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Touseef Amna,1 M Shamshi Hassan,2 Jieun Yang,1 Myung-Seob Khil,2 Ki-Duk Song,3 Jae-Don Oh,3 Inho Hwang1 1Department of Animal Sciences and Biotechnology, 2Department of Organic Materials and Fiber Engineering, Chonbuk National University, Jeonju, South Korea; 3Genomic Informatics Center, Hankyong National University, Anseong, South Korea Abstract: Recently, substantial interest has been generated in using electrospun biomimetic nanofibers of hybrids, particularly organic/inorganic, to engineer different tissues. The present work, for the first time, introduced a unique natural and synthetic hybrid micronanofiber wound dressing, composed of virgin olive oil/copper oxide nanocrystals and polyurethane (PU), developed via facile electrospinning. The as-spun organic/inorganic hybrid micronanofibers were characterized by scanning electron microscopy (SEM), energy dispersive X-ray analysis, X-ray diffraction, electron probe microanalysis, and transmission electron microscopy. The interaction of cells with scaffold was studied by culturing NIH 3T3 fibroblasts on an as-spun hybrid micronanofibrous mat, and viability, proliferation, and growth were assessed. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay results and SEM observation showed that the hybrid micronanofibrous scaffold was noncytotoxic to fibroblast cell culture and was found to benefit cell attachment and proliferation. Hence our results suggest the potential utilization of as-spun micronanoscaffolds for tissue engineering. Copper oxide–olive oil/PU wound dressing may exert its positive beneficial effects at every stage during wound-healing progression, and these micronanofibers may serve diverse biomedical applications, such as tissue regeneration, damaged skin treatment, wound healing applications, etc. Conclusively, the fabricated olive oil–copper oxide/PU micronanofibers combine the benefits of virgin olive oil and copper oxide, and therefore hold great promise for biomedical applications in the near future. Keywords: micronanofibers, copper oxide, wound healing, polyurethane, olive oil

Traditionally, the p -value is the criterion for the cutoff threshold to determine significant markers in genome-wide association studies (GWASs). Choosing the best subset of markers for the best linear unbiased prediction (BLUP) for improved prediction ability (PA) has become an interesting issue. However, when dealing with many traits having the same marker information, the p -values' themselves cannot be used as an obvious solution for having a confidence in GWAS and BLUP. We thus suggest a genomic estimated breeding value-assisted reduction method of the single nucleotide polymorphism (SNP) set (GARS) to address these difficulties. GARS is a BLUP-based SNP set decision presentation. The samples were Landrace pigs and the traits used were back fat thickness (BF) and daily weight gain (DWG). The prediction abilities (PAs) for BF and DWG for the entire SNP set were 0.8 and 0.8, respectively. By using the correlation between genomic estimated breeding values (GEBVs) and phenotypic values, selecting the cutoff threshold in GWAS and the best SNP subsets in BLUP was plausible as defined by GARS method. 6,000 SNPs in BF and 4,000 SNPs in DWG were considered as adequate thresholds. Gene Ontology (GO) analysis using the GARS results of the BF indicated neuron projection development as the notable GO term, whereas for the DWG, the main GO terms were nervous system development and cell adhesion., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Beef consumers valued meat quality traits such as texture, tenderness, juiciness, flavor, and meat color that determining consumers' purchasing decision. Most research on meat quality has focused on marbling, a key characteristic related to meat eating quality. However, other important traits such as meat texture, tenderness, and color have not much studied in cattle. Among these traits, meat tenderness and texture of cattle are among the most important factors affecting quality evaluation of consumers. Collagen is the main component of connective tissues.It greatly affects meat tenderness. The objective of this study was to determine significant variants and candidate genes associated with collagen contents trait (total collagen) through genome-wide association studies (GWAS). Phenotypic and genomic data from 135 Hanwoo were used. The BLUPF90 family program and GRAMMAR method for GWAS were applied in this study. A total of 73 potential single nucleotide polymorphisms (SNPs) showed significant associations with collagen content. They were located in or near 108 candidate genes. TMEM135 and ME3 genes were identified to have the most significant SNPs associated with collagen contents trait. Data indicated that these genes were related to collagen. Biological processes and pathways for the prediction of biological functions of candidate genes were confirmed. We found that candidate genes were involved in positive regulation of CREB transcription factor activity and actin cytoskeleton related to tenderness and texture of beef. Three genes (CRTC3, MYO1C and MYLK4) belonging to these biological functions were related to tenderness. These results provide a basis for improving genomic characteristics of Hanwoo for the production of tender beef. Furthermore, they could be used they could be used as an index to select desired traits for consumers., Competing Interests: No potential conflict of interest relevant to this article was reported., (© Copyright 2023 Korean Society of Animal Science and Technology.)

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry., Competing Interests: No potential conflict of interest relevant to this article was reported., (© Copyright 2022 Korean Society of Animal Science and Technology.)

Myxovirus resistance (Mx) proteins are antiviral GTPases induced by type I interferons (IFNs). In chickens, a single Mx protein variant, S631N, has been suggested to possess antiviral activity. However, the impact of this variant on chicken Mx (chMx) protein structure and conformation has not been investigated. Hence, in this study, we applied computational methods such as molecular modeling, molecular dynamic simulation, inter domain motion and residue networks to examine the structure and dynamic behavior of wild-type and mutant chMx. At first, we built 3-dimensional structural models for both wild-type and mutant chMx proteins, which revealed that the structural organization of chMx was similar to that of human Mx proteins. Subsequently, molecular dynamics simulations revealed that angle variation around the hinge1 region led to the different stalk domain conformations between the wild-type and mutant chMx proteins. Domain motion analysis further suggested that the conformational differences in the loop region surrounded by the mutant residue may lead to an inclined stalk domain conformation in the mutant compared to the wild-type protein. In addition, we performed betweenness centrality analysis from residue interaction networks, to identify the crucial residues for intramolecular signal flow in chMx. The results of this study provided information on the differences in structure and dynamics between wild-type and mutant chMx, which may aid in understanding the structural features of the S631N mutant, that may be associated with chMx protein antiviral activity.Communicated by Ramaswamy H. Sarma.

