An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay

<p>Abstract</p> <p>Background</p> <p>Aside from single nucleotide polymorphisms, copy number variations (CNVs) are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time PCR, invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed.</p> <p>Results</p> <p>PCR followed by a quantitative oligonucleotide ligation assay (qOLA) was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine <it>KIT</it>, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine <it>KIT</it>. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of <it>KIT </it>copies with spliced forms, we confirmed the segregation of <it>KIT </it>alleles in 145 F₁animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement), confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high <it>KIT </it>copy numbers (>4 per diploid genome). Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used.</p> <p>Conclusion</p> <p>We have established a high resolution quantification method using an oligonucleotide ligation assay to measure CNVs, and verified the reliability of genotype assignment for random animal samples using the nearest centroid sorting method. This new method will make it more practical to determine <it>KIT </it>CNV and to genotype the complicated <it>Dominant White/KIT </it>locus in pigs. This procedure could have wide applications for studying gene or segment CNVs in other species.</p

An SREBP-Responsive microRNA Operon Contributes to a Regulatory Loop for Intracellular Lipid Homeostasis

SummarySterol regulatory element-binding proteins (SREBPs) have evolved as a focal point for linking lipid synthesis with other pathways that regulate cell growth and survival. Here, we have uncovered a polycistrionic microRNA (miRNA) locus that is activated directly by SREBP-2. Two of the encoded miRNAs, miR-182 and miR-96, negatively regulate the expression of Fbxw7 and Insig-2, respectively, and both are known to negatively affect nuclear SREBP accumulation. Direct manipulation of this miRNA pathway alters nuclear SREBP levels and endogenous lipid synthesis. Thus, we have uncovered a mechanism for the regulation of intracellular lipid metabolism mediated by the concerted action of a pair of miRNAs that are expressed from the same SREBP-2-regulated miRNA locus, and each targets a different protein of the multistep pathway that regulates SREBP function. These studies reveal an miRNA “operon” analogous to the classic model for genetic control in bacterial regulatory systems

Immediate and Sustained Improvement in Behavior and Life Quality by Adenotonsillectomy in Children With Sleep-Disordered Breathing

Objectives To investigate longitudinal changes in behavior and quality-of-life (QoL) in children with sleep disordered breathing (SDB) after adenotonsillectomy (AT). Methods This study prospectively enrolled 148 children who underwent AT for SDB. Caregivers filled out Korean attention deficit hyperactivity disorder (ADHD) rating scale (K-ARS) and Korean version of the obstructive sleep apnea-18 (KOSA-18) at preoperative 1 day, postoperative 1 month, and postoperative 6 months. Longitudinal changes in K-ARS and KOSA-18 were evaluated and compared among subgroups. Results Both K-ARS and KOSA-18 scores improved immediately at postoperative 1 month and were maintained at postoperative 6 months. The mean preoperative K-ARS scores of the non-ADHD, ADHD-trait, and overt-ADHD groups showed uniformly immediate and sustained improvements. Also, the mean preoperative KOSA-18 scores of the small, moderate, and large impact groups were significantly improved both at postoperative 1 month and 6 months. The changes in behavior and QoL showed no significant differences with regard to the aforementioned factors. Conclusion After AT, we may expect immediate and sustained improvements in behavior and QoL in children with SDB regardless of preoperative symptom severity. Moreover, by performing AT, improvements in behavior and QoL are expected regardless of sex, age, allergic trait, or concurrent coblation-assisted turbinoplasty. These findings may help our colleague physicians counselling pediatric SDB patients and their caregivers

Is there any vindication for low dose nonselective β-blocker medication in patients with liver cirrhosis?

