibits anti-inflammatory activity. In this study we characterized the therapeutic potential of BeG against bacterial infection and inflammation-related disorders, and elucidated the underlying mechanisms. We showed that pre-treatment with BeG (20 µM) effectively inhibited NLRP3 inflammasome activation in both lipopolysaccharides (LPS)-primed J774A.1 cells and bone marrow-derived macrophages (BMDMs), evidenced by attenuated cleaved caspase-1 and mature IL-1ß release, as well as reduced ASC speck formation and subsequent gasdermin D (GSDMD)-mediated pyroptosis. Transcriptome analysis revealed that BeG regulated the expression of genes involved in mitochondrial and reactive oxygen species (ROS) metabolism in BMDMs. Moreover, BeG treatment reversed the diminished mitochondrial activity and ROS production after NLRP3 activation, and elevated the expression of LC3-II and enhanced the co-localization of LC3 with mitochondria. Treatment with 3-methyladenine (3-MA, 5 mM) reversed the inhibitory effects of BeG on IL-1ß, cleaved caspase-1 and LDH release, GSDMD-N formation as well as ROS production. In mouse model of Escherichia coli-induced sepsis and mouse model of Citrobacter rodentium-induced intestinal inflammation, pre-treatment with BeG (50 mg/kg) significantly ameliorated tissue inflammation and injury. In conclusion, BeG inhibits NLRP3 inflammasome activation and pyroptosis by promoting mitophagy and maintaining mitochondrial homeostasis. These results suggest BeG as a promising drug candidate for the treatment of bacterial infection and inflammation-related disorders.

Scoparone suppresses mitophagy-mediated NLRP3 inflammasome activation in inflammatory diseases.

Recent evidence shows that targeting NLRP3 inflammasome activation is an important means to treat inflammasome-driven diseases. Scoparone, a natural compound isolated from the Chinese herb Artemisia capillaris Thunb, has anti-inflammatory activity. In this study we investigated the effect of scoparone on NLRP3 inflammasome activation in inflammatory diseases. In LPS-primed, ATP or nigericin-stimulated mouse macrophage J774A.1 cells and bone marrow-derived macrophages (BMDMs), pretreatment with scoparone (50 µM) markedly restrained canonical and noncanonical NLRP3 inflammasome activation, evidenced by suppressed caspase-1 cleavage, GSDMD-mediated pyroptosis, mature IL-1ß secretion and the formation of ASC specks. We then conducted a transcriptome analysis in scoparone-pretreated BMDMs, and found that the differentially expressed genes were significantly enriched in mitochondrial reactive oxygen species (ROS) metabolic process, mitochondrial translation and assembly process, as well as in inflammatory response. We demonstrated in J774A.1 cells and BMDMs that scoparone promoted mitophagy, a well-characterized mechanism to control mitochondrial quality and reduce ROS production and subsequent NLRP3 inflammasome activation. Mitophagy blockade by 3-methyladenine (3-MA, 5 mM) reversed the protective effects of scoparone on mitochondrial damage and inflammation in the murine macrophages. Moreover, administration of scoparone (50 mg/kg) exerted significant preventive effects via inhibition of NLRP3 activation in mouse models of bacterial enteritis and septic shock. Collectively, scoparone displays potent anti-inflammatory effects via blocking NLRP3 inflammasome activation through enhancing mitophagy, highlighting a potential action mechanism in treating inflammasome-related diseases for further clinical investigation.

Epileptic Seizure after Use of Moxifloxacin in Man with Legionella longbeachae Pneumonia.

Legionellosis caused by Legionella longbeachae is diagnosed mainly by PCR. We report a case of L. longbeachae infection in mainland China, which was diagnosed by metagenomic next-generation sequencing, in a man who developed an epileptic seizure after using moxifloxacin. Metagenomic next-generation sequencing may be a useful tool to detect Legionella spp.

circRNA on animal skeletal muscle development regulation.

Circular RNA (circRNA) is a type of closed circular RNA molecules formed by reverse splicing, which exists widely in organisms and has become a research hotspot in non-coding RNAs in recent years. Skeletal muscle plays the role of coordinating movement and maintaining normal metabolism and endocrine in organisms. With the development of sequencing and bioinformatics analysis technology, the functions and regulation mechanisms of circRNAs in skeletal muscle development have been gradually revealed. In this review, we summarize the types of molecular regulatory mechanisms, the classical research ideas and the functional research methods of circRNAs, and the research progress of circRNAs involved in normal development of skeletal muscle and regulation of skeletal muscle disease, in order to provide a reference to further study of the genetic mechanisms of circRNAs in the regulation of skeletal muscle development.

