Application of deep learning with bivariate models for genomic prediction of sow lifetime productivity-related traits

OBJECTIVE

Pig breeders cannot obtain phenotypic information at the time of selection for sow lifetime productivity (SLP). They would benefit from obtaining genetic information of candidate sows. Genomic data interpreted using deep learning (DL) techniques could contribute to the genetic improvement of SLP to maximize farm profitability because DL models capture nonlinear genetic effects such as dominance and epistasis more efficiently than conventional genomic prediction methods based on linear models. This study aimed to investigate the usefulness of DL for the genomic prediction of two SLP-related traits; lifetime number of litters (LNL) and lifetime pig production (LPP).

METHODS

Two bivariate DL models, convolutional neural network (CNN) and local convolutional neural network (LCNN), were compared with conventional bivariate linear models (i.e., genomic best linear unbiased prediction, Bayesian ridge regression, Bayes A, and Bayes B). Phenotype and pedigree data were collected from 40,011 sows that had husbandry records. Among these, 3,652 pigs were genotyped using the PorcineSNP60K BeadChip.

RESULTS

The best predictive correlation for LNL was obtained with CNN (0.28), followed by LCNN (0.26) and conventional linear models (approximately 0.21). For LPP, the best predictive correlation was also obtained with CNN (0.29), followed by LCNN (0.27) and conventional linear models (approximately 0.25). A similar trend was observed with the mean squared error of prediction for the SLP traits.

CONCLUSION

This study provides an example of a CNN that can outperform against the linear model-based genomic prediction approaches when the nonlinear interaction components are important because LNL and LPP exhibited strong epistatic interaction components. Additionally, our results suggest that applying bivariate DL models could also contribute to the prediction accuracy by utilizing the genetic correlation between LNL and LPP.

[Microanatomy and functional MRI study of arcuate fasciculus and superior longitudinal fasciculus]

Objectives: To explore the microanatomy and functional MRI(fMRI) of arcuate fasciculus(AF) and superior longitudinal fasciculus(SLF),and to analyze their functions. Methods: Ten normal adult cadaveric head specimens (20 cerebral hemispheres) were fixed with 10% methanal at the Translational Research Institute for Neurological Disorders of the Wannan Medical Collegefrom February to December 2022.The Klingler fiber dissection technique was utilized to perform white matter fiber dissection,with a magnification ranging from 6 to 40.The study focused on the microanatomical structures of the AF and SLF,aiming to explore their relationships with deep brain fibers.Furthermore, six healthy adult volunteers who underwent fMRI of the brain were included.The collected diffusion tensor imaging (DTI) data were processed and integrated with the microanatomical findings for a comprehensive analysis. Results: After removing the gray matter of the cerebral cortex,the superficial U fibers were exposed.The long association fibers that beneath the U fibers were the AF and SLF,which were the main long association fibers in the superficial layers of the brain.The AF could be divided into dorsal and ventral parts,while the SLF could be divided into Ⅰ,Ⅱ,and Ⅲ.SLF Ⅰ lied within the upper bank of the cingulate sulcus,travels medial to the callosal sulcus.The SLF Ⅱ,Ⅲ,and the AF were located on the lateral surface of the brain.By removing the gray matter of the insular cortex and the extreme capsule,exposing the external capsule and claustrum.Subsequently,the AF and SLF Ⅱ,Ⅲ were dissected,revealing the corona radiata and sagittal stratum,along with other deep brain fibers.During the dissection,it was observed that there was a close connection between the AF,SLF Ⅱ,and the deep brain fibers.Furthermore,in the regions above the lateral fissure of the cerebral hemisphere,there was no direct connection of long association fibers between the gray matter cortex and the deep U fibers in the coronal plane.These findings were further supported by DTI studies. Conclusions: The AF and SLF are the major long association fibers that located in the superficial layers of the brain,and closely connect to the gray matter cortex and U fibers,even closely relate with deep brain fibers.In the regions above the lateral fissure of the hemisphere,only the AF and SLF Ⅱ and Ⅲ serve as superficial long association fibers in the anterior-posterior direction.These fibers are likely involved in the transmission of brain functional information between the top and bottom gray matter cortex in the coronal plane above the lateral fissure.

