Haplotype-resolved 3D chromatin architecture of the hybrid pig

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Surgical sensation during caesarean section: a qualitative analysis

BACKGROUND

Caesarean section (CS) is a major abdominal surgery performed usually on a young and healthy population under neuraxial anesthesia with little to no sedation. This creates a distinct surgical experience whereby patients are aware of the surgical process, physical sensations, and their environment. This study aimed to provide an in-depth descriptive assessment of subjective surgical experience during CS under regional anaesthesia. We expected the information gained would enhance our current understanding and better alleviate patient anxiety through informed counselling.

METHODS

This qualitative descriptive study was conducted at a Canadian academic centre. Twenty patients participated in semi-structured interviews within a week of CS, using an interview guide developed for this study. Patient medical records were reviewed to collect demographic and surgical information. Thematic analysis was conducted using an inductive approach to determine common themes.

RESULTS

Nine themes were identified. Five themes were identified in the category of surgical sensation and four themes were identified in the category of peri-operative education.

CONCLUSIONS

Patients commonly experienced pressure and movement sensations at varying intensity, and most did not experience pain. Environmental factors, including sounds and distraction by the newborn, affected perception of surgical sensation. Patients wish to receive pre-operative counselling regarding potential surgical sensations, as well as ongoing communication from their anaesthesiologist. These results can be used to guide informed discussions with patients and direct further investigation in this area.

Increased Sparc release from subchondral osteoblasts promotes articular chondrocyte degeneration under estrogen withdrawal

OBJECTIVE

The incidence of osteoarthritis (OA) in menopausal women is significantly higher than in same-aged men. Investigating the role of subchondral osteoblasts in estrogen deficiency-induced OA may help elucidate the pathological mechanism, providing new insights for the diagnosis and treatment of menopausal OA.

METHODS

A classical ovariectomy-induced OA (OVX-OA) rat model was utilized to isolate primary articular chondrocytes and subchondral osteoblasts, which were identified and then cocultured in Transwell. The expression of chondrocyte anabolic and catabolic indicators was evaluated. The differentially expressed proteins in the conditioned medium (CM) of osteoblasts were identified by Liquid Chromatograph-Mass Spectrometer (LC-MS/MS). Normal chondrocytes were treated with osteoblast CM, and then RNA sequencing was performed on the treated chondrocytes. KEGG was used to identify significant enrichment of signaling pathways, and Simple Western was used to verify the expression of related proteins in the signaling pathways.

RESULTS

Coculture of OVX-OA subchondral osteoblasts with chondrocytes significantly downregulated the expression of the anabolic indicators and upregulated the expression of the catabolic indicators in chondrocytes. 1,601 proteins were identified in both normal and OVX osteoblast culture supernatants. Protein-protein interaction network analysis revealed that Sparc was one of the hub proteins. The AMPK/Foxo3a signaling pathway of chondrocytes was downregulated by OVX-OA osteoblasts CM. AICAR, the AMPK agonist, partially reversed the catabolic effect of OVX-OA osteoblasts on chondrocytes.

CONCLUSIONS

Sparc secreted by OVX-OA subchondral osteoblasts can downregulate the AMPK/Foxo3a signaling pathway of chondrocytes, thereby promoting chondrocyte degeneration.

Correlation between oral fluid and blood THC concentration: A systematic review and discussion of policy implications

Cannabis is the second most commonly used impairing substance by drivers, after alcohol. As more countries legalize cannabis, there is concern that cannabis-impaired driving will increase. In many countries, police use roadside devices to test for oral fluid THC (the primary psychotropic component in cannabis) to identify drivers who used cannabis; including in countries with non-zero per se limits for THC in blood. This practice is questioned as previous research demonstrates a poor correlation between oral fluid and blood THC concentrations at the individual level. We conducted a meta-analysis to identify all research that compared oral fluid with blood THC levels. We obtained individual-level data from study authors and analyzed pooled individual-level data to calculate sensitivity and specificity of oral fluid THC (at various cut-off values) to detect blood THC above different concentration limits. Finally, we explored practical implications of using oral fluid THC in an enforcement context. Our review found THC concentrations measured in over 18,000 paired samples of oral fluid and blood. We found a good correlation between the presence of THC in oral fluid and presence of THC in blood (sensitivity = 71.2%, specificity = 97.7%). However oral fluid THC, at commonly used cut-off values, is less sensitive and less specific when used as a biomarker to detect people with blood THC concentrations above commonly used per se limits (such as 5 ng/mL). As such, there will be a large number of "false positive" tests if oral fluid THC testing were used as a biomarker for "illegal" THC concentrations in randomly selected drivers. We argue that the adverse implications of false positive oral fluid THC tests in this context outweigh the possible road safety benefits and we recommend against oral fluid THC screening in randomly selected drivers in countries with non-zero per se limits for blood THC. In contrast, oral fluid THC tests appear to be useful for investigating "high-risk" drivers who come to police attention because of evidence of impairment.

Crucial functions of alpha-actinin 2 in the embryonic heart

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): Wellcome Trust; British Heart Foundation

Background/Introduction

Alpha-actinin is an integral protein of the Z-discs in heart and skeletal muscle cells, with important structural and signalling functions.  Missense variants in alpha-actinin can cause inherited conditions, e.g. myopathies and cardiomyopathies. The underlying disease mechanisms are still unknown.