[Preliminary survey on the host of Angiostrongylus cantonensis in three plateau lakes of Yunnan Province].

OBJECTIVE: To investigated the intermediate hosts of Angiostrongylus cantonensis in three plateau lakes of Yunnan Province, and analyze the effect of temperature on A. cantonensis during 1991-2010. METHODS: An epidemiological investigation of angiostrongyliasis cantonensis in Erhai Lake, Fuxian Lake and Xingyun Lake was conducted from April to September in 2012. Snails were examined for the third stage larvae by enzyme digestion or lung examination. Rodents were captured in the fields, and their hearts and lungs were dissected for adult worms. The potential distribution of A. cantonensis and its main intermediate host Pomacea canaliculata were predicted based on degree-day models using GIS technique. RESULTS: A total of 4 950 snails were collected, belonging to 4 species, P. canaliculata, Cipangopaludina chinensis, Bellamya aeruginosa, and B. quadrata. 174 rodents were captured, belonging to 5 species. No positive samples were found. The potential distribution map showed that the distribution of A. cantonensis and P. canaliculata in Yunnan would expand with the rise of temperature, and with the passage of time they could complete one generation in the region which couldn't finish one generation in one year along with time passing. CONCLUSION: A. cantonensis are not found in the hosts. The natural environment and ecological system of the three lakes match the condition of A. cantonensis transmission.

Molecular characterization, polymorphism and association of porcine SPATA19 gene.

Spermatogenesis associated 19 (SPATA19) is an important reproduction related gene. In this study, we cloned the full-length cDNA sequence of porcine SPATA19 gene through the rapid amplification of cDNA ends (RACE) method. The porcine SPATA19 gene encodes a protein of 154 amino acids which shares high homology with the SPATA19 of ten species: giant panda (87 %), dog (86 %), cattle (84 %), rabbit (78 %), sumatran orangutan (72 %), human (71 %), rhesus monkey (71 %), chimpanzee (70 %), mouse (71 %) and rat (69 %). The phylogenetic analysis revealed that the porcine SPATA19 gene has a closer genetic relationship with the SPATA19 gene of dog. This gene is structured in six exons and five introns as revealed by computer-assisted analysis. PCR-RFLP was established to detect the GU475012:c.515T>C substitution of porcine SPATA19 gene mRNA and association of this mutation with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations. Results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White sows and Landrace sows. Therefore, SPATA19 gene could be an useful candidate gene in selection for increasing litter size in pigs. These data serve as a foundation for further insight into this novel porcine gene.

A novel porcine gene, POT1, differentially expressed in the longissimus muscle tissues from Wujin and Large White pigs.

The mRNA differential display technique was performed to investigate the differences of gene expression in the longissimus muscle tissues from Wujin and Large White pigs. One novel gene differentially expressed was identified through quantitative real time PCR and the cDNA complete sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 507 amino acids that shares high homology with the protection of telomeres 1 isoform 4 (POT1) of human (86%)-so that this gene can be defined as swine POT1 gene. This gene is structured in 12 exons and 11 introns as revealed by computer-assisted analysis. The tissue expression analysis indicated that the swine POT1 gene is differentially expressed in tissues including muscle, heart, liver, fat, kidney, lung, pancreas and spleen. Our experiment is the first to establish the primary foundation for further research on the swine POT1 gene.

Service users' personal experience and interpretation of mental illness: oriental narratives.

BACKGROUND: Service users' perception of mental illness is vital because it points out a viable direction that practitioners can follow to fully understand service users in their own sociocultural context. MATERIAL: Qualitative research findings include mental health service users' roles and identities, their perceptions of mental illness and their personal experiences of psychiatric stigma. DISCUSSION: While there are similar phenomena regarding mental illness stigma between East and West, there are culturally distinctive characteristics found in Taiwan. CONCLUSIONS: Based on personal perceptions and experiences, mental health service users have interpreted illness and performed the patient role in their own way.

The chemical composition and ultrastructure of uroliths in Boer goats.