Development of a Pedicle Screw Fixation Simulation Model for Surgical Training Using a 3-Dimensional Printer

OBJECTIVE

Training surgeons in pedicle screw fixation (PSF) techniques during actual surgery is limited because of patient safety, complications, and surgical efficiency issues. Recent technical developments are leading the world to an era of personalized three-dimensional (3D) printing. This study aimed to evaluate the educational effect of using a 3D-printed spine model to train beginners in PSF techniques to improve screw accuracy and procedure time.

METHODS

Computed tomography (CT) scan data were used in a 3D printer to produce a life-size lumbar spine replica of L1-3 vertebrae. Four residents performed PSF thrice. Each resident performed 18 screw fixations on both sides (6 screws per trial). The time to complete the procedure and pedicle violation was recorded.

RESULTS

The average time for the 3 procedures was 42.1±2.9 minutes, 38.8±3.3 minutes, and 32.1±2.5 minutes, respectively. Furthermore, the average pedicle screw score for the 3 procedures was 13.0±0.8, 14.5±0.6, and 16.0±0.8, respectively. As the trial was repeated, the procedure time decreased and the accuracy of screw fixation tended to be more accurate.

CONCLUSIONS

It was possible to decrease the procedure time and increase accuracy through repeated training using the 3D-printed spine model. By implementing a 3Dprinted spine model based on the patient's actual CT data, surgeons can perform simulation surgery before the actual surgery. Therefore, this technology can be useful in educating residents to improve their surgical skills.

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

Association of the ubiquitin specific peptidase 9X -linked and Afadin expression patterns with sexual maturation in boar testis

Closely correlated expression patterns between ubiquitin specific peptidase 9X-linked (USP9X) and adherens junction formation factor (Afadin) in mouse testis development suggests that Usp9x regulates the deubiquitination of Af-6 (also known as Afadin, AFDN), and subsequently, the cell adhesion dynamics during gametogenesis. However, this relationship has not yet been tested in other domestic animals. The study was examined the temporal and spatial expression patterns of porcine USP9X and AFDN from the pre-pubertal to adult stages using real time-PCR and immunohistochemistry. Furthermore, we detected the transcripts of USP9X and AFDN in the testis of 1-, 6- and 12-months old boar, respectively. USP9X and AFDN were found to have similar expressions patterns, with basal expression after 1 month followed by a significant up-regulation from 6 months (puberty) onwards. In addition, neither the AFDN or USP9X proteins were detected in spermatogenic cells but they were expressed in the leydig cells and sertoli cells. USP9X was detected around the basal lamina during pre-puberty, and predominantly expressed in the leydig cells at puberty. Finally, in adult testis, USP9X was increased at the sertoli cell-cell interface and the sertoli cell-spermatid interface. In summary, closely correlated expression patterns between USP9X and AFDN in boar testis supports the previous findings in mice. Furthermore, the junction connections between the sertoli cells may be regulated by the ubiquitination process mediated via USP9X.

Modeling and optimization of process parameters of biofilm reactor for wastewater treatment

The efficiency of heavy metal in biofilm reactors depends on absorption process parameters, and those relationships are complicated. This study explores artificial neural networks (ANNs) feasibility to correlate the biofilm reactor process parameters with absorption efficiency. The heavy metal removal and turbidity were modeled as a function of five process parameters, namely pH, temperature(°C), feed flux(ml/min), substrate flow(ml/min), and hydraulic retention time(h). We developed a standalone ANN software for predicting and analyzing the absorption process in handling industrial wastewater. The model was tested extensively to confirm that the predictions are reasonable in the context of the absorption kinetics principles. The model predictions showed that the temperature and pH values are the most influential parameters affecting absorption efficiency and turbidity.

Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip

BACKGROUND

Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome.

OBJECTIVE

This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level.

METHODS

Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure.

RESULTS

KWB showed the lowest average expected heterozygosity (H_E = 0.1904), while KWH showed the highest genetic diversity (H_E = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations.

CONCLUSION

This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC.

Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.

Clinico-radiologic features of molar-incisor malformation in a case series of 38 patients: A retrospective observational study

Molar-incisor malformation (MIM) is a recently defined dental abnormality of molar root and incisors, and introduced as one of the causes of periapical and periodontal abscess. The purpose of this study was to investigate the clinical and radiological features of MIM, with special emphasis on various medical history. A total of 38 patients with MIM were included in this study. Radiographic features and clinical data, including medical history, chief complaint, associated complications, treatment, and prognosis, were retrospectively investigated. On radiographs, the affected molars showed short, slender, underdeveloped roots and constricted pulp chambers. All affected incisors and canines exhibited dilacerated short roots, wedge-shaped defect on the cervical part of the crown. Complications included periodontal bone loss (52.6%), endodontic lesion (50.0%), and endodontic-periodontal lesion (28.9%). The medical histories of the patients with MIM indicate that almost all (94.7%) were hospitalized due to problems during the neonatal period. MIM may cause various dental problems, such as periapical and periodontal abscess and early loss of the affected teeth. The early diagnosis of MIM on radiographs and appropriate treatment will contribute to a favorable prognosis, especially for young and adolescent patients.

Behaviors and body weight of suckling piglets in different social environments

OBJECTIVE

This study was conducted to characterize the behaviors and the body weight of suckling piglets in different social environments.

METHODS

Two groups of sows and suckling piglets housed either in individual farrowing crates in separate pens (1.8×2.4 m, the control group) or in groups of three sows with their piglets in farrowing crates in a large common enclosure (5.4×2.2 m, the treatment group) were observed with the aid of video technology for 9 consecutive hours on days 1, 2, and 3, after mixing.

RESULTS

Suckling, agonistic, and elimination behaviors of suckling piglets were significantly higher in the control group than in the treatment group. Inactive behavior was higher in the treatment group than in the control group. Most of the effects of the social environment on the suckling piglets seem to be the result of large reductions in behaviors and body weight for piglets switching from high activity to low activity. Moreover, suckling behavior and birth body weight were highly correlated with body weight at the end of the test.

CONCLUSION

The social environment that resulted from mixing, thus, had significant effects on the behavior and body weight of suckling piglets, and behavioral characteristics, therefore, should be considered when making improvements to the husbandry and care methods used in swine production.

Isolation and characterization of novel microsatellites for Abies koreana and A. nephrolepis (Pinaceae)

Abies koreana is an endemic and rare species from Korea and is classified as endangered by the International Union for Conservation of Nature. Although the genetic diversity assessment for current population of A. koreana needs to be performed urgently, no microsatellite markers have been developed for this species. In the present study, we developed 22 novel polymorphic microsatellite loci and the characteristics of these loci were determined in A. koreana as well as in Abies nephrolepis, the most closely related species, and these loci were compared with previously reported microsatellite markers developed for the Abies genus. Genomic sequence (161 Mbp; 325,776 reads) was obtained from one individual of A. koreana using Roche 454 GS-FLX Titanium sequencing and 19,258 repeat motifs were identified from it. A total of 288 primer pairs with high copy numbers of di-repeat motifs were evaluated for amplification in A. koreana and A. nephrolepis. A total of 71 primer pairs successfully amplified fragments, of which 22 showed polymorphisms in A. koreana and A. nephrolepis. The average expected diversity was 0.767 and 0.717 in A. koreana and A. nephrolepis, respectively; these heterozygosity levels were moderate compared to the previously reported microsatellite loci from Abies species. This is the first set of microsatellite markers developed for A. koreana as well as A. nephrolepis and further population genetic studies of both species and genetic delimitation can be carried out for the species conservation and management.