Malignant melanoma is highly resistant to conventional treatments and is one of the most aggressive types of skin cancers. Conventional cancer treatments are limited due to drug resistance, tumor selectivity, and solubility. Therefore, new treatments with fewer side effects and excellent effects should be developed. In previous studies, we have analyzed antimicrobial peptides (AMPs), which showed antibacterial and anti-inflammatory effects in insects, and some AMPs also exhibited anticancer efficacy. Anticancer peptides (ACPs) are known to have fewer side effects and high anticancer efficacy. In this study, the insect-derived peptide poecilocorisin-1 (PCC-1) did not induce toxicity in the human epithelial cell line HaCaT, but its potential as an anticancer agent was confirmed through specific effects of antiproliferation, apoptosis, and cell cycle arrest in two melanoma cell lines, SK-MEL-28 and G361. Additionally, we discovered a novel anticancer mechanism of insect-derived peptides in melanoma through the regulation of transcription factor Sp1 protein, which is overexpressed in cancer, apoptosis, and cell cycle-related proteins. Taken together, this study aims to clarify the anticancer efficacy and safety of insect-derived peptides and to present their potential as future therapeutic agents., (© 2021. The Author(s).)

Whole-genome sequence (WGS) data are increasingly being applied into genomic predictions, offering a higher predictive ability by including causal mutations or single-nucleotide polymorphisms (SNPs) putatively in strong linkage disequilibrium with causal mutations affecting the trait. This study aimed to improve the predictive performance of the customized Hanwoo 50 k SNP panel for four carcass traits in commercial Hanwoo population by adding highly predictive variants from sequence data. A total of 16,892 Hanwoo cattle with phenotypes (i.e., backfat thickness, carcass weight, longissimus muscle area, and marbling score), 50 k genotypes, and WGS imputed genotypes were used. We partitioned imputed WGS data according to functional annotation [intergenic (IGR), intron (ITR), regulatory (REG), synonymous (SYN), and non-synonymous (NSY)] to characterize the genomic regions that will deliver higher predictive power for the traits investigated. Animals were assigned into two groups, the discovery set (7324 animals) used for predictive variant detection and the cross-validation set for genomic prediction. Genome-wide association studies were performed by trait to every genomic region and entire WGS data for the pre-selection of variants. Each set of pre-selected SNPs with different density (1000, 3000, 5000, or 10,000) were added to the 50 k genotypes separately and the predictive performance of each set of genotypes was assessed using the genomic best linear unbiased prediction (GBLUP). Results showed that the predictive performance of the customized Hanwoo 50 k SNP panel can be improved by the addition of pre-selected variants from the WGS data, particularly 3000 variants from each trait, which is then sufficient to improve the prediction accuracy for all traits. When 12,000 pre-selected variants (3000 variants from each trait) were added to the 50 k genotypes, the prediction accuracies increased by 9.9, 9.2, 6.4, and 4.7% for backfat thickness, carcass weight, longissimus muscle area, and marbling score compared to the regular 50 k SNP panel, respectively. In terms of prediction bias, regression coefficients for all sets of genotypes in all traits were close to 1, indicating an unbiased prediction. The strategy used to select variants based on functional annotation did not show a clear advantage compared to using whole-genome. Nonetheless, such pre-selected SNPs from the IGR region gave the highest improvement in prediction accuracy among genomic regions and the values were close to those obtained using the WGS data for all traits. We concluded that additional gain in prediction accuracy when using pre-selected variants appears to be trait-dependent, and using WGS data remained more accurate compared to using a specific genomic region., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Lopez, An, Srikanth, Lee, Oh, Shin, Park, Chai, Park and Lim.)

Despite the various existing studies about nonsynonymous single nucleotide polymorphisms (nsSNPs), genome-wide studies based on nsSNPs are rare. NsSNPs alter amino acid sequences, affect protein structure and function, and have deleterious effects. By predicting the deleterious effect of nsSNPs, we determined the total risk score per individual. Additionally, the machine learning technique was utilized to find an optimal nsSNP subset that best explains the complete nsSNP effect. A total of 16,100 nsSNPs were selected as the best representatives among 89,519 regressed nsSNPs. In the gene ontology analysis encompassing the 16,100 nsSNPs, DNA metabolic process, chemokine- and immune-related, and reproduction were the most enriched terms. We expect that our risk score prediction and nsSNP marker selection will contribute to future development of extant genome-wide association studies and breeding science more broadly., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Background: Lactobacillus reuteri is a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts., Objective: Because the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L. reuteri and investigate modified, acquired, or lost genetic features that have facilitated the evolution and adaptation of strains to specific environmental niches by this study., Methods: To examine canine L. reuteri, we sequenced an L. reuteri strain isolated from a dog in Korea. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to different hosts based on 27 published genomic sequences., Results: The pan-genome of 28 L. reuteri strains contained 7,369 gene families, and the core genome contained 1070 gene families. The ANI tree based on the core genes in the canine L. reuteri strain (C1) was very close to those for three strains (IRT, DSM20016, JCM1112) from humans. Evolutionarily, these four strains formed one clade, which we regarded as C1-clade in this study. We could investigate a total of 32,050 amino acid substitutions among the 28 L. reuteri strain genomes. In this comparison, 283 amino acid substitutions were specific to strain C1 and four strains in C1-clade shared most of these 283 C1-strain specific amino acid substitutions, suggesting strongly similar selective pressure. In accessory genes, we could identify 127 C1-clade host-specific genes and found that several genes were closely related to replication, recombination, and repair., Conclusion: This study provides new insights into the adaptation of L. reuteri to the canine intestinal habitat, and suggests that the genome of L. reuteri from canines is closely associated with their living and shared environment with humans.

Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle., Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genes., Results: In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight., Conclusion: This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.

Myeloid differentiating factor 88 (Myd88) is a universal adaptor protein that plays a critical role in innate immunity by mediating TLR downstream signaling. Myd88 death domain (DD) forms an oligomeric complex by association with other DD-containing proteins such as IRAK4. Despite its universal role, polymorphisms in Myd88 can result in several diseases. Previous studies have suggested that, out of several non-synonymous single-nucleotide polymorphisms (nsSNPs), the variants S34Y and R98C in the DD of Myd88 disrupt the formation of the Myddosome complex. Therefore, we performed molecular dynamics (MD) simulations on wild-type (Myd88 WT ) and mutant (Myd88 S34Y , Myd88 R98C ) DDs to evaluate the subtle conformational changes induced by these mutations. Our results suggest that the S34Y variant induces large structural transitions compared to the R98C variant as evidenced by residual flexibility at the variable loop regions, particularly in the H1-H2 loop, and variations in the collective modes of motion observed for wild-type and mutant Myd88 DDs. The residue interaction network strongly suggests a distortion in the interaction pattern at the location of the mutated residue between the wild type and mutants. Moreover, betweenness centrality values indicate that variations in the distribution of functionally important residues may be reflected by distinct residue signal transductions in both wild-type and mutant Myd88 DDs, which may influence the interaction with other DDs in TLR downstream signaling., (Copyright © 2020 Gosu, Won, Oh and Shin.)

Background: The objective of this qualitative study is to better understand primary care clinician decision making for managing chronic pain. Specifically, we focus on the factors that influence changes to existing chronic pain management plans. Limitations in guidelines and training leave clinicians to use their own judgment and experience in managing the complexities associated with treating patients with chronic pain. This study provides insight into those judgments based on clinicians' first-person accounts. Insights gleaned from this study could inspire innovations aimed at supporting primary care clinicians (PCCs) in managing chronic pain., Methods: We conducted 89 interviews with PCCs to obtain their first-person perspective of the factors that influenced changes in treatment plans for their patients. Interview transcripts were analyzed thematically by a multidisciplinary team of clinicians, cognitive scientists, and public health researchers., Results: Seven themes emerged through our analysis of factors that influenced a change in chronic pain management: 1) change in patient condition; 2) outcomes related to treatment; 3) nonadherent patient behavior; 4) insurance constraints; 5) change in guidelines, laws, or policies; 6) approaches to new patients; and 7) specialist recommendations., Conclusions: Our analysis sheds light on the factors that lead PCCs to change treatment plans for patients with chronic pain. An understanding of these factors can inform the types of innovations needed to support PCCs in providing chronic pain care. We highlight key insights from our analysis and offer ideas for potential practice innovations., Competing Interests: Conflict of interest: CAH is a principal investigator on past and current research grants from the Agency for Healthcare Research and Quality (AHRQ) and Pfizer, Inc. related to chronic pain care. RC receives funding from the National Institutes of Health (NIH) and the Florida Department of Health. RWH receives funding from AHRQ, NIH, Medtronic (educational grant to Wake Forest University School of Medicine), Medtronic (consultancy), and the Robert Wood Johnson Foundation (research funding as a Clinical Scholar). BTAC serves as a coinvestigator on an NIH R01 examining effects of state policies on pain management. The authors, JD, LGM, SMD, SA, ECD, and BWM declare that they have no affiliations with or involvement in any organization or entity with any financial interest in the subject matter or materials discussed in this paper., (© Copyright 2020 by the American Board of Family Medicine.)

The genomic best linear unbiased prediction (GBLUP) method has been widely used in routine genomic evaluation as it assumes a common variance for all single nucleotide polymorphism (SNP). However, this is unlikely in the case of traits influenced by major SNP. Hence, the present study aimed to improve the accuracy of GBLUP by using the weighted GBLUP (WGBLUP), which gives more weight to important markers for various carcass traits of Hanwoo cattle, such as backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Linear and different nonlinearA SNP weighting procedures under WGBLUP were evaluated and compared with unweighted GBLUP and traditional pedigree-based methods (PBLUP). WGBLUP methods were assessed over ten iterations. Phenotypic data from 10,215 animals from different commercial herds that were slaughtered at approximately 30-month-old of age were used. All these animals were genotyped using Illumina Bovine 50k SNP chip and were divided into a training and a validation population by birth date on 1 November 2015. Genomic prediction accuracies obtained in the nonlinearA weighting methods were higher than those of the linear weighting for all traits. Moreover, unlike with linear methods, no sudden drops in the accuracy were noted after the peak was reached in nonlinearA methods. The average accuracies using PBLUP were 0.37, 0.49, 0.40, and 0.37, and 0.62, 0.74, 0.67, and 0.65 using GBLUP for BFT, CWT, EMA, and MS, respectively. Moreover, these accuracies of genomic prediction were further increased to 4.84% and 2.70% for BFT and CWT, respectively by using the nonlinearA method under the WGBLUP model. For EMA and MS, WGBLUP was as accurate as GBLUP. Our results indicate that the WGBLUP using a nonlinearA weighting method provides improved predictions for CWT and BFT, suggesting that the ability of WGBLUP over the other models by weighting selected SNPs appears to be trait-dependent.

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene's effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.

Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information., Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity (HE), polymorphism information content, F-statistics (FST), linkage disequilibrium (LD) and effective population size (Ne)., Results: The chromosome-wise distribution of FST in BS, LR, and YS populations were within the range of 0-0.36, and the average FST value was estimated to be 0.07±0.06. This result indicated some level of genetic segregation. An average LD (r2) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average Ne of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster Ne decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past., Conclusion: To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.