Purpose

In order to study the disease mechanisms of an alpha-actinin missense variant, which is known to cause Hypertrophic Cardiomyopathy in human patients, a mouse model was generated.

Methods

Mice carrying the alpha-actinin missense variant were generated by CRISPR-Cas9 genome editing. The heterozygous adult mice carrying the alpha-actinin variant were characterised by echocardiography and quantitative PCR. Hearts of homozygous embryos were analysed at E15.5 by high-resolution episcopic microscopy (HREM).

Results

Mice carrying a single copy of the missense variant were viable and had normal appearance. Adult heterozygous mice showed no signs of cardiomyopathy on echocardiography. However, mature male mice displayed molecular signs of cardiomyopathy, such as induction of the fetal gene programme at transcript level.

The attempt to generate adult mice homozygous for the variant failed: 9 breeding pairs produced 18 litters with 83 weaned pups, but no homozygous offspring. Embryonic lethality was confirmed and E15.5 was the latest stage homozygous pups were reliably found to be viable. At this timepoint, genotype distribution was within the expected Mendelian ratios.

HREM of the hearts at this stage revealed increased right ventricular chamber size and decreased left atrial size, when compared to wildtype littermates. Membranous ventricular septal defects were observed in 3 out of 8 homozygous hearts. Further these embryos displayed aortic stenosis and dysplasic leaflets of the pulmonary valve.

Conclusions

Heterozygous adult mice only displayed sub-clinical signs of disease. In contrast, the missense variant is embryonic lethal in the homozygous setting and leads to a range of morphological abnormalities in E15.5 hearts. Future work will identify how altered functions of alpha-actinin cause these changes.

Yak miR-2285o-3p attenuates hypoxia-induced apoptosis by targeting caspase-3

miRNAs are a class of hairpin‐derived RNAs, 21–24 nucleotides in length, which are involved in a range of biological processes. The bta‐miR‐2285 family has over 40 members spanning the entire bovine genome. We previously found that bta‐miR‐2285o‐3p was highly expressed in yak heart and lung when compared with cattle, which prompted us to investigate its potential function in high‐altitude adaptation of yaks. In this study, we detected wide‐spread high expression of bta‐miR‐2285o‐3p in yak tissues. Further experiments revealed that the protein tyrosine phosphatase receptor type M (PTPRM) gene was the host gene of bta‐miR‐2285o‐3p and that two linked SNPs in bta‐mir‐2285o precursor affected the biogenesis of mature miRNA (bta‐miR‐2285o‐3p). Functional analysis in vitro indicated that bta‐miR‐2285o‐3p attenuated hypoxia‐induced apoptosis by targeting very low‐density lipoprotein receptor (VLDLR), phosphatase and tensin homolog (PTEN) and caspase‐3. Expression level analysis in vivo revealed the high negative Pearson’s correlation between bta‐miR‐2285o‐3p and caspase3 in yak, highlighting the potential important roles of bta‐miR‐2285o‐3p in yak high‐altitude adaptation. Our study provides a typical model for deciphering the function of miRNAs in environmental adaptation.

Parsing the microRNA genetics basis regulating skeletal muscle fiber types and meat quality traits in pigs

Muscle fibers are closely related to human diseases and livestock meat quality. However, the genetics basis of microRNAs (miRNAs) in regulating muscle fibers is not completely understood. In this study, we constructed the whole genome-wide miRNA expression profiles of porcine fast-twitch muscle [biceps femoris (Bf)] and slow-twitch muscle [soleus (Sol)], and identified hundreds of miRNAs, including four skeletal muscle-highly expressed miRNAs, ssc-miR-378, ssc-let-7f, ssc-miR-26a, and ssc-miR-27b-3p. Moreover, we identified 63 differentially expressed (DE) miRNAs between biceps femoris vs. soleus, which are the key candidate miRNAs regulating the skeletal muscle fiber types. In addition, we found that the expression of DE ssc-miR-499-5p was significantly correlated to the expression of Myoglobin (r = 0.6872, P < 0.0001) and Myosin heavy chain 7 (MYH7; r = 0.5408, P = 0.0020), and pH_45 min (r = 0.3806, P = 0.0380) and glucose content (r = -0.4382, P = 0.0154); while the expression of DE ssc-miR-499-3p was significantly correlated to the expression of Myoglobin (r = 0.5340, P = 0.0024) and pH_45 min (r = 0.4857, P = 0.0065). Taken together, our data established a sound foundation for further studies on the regulatory mechanisms of miRNAs in skeletal muscle fiber conversion and meat quality traits in livestock, and could provide a genetic explanation of the role of miRNAs in human muscular diseases.

Effect of salt concentration on microbial communities, physicochemical properties and metabolite profile during spontaneous fermentation of Chinese northeast sauerkraut

AIM

The aim of this study was to study the effects of salt concentrations on the microbial communities, physicochemical properties, metabolome profiles and sensory characteristics during the fermentation of traditional northeast sauerkraut.