Behavioral Characteristics of Weaned Piglets Mixed in Different Groups

With regard to animal welfare concerns, behavioral information of weaned and mixed piglets is great interest in swine production. The aim of this study was to demonstrate the change in behavior of weaned piglets over time in two different groups (littermates and piglets from different litters) after mixing. Two weaned groups of piglets (72 individuals in all) housed either with littermates or with foreign piglets (6 individuals in 1.8 m×1.4 m pens, 28°C±1°C temperature) were observed with the aid of video technology for 9 consecutive hours on days 1, 2, and 3 after mixing. The behaviors of the weaned piglets in the control and treatment groups were significantly different among the days after mixing. Piglets were, however, more active and aggressive in the groups with foreign piglets. This study reveals a lower level of agonistic behavior in groups of piglets that came from the same litter.

Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds

Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.

Effects of Mixing on the Aggressive Behavior of Commercially Housed Pigs

In this study, we investigated the effects of mixing on the aggressive behavior of commercially housed pigs. The behavioral patterns of 36 groups of pigs (a total of 360 animals) were observed over 3 consecutive days directly after weaning (25±1.2 days of age), and 25 and 50 days later with the aid of video technology. Fight latency and total duration and frequency of fighting were significantly different among the age groups. The aggressive behaviors decreased in 75-day old pigs if compared to 25- and 50-day old animals. Moreover, dominance index (DI) was higher in 25-day old and lower in 75-day old pigs. A comparison of dominant (DI>0) and submissive (DI<0) pigs showed significant differences (p<0.05) for major aggressive behaviors in all age groups. Dominant pigs were involved in more aggressive interactions, had longer fights, and initiated more fights than submissive pigs. Post-mixing aggressive behavior was altered by previous experience of mixing. Aggressive behavior and DI are suitable methods for analyzing the effects of mixing on commercially housed growing pigs.

Effect of dietary supplementation of procyanidin on growth performance and immune response in pigs

This study was performed to determine the effect of dietary supplementation of procyanidin on growth performance, blood characteristics, and immune function in growing pigs. In experiment 1 (Exp. 1), thirty-two crossbred pigs with an initial BW of 19.2±0.3 kg were allocated into 4 treatments for an 8-wk experiment: i) CON (basal diet), ii) MOS 0.1 (basal diet+0.1% mannanoligosaccharide), iii) Pro-1 (basal diet+0.01% procyanidin), and iv) Pro-2 (basal diet+0.02% procyanidin). Pigs fed Pro-1 and Pro-2 diets had greater (p<0.05) gain:feed ratio compared with those fed CON or MOS 0.1 diets. Serum creatinine concentration was less (p<0.05) in Pro-2 treatment than those in CON, MOS 0.1 and Pro-1 treatments. In Exp. 2, twelve pigs (BW 13.4±1.3 kg) received basal diet with i) 0 (CON), ii) 0.02% (Pro-0.02%), and iii) 0.04% procyanidin (Pro-0.04%) for 4 wk. Concentration of platelets was lower (p<0.05) in the Pro-0.04% group compared to CON at 24 h after lipopolysaccharide (LPS) challenge. In addition, secretion of cytokines from cultured peripheral blood mononuclear cells (PBMC) in the presence or absence of procyanidin was examined. The levels of interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α were lower (p<0.05) in Pro (LPS-stimulated PBMCs+procyanidin) than those in CON (LPS-stimulated PBMCs+PBS) at 4 h after LPS challenge. These data suggest that dietary addition of procyanidin improves feed efficiency and anti-inflammatory cytokines of pigs.