Long noncoding RNAs (lncRNAs) regulate the expression of mRNA and can affect various biological processes and phenotypes. Currently, studies of lncRNAs in cattle are under way, but their exact function for several tissues has not yet been established. Hanwoo cattle ( Bos taurus coreanae ) have inhabited the Korean peninsula for about 6000 years and are one of the representative domesticated animals in Korea. As a result of intensive breeding, the meat of Hanwoo cattle is high in marbling content and is preferred by Koreans and other East Asian people. In this study, the expression of lncRNAs was identified in 36 samples from skeletal muscle and three adipose tissues (intramuscular, subcutaneous, and omental) of nine Hanwoo individuals. We identified 76 tissue-specific lncRNAs for each of the four tissues using the differences in expression levels. Through QTL information, we could identify 12 lncRNAs associated with shear force and six lncRNAs associated with body weight, which are two important traits in the Hanwoo population breeding strategy. By the physical position comparison of lncRNA and Bovine transcripts information, we could identify 11 lncRNAs that were in bovine transcripts, and four of the 11 genes related to transcripts of lncRNAs were biologically associated with muscle function. We believe this Hanwoo lncRNAs study will help reveal the lncRNA role in the physiological mechanisms of these four tissues.

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs., Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs., Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits., Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

Objective: This study aimed to test the expression patterns of ERBB receptor feedback inhibitor 1 ( ERRFI1 ) before and after exercise and the association of non-synonymous single-nucleotide polymorphisms (nsSNPs) of horse ERRFI1 with racing traits in Thoroughbreds., Methods: We performed bioinformatics and gene expression analyses for horse ERRFI1 . Transcription factor (TF) binding sites in the 5'-regulatory region of this gene were identified through a tool for prediction of TF-binding site (PROMO). A general linear model was used to detect the association between the nsSNP (LOC42830758 A to G) and race performance., Results: Quantitative polymerase chain reaction analysis showed that expression level of ERRFI1 after exercise was 1.6 times higher than that before exercise. Ten transcription factors were predicted from the ERRFI1 regulatory region. A novel nsSNP (LOC42830758 A to G) was found in ERRFI1 , which was associated with three racing traits including average prize money, average racing index, and 3-year-old starts percentile ranking., Conclusion: Our analysis will be helpful as a basis for studying genes and SNPs that affect race performance in racehorses.

Objective: This study was to determine the relationship between estimated breeding value and phenotype information after farrowing when juvenile selection was made in candidate pigs without phenotype information., Methods: After collecting phenotypic and genomic information for the total number of piglets born by Landrace pigs, selection accuracy between genomic breeding value estimates using genomic information and breeding value estimates of best linear unbiased prediction (BLUP) using conventional pedigree information were compared., Results: Genetic standard deviation ( σ a ) for the total number of piglets born was 0.91. Since the total number of piglets born for candidate pigs was unknown, the accuracy of the breeding value estimated from pedigree information was 0.080. When genomic information was used, the accuracy of the breeding value was 0.216. Assuming that the replacement rate of sows per year is 100% and generation interval is 1 year, genetic gain per year is 0.346 head when genomic information is used. It is 0.128 when BLUP is used., Conclusion: Genetic gain estimated from single step best linear unbiased prediction (ssBLUP) method is by 2.7 times higher than that the one estimated from BLUP method, i.e., 270% more improvement in efficiency.

Aim: This integrative review aims to summarize the evidence regarding the health-related quality of life, psychological well-being, and the relevant influencing factors in men with benign prostatic hyperplasia., Methods: An integrative published work review was adopted. Articles published in English from 2002 to 2014 that addressed the variables of health-related quality of life, psychological well-being, or the relevant influencing factors in men with benign prostatic hyperplasia were included., Results: Of the 4708 articles retrieved, 16 were deemed relevant. Analysis of the published work suggests that benign prostatic hyperplasia has a negative impact on health-related quality of life, citing two major predictive factors: lower urinary tract symptoms and medical management. The psychological well-being of men with benign prostatic hyperplasia remains inconclusive as very limited studies have been conducted to investigate this aspect in these men. Limited studies collectively investigate the relationship among concepts such as health-related quality of life, psychological well-being, and sociodemographic and clinical factors related to benign prostatic hyperplasia., Conclusion: This review highlights the need to conduct further study on health-related quality of life and the psychological well-being of patients with benign prostatic hyperplasia, especially in an Asian context. Such efforts promote patient-centric care and improve patient satisfaction through incorporating the concept of health-related quality of life into clinical practices., (© 2016 Japan Academy of Nursing Science.)

c-MYC (v-myelocytomatosis viral oncogene homologue) is a transcription factor that plays important role in many biological process including cell growth and differentiation, such as myogenesis and adipogenesis. In this study, we aimed to detect MYC gene polymorphisms, their genotype frequencies and to determine associations between these polymorphisms and meat quality traits in Berkshire pigs. We identified a single nucleotide polymorphism (SNP) in intron 2 of MYC gene by Sanger sequencing, i.e., g.3350G>C (rs321898326), that is only found in Berkshire pigs, but not in other breeds including Duroc, Landrace, and Yorkshire pigs that were used in this study. Genotypes of total 378 Berkshire pigs (138 sows and 240 boars) were determined using Hha I restriction enzyme digestion after polymerase chain reaction. Observed allele frequencies of GG, GC, and CC genotypes were 0.399, 0.508, and 0.093 respectively. Statistical analysis indicated that the g.3350G>C polymorphism was significantly associated with pH45min and cooking loss (p<0.05), suggesting that g.3350G>C SNP can be used for pre-selection of pH45min and cooking loss traits in Berkshire pigs.

Japanese quail (Coturnix coturnix japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight). Differentially expressed genes shared between female and male tissue contrast groups were analyzed to identify genes related to sexual dimorphism as well as potential novel candidate genes for molecular sexing. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (CHKA, NYAP), as well as body development and size differentiation (ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes (HXC4, ISL1) shared between our two sex-related contrast groups (Female Brain vs. Male Brain and Ovary vs. Testis) indicates that these genes may regulate sex-specific anatomical development. Results reveal genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.