METHODS AND RESULTS

Northeast sauerkraut was spontaneously fermented under four salt concentrations (0·5, 1·5, 2·5 and 3·5%, w/w). The result of microbiological analysis showed that the population of lactic acid bacteria in 2·5%-salted sauerkraut was significantly higher than that in the other samples. Correspondingly, the speed of decrease in pH and accumulation of acids were the highest in 2·5%-salted sauerkraut. The glucose (analysed by HPLC) in 2·5%-salted sauerkraut was consumed more completely to produce higher levels of organic acids compared to those in the other samples. Principle component analysis showed clear differences in the metabolites of sauerkraut according to different salt concentrations. A higher level of volatiles (detected by HS-SPME/GC-MS) was identified in 2·5%-salted sauerkraut, and sensory evaluation demonstrated that 2·5%-salted sauerkraut had the best sensory characteristics.

CONCLUSION

The best quality of sauerkraut was obtained from fermented under 2·5% salt concentration.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study facilitated the understanding of the effects of salt on the sauerkraut fermentation and may be useful for developing the quality of sauerkraut.

Genetic parameter estimation for reproductive traits in QingYu pigs and comparison of carcass and meat quality traits to Berkshire×QingYu crossbred pigs

OBJECTIVE

The QingYu pig is well known for its excellent meat quality attributes in Sichuan province, China. In order to improve its production efficiency, the determination of genetic factors contributing to quantifiable economic traits of livestock is important. Moreover, the cross-breeding of QingYu pigs with western breeds possessing strong growth attributes is an efficient way to improve the performance of this breed.

METHODS

Here, the genetic parameters of several important reproductive traits of QingYu pigs were estimated, include total number born (TNB), number born alive, litter birth weight, individual birth weight, number of piglets weaned, litter weaning weight, and individual weaning weight. The data was analyzed using the ASReml 3.0 software (NSW Inc., Sydney, Australia). Furthermore, the effects of crossing Berkshire with QingYu (BQ) pigs on carcass and meat quality traits, as well as the effects of slaughter weight on carcass and meat quality of BQ were characterized.

RESULTS

QingYu pigs exhibited superior reproductive traits. The TNB available to QingYu pigs was more than 8 per parity. The observed repeatability of the reproductive traits of the QingYu pigs was between 0.10 and 0.23. The significantly correlated genetic and phenotypic of reproduction traits were consistent. Interestingly, the BQ pigs exhibited improved carcass quality, with a significant increase in loin muscle area, lean percentage and reduction in sebum percentage. As a result, BQ had higher L45min, lower cooking scores, and lower drip loss. In addition, the loin muscle area, body length, and sebum percentage were significantly higher in 90 and 100 kg animals. Cooking loss showed a significant increase at 80 kg, and marbling increased significantly from 90 kg.

CONCLUSION

The results of this study suggest that QingYu pigs exhibit excellent reproductive properties and heritability of these traits. Crossing with Berkshire is an efficient strategy to improve the carcass and meat quality of QingYu pigs for commercial operations. Furthermore, it appears as though the optimal slaughter weight of BQ pigs is at approximately 90 kg.

Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives

High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region's genetic diversity is conspicuous in high-altitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high- and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.

The Pro-angiogenesis Of Exosomes Derived From Umbilical Cord Blood Of Intrauterine Growth Restriction Pigs Was Repressed Associated With MiRNAs

Dysfunctional umbilical cord blood (UCB) is a key factor for the development of intrauterine growth restriction (IUGR) in utero. Poor degrees of angiogenesis were observed during IUGR development. Here, it was demonstrated that NV-EXO (normal piglet's Umbilical Veins derived exosomes) promoted angiogenesis within the subdued pro-angiogenesis context of IV-EXO (IUGR piglet's Umbilical Veins derived exosomes). Investigation of the miRNA transcriptome of umbilical cord vein and artery exosomes between IUGR and normal littermates showed significant differences between umbilical veins from normal (NV) and IUGR (IV) piglets. Similar patterns were observed in normal (NA) and IUGR (IA) umbilical arteries as well. Moreover, the miRNAs expession level was more stable in NV. Further analysis revealed that miRNAs related to angiogenesis exhibited aberrant expression in IUGR pigs. The miRNA expression patterns between IUGR and normal piglets showed great difference. Expression of miR-150 in the tissues and UCB exosomes of IUGR pigs was significantly decreased. Up-regulation of miR-150 was able to increase proliferation, migration and tube formation of Human umbilical vein endothelial cells (HUVECs), suggesting a pro-angiogenic role. Furthermore, the data demonstrated that UCB derived miRNAs participate in fetal epigenetic regulation during pregnancy, suggesting a novel possible explanation for abnormal embryologic vascular development and several congenital cardiovascular diseases.

Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives

Background

Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown.

Findings

We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation.

Conclusions

These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.

