Genome-wide scan reveals divergent selection among taurine and zebu cattle populations from different regions.

In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (FST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (FST  ≥ 0.53), representing the top 1% smoothed FST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.

Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip.

The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation. These results could be a basis for investigating the underlying mutations associated with observed phenotypic variation. Validation using genome-wide association analysis would also facilitate the inclusion of some of these markers in genetic evaluation programs.

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

Object tracking mask-based NLUT on GPUs for real-time generation of holographic videos of three-dimensional scenes.

A new object tracking mask-based novel-look-up-table (OTM-NLUT) method is proposed and implemented on graphics-processing-units (GPUs) for real-time generation of holographic videos of three-dimensional (3-D) scenes. Since the proposed method is designed to be matched with software and memory structures of the GPU, the number of compute-unified-device-architecture (CUDA) kernel function calls and the computer-generated hologram (CGH) buffer size of the proposed method have been significantly reduced. It therefore results in a great increase of the computational speed of the proposed method and enables real-time generation of CGH patterns of 3-D scenes. Experimental results show that the proposed method can generate 31.1 frames of Fresnel CGH patterns with 1,920 × 1,080 pixels per second, on average, for three test 3-D video scenarios with 12,666 object points on three GPU boards of NVIDIA GTX TITAN, and confirm the feasibility of the proposed method in the practical application of electro-holographic 3-D displays.

2009 H1N1 influenza infection in Korean healthcare personnel.

Healthcare personnel (HCP) can acquire influenza and transmit it to patients and other hospital staff. The aim of this study was to evaluate the attack rate of HCP by the 2009 H1N1 influenza virus during the 2009 pandemic influenza season in Korea. HCP infected with H1N1 virus were asked to fill out a questionnaire, which included job type, method of diagnosis, facility type, history of contact with patients infected by H1N1 virus, vaccination status, and use of personal protective equipment. A total of 328 HCP (female 68.6%, 225/328) were infected with H1N1 virus at the nine study centers. The highest attack rate was in physicians, followed by nurses and nurses' aides. Transmission occurred primarily after contact with outpatients (27.8%), followed by contact with inpatients (21.6%). Most (77.3%) of the infected HCP never used an N95 mask during contact with patients. Surgical masks were always used by 29.4% of the subjects and usually or intermittent used by 46.9%. The peak incidence of the H1N1 infection among HCP preceded that among the general population. Among HCPs, physicians, nurses, and nurses' aides were at the greatest risk of H1N1 infection. HCP should be more vigilant and protect themselves with appropriate personal protective equipment during the influenza season.

Genetic effects analysis of myeloid leukemia factor 2 and T cell receptor-beta on resistance to coccidiosis in chickens.

Associations between the parameters of resistance to coccidiosis and SNP in 3 candidate genes located on chromosome 1 [T cell receptor-beta (TCR-beta), myeloid leukemia factor 2 (MLF2), and lymphotactin] were determined. Single nucleotide polymorphisms were genotyped in 24 F1 generation and 290 F2 generation birds. Four SNP were identified in the lymphotactin gene, 12 were located in the TCR-beta gene, and 4 in the MLF2 gene. At various times after experimental infection of the F2 generation with Eimeria maxima, BW, fecal oocyst shedding, and biochemical parameters were measured as parameters of coccidiosis resistance. Single marker association test was applied to determine the associations between the 20 SNP and the parameters of coccidiosis resistance. The maximum additive genetic effect on disease resistance of an SNP in MLF2 was explained by BW (P = 0.0002). The SNP in MLF2 significantly associated with BW was also associated with fecal oocyst shedding (P = 0.001). Four SNP associated with oocyst shedding were found within the coding region of TCR-beta (P < 0.05). Although none of the lymphotactin SNP were associated with oocyst shedding, interferon-gamma level was associated with 2 SNP in lymphotactin. These results suggest that the SNP in the MLF2 gene can be one of the markers to select coccidiosis resistance in chickens.

Linkage disequilibrium in the North American Holstein population.