Background: Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data., Results: We generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism., Conclusions: Results revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.

Since being domesticated about 10,000-12,000 years ago, domestic pigs (Sus scrofa domesticus) have been selected for traits of economic importance, in particular large body size. However, Yucatan miniature pigs have been selected for small body size to withstand high temperature environment and for laboratory use. This renders the Yucatan miniature pig a valuable model for understanding the evolution of body size. We investigate the genetic signature for selection of body size in the Yucatan miniature pig. Phylogenetic distance of Yucatan miniature pig was compared to other large swine breeds (Yorkshire, Landrace, Duroc and wild boar). By estimating the XP-EHH statistic using re-sequencing data derived from 70 pigs, we were able to unravel the signatures of selection of body size. We found that both selections at the level of organism, and at the cellular level have occurred. Selection at the higher levels include feed intake, regulation of body weight and increase in mass while selection at the molecular level includes cell cycle and cell proliferation. Positively selected genes probed by XP-EHH may provide insight into the docile character and innate immunity as well as body size of Yucatan miniature pig.

A genome wide association study was conducted using estimated breeding value (EBV) for milk production traits from 1st to 4th lactation. Significant single nucleotide polymorphism (SNP) markers were selected for each trait and the differences were compared by lactation. DNA samples were taken from 456 animals with EBV which are Holstein proven bulls whose semen is being sold or the daughters of old proven bulls whose semen is no longer being sold in Korea. High density genome wide SNP genotype was investigated and the significance of markers associated with traits was tested using the breeding value estimated by a multiple lactation model as a dependent variant. As the result of significance comparisons by lactations, several differences were found between the first lactation and subsequent lactations (from second to 4th lactation). A similar trend was noted in mean deviation and correlation of the estimated effects by lactation. Since there was a difference in the genes associated with EBV for each trait between first and subsequent lactations, a multi-lactation model in which lactation is considered as a different trait is genetically useful. Also, significant markers in all lactations and common markers for different traits were detected, which can be used as markers for quantitative trait loci exploration and marker assisted selection in milk production traits.

Aims and Objectives: To examine the health-related quality of life and psychological well-being of patients with benign prostatic hyperplasia and identify the predictive factors of health-related quality of life., Background: Benign prostatic hyperplasia is highly prevalent in ageing men and causes bothersome lower urinary tract symptoms, which has a negative impact on their health-related quality of life. The current practice of managing benign prostatic hyperplasia focuses on relieving physical symptoms. However, the impact of benign prostatic hyperplasia on the patients' health-related quality of life and psychological well-being remains understudied, especially in the Asian population., Design: A descriptive correlational survey study., Methods: A convenience sample of 97 patients with benign prostatic hyperplasia was recruited at an outpatient urology clinic of a tertiary hospital in Singapore. The health-related quality of life, lower urinary tract symptoms and psychological well-being of the participants were assessed using the 12-item Short-Form Health Survey, International Prostate Symptom Score and the Hospital Anxiety and Depression Scale, respectively., Results: The health-related quality of life scores were low with physical and mental health component scores of 47·0 and 48·9, respectively, as assessed by the 12-item Short-Form Health Survey. There was a high prevalence of anxiety (10·3%) and depression (21·6%). Correlation analysis revealed significantly negative relationships between lower urinary tract symptoms, anxiety, depression and physical and mental health dimensions of the 12-item Short-Form Health Survey. Multiple linear regression analysis further identified that postvoid residual urine and lower urinary tract symptoms were predictive factors of the physical health dimension, whereas anxiety and depression were predictive factors of the mental health dimension of the 12-item Short-Form Health Survey., Conclusions: The health-related quality of life of patients with benign prostatic hyperplasia was poor, and their psychological well-being was severely affected. Postvoid residual urine, lower urinary tract symptoms, anxiety and depression were identified to be significant predictive factors of the health-related quality of life of patients with benign prostatic hyperplasia., Relevance to Clinical Practice: Findings from this study provide useful evidence-based information for healthcare professionals in the development and implementation of effective and culturally sensitive interventions to improve the health-related quality of life and psychological well-being of patients with benign prostatic hyperplasia., (© 2014 John Wiley & Sons Ltd.)

There are five native chicken lines in Korea, which are mainly classified by plumage colors (black, white, red, yellow, gray). These five lines are very important genetic resources in the Korean poultry industry. Based on a next generation sequencing technology, whole genome sequence and reference assemblies were performed using Gallus&#95;gallus&#95;4.0 (NCBI) with whole genome sequences from these lines to identify common and novel single nucleotide polymorphisms (SNPs). We obtained 36,660,731,136 ± 1,257,159,120 bp of raw sequence and average 26.6-fold of 25-29 billion reference assembly sequences representing 97.288 % coverage. Also, 4,006,068 ± 97,534 SNPs were observed from 29 autosomes and the Z chromosome and, of these, 752,309 SNPs are the common SNPs across lines. Among the identified SNPs, the number of novel- and known-location assigned SNPs was 1,047,951 ± 14,956 and 2,948,648 ± 81,414, respectively. The number of unassigned known SNPs was 1,181 ± 150 and unassigned novel SNPs was 8,238 ± 1,019. Synonymous SNPs, non-synonymous SNPs, and SNPs having character changes were 26,266 ± 1,456, 11,467 ± 604, 8,180 ± 458, respectively. Overall, 443,048 ± 26,389 SNPs in each bird were identified by comparing with dbSNP in NCBI. The presently obtained genome sequence and SNP information in Korean native chickens have wide applications for further genome studies such as genetic diversity studies to detect causative mutations for economic and disease related traits.