[Application of next generation sequencing in congenital sensorineural deafness]

Objective:The next-generation sequencing technology (NGS) was used to perform genetic testing on children diagnosed with sensorineural hearing loss in outpatient clinics.The information on the status and inheritance of disease causing genes in deafness was analyzed to provide a theoretical basis for genetic counseling, prenatal diagnosis, and birth defects prevention.Method:Ninety-four cases of sensorineural deafness diagnosed by medical history, audiological examination, and imaging examination were collected in our department.Next-generation sequencing was used to detect the region of exons of 159 genes, 6 mitochondrial genes, and 3 miRNAs related to deafness. The Sanger sequencing verification was performed on the parents of the probands to find out the gene expression status and relationship between the probands and the parents.Result:Of the 94 children with deafness,70 had severe sensorineural hearing loss, 13 had moderate to severe hearing loss, 8 had moderate hearing loss, and 3 had mild hearing loss.Twenty-three cases of cariogenic mutations were detected by next generation sequencing,and the total mutation rate was 24.5%. There were 11 cases of GJB2 mutations, including 6 homozygous mutations of 235delC, 4 heterozygous mutations of 235delC and 299_300del heterozygous mutation of 235delC and c.176_191del.There are 5 cases of SLC26A4 gene mutations, including 2 cases of homozygous mutations of c.919-2A> G, one case of c.919-2A> G and c.2168A>G compound heterozygous mutations, c.919-2A> G and c.754T> C compound heterozygous mutation in 1 case, c.919 2A> G and c.416-418del complex heterozygous mutation in 1 case. There were 2 cases of MT RNR1 mutations, and 1 case of STRC,KCNQ1,USH2A,POU3F4, and MITF mutations.Conclusion:The next-generation sequencing has features such as rapid, high throughput, and low cost, which is beneficial to medication guidance, genetic counseling, and marriage and parenting guidance,and help to effectively prevent or reduce the occurrence of hereditary deafness..

Betaine Supplementation Enhances Lipid Metabolism and Improves Insulin Resistance in Mice Fed a High-Fat Diet

Obesity is a major driver of metabolic diseases such as nonalcoholic fatty liver disease, certain cancers, and insulin resistance. However, there are no effective drugs to treat obesity. Betaine is a nontoxic, chemically stable and naturally occurring molecule. This study shows that dietary betaine supplementation significantly inhibits the white fat production in a high-fat diet (HFD)-induced obese mice. This might be due to betaine preventing the formation of new white fat (WAT), and guiding the original WAT to burn through stimulated mitochondrial biogenesis and promoting browning of WAT. Furthermore, dietary betaine supplementation decreases intramyocellular lipid accumulation in HFD-induced obese mice. Further analysis shows that betaine supplementation reduced intramyocellular lipid accumulation might be associated with increasing polyunsaturated fatty acids (PUFA), fatty acid oxidation, and the inhibition of fatty acid synthesis in muscle. Notably, by performing insulin-tolerance tests (ITTs) and glucose-tolerance tests (GTTs), dietary betaine supplementation could be observed for improvement of obesity and non-obesity induced insulin resistance. Together, these findings could suggest that inhibiting WAT production, intramyocellular lipid accumulation and inflammation, betaine supplementation limits HFD-induced obesity and improves insulin resistance.

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice

Galacto-oligosaccharides (GOS) are prebiotics that positively affect the host's gut microbiota, which is important for the health of the host.

[Study on the recent application of ear correction model in children with congenital auricular deformity]

Objective:To study the short-term effect of Earwell ear correction model on congenital auricular deformity in children. Method:Selected 38 children with ear malformation, a total of 42 ears, born at the age of 7 days to 176 days, and the average age was 62.40 days, and all of patients were used the U.S. Earwell correction model for correction. Result:Final auricular morphologic results were classified as excellent (normal shape), good (nearnormal shape), and poor (slight or no improvement). And the patients were divided into group 1 (neonatal period), group 2 (28-90 days) and group 3 (more than 90 days) according to age, after using the Earwell ear correction device, the result which evaluated excellent are 100.00%, 89.47% and 72.73% respectively, and the average correction times are 16.75 days, 26.26 days and 38.91 days respectively, the ratio of complications are 0, 73.68% and 100.00% respectively. Conclusion:The effection of Earwell ear correction model is significant for the correction of children with congenital auricular deformity , the earlier treatment cause the better result, the shorter of the correcting time , and the lower of the complication rate.

Psychiatric and behavioral side effects of anti-epileptic drugs in adolescents and children with epilepsy

PURPOSE

The objective of the study was to compare the psychiatric and behavioral side effect (PBSE) profiles of both older and newer antiepileptic drugs (AEDs) in children and adolescent patients with epilepsy.

METHOD

We used logistic regression analysis to test the correlation between 83 non-AED/patient related potential predictor variables and the rate of PBSE. We then compared for each AED the rate of PBSEs and the rate of PBSEs that led to intolerability (IPBSE) while controlling for non-AED predictors of PBSEs.

RESULTS

922 patients (≤18 years old) were included in our study. PBSEs and IPBSEs occurred in 13.8% and 11.2% of patients, respectively. Overall, a history of psychiatric condition, absence seizures, intractable epilepsy, and frontal lobe epilepsy were significantly associated with increased PBSE rates. Levetiracetam (LEV) had the greatest PBSE rate (16.2%). This was significantly higher compared to other AEDs. LEV was also significantly associated with a high rate of IPBSEs (13.4%) and dose-decrease rates due to IPBSE (6.7%). Zonisamide (ZNS) was associated with significantly higher cessation rate due to IPBSE (9.1%) compared to other AEDs.

CONCLUSION

Patients with a history of psychiatric condition, absence seizures, intractable epilepsy, or frontal lobe epilepsy are more likely to develop PBSE. PBSEs appear to occur more frequently in adolescent and children patients taking LEV compared to other AEDs. LEV-attributed PBSEs are more likely to be associated with intolerability and subsequent decrease in dose. The rate of ZNS-attributed IPBSEs is more likely to be associated with complete cessation of AED.