Linkage disequilibrium was estimated using 7119 single nucleotide polymorphism markers across the genome and 200 animals from the North American Holstein cattle population. The analysis of maternally inherited haplotypes revealed strong linkage disequilibrium (r(2) > 0.8) in genomic regions of approximately 50 kb or less. While linkage disequilibrium decays as a function of genomic distance, genomic regions within genes showed greater linkage disequilibrium and greater variation in linkage disequilibrium compared with intergenic regions. Identification of haplotype blocks could characterize the most common haplotypes. Although maximum haplotype block size was over 1 Mb, mean block size was 26-113 kb by various definitions, which was larger than that observed in humans ( approximately 10 kb). Effective population size of the dairy cattle population was estimated from linkage disequilibrium between single nucleotide polymorphism marker pairs in various haplotype ranges. Rapid reduction of effective population size of dairy cattle was inferred from linkage disequilibrium in recent generations. This result implies a loss of genetic diversity because of the high rate of inbreeding and high selection intensity in dairy cattle. The pattern observed in this study indicated linkage disequilibrium in the current dairy cattle population could be exploited to refine mapping resolution. Changes in effective population size during past generations imply a necessity of plans to maintain polymorphism in the Holstein population.

Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium.

Twinning is a complex trait with negative impacts on health and reproduction, which cause economic loss in dairy production. Several twinning rate quantitative trait loci (QTL) have been detected in previous studies, but confidence intervals for QTL location are broad and many QTL are unreplicated. To identify genomic regions or genes associated with twinning rate, QTL analysis based on linkage combined with linkage disequilibrium (LLD) and individual marker associations was conducted across the genome using high-throughput single nucleotide polymorphism (SNP) genotypes. A total of 9919 SNP markers were genotyped with 200 sires and sons in 19 half-sib North American Holstein dairy cattle families. After SNPs were genotyped, informative markers were selected for genome-wide association tests and QTL searches. Evidence for twinning rate QTL was found throughout the genome. Thirteen markers significantly associated with twinning rate were detected on chromosomes 2, 5 and 14 (P < 2.3 x 10(-5)). Twenty-six regions on fourteen chromosomes were identified by LLD analysis at P < 0.0007. Seven previously reported ovulation or twinning rate QTL were supported by results of single marker association or LLD analyses. Single marker association analysis and LLD mapping were complementary tools for the identification of putative QTL in this genome scan.

Association of resistance to avian coccidiosis with single nucleotide polymorphisms in the zyxin gene.

Our previous genetic studies demonstrated that resistance to avian coccidiosis is linked with microsatellite markers LEI0071 and LEI0101 on chromosome 1. In this study, the associations between parameters of resistance to coccidiosis and single nucleotide polymorphisms (SNP) in 3 candidate genes located between LEI0071 and LEI0101 [zyxin, CD4, and tumor necrosis factor receptor super family 1A (TNFRSF1A)] were determined. The SNP were genotyped in 24 F(1) generation and 290 F(2) generation animals. No SNP were identified in the TNFRSF1A gene, whereas 10 were located in the zyxin gene and 4 in the CD4 gene. At various times following experimental infection of the F(2) generation with Eimeria maxima, BW, fecal oocyst shedding, and plasma levels of carotenoid, nitrite plus nitrate (NO(2)(-) + NO(3)(-)), and interferon-gamma (IFN-gamma) were measured as parameters of resistance. Single marker and haplotype-based tests were applied to determine the associations between the 14 SNP and the parameters of coccidiosis resistance. None of the CD4 SNP were correlated with disease resistance. However, by single marker association, several of the zyxin SNP were significantly associated with carotenoid or NO(2)(-) + NO(3)(-) concentrations. These were the SNP at nucleotide 149 associated with carotenoid at d 3 postinfection (PI), nucleotide 187 with carotenoid at d 6 and 9 PI, and nucleotide 159 with carotenoid between d 3 and 9 PI. In addition, the zyxin SNP at nucleotide 191 was significantly associated with increased levels of NO(2)(-) + NO(3)(-) at d 3 PI. By haplotype association, the zyxin SNP also were found to be highly associated with NO(2)(-) + NO(3)(-) at d 3 PI and increased IFN-gamma at d 6 PI. These results suggest that zyxin is a candidate gene potentially associated with increased resistance to experimental avian coccidiosis.

C-reactive protein binds to integrin α2 and Fcγ receptor I, leading to breast cell adhesion and breast cancer progression.