The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10(-14) in population J, 3.17×10(-9) in population B, and 1.03×10(-12) in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

Necrotic enteritis (NE) is a re-emerging disease as a result of increased restriction on the use of antibiotics in poultry. However, the molecular mechanisms underlying the pathogenesis of NE are unclear. Small RNA transcriptome analysis was performed using spleen and intestinal intraepithelial lymphocytes (IEL) from 2 inbred chicken lines selected for resistance or susceptibility to Marek's disease (MD) in an experimentally induced model of avian NE to investigate whether microRNA (miRNA) control the expression of genes associated with host response to pathogen challenge. Unique miRNA represented only 0.02 to 0.04% of the total number of sequences obtained, of which 544 were unambiguously identified. Hierarchical clustering revealed that most of miRNA in IEL were highly expressed in the MD-susceptible line 7.2 compared with MD-resistant line 6.3. Reduced CXCL14 gene expression was correlated with differential expression of several unique miRNA in MD-resistant chickens, whereas TGFβR2 gene expression was correlated with altered gga-miR-216 miRNA levels in MD-susceptible animals. In conclusion, miRNA profiling and deep sequencing of small RNA in experimental models of infectious diseases may be useful for further understanding of host-pathogen interactions, and for providing insights into genetic markers of disease resistance., (Poultry Science Association Inc.)

Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.

Phospholipid transfer protein (PLTP) regulates high-density lipoprotein metabolism. The gene encoding PLTP is located on bovine chromosome 13. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the Hanwoo (Bos taurus coreanae) PLTP gene to detect novel mutations affecting economically important traits. Five SNPs were identified in the coding region (C7368T, G7453A, C9888T, and C9905T) and intron (A1750G). G7453A changes amino acid 362 of PLTP from alanine to threonine, and C9888T changes amino acid 491 of PLTP from proline to serine. Statistical analyses revealed that the G7453A and C9888T polymorphisms in the PLTP gene were significantly associated with marbling score (P < 0.05). The relationship between haplotype and economic traits was analyzed and found to be significantly associated with marbling score (P < 0.05). The results suggest that PLTP polymorphisms might be an important genetic influence on economic traits in Hanwoo.

The contribution of striatal protein kinase C (PKC) isoform changes in levodopa (L-DOPA) induced motor response complications in parkinsonian rats was investigated and the ability of tamoxifen, an antiestrogen with a partial PKC antagonist property, to prevent these response alterations in 6-hydroxydopamine (6-OHDA) lesioned rats as well as in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treated cynomologous monkeys was studied. Following treatment of adult male rats with L-DOPA twice daily for 3 weeks, protein levels of left (lesioned) and right (intact) striatal PKC isoforms were measured. Western blot analysis showed increased protein expression of both the novel PKC epsilon isoform and the atypical PKC lambda isoform ipsilateral to the lesion (174+/-17% for epsilon, 140+/-9% for lambda, of intact striatum in 6-OHDA lesioned plus chronic L-DOPA treated animals) in acute L-DOPA treated rats. No enhancement was observed in PKC immunoreactivity for other isoforms. Tamoxifen (5.0 mg/kg p.o.) significantly attenuated the L-DOPA induced augmentation of protein expression of PKC epsilon and PKC lambda, but had no effect on immunoreactivity for other PKC isoforms. In chronic L-DOPA treated parkinsonian rats, tamoxifen prevented (5.0 mg/kg p.o.) as well as ameliorated (5.0 mg/kg p.o.) the characteristic shortening in duration of motor response to L-DOPA challenge. In MPTP lesioned primates, similar to the ameliorative effect seen in rats, tamoxifen (1 and 3 mg/kg p.o) reduced the appearance of L-DOPA induced dyskinesia by 61% and 55% respectively (p<0.05). These results suggest that changes in specific striatal PKC isoforms contribute to the pathogenesis of L-DOPA induced motor complications and further that drugs able to selectively inhibit these signaling kinases might provide adjunctive benefit in the treatment of Parkinson's disease.

Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1's response to acid during in vitro growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with H. pylori's adaptation to ChAG.

Chronic atrophic gastritis (ChAG), a Helicobacter pylori-associated risk factor for the development of gastric cancer, involves loss of acid-producing parietal cells. Recent studies in gnotobiotic mouse models of ChAG have shown that parietal cell loss results in amplification of multi- and oligo-potential gastric stem cells that express sialylated glycan receptors recognized by H. pylori adhesins. Moreover, H. pylori resides within a subset of these stem cells. Studies of the transcriptomes of gastric stem cells, harvested directly from the stomachs of uninfected mice, using laser capture microdissection, suggest that they have the ability to complement some of the metabolic needs of H. pylori. These findings indicate that proliferating and non-proliferating gastric stem cells provide a habitat that could support H. pylori persistence in a gastric ecosystem that has lost its acid barrier to colonization by environmental, oral and intestinal microbes. One consequence to the host might be an increased risk of tumorigenesis.

AMPA and NMDA receptors, abundantly expressed on striatal medium spiny neurons, have been implicated in the regulation of corticostriatal synaptic efficacy. To evaluate the contribution of both glutamate receptor types to the pathogenesis of motor response alterations associated with dopaminergic treatment, we studied the ability of the selective AMPA receptor antagonist GYKI-47261 and the selective NMDA receptor antagonists, MK-801 and amantadine, to mitigate these syndromes in rodent and primate models of Parkinson's disease. The effects of GYKI-47261 and amantadine (or MK-801), alone and in combination, were compared for their ability to modify dyskinesias induced by levodopa. In rats, simultaneous administration of subthreshold doses of AMPA and NMDA receptor antagonists completely normalized the wearing-off response to acute levodopa challenge produced by chronic levodopa treatment (P < 0.05). In primates, the glutamate antagonists GYKI-47261 and amantadine, co-administered at low doses (failing to alter dyskinesia scores), reduced levodopa-induced dyskinesias by 51% (P < 0.05). The simultaneous AMPA and NMDA receptor blockade acts to provide a substantially greater reduction in the response alterations induced by levodopa than inhibition of either of these receptors alone. The results suggest that mechanisms mediated by both ionotropic glutamate receptors make an independent contribution to the pathogenesis of these motor response changes and further that a combination of both drug types may provide relief from these disabling complications at lower and thus safer and more tolerable doses than required when either drug is used alone.