The chemical composition and ultrastructure of urinary calculi obtained from male Boer goats were studied using qualitative chemical analysis, scanning electron microscopy, X-ray diffraction, X-ray energy dispersive spectrometry and Fourier transform infra-red spectroscopy. The calculi came from 10 naturally-occurring cases of urolithiasis and from seven cases of urolithiasis experimentally-induced by feeding a cottonseed meal-rice straw diet supplemented with magnesium oxide. The results indicated that the major component of urinary calculi collected from naturally-occurring and experimentally-induced cases of urolithiasis was struvite (magnesium ammonium phosphate). The study also identified previously unreported prismatic crystals in the uroliths of goats, similar to struvite but rich in potassium. The characteristic ultrastructure of struvite uroliths is described along with a brief discussion of their formation.

Study on precipitation of struvite and struvite-K crystal in goats during onset of urolithiasis.

To learn more about the biomineralization process of struvite in ruminants, a seldom noticeable crystal, struvite-K, was investigated in six goats in which urolithiasis was induced by feeding a cottonseed meal and rice straw diet supplemented with MgO. The compositions of crystals and calculi were studied by chemical qualitative analysis and X-ray energy dispersive spectrometry (EDS). The activity product (AP) and relative supersaturation (RSS) of magnesium ammonium phosphate (MAP) and potassium magnesium phosphate (MKP) were calculated to compare the difference of crystals formed in this process. The results showed that calculi consisted of MAP with a little MKP. Crystals in the urine consisted of MAP and MKP before stone formation, but crystals in urine after stone formation mainly consisted of MKP. The AP and RSS of MAP and MKP significantly decreased after stone formation. It was concluded that MAP and MKP may coexist in the crystals of urine before struvite calculi formation but MKP did not precipitate to struvite calculi and was separated out as crystal sedimentation of urine. The changes of crystallization of MAP and MKP contributed partially to the supersaturation status of MAP and MKP during struvite stone formation.

[Developmental expression changes of insulin-like growth factors (IGFs) system genes in longissimus dorsi muscle of two pig breeds].

Real-time fluorescence quantitative PCR was applied to investigate the developmental expression patterns of insulin like growth factor-1 and -2 (IGF-1 and -2), insulin like growth factor receptor -1 and -2 (IGF-1R and -2R), insulin like growth factor binding protein-3 and -5 (IGFBP-3 and -5) genes at the age of birth (0), 1, 2, 3, 4, and 5 months in longissimus dorsi muscle of Landrace and Meishan pigs. The expression level of IGF-1 exhibited up-regulation, in contrast, the expression level of IGF-2 showed down-regulation after birth in the two pig breeds. These findings are consistent with the previous knowledge that IGF-2 is mainly expressed during the embryonic phase, IGF-1 is mainly expressed during the postnatal period, which could promote cell proliferation and ontogenesis. The expression patterns of IGFRs and IGFs were dissimilar from 0 to 5 months in the two pig breeds, which suggest that the expression changes of IGFRs may not be subjected to the regulation by local secretion of IGFs. Strikingly, at the age of 2 months, the expression levels of IGF-1R, IGF-2R, and IGFBP-3 reached their maximum peak values in Landrace pigs, which suggest that the 2 months after birth may be the most important growth stage for genes of insulin-like growth factors (IGFs) system to exert their biological functions from birth to 5 months. These results indicate that the mRNAs of IGFs system genes exhibit specific developmental expression changes between Landrace and Meishan pigs, and provides some data for further study on the mutual regulation mechanism of genes in IGFs system.

Comparison of effect of high intake of magnesium with high intake of phosphorus and potassium on urolithiasis in goats fed with cottonseed meal diet.

The effect of high intake of Mg on urolithiasis was compared with high intake of P and K in goats being fed with a cottonseed meal and rice straw diet. Eighteen wether goats were randomly allocated into group A, B and C evenly and fed with cottonseed meal and rice straw diet for three months. From day 60 onwards, KH(2)PO(4) and K(2)HPO(4) were provided via drinking water to goats in group B to increase the intake of P, K, and MgO to goats in group C to increase the intake of Mg. Blood and urine samples were collected to analyze the concentration of P, K, Mg and Ca, and the activity product (AP) of potassium magnesium phosphate (MKP) in urine was also calculated. The composition of calculi and urinary sedimentary crystals were examined by chemical qualitative analysis, X-ray diffraction, X-ray energy dispersive spectrometry and Fourier transform infrared spectroscopy. The results showed that the incidence of urolithiasis in group C (6/6) was higher than that in group A (1/6) and B (1/6) (P<0.05). The calculi were mainly composed of magnesium ammonium phosphate (MAP) and partly composed of MKP. MKP presented in crystals of different phases in this experiment. The high intake of Mg contributed to a significant increase of plasma Mg, but additional P, K did not cause a further increase of plasma P, K. Urine P, K, Mg and Ca and AP of MKP in group C decreased significantly after the onset of urolithiasis. In conclusion, high intake of Mg was more important in inducing struvite calculi compared with high intake of K and P in goats under these feeding conditions. Cottonseed meal and rice straw with additional Mg is a good dietary model for inducing struvite calculi in castrated goats.