C-reactive protein (CRP) is an acute phase protein synthesized upon the inflammatory responses, associated with breast cancer. The process of tumor cell invasion and metastasis involves the adherence of cells to the extracellular matrix via integrin as a receptor for matrix molecules. The present study investigated the role of CRP in the adhesive phenotype of breast cells and the underlying mechanisms. Here, we first showed that CRP induces adhesion of MCF10A human breast epithelial cells through the activation of integrin α2 signaling. Expression of integrin α2 was induced by CRP in which transcription factors c-fos and SP1 may be involved. Binding of CRP with integrin α2 leads to the activation of focal adhesion kinase (FAK), paxillin and ERKs. CRP also binds to an Fcγ receptor Fcγ receptor I (FcγRI), and induces activation of paxillin, FAK and ERKs. Integrin α2 and FAK have crucial roles in the adhesive and invasive phenotypes as well as MMP-9 upregulation induced by CRP in MCF10A cells. Treatment with an inflammatory lipid sphingosine-1-phosphate induced CRP, which may be secreted and exert an autocrine effect by binding to FcγRI and integrin α2. Involvement of CRP in adhesion, invasion, anchorage-independent growth and upregulation of integrin α2, paxillin and FAK was observed in MDA-MB-231 triple-negative human breast cancer (TNBC) cells. Using an in vivo invasion model and an orthotopic mouse tumor model with MDA-MB-231 cells, we showed that CRP has an important role in intravasation and tumor growth in vivo, demonstrating the in vivo relevance of our in vitro results. The present study elucidates a critical molecular basis between CRP, integrin α2 and FcγRI pathways in MCF10A breast cells and MDA-MB-231 TNBC cells, thereby providing useful information on CRP-induced aggressiveness of breast cells in the inflammatory microenvironment.

Identification of aldo-keto reductase (AKR7A1) and glutathione S-transferase pi (GSTP1) as novel renal damage biomarkers following exposure to mercury.

The kidney is one of the main targets for toxicity induced by xenobiotics. Sensitive detection of early impairment is critical to assess chemical-associated renal toxicity. The aim of this study was to identify potential nephrotoxic biomarkers in rat kidney tissues after exposure to mercury (Hg), a representative nephrotoxicant, and to evaluate these new biomarkers employing in vivo and in vitro systems. Mercuric chloride was administered orally to Sprague-Dawley rats for 2 weeks. Proteomic analysis revealed that aldo-keto reductase (AKR7A1) and glutathione S-transferase pi (GSTP1) were significantly elevated in kidney after Hg exposure. While the levels of conventional nephrotoxic clinical markers including blood urea nitrogen and serum creatinine were not elevated, the mRNA and protein levels of AKR7A1 and GSTP1 were increased upon Hg exposure in a dose-dependent manner. The increases in AKR7A1 and GSTP1 were also observed in rat kidneys after an extended exposure for 6 weeks to low-dose Hg. In in vitro rat kidney proximal tubular cells, changes in AKR7A1 and GSTP1 levels correlated well with the extent of cytotoxicity induced by Hg, cadmium, or cisplatin. AKR7A1 and GSTP1 were identified as new candidates for Hg-induced nephrotoxicity, suggesting that these biomarkers have potential for evaluating or predicting nephrotoxicity.

Fine-mapping of coccidia-resistant quantitative trait loci in chickens.

Two commercial, pure broiler lines with different susceptibility to coccidiosis were used to fine-map QTL associated with the previously identified marker LEI0101, located at 259 cM on chromosome 1 and shown to be significantly associated with disease resistance. Eight additional microsatellite markers linked to LEI0101 were used for genotyping of F(1) parents and F(2) offspring (n = 314), and their associations with oocyst shedding, as a marker of disease resistance, were determined in birds experimentally infected with Eimeria maxima. Single-point analysis of 4 families showed that logarithm of odds (LOD) scores at all marker loci were > 0.5, with the exception of marker LEI0071, located at 242 cM (LOD score = 2.45). Multipoint analysis showed a maximum LOD score between LEI0071 and LEI0101 at 254 cM (LOD score = 3.74). Although the LEI0071 marker was mapped near LEI0101 by linkage analysis, the physical location of LEI0071 was not identified. Further studies to determine the physical locations of these and other markers will allow additional application association mapping techniques using single nucleotide polymorphism markers.