Helicobacter pylori is generally viewed as an extracellular pathogen. We have analyzed the tropism of H. pylori clinical isolates in a gnotobiotic transgenic mouse model of human chronic atrophic gastritis, a preneoplastic condition. These mice lack acid-producing parietal cells and have an amplified population of dividing gastric epithelial progenitors (GEPs) that express NeuAc alpha 2,3Gal beta 1,4-glycans recognized by H. pylori adhesins. Scanning confocal and transmission electron microscopic studies of stomachs that had been colonized for 1 month or 1 year revealed intracellular bacterial collections (IBCs) in a small subset of multi- and oligopotential epithelial progenitors. Transmission electron microscopic and multilabel immunohistochemical analyses disclosed bacteria with several morphotypes, including spiral-shaped, in the cytoplasm and endosomes. Several stages in IBC evolution were documented, from a few solitary bacteria to consolidated populations in dividing and nondividing GEPs, to microorganisms traversing breaches in the GEP plasma cell membrane. IBC formation was not a unique feature of H. pylori strains isolated from patients with chronic atrophic gastritis. The notion that adult mammalian epithelial progenitors can function as a repository for H. pylori broadens the view of host habitats available to this and perhaps other pathogens.

Sensitization of NMDA receptors containing the NR2B subunit has been increasingly associated with various forms of synaptic plasticity, including those implicated in the pathogenesis of extrapyramidal motor dysfunction. To determine whether activation of NR2B containing receptors contributes to the development and maintenance of levodopa-induced response changes in parkinsonian animals, we evaluated the effects of the selective NR2B antagonist CP-101,606 on these response alterations in unilateral 6-hydroxydopamine (6-OHDA) lesioned rats. Three weeks of twice-daily levodopa treatment decreased the duration of the rotational response to acute levodopa challenge. The response alteration was associated with an increase in GluR1 (S831) phosphorylation in medium spiny neurons of the dorsolateral striatum. Both the attenuated rotational response and augmented GluR1 phosphorylation were decreased by CP-101,606 treatment. These CP-101,606 effects were observed when the compound was administered either at the end of chronic levodopa treatment (ameliorative effect) or together with the twice-daily levodopa treatment for 3 weeks (preventive effect). Furthermore, concurrent administration of CP-101,606 with levodopa potentiated the ability of levodopa challenge to reverse the 6-OHDA lesion-induced contralateral forelimb movement deficit as measured in a drag test. These results suggest that activation of NR2B subunit containing NMDA receptors contributes to both the development and maintenance of levodopa-induced motor response alterations, through a mechanism that involves an increase in GluR1 phosphorylation in striatal spiny neurons.

Adenosine A(2A) receptors, abundantly expressed on striatal medium spiny neurons, appear to activate signaling cascades implicated in the regulation of coexpressed ionotropic glutamatergic receptors. To evaluate the contribution of adenosinergic mechanisms to the pathogenesis of the response alterations induced by dopaminergic treatment, we studied the ability of the selective adenosine A(2A) receptor antagonist KW-6002 to prevent as well as palliate these syndromes in rodent and primate models of Parkinson's disease. In rats, KW-6002 reversed the shortened motor response produced by chronic levodopa treatment while reducing levodopa-induced hyperphosphorylation at S845 residues on AMPA receptor GluR1 subunits. In primates, KW-6002 evidenced modest antiparkinsonian activity when given alone. Once-daily coadministration of KW-6002 with apomorphine prevented the development of dyskinesias, which appeared in control animals 7-10 days after initiating apomorphine treatment. Animals initially given apomorphine plus KW-6002 for 3 weeks did not begin to manifest apomorphine-induced dyskinesias until 10-12 days after discontinuing the A(2A) antagonist. These results suggest that KW-6002 can attenuate the induction as well as the expression of motor response alterations to chronic dopaminergic stimulation in parkinsonian animals, possibly by blocking A(2A) receptor-stimulated signaling pathways. Our findings strengthen the rationale for developing A(2A) antagonists as an early treatment strategy for Parkinson's disease.

Activation of cAMP responsive element binding protein (CREB) has been increasingly implicated in the formation and maintenance of long-term memory. To elucidate molecular mechanisms that underlie the persisting alterations in motor response occurring with levodopa (L-dopa) treatment of parkinsonian patients, we evaluated the time course of these changes in relation to the activation of striatal CREB in 6-hydroxydopamine (6-OHDA) lesioned animals. Three weeks of twice-daily L-dopa treatment reduced the duration of the rotational response to acute L-dopa challenge in hemiparkinsonian rats, which lasted about 5 weeks after withdrawal of chronic L-dopa therapy. This shortened response duration, resembling human wearing-off fluctuations, was associated with a marked increase in Ser-133 phosphorylated CREB (pCREB) immunoreactivity in medium spiny neurons in dorsolateral striatum in response to acute dopaminomimetic challenge. Intermittent treatment with the D1 receptor-preferring agonist SKF 38393, but not the D2 receptor-preferring agonist quinpirole, produced a similar rise in CREB phosphorylation. The time course of changes in CREB phosphorylation correlated with the time course of changes in motor behavior after cessation of chronic L-dopa therapy. Both the altered motor response duration and the degree of CREB phosphorylation were attenuated by the intrastriatal administration of CREB antisense or protein kinase A inhibitor Rp-cAMPS. The results suggest that region-specific Ser-133 CREB phosphorylation in D1 receptor containing spiny neurons contributes to the persistence of the motor response alterations produced by intermittent stimulation of striatal dopaminergic receptors., (Copyright 2003 Wiley-Liss, Inc.)