Pepper gene encoding a basic class II chitinase is inducible by pathogen and ethephon

A chitinase cDNA clone (designated CAChi2) was isolated from the cDNA library of pepper leaves infected with Xanthomonas campestris pv. vesicatoria. The 1004-bp full-length CAChi2 cDNA encodes a basic chitinase with an N-terminal 24 amino acid signal peptide followed by a catalytic region. An analysis of its sequence indicates that CAChi2 is a class II chitinase, because it does not have chitin-binding domain and C-terminal extension sequences. The deduced amino acid sequence of CAChi2 has a high level of identity with class II chitinases from potato, tomato, tobacco and petunia. Southern analysis demonstrated that the CAChi2 chitinase is encoded by a single or two copy genes in the pepper genome. Following X. campestris pv. vesicatoria or Phytophthora capsici infection, the CAChi2 chitinase mRNA was more highly expressed in the incompatible interaction, compared to expression in the compatible interaction. Treatment with ethylene-releasing ethephon resulted in a strong accumulation of the transcripts in the leaves. In contrast, DL-beta-amino-n-butyric acid, salicylic acid and methyl jasmonate were not effective in inducing CAChi2 transcripts in pepper leaves.

Concomitant lichen scrofulosorum and erythema induratum

We describe a patient in whom two tuberculids, lichen scrofulosorum, and erythema induratum occurred simultaneously. The clinical and histopathologic features were characteristic and a Mantoux test showed a positive reaction. There was no extracutaneous focus of tuberculosis. Polymerase chain reaction for mycobacteria in the skin lesions was negative, but her lesions responded rapidly to antituberculous chemotherapy.

MR566A and MR566B, new melanin synthesis inhibitors produced by Trichoderma harzianum. II. Physico-chemical properties and structural elucidation

New melanin synthesis inhibitors (MR566A and B) and six related known isocyanocyclopentenes were isolated from the fermentation broth of Trichoderma harzianum, and their structures were elucidated by spectroscopic methods. The structures of novel isocyanides, MR566A (1) and B (2), were elucidated as 1-(3-chloro-1,2-dihydroxy-4-isocyano-4-cyclopenten-1-yl)etha nol, 1-(1,2,3-trihydroxy-3-isocyano-4-cyclopenten-1-yl)ethanol, respectively. The structure of novel oxazole, MR93B (9), was elucidated as 4-[(1Z)-3-hydroxy-2-hydroxymethyl-1-propen-1-yl]oxazole.

Determination of phenolalkylamines, narcotic analgesics, and beta-blockers by gas chromatography/mass spectrometry

An analytical procedure for determination of phenolalkylamines, narcotic analgesics, and beta-blockers in urine by gas chromatography/mass spectrometry (GC/MS) is described. The detection of phenolalkylamines, narcotic analgesics, and beta-blockers is based on acid hydrolysis, liquid-liquid extraction, and selective derivatization. For screening of phenolalkylamines the m/e 179 and 267 ions were monitored by GC/MS. With narcotic analgesics, the extracted ion corresponded to the molecular ion (M+) of the drug and two additional characteristic ions. Beta-blockers were analyzed as the selectively derivatized forms of the parent molecule and its metabolites by GC/MS with selected ion monitoring. The ions monitored for screening of beta-blockers containing an isopropylamine group were m/e 284 and 129 ions. The ion at m/e 86 was monitored to characterize the tert-butylamine group of beta-blockers.

Demonstration of opsonic and protective activity of human cord sera against type III group B streptococcus that are independent of type-specific antibody

In an effort to further understand the host defense against group B streptococcus (GBS), we examined 71 human cord sera for their content of type III GBS IgG antibody by enzyme-linked immunosorbent assay and correlated the results with opsonic and protective activity against type III GBS. Most cord sera (67%) containing greater than 0.1 microgram/ml of type III GBS IgG antibody promoted phagocytosis and killing in vitro and protection against type III GBS in neonatal rats. However, 26% of cord sera containing less than 0.1 microgram/ml of type III IgG antibody exhibited similar activity in vitro and in vivo against type III GBS. This opsonic and protective activity was retained in IgG fraction of whole serum, and was not directly associated with complement activity or with fibronectin. Further studies are needed to understand the mechanisms responsible for the opsonic and protective activity of some cord sera against type III GBS that may be independent of antibody to the type-specific polysaccharide antigen.