Gα12 gep oncogene deregulation of p53-responsive microRNAs promotes epithelial-mesenchymal transition of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) has a poor prognosis owing to aggressive phenotype. Gα12 gep oncogene product couples to G-protein-coupled receptors, whose ligand levels are frequently increased in tumor microenvironments. Here, we report Gα12 overexpression in human HCC and the resultant induction of zinc-finger E-box-binding homeobox 1 (ZEB1) as mediated by microRNA deregulation. Gα12 expression was higher in HCC than surrounding non-tumorous tissue. Transfection of Huh7 cell with an activated mutant of Gα12 (Gα12QL) deregulated microRNA (miRNA or miR)-200b/a/429, -194-2/192 and -194-1/215 clusters in the miRNome. cDNA microarray analyses disclosed the targets affected by Gα12 gene knockout. An integrative network of miRNAs and mRNA changes enabled us to predict ZEB1 as a key molecule governed by Gα12. Decreases of miR-200a/b, -192 and -215 by Gα12 caused ZEB1 induction. The ability of Gα12 to decrease p53 levels, as a result of activating protein-1 (AP-1)/c-Jun-mediated mouse double minute 2 homolog induction, contributed to transcriptional deregulation of the miRNAs. Gα12QL induced ZEB1 and other epithelial-mesenchymal transition markers with fibroblastoid phenotype change. Consistently, transfection with miR-200b, -192 or -215 mimic prevented the ability of Gα12QL to increase tumor cell migration/invasion. In xenograft studies, sustained knockdown of Gα12 decreased the overall growth rate and average volume of tumors derived from SK-Hep1 cell (mesenchymal-typed). In HCC patients, miR-192, -215 and/or -200a were deregulated with microvascular invasion or growth advantage. In the HCC samples with higher Gα12 level, a correlation existed in the comparison of relative changes of Gα12 and ZEB1. In conclusion, Gα12 overexpressed in HCC causes ZEB1 induction by deregulating p53-responsive miRNAs, which may facilitate epithelial-mesenchymal transition and growth of liver tumor. These findings highlight the significance of Gα12 upregulation in liver tumor progression, implicating Gα12 as an attractive therapeutic target.

Inflammatory lipid sphingosine-1-phosphate upregulates C-reactive protein via C/EBPß and potentiates breast cancer progression.

A crucial role of the inflammatory lipid sphingosine-1-phosphate (S1P) in breast cancer aggressiveness has been reported. Recent clinical studies have suggested that C-reactive protein (CRP) has a role in breast cancer development. However, limited information is available on the molecular basis for the expression of CRP and its functional significance in breast cell invasion. The present study aimed to elucidate the molecular link between S1P and CRP during the invasive process of breast epithelial cells. This is the first report showing that transcription of CRP was markedly activated by S1P in breast cells. Our data suggest that not only S1P treatment but also the endogenously produced S1P may upregulate CRP in breast carcinoma cells. Transcription factors CCAAT/enhancer-binding protein beta and c-fos were required for S1P-induced CRP expression. Coupling of S1P3 to heterotrimeric Gαq triggered the expression of CRP, utilizing signaling pathways involving reactive oxygen species (ROS), Ca(2+) and extracellular signal-related kinases (ERKs). S1P-induced CRP expression was crucial for the transcriptional activation of matrix metalloproteinase-9 through ERKs, ROS and c-fos, leading to breast cell invasion. Using a xenograft mice tumor model, we demonstrated that S1P induced CRP expression both in vitro and in vivo. Taken together, our findings have revealed a molecular basis for S1P-induced transcriptional activation of CRP and its functional significance in the acquisition of the invasive phenotype of human breast epithelial cells under inflammatory conditions. Our findings may provide useful information on the identification of useful therapeutic targets for inflammatory breast cancer.

Various Quantum- and Nano-Structures by III-V Droplet Epitaxy on GaAs Substrates.