Alterations in motor response that complicate levodopa treatment of Parkinson's disease appear to involve sensitization of striatal ionotropic glutamate receptors. Since protein kinase C (PKC)-mediated phosphorylation regulates glutamatergic receptors of the alpha-amino-3-hydroxyl-5-methyl-4-isoxazole propionic acid (AMPA) subtype and has been linked to several forms of behavioral plasticity, activation of PKC signaling in striatal spiny neurons may also contribute to the motor plasticity changes associated with chronic levodopa therapy. To evaluate this possibility, we sought to augment PKC signaling by using Herpes Simplex Virus type 1 vectors (pHSVpkcDelta) to directly transfer the catalytic domain of the PKCbetaII gene into striatal neurons of parkinsonian rats. Microinjection of pHSVpkcDelta vectors lead to the persistent expression of PkcDelta (35% loss over 21 days) in medium spiny neurons together with an increase in serine 831 phosphorylation on AMPA receptor GluR1 subunits and hastened the appearance of the shortened response duration produced by chronic levodopa treatment (P<0.05). In pHSVpkcDelta-infected animals, intrastriatal injection of the PKC inhibitor NPC-15437 (1.0 microg) attenuated both the increased GluR1 phosphorylation (P<0.01) and the accelerated onset of the levodopa-induced response modifications (P<0.01). However, in rats that received levodopa treatment for 21 days without the gene transfer, intrastriatal NPC-15437 had no effect on the response shortening or on GluR1 S831 phosphorylation. The results suggest that an increase in PKC-mediated signaling, including, in part, phosphorylation of AMPA receptors, on striatal spiny neurons may be sufficient to promote the initial appearance, but not necessary the ultimate expression, of the levodopa-induced motor response changes occurring in a rodent model of the human motor complication syndrome.

Helicobacter pylori infection of the human stomach is common and typically benign, although a subset of hosts develops severe pathology. Infection occurs in an organ with distinct microenvironments characterized by pronounced differences in the composition of acid-producing parietal cells. In this study, we examine determinants of bacterial tropism to various gastric niches by using germ-free normal and transgenic mice with an engineered parietal cell ablation. Mice were colonized for 8 weeks with a clinical isolate (Hp1) that expresses adhesins recognized by epithelial NeuAcalpha2,3Galbeta1,4 glycan receptors. In normal mice, Hp1 has tropism for a parietal cell-deficient niche where sialylated glycans are expressed by a narrow band of pit cells positioned at the boundary between the squamous epithelium (forestomach) and the proximal glandular epithelium. Lymphoid aggregates that develop in this niche, but not elsewhere in the stomach, were analyzed by GeneChip and quantitative RT-PCR studies of laser capture microdissected mucosa and yielded a series of biomarkers indicative of immune cell activation and maturation. Genetic ablation of parietal cells produced a new source of NeuAcalpha2,3Galbeta1,4 glycans in amplified gastric epithelial lineage progenitors, with accompanying expansion of Hp1 within the glandular epithelium. Lymphoid aggregates that develop in this formerly acid-protected epithelium have molecular features similar to those observed at the forestomach/glandular junction. These findings demonstrate the important roles played by parietal cells and glycan receptors in determining the positioning of H. pylori within the gastric ecosystem, and emphasize the need to consider the evolution of pathology within a given host in a niche-specific context.

The nonphysiologic stimulation of striatal dopaminergic receptors, as a result of disease- or drug-related denervation or intermittent excitation, triggers adaptive responses in the basal ganglia which contribute to the appearance of parkinsonian symptoms and later to the dyskinesias and other alterations in motor response associated with dopaminergic therapy. Current evidence suggests that these altered responses involve activation of signal transduction cascades in striatal medium spiny neurons linking dopaminergic to coexpressed ionotropic glutamatergic receptors of the N-methyl-D-aspartate (NMDA) and Alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid (AMPA) classes. These intraneuronal signaling pathways appear capable of modifying the phosphorylation state of NMDA and AMPA receptor subunits; resultant sensitization enhances cortical glutamatergic input which in turn modifies striatal output in ways that compromise motor behavior. The regulation of these spiny neuron glutamate receptors can also be affected by the activation state of coexpressed nondopaminergic receptors as well as by changes associated with Huntington's disease. These observations lend new insight into molecular mechanisms contributing to the integration of synaptic inputs to spiny neurons. They also suggest novel approaches to the pharmacotherapy of extrapyramidal motor dysfunction.

The contribution of serotoninergic mechanisms to motor dysfunction in Parkinson's disease (PD) has yet to be fully elucidated. Recent clinical observations increasingly suggest that drugs able to block serotonin 5HT2A/C receptors can benefit patients with certain extrapyramidal movement disorders. To further explore the roles of these and other neurotransmitter receptors in the pathogenesis of parkinsonian signs and levodopa-induced dyskinesias; we evaluated the effects of quetiapine, an atypical antipsychotic with 5HT2A/C and D2/3 antagonistic activity, on motor behavior in 6-hydroxydopamine-lesioned rats and MPTP-lesioned nonhuman primates. In hemiparkinsonian rats, quetiapine (5 mg/kg, po) reversed the shortened motor response to levodopa challenge produced by 3 weeks of twice-daily levodopa treatment (P < 0.01). Quetiapine (5 mg/kg po) also normalized the shortened response to the acute injection of either a dopamine D1 receptor agonist (SKF 38392) or a D2 agonist (quinpirole) in rats that had received chronic levodopa treatment. Quetiapine had no effect on parkinsonian dysfunction when given alone or with levodopa to parkinsonian rats and monkeys. Quetiapine (4 mg/kg, po) did, however, substantially reduce levodopa-induced dyskinesias when coadministered with levodopa (P < 0.05). These results suggest that quetiapine could confer therapeutic benefits to patients with levodopa-induced motor complications. Moreover, our findings may indicate that 5HT2A/C receptor-mediated mechanisms, alone or in combination with other mechanisms, contribute to the pathogenesis of the altered motor responses associated with the treatment of PD.