Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

Treatment Protocol, Long-Term Follow-Up, and Predictors of Mortality in 302 Cases of Atypical Meningioma.

OBJECTIVE: Because of the paucity of relevant data, treatment and outcomes in intracranial atypical meningioma (AM) remain unclear. The aim of this study was to find useful factors predicting survival and to evaluate the role of postoperative radiation after surgery. METHODS: Data were obtained from 302 patients with AM who underwent surgery between January 2008 and December 2015. RESULTS: A series of 302 patients, including 166 female and 136 male, underwent surgery at our institution. Gross total resection (GTR) was achieved in 201 (66.6%) patients. Seventy-five patients (24.8%) underwent postoperative radiation after surgery. For the entire cohort, there were 131 (43.4%) recurrences, 1 (0.33%) metastasis, and 56 (18.5%) mortalities during a median follow-up duration of 41.6 months. The median recurrence-free survival (RFS) was 55.2 months after the date of the first AM surgery, with 1-year, 3-year, and 5-year RFS rates of 87.6%, 63.3% and 47.7%, respectively. The median overall survival (OS) for patients was 99.8 months, and the actuarial OS rates from the time of the first AM surgery at 1, 3, and 5 years were 97.0%, 90.6%, and 78.8%, respectively. In multivariate analysis, preoperative Karnofsky Performance Scale score (≥80), primary tumor, tumor invasiveness, and GTR were associated with increased RFS, whereas preoperative Karnofsky Performance Scale score (≥80), primary tumor, supratentorial location, lack of peritumoral edema, radiotherapy, and GTR were associated with increased OS. CONCLUSIONS: GTR is the first choice for patients with AM. We recommend that patients with secondary tumors receive radiotherapy after surgery.

Relationship between Residual Feed Intake and Production Traits in a Population of F2 Ducks.

Improving feed efficiency is important for decreasing feed cost in poultry production, because feed account for approximately 70% of the total production costs. The selection of feed efficiency may affect other important economic traits. Therefore, the objectives of this present study was to evaluate the relationships of the residual feed intake (RFI) with live body weight, carcass weight, carcass composition, and size of small intestines in a population of F2 Pekin ducks. Nine-hundred and eighty F2 ducks were derived from a cross between 40 Pekin ducks and 10 Mallard ducks. The results showed no significant correlation of RFI with live body weight and eviscerated carcass weight. RFI had negative effects on breast meat weight and gizzard weight. A positive correlation of RFI with abdominal fat weight, skin weight, and jejunum length was detected. Our results indicated that the selection of RFI could improve the feed efficiency of ducks without affecting their carcass compositions.

Prognostic Factors, Survival, and Treatment for Intracranial World Health Organization Grade II Chordoid Meningiomas and Clear-Cell Meningiomas.

OBJECTIVE: Chordoid meningioma (CM) and clear-cell meningioma (CCM) are rare World Health Organization grade II meningioma subtypes. This study aimed to evaluate favorable factors and appropriate therapeutic strategies for these lesions. METHODS: We retrospectively reviewed clinical data from 111 cases of grade II meningiomas, including 55 cases of CM and 56 cases of CCM, between January 2011 and December 2015. RESULTS: The mean follow-up time of the rare World Health Organization grade II meningiomas (n = 111) was 45.3 months. In the CM group, 8 patients (14.5%) experienced recurrence, and 2 patients (3.6%) died. In the CCM group, 22 patients (39.3%) experienced recurrence, and 9 patients (16.1%) died. Significant differences were observed between the CM and CCM groups in tumor size (P = 0.019), history of surgery (P = 0.038), and peritumoral edema (P = 0.004). In the CM group, gross total resection was associated with favorable progression-free survival (hazard ratio, 0.144; 95% confidence interval, 0.029-0.714; P = 0.018). In the CCM group, univariate analyses showed that preoperative Karnofsky Performance Status <80 (P < 0.001), tumor size ≥5 cm (P = 0.015), tumor size (per-centimeter increase) (P = 0.022), bone invasion