We report on various self-assembled In(Ga)As nanostructures by droplet epitaxy on GaAs substrates using molecular beam epitaxy. Depending on the growth condition and index of surfaces, various nanostructures can be fabricated: quantum dots (QDs), ring-like and holed-triangular nanostructures. At near room temperatures, by limiting surface diffusion of adatoms, the size of In droplets suitable for quantum confinement can be fabricated and thus InAs QDs are demonstrated on GaAs (100) surface. On the other hand, at relatively higher substrate temperatures, by enhancing the surface migrations of In adatoms, super lower density of InGaAs ring-shaped nanostructures can be fabricated on GaAs (100). Under an identical growth condition, holed-triangular InGaAs nanostructures can be fabricated on GaAs type-A surfaces, while ring-shaped nanostructures are formed on GaAs (100). The formation mechanism of various nanostructures can be understood in terms of intermixing, surface diffusion, and surface reconstruction.

Refined mapping of twinning-rate quantitative trait loci on bovine chromosome 5 and analysis of insulin-like growth factor-1 as a positional candidate gene.

Twinning in cattle is a complex trait that is associated with economic loss and health issues such as abortion, dystocia, and reduced calf survival. Twinning-rate QTL have been detected previously on BTA5 in the North American Holstein and Norwegian dairy cattle populations and in a USDA herd selected for high twinning rate. In previous work with the North American Holstein population, the strongest evidence for a QTL was obtained from analysis of an extended, multiple-generation family. Using additional animals, an increased density of SNP marker association tests, and a combined linkage and linkage disequilibrium mapping method, we refined the position of this QTL in the North American Holstein population. Two sets of twinning-rate predicted transmitting abilities estimated during 2 different time periods in the North American dairy cattle population were used to provide validation of results. A total of 106 SNP and 3 microsatellites were used to scan the genomic region between 5 and 80 Mb on BTA5. Combined linkage-linkage disequilibrium analysis identified significant evidence for QTL within the 25- to 35-Mb and 64- to 70-Mb regions of BTA5. The IGF-1 gene (IGF1) was examined as a positional candidate gene and an SNP in intron 2 of IGF1 was significantly associated with twinning rate by using both data sets (P = 0.003 and P = 1.05 x 10(-6)). Replication of this association in other cattle populations will be required to examine the extent of linkage disequilibrium with the underlying quantitative trait nucleotide across breeds.

Haemodynamic and clinical assessment of lateral marginal vein excision in patients with a predominantly venous malformation of the lower extremity.

OBJECTIVE: The purpose of the present study was to determine the effects of the surgical excision of lateral marginal veins (LMVs) in patients with a venous malformation (VM) affecting the lower extremity. METHODS: Preoperative and postoperative air plethysmography (APG), CEAP classification C scores, and venous clinical severity scores (VCSS) of the 25 VM patients who underwent LMV excision were compared. RESULTS: After LMV excision, venous haemodynamic parameters revealed significantly increased ejection fraction (EF, 33.2 S.D.18.5% vs. 39.7 S.D.21.2%, P=.020), and reduced venous volume (VV, 235.0 S.D.141.8 ml vs. 198.0 S.D.114.1 ml, P=.016) and residual venous fraction (RVF, 62.4 S.D. 26.6% vs. 56.9 S.D. 25.3%, P=.046). Clinical assessments of affected limbs revealed significantly improved mean CEAP C scores and VCSS (preoperative score, 4.4 S.D.1.7 vs. postoperative score 2.4 S.D.1.7, P=.026) after LMV excision versus preoperative data. CONCLUSION: Haemodynamic and clinical improvements were observed in patients with lower extremity VM after LMV excision.

Avermectin: biochemical and molecular basis of its biosynthesis and regulation.

Avermectin and its analogues, produced by Streptomyces avermitilis, are major commercial antiparasitic agents in the field of animal health, agriculture, and human infections. They are 16-membered pentacyclic lactone compounds derived from polyketide and linked to a disaccharide of the methylated deoxysugar l-oleandrose. Labeling studies, analyses of the biosynthetically blocked mutants, and the identification of the avermectin gene cluster allows characterization of most of the biosynthetic pathway. Recent completion of S. avermitilis genome sequencing is also expected to help in revealing the precise biosynthetic sequence and the complicated regulatory mechanism for avermectin biosynthesis, which has been long-awaited to be elucidated. The well characterized avermectin biosynthetic pathway and availability of S. avermitilis genome information in combination with the recent development of combinatorial biosynthesis should allow us to redesign more potent avermectin analogues and to engineer S. avermitilis as a more efficient host for the production of important commercial analogues.