[Identification of porcine reproductive and respiratory syndrome virus regulation sequence in 3'-untranslated region].

Based on our established infectious clone of PRRSV, designated as pCBC2, a series of mutagenesis of 3'-untranslated region (3'-UTR) at primary structure and secondary structure level were constructed. Then the full length mutant clones were transfected into MARC-145 cells, from which the influences of the discrete 3'-UTR mutation on PRRSV replication and transcription were analyzed. The properties of the rescued mutant viruses were then further characterized by Northern Blot and plaque morphology analysis. Our results demonstrated that PRRSV could tolerate more than 41 nucleotides deletion and 23nt insertion in the 3'-UTR, however, minor changes in the conserved stem loop region destroyed virus infectivity. To sum up, the stem-loop structure was essential for virus viability, but 5' end of the 3'-UTR tolerates certain level of nucleotide deletion or insertion. This is the first report to define the essential sequence and secondary structure for PRRSV genome replication and it is useful for future research about the regulation element.

The injury effect of oxygen free radicals in vitro on cultured pulmonary artery endothelial cells from broilers.

Pulmonary artery endothelial cells (PAEC) were isolated from broilers by the method of tissue explantation. The cells were identified using morphological features and immunocytochemical staining using a specific antiserum against factor VIII related antigen. Xanthine/Xanthine oxidase (X/XO) served as the oxygen free radical (OFR) generating system. In vitro model of oxidative injury of PAEC was established based on the X/XO system. The effect of OFR on the growth and viability of PAEC was determined with methylthiazol tetrazolium (MTT) colorimetric assay. Malondialdehyde (MDA, a product of lipid peroxidation) in culture medium of PAEC was detected by a thiobarbituric acid colorimetric assay. The results showed that PAEC survive in vitro and can be subcultured for 5-6 passages. Morphological and immunocytochemical observations of cultured cells demonstrated specific characteristics of endothelial cells. PAECs were severely damaged by OFR. The viability of cells was reduced by the X/XO system, and a dose-dependent decrease in cell viability was found with increasing XO dosages. OFR promoted lipid peroxidation of PAEC and increased the MDA concentration in culture media. These results suggest that OFR can injure the endothelial cells from broiler pulmonary arteries in vitro, which confirms previous results obtained in vivo. Oxidative injury may play an important role in the pathogenesis of pulmonary hypertension syndrome in broiler.

L-arginine prevents reduced expression of endothelial nitric oxide synthase (NOS) in pulmonary arterioles of broilers exposed to cool temperatures.

This study investigated nitric oxide synthase (NOS) expression in the endothelium of pulmonary arterioles of broilers during the development of pulmonary hypertension syndrome (PHS). PHS was triggered by exposing broilers to sub-thermoneutral (cool) temperatures and an additional 1.0% L-arginine was added to the basal diet to evaluate the effects of supplemental L-arginine on nitric oxide (NO) production, endothelial NOS expression, and the incidence of PHS. Cumulative mortality from PHS, right/total ventricle weight ratios (RV/TV), and body weights were recorded. Plasma NO concentration and NOS expression in the endothelium of pulmonary arterioles with an outer diameter ranging from 100 to 200 microm were determined. Birds exposed to cool temperatures had increased pulmonary hypertension and PHS mortality and diminished endothelial NOS expression. Supplemental dietary L-arginine reduced PHS mortality and elicited higher NOS expression within the pulmonary endothelium coincident with elevated NO production. The results demonstrated that broilers developing PHS exhibited diminished NOS expression in the endothelium of their pulmonary arterioles. Supplemental L-arginine prevented the reduced expression of NOS in the pulmonary endothelium, which might contribute to the increased production of NO by the pulmonary vasculature.

cDNA cloning and functional analysis of goose interleukin-2.