Protective effects of salidroside against isoflurane-induced cognitive impairment in rats

Postoperative cognitive dysfunction, which is associated with a wide range of cognitive functions including working memory, long-term memory, information processing, attention, and cognitive flexibility, is a major clinical issue in geriatric surgical patients. The aim of the current study was to determine the protective role and possible mechanisms of salidroside against isoflurane-induced cognitive impairment. Sprague Dawley rats were randomly assigned to five groups and were treated with or without salidroside before isoflurane exposure. Open-field and fear conditioning tests were conducted to evaluate the cognitive function of the rats. Moreover, the hippocampus tissues were obtained for biochemical analysis. The results showed that the isoflurane anesthesia decreased the freezing time to context significantly at 48 h after the isoflurane exposure in the fear conditioning test. Salidroside could ameliorate isoflurane-induced cognitive dysfunction. Further analysis demonstrated salidroside markedly suppressed the release of tumor necrosis factor-α and interleukin-1β. Moreover, salidroside reversed the decreased activity of choline acetyltransferase, superoxide dismutase, glutathione peroxidase, and content of acetylcholine, as well as the increased activity of acetylcholine esterase and content of malondialdehyde in hippocampal tissue of isoflurane-exposed rats. According to the results, we concluded that that salidroside has a protective effect against isoflurane-induced cognitive dysfunction by inhibiting excessive inflammatory responses, decreasing oxidative stress, and regulating the cholinergic system.

Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose

A better understanding of the control of lipogenesis is of critical importance for both human and animal physiology. This requires a better knowledge of the changes of gene expression during the process of adipose tissue development. Thus, the objective of the current study was to determine the effects of development on subcutaneous adipose tissue gene expression in growing and adult pigs. Here, we present a comprehensive investigation of mRNA transcriptomes in porcine subcutaneous adipose tissue across four developmental stages using digital gene expression profiling. We identified 3,274 differential expressed genes associated with oxidative stress, immune processes, apoptosis, energy metabolism, insulin stimulus, cell cycle, angiogenesis and translation. A set of universally abundant genes (ATP8, COX2, COX3, ND1, ND2, SCD and TUBA1B) was found across all four developmental stages. This set of genes may play important roles in lipogenesis and development. We also identified development-related gene expression patterns that are linked to the different adipose phenotypes. We showed that genes enriched in significantly up-regulated profiles were associated with phosphorylation and angiogenesis. In contrast, genes enriched in significantly down-regulated profiles were related to cell cycle and cytoskeleton organization, suggesting an important role for these biological processes in adipose growth and development. These results provide a resource for studying adipose development and promote the pig as a model organism for researching the development of human obesity, as well as being used in the pig industry.

Deciphering the microRNA transcriptome of skeletal muscle during porcine development

MicroRNAs (miRNAs) play critical roles in many important biological processes, such as growth and development in mammals. Various studies of porcine muscle development have mainly focused on identifying miRNAs that are important for fetal and adult muscle development; however, little is known about the role of miRNAs in middle-aged muscle development. Here, we present a comprehensive investigation of miRNA transcriptomes across five porcine muscle development stages, including one prenatal and four postnatal stages. We identified 404 known porcine miRNAs, 118 novel miRNAs, and 101 miRNAs that are conserved in other mammals. A set of universally abundant miRNAs was found across the distinct muscle development stages. This set of miRNAs may play important housekeeping roles that are involved in myogenesis. A short time-series expression miner analysis indicated significant variations in miRNA expression across distinct muscle development stages. We also found enhanced differentiation- and morphogenesis-related miRNA levels in the embryonic stage; conversely, apoptosis-related miRNA levels increased relatively later in muscle development. These results provide integral insight into miRNA function throughout pig muscle development stages. Our findings will promote further development of the pig as a model organism for human age-related muscle disease research.

Combined low dose local anesthetics and opioids versus single use of LA for transurethral urological surgery: a meta-analysis

INTRODUCTION

The combination of reduced dose of local anesthetics (LA) and highly lipid-soluble synthetic opioids for patients undergoing transurethral surgery could reduce block duration and side-effects. However, it remains unclear what are the most appropriate levels of low dose and the extent to which the side-effects could be controlled. A meta-analysis was conducted to address this concern.

MATERIALS AND METHODS

Based on twelve randomized controlled trials, this meta-analysis pooled previous results to generate integrated evidence.

RESULTS

Combined low dose of LA and opioids had similar sensory block and significantly shorter motor block duration (weighted mean difference: -39.31 min, 95% confidence interval (CI): -50.58--28.05, P < 0.00001) compared with single use of LA. There was no evidence of higher risk of analgesic failure in the combination group. In addition, combined low dose LA and opioids was associated with significantly reduced rate of postoperative hypotension (risk ratios (RR): 0.60, 95% CI: 0.37-0.96, P = 0.03) and shivering (RR: 0.27, 95% CI: 0.11-0.64, P = 0.003), but with higher rate of sedation (RR: 3.14, 95% CI: 1.02-9.66, P = 0.05).

CONCLUSION

Combined low dose LA and opioids is a better choice for patients received transurethral surgery compared with single use of intrathecal LA.

Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs

BACKGROUND

Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach.

RESULTS

We observed a tendency toward a global loss of DNA methylation in the gene-body region of the skeletal muscle of the middle-aged pigs compared with the young group. We determined the genome-wide gene expression pattern in the longissimus dorsi muscle using microarray analysis and performed a correlation analysis using DMR (differentially methylated region)-mRNA pairs, and we found a significant negative correlation between the changes in methylation levels within gene bodies and gene expression. Furthermore, we identified numerous genes that show age-related methylation changes that are potentially involved in the aging process. The methylation status of these genes was confirmed using bisulfite sequencing PCR. The genes that exhibited a hypomethylated gene body in middle-aged pigs were over-represented in various proteolysis and protein catabolic processes, suggesting an important role for these genes in age-related muscle atrophy. In addition, genes associated with tumorigenesis exhibited aged-related differences in methylation and expression levels, suggesting an increased risk of disease associated with increased age.

CONCLUSIONS

This study provides a comprehensive analysis of genome-wide DNA methylation patterns in aging pig skeletal muscle. Our findings will serve as a valuable resource in aging studies, promoting the pig as a model organism for human aging research and accelerating the development of comparative animal models in aging research.

Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native and domesticated pigs provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection. Here we used whole-genome sequencing to explore the genetic relationships among the European native pig Berkshire and breeds that are distributed worldwide, and to identify genomic footprints left by selection during the domestication of Berkshire. Numerous nonsynonymous SNPs-containing genes fall into olfactory-related categories, which are part of a rapidly evolving superfamily in the mammalian genome. Phylogenetic analyses revealed a deep phylogenetic split between European and Asian pigs rather than between domestic and wild pigs. Admixture analysis exhibited higher portion of Chinese genetic material for the Berkshire pigs, which is consistent with the historical record regarding its origin. Selective sweep analyses revealed strong signatures of selection affecting genomic regions that harbor genes underlying economic traits such as disease resistance, pork yield, fertility, tameness and body length. These discoveries confirmed the history of origin of Berkshire pig by genome-wide analysis and illustrate how domestication has shaped the patterns of genetic variation.

Intrinsic features in microRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk

MicroRNAs (miRNAs) are non-coding small RNA ∼22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNA-sequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f-5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders.

Purification and identification of five novel antioxidant peptides from goat milk casein hydrolysates

The present research described the preparation, purification, and identification of antioxidant peptides from goat milk casein (GMC). Goat milk casein was hydrolyzed by using a combination of neutral and alkaline proteases to obtain goat milk casein hydrolysates (GMCH) with high antioxidant activity. After desalting by nonpolar macroporous absorption resin, GMCH was isolated and purified by gel filtration chromatography and reversed-phase HPLC, respectively, and further identified by nanoliter electrospray ionization-tandem mass spectrometry. Antioxidant activities of GMC, GMCH, and pure peptides were evaluated and compared using free radical scavenging activity, metal ion chelating ability, and anti-lipid peroxidation ability. Compared with GMC, the free radical-scavenging ability and ferrous ion-chelating ability of GMCH increased significantly. The inhibition effect of lipid peroxidation of GMCH was much stronger than that of tert-butylhydroquinone and phytogermine and a little lower than that of ascorbic acid. The antioxidant activity of GMCH could be attributed to the high antioxidant activity of oligopeptides, especially 5 novel oligopeptides: Val-Tyr-Pro-Phe, Phe-Gly-Gly-Met-Ala-His, Phe-Pro-Tyr-Cys-Ala-Pro, Tyr-Val-Pro-Glu-Pro-Phe, and Tyr-Pro-Pro-Tyr-Glu-Thr-Tyr, which were first observed in GMCH. The antioxidant activity of these 5 novel oligopeptides and GMCH increased 3.59 to 380 times compared with GMC, combining anti-lipid peroxidation ability of GMCH, which indicated that GMCH and its purified fractions in different stages could be used as functional food ingredients, food additives, and pharmaceutical agents in the future.

Clinical features of atopic dermatitis in a hospital-based setting in China

BACKGROUND

Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease. There have been few detailed reports of the clinical evaluation of Chinese patients with AD.

OBJECTIVES

To give a profile of the clinical features of Chinese AD patients in a university hospital setting.

METHODS

A total of 1008 cases met Hanifin and Rajka diagnostic criteria of AD were recruited at Xinhua Hospital, Shanghai Jiaotong University School of Medicine, China.

RESULTS

In our survey, 22.7% patients were mild, 66.6% were moderate and 10.7% were severe according to the SCORAD index. Both the frequency and severity of the male patients were slightly higher. The frequency of asthma among the AD patients was 16.7% and it was increased with the age (χ2 = 205.20, P = 0.000). The frequencies of objective minor signs were demonstrated with age-related changes. Besides, three localized variants including eyelid eczema (49.8%), scalp dermatitis (49.7%), infra-auricular and retroauricular fissuring (44.8%) were commonly observed, especially in the infantile phase (P < 0.01). It was showed significant differences in serum total immunoglobulin E (IgE) and eosinophil cationic protein (ECP) levels of different age groups. The positive rate of Phadiatop was raised after 3 years old and that of the common food allergens were decreased after 6 years old.

CONCLUSIONS

More males than females had ongoing AD in our survey. Most AD debuted in the first year of the cases. High incidence of the three clinical signs: eyelid eczema, scalp dermatitis and infra-auricular and retroauricular fissuring among the patients suggests it can be a potential valuable diagnostic clue to AD.

DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway

Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer in its clinical behavior, with a 5-year overall survival as low as 5%. Despite years of research in the field, molecular determinants of SCLC behavior are still poorly understood, and this deficiency has translated into an absence of specific diagnostics and targeted therapeutics. We hypothesized that tumor DNA copy number alterations would allow the identification of molecular pathways involved in SCLC progression. Array comparative genomic hybridization was performed on DNA extracted from 46 formalin-fixed paraffin-embedded SCLC tissue specimens. Genomic profiling of tumor and sex-matched control DNA allowed the identification of 70 regions of copy number gain and 55 regions of copy number loss. Using molecular pathway analysis, we found a strong enrichment in these regions of copy number alterations for 11 genes associated with the focal adhesion pathway. We verified these findings at the genomic, gene expression and protein level. Focal Adhesion Kinase (FAK), one of the central genes represented in this pathway, was commonly expressed in SCLC tumors and constitutively phosphorylated in SCLC cell lines. Those were poorly adherent to most substrates but not to laminin-322. Inhibition of FAK phosphorylation at Tyr(397) by a small-molecule inhibitor, PF-573,228, induced a dose-dependent decrease of adhesion and an increase of spreading in SCLC cell lines on laminin-322. Cells that tended to spread also showed a decrease in focal adhesions, as demonstrated by a decreased vinculin expression. These results support the concept that pathway analysis of genes in regions of copy number alterations may uncover molecular mechanisms of disease progression and demonstrate a new role of FAK and associated adhesion pathways in SCLC. Further investigations of FAK at the functional level may lead to a better understanding of SCLC progression and may have therapeutic implications.

Loss of PTEN engages ErbB3 and IGF-I receptor signaling to promote antiestrogen resistance in breast cancer

Abstract #73

We sought to determine whether loss of the lipid phosphatase PTEN confers resistance to antiestrogens in estrogen receptor (ER)-positive breast cancer cells and primary tumors. Stable knockdown of PTEN expression (PTEN-kd) with shRNA in MCF-7, T47D, and MDA-361 ER+ human breast cancer cells resulted in upregulation of PI3K and P-Akt, resistance to tamoxifen and faslodex, and estrogen-independent growth. Upon PTEN-kd, ER levels were maintained in MCF-7 cells but markedly reduced in T47D and MDA-361 cells. While PTEN-kd upregulated ER transcriptional reporter activity in MCF-7 cells, opposite effects were seen in T47D and MDA-361 cells.&#x2028; We evaluated mechanisms of PI3K activation in PTEN-kd cells by immunoprecipitating the p85 regulatory subunit of PI3K and examining p85-bound tyrosine-phosphorylated adaptors or receptors. PTEN-kd increased the binding of p85 to IRS-1 (MCF-7) and ErbB3 (T47D). PTEN-kd increased PI3K pathway sensitivity to IGF-I (MCF-7) and endogenous ligand (T47D, MDA-361). PTEN-kd cells had increased and prolonged activation of IGF-IR and ErbB3, thus implicating PTEN in the regulation of signaling upstream of PI3K. Further, PTEN-kd increased non-genomic, estrogen-induced signaling via IGF-IR by increasing p85-IRS-1 binding and activation of PI3K/Akt in MCF-7 cells. Inhibition of PI3K and mTOR with the small molecule BEZ235, of IGF-IR with the small molecule AEW541, and/or of ErbB2-mediated activation of ErbB3 with lapatinib restored the growth inhibitory effect of antiestrogens.&#x2028; We generated gene expression signatures of PTEN loss in each cell line by microarray analyses. Comparison of these signatures to the Connectivity Map (Science 313:1929, 2006) suggested activation of PI3K, as signatures of PTEN loss negatively connected with those induced by the PI3K inhibitors wortmannin and LY294002 (all p&lt;0.06). We found a 24-gene signature of PTEN loss common to all 3 lines, which we used to score the gene expression profiles of tumors from a cohort of 268 patients with ER+ breast cancer treated with adjuvant tamoxifen for 5 yrs and a median follow-up of 9.1 years (BMC Genomics 9:239, 2008). Patients with tumors exhibiting a signature of PTEN loss had shorter relapse-free survival (p&lt;0.0001; log rank test). Eleven genes in the PTEN signature were individually predictive of disease outcome (p&lt;0.05). In a separate, smaller cohort of patients with ER+ cancers treated with adjuvant tamoxifen (n=34), undetectable PTEN in tumor cells (measured by IHC) correlated with shorter relapse-free survival vs. tumors with detectable PTEN (p=0.06). These data suggest that 1) PTEN loss confers antiestrogen resistance to ER+ breast cancer by genomic and non-genomic mechanisms; 2) PTEN loss is permissive for activation of IGF-IR and ErbB3 signaling; 3) inhibition of IGF-IR and/or ErbB signaling pathways overcomes the resistance to antiestrogens conferred by PTEN loss; and 4) a gene expression signature reflective of loss of PTEN and/or absence of PTEN protein can predict poor patient outcome after adjuvant hormonal therapy.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 73.

The Notch pathway mediates expansion of a progenitor pool and neuronal differentiation in adult neural progenitor cells after stroke

Molecular mechanisms by which stroke increases neurogenesis have not been fully investigated. Using neural progenitor cells isolated from the subventricular zone (SVZ) of the adult rat subjected to focal cerebral ischemia, we investigated the Notch pathway in regulating proliferation and differentiation of adult neural progenitor cells after stroke. During proliferation of neural progenitor cells, ischemic neural progenitor cells exhibited substantially increased levels of Notch, Notch intracellular domain (NICD), and hairy enhancer of split (Hes) 1, which was associated with a significant increase of proliferating cells. Blockage of the Notch pathway by short interfering ribonucleic acid (siRNA) against Notch or a gamma secretase inhibitor significantly reduced Notch, NICD and Hes1 expression and cell proliferation induced by stroke. During differentiation of neural progenitor cells, Notch and Hes1 expression was downregulated in ischemic neural progenitor cells, which was coincident with a significant increase of neuronal population. Inhibition of the Notch pathway with a gamma secretase inhibitor further substantially increased neurons, but did not alter astrocyte population in ischemic neural progenitor cells. These data suggest that the Notch signaling pathway mediates adult SVZ neural progenitor cell proliferation and differentiation after stroke.

Reduced carbon solubility in Fe nanoclusters and implications for the growth of single-walled carbon nanotubes

Fe nanoclusters are becoming the standard catalysts for growing single-walled carbon nanotubes via chemical vapor decomposition. Contrary to the Gibbs-Thompson model, we find that the reduction of the catalyst size requires an increase of the minimum temperature necessary for the growth. We address this phenomenon in terms of solubility of C in Fe nanoclusters and, by using first-principles calculations, we devise a simple model to predict the behavior of the phases competing for stability in Fe-C nanoclusters at low temperature. We show that, as a function of particle size, there are three scenarios compatible with steady state growth, limited growth, and no growth of single-walled carbon nanotubes, corresponding to unaffected, reduced, and no solubility of C in the particles.

Novel magnetic rings for rapid vascular reconstruction in canine liver transplantation model

OBJECTIVE

Magnetic rings were used for rapid vascular reconstruction in a canine liver transplantation model.

MATERIALS AND METHODS

Thirty-two adult mongrel dogs weighing 13 to 16 kg were randomly selected as donors or recipients of transplantations. The recipients were randomly divided into two groups: group A (n = 10) had magnetic rings used for vascular reconstruction without venovenous bypass; group B (n = 6) had vascular reconstruction performed by continuous suturing with splenojugular venovenous bypass.

RESULTS

In group A, the entire operative period was 3.24 +/- 0.49 hours, the durations of clamping the portal vein and the infrahepatic vena cava of the recipient were 5.89 +/- 2.27 minutes and 3.89 +/- 0.73 minutes, respectively. In group B, the entire operative period was 4.12 +/- 0.51 hours with the duration of clamping portal vein and infrahepatic vena cava, 28.33 +/- 6.04 minutes and 12.16 +/- 3.72 minutes (P < .01 vs group A). In group A, mean arterial pressure dropped during the anhepatic phase but recovered quickly after reperfusion. The fluid infusion was about 730.56 +/- 50.56 mL in the group A and a pressor agent was unnecessary. In group B, blood pressure dropped during the anhepatic phase and slowly recovered. The fluid infusion was about 2241.67 +/- 390.78 mL and a pressor agent was used to maintain the blood pressure of the recipient. No twist or thrombus was discovered in the anastomoses group A and the endothelium at the site of anastomosis was entire. In group B, errhysis was common in the anastomotic stomas. Nine of 10 dogs in group A survived more than 3 days, the longest being 8 days, whereas four of the six dogs in group B survived less than 3 days.

CONCLUSION

The results showed that the anhepatic time was significantly shortened (about 5.89 +/- 2.27 minutes) in group A compared with group B and venovenous bypass was unnecessary. Magnetic rings could be used for rapid vascular reconstruction in canine liver transplantation model. The long-term results of this procedure should be clarified before it is applied in clinical practice in the future.

Efficiencies of residual organic pollutants removal from secondary effluent by switching of coagulation- air flotation -filtration processes

It is an essential task to remove the residual organic pollutants (ROP) from secondary effluent of a Wastewater Treatment Plant (WWTP) in wastewater reclamation and reuse processes. Four different compared flow schemes would be achieved for further purification of the secondary effluent by switching of different valves. In order to mainly remove non-biodegradable residual organic pollutants under various operating conditions, the optimum technology and economic process was obtained in the advanced purification flow scheme at a flow of 3200 m(3)/d in Harbin Wenchang WWTP. Conclusions under a lot of experiments show that: choosing the coagulation-settler plus biofilm filter for advanced purification process is reasonable; during the stable operation phase, this process showed good performance in removing the COD, BOD5, TP, NH3-N and SS; the removal rates are 50%, 39%, 67%, 50%, 80% respectively. The effluent is able to excel the requirements for wastewater reuse standards. The unit cost of the water is 0.542 yuan/m(3), which is far below the fee paid for supply water, long-distance transfer water or seawater desalination through economic analysis.