Background/AimsNonselective β-blockers (NSBBs), such as propranolol, reportedly exert a pleiotropic effect in liver cirrhosis. A previous report suggested that survival was higher in patients receiving adjusted doses of NSBBs than in ligation patients. This study investigated whether low-dose NSBB medication has beneficial effects in patients with liver cirrhosis, especially in terms of overall survival.MethodsWe retrospectively studied 273 cirrhotic patients (199 males; age 53.6±10.2 years, mean±SD) who visited our institution between March 2003 and December 2007; follow-up data were collected until June 2011. Among them, 138 patients were given a low-dose NSBB (BB group: propranolol, 20-60 mg/day), and the remaining 135 patients were not given an NSBB (NBB group). Both groups were stratified randomly according to Child-Turcotte-Pugh (CTP) classification and age.ResultsThe causes of liver cirrhosis were alcohol (n=109, 39.9%), hepatitis B virus (n=125, 45.8%), hepatitis C virus (n=20, 7.3%), and cryptogenic (n=19, 7.0%). The CTP classes were distributed as follows: A, n=116, 42.5%; B, n=126, 46.2%; and C, n=31, 11.4%. Neither the overall survival (P=0.133) nor the hepatocellular carcinoma (HCC)-free survival (P=0.910) differed significantly between the BB and NBB groups [probability of overall survival at 4 years: 75.1% (95% CI=67.7-82.5%) and 81.2% (95% CI=74.4-88.0%), respectively; P=0.236]. In addition, the delta CTP score did not differ significantly between the two groups.ConclusionsUse of low-dose NSBB medication in patients with liver cirrhosis is not indicated in terms of overall and HCC-free survival

Zinc-chelated Vitamin C Stimulates Adipogenesis of 3T3-L1 Cells

Adipose tissue development and function play a critical role in the regulation of energy balance, lipid metabolism, and the pathophysiology of metabolic syndromes. Although the effect of zinc ascorbate supplementation in diabetes or glycemic control is known in humans, the underlying mechanism is not well described. Here, we investigated the effect of a zinc-chelated vitamin C (ZnC) compound on the adipogenic differentiation of 3T3-L1 preadipocytes. Treatment with ZnC for 8 d significantly promoted adipogenesis, which was characterized by increased glycerol-3-phosphate dehydrogenase activity and intracellular lipid accumulation in 3T3-L1 cells. Meanwhile, ZnC induced a pronounced up-regulation of the expression of glucose transporter type 4 (GLUT4) and the adipocyte-specific gene adipocyte protein 2 (aP2). Analysis of mRNA and protein levels further showed that ZnC increased the sequential expression of peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT/enhancer-binding protein alpha (C/EBPα), the key transcription factors of adipogenesis. These results indicate that ZnC could promote adipogenesis through PPARγ and C/EBPα, which act synergistically for the expression of aP2 and GLUT4, leading to the generation of insulin-responsive adipocytes and can thereby be useful as a novel therapeutic agent for the management of diabetes and related metabolic disorders

Expression analysis and functional characterization of the monosaccharide transporters, OsTMTs, involving vacuolar sugar transport in rice (Oryza sativa)

In Arabidopsis, the compartmentation of sugars into vacuoles is known to be facilitated by sugar transporters. However, vacuolar sugar transporters have not been studied in detail in other plant species. To characterize the rice (Oryza sativa) tonoplast monosaccharide transporters, OsTMT1 and OsTMT2, we analysed their subcellular localization using green fluorescent protein (GFP) and expression patterns using reverse-transcription polymerase chain reaction (RT-PCR), performed histochemical beta-glucuronidase (GUS) assay and in situ hybridization analysis, and assessed sugar transport ability using isolated vacuoles. Expression of OsTMT-GFP fusion protein in rice and Arabidopsis revealed that the OsTMTs localize at the tonoplast. Analyses of OsTMT promoter-GUS transgenic rice indicated that OsTMT1 and OsTMT2 are highly expressed in bundle sheath cells, and in vascular parenchyma and companion cells in leaves, respectively. Both genes were found to be preferentially expressed in the vascular tissues of roots, the palea/lemma of spikelets, and in the main vascular tissues and nucellar projections on the dorsal side of the seed coats. Glucose uptake studies using vacuoles isolated from transgenic mutant Arabidopsis (tmt1-2-3) expressing OsTMT1 demonstrated that OsTMTs are capable of transporting glucose into vacuoles. Based on expression analysis and functional characterization, our present findings suggest that the OsTMTs play a role in vacuolar glucose storage in rice