cDNA encoding goose IL-2 (GoIL-2) was cloned from Con A-stimulated goose splenic mononuclear cells (SMC) using oligonucleotide primers based on the conserved sequence of duck (DuIL-2), chicken (ChIL-2) and turkey IL-2s (TuIL-2). The GoIL-2 cDNA is 718nt long, which contains an open reading frame (ORF) of 423 base pairs encoding a protein of 141 aa. The GoIL-2 shows, respectively, 79%, 82-85%, and 91-92% identities with TuIL-2, ChIL-2 and DuIL-2 in cDNA, and also shows, respectively, 63%, 63-64%, and 82-85% identities with TuIL-2, ChIL-2 and DuIL-2 in amino acid sequence. Recombinant GoIL-2 (rGoIL-2) protein expressed in Escherichia coli has an approximate molecular weight of 18kDa. The rGoIL-2 has biological effect on goose and duck as well as chicken lymphocytes in a dose-dependent manner, though the effect on duck and chicken lymphocytes has been found to be relatively weak. In addition, rGoIL-2 also strengthens goose immune responses induced by vaccinating the inactivated oil emulsion vaccine against avian influenza virus. The monoclonal antibodies (mAb) to rGoIL-2 recognized the binding epitopes of nature GoIL-2 protein expressed in vero cells. Antiserum and mAb 5B10 to rGoIL-2 can inhibit the biological activity of rGoIL-2 and endogenous GoIL-2. The results, at the first time, indicated that goose IL-2 reserves species-specialties in the biological functions and can be used as a potential immunoadjuvant for goose vaccination and immunotherapeutic purposes. Finally, the mAbs to rGoIL-2 also provide a useful tool for further immunobiological studies of IL-2 in avian immune systems.

Cloning, in vitro expression and bioactivity of duck interleukin-2.

In this report, the cDNA sequences of Shaoxing (SX) and Muscovy (MV) duck IL-2 were cloned, then recombinant duck IL-2 (rduIL-2) was produced in prokaryotic expression system. In vitro bioactivity of rduIL-2 was determined by lymphocyte proliferation assay and in vivo bioactivity of rduIL-2 was assessed by vaccine immunization. Monoclonal antibodies (mAbs) and polyclonal antibodies (pAbs) specific for rduIL-2 were generated and characterized by ELISA, Western blot and neutralizing assays. The cDNA contains an open reading frame (ORF) of 420-base pairs encoding a protein of 140 amino acids (aa) with a putative signal peptide of 21aa. The His-duIL-2 fusion protein was recognized in Western blot by mAb against chicken IL-2 (chIL-2), but not by mAbs against human IL-2 and mouse IL-2. Recombinant duIL-2 induces in vitro proliferation of Con A-stimulated duck splenocytes in MTT assay and strengthens duck immune responses induced by vaccinating the inactivated oil emulsion vaccine against avian influenza virus. Polyclonal antibodies and mAb 2B3 against rduIL-2 were shown to have effective neutralizing ability by inhibiting the biological activities of both recombinant duIL-2 and endogenous duIL-2. Despite the fact that duck and chicken IL-2s only share identity of 55.0-56.7% in amino acid sequence, duck and chicken IL-2 molecules displayed similar cross-priming activity in in vitro lymphocyte proliferation assays. The results, at the first time, indicated that rduIL-2 has the potential to be used as an immunoadjuvant for enhancing vaccine efficacy and an immunotherapeutic, and the mAbs against rduIL-2 further facilitate basic immunobiological studies of the role of IL-2 in avian immune system.

Generation of the transgenic potato expressing full-length spike protein of infectious bronchitis virus.

To seek a new delivery system of vaccine for infectious bronchitis virus (IBV), transgenic potato expressing full-length spike (S) protein of IBV was produced and its immunogenicity in chickens was investigated. One to three copies of S gene of IBV were randomly and stably inserted into potato (Solanum tuberrosum cv. Dongnong 303) genome by Agrobacterium tumefaciens-mediated transformation. Transcription and translation of S gene for IBV were confirmed by Northern blot and Western blot analyses in transgenic plantlets. Chickens immunized orally and intramuscularly with transgenic potato tubers expressing S protein generated the detectable levels of serum neutralizing antibodies and were protected against the challenge with the virulent IBV. In vitro secretion of interleukin 2 and T lymphocyte proliferation of spleen cells from the immunized chickens varied with the dose and the manner of vaccination with S protein derived from transgenic plants. The results indicated that S protein expressed in transgenic plants might be a new source for the production of Coronaviridae IBV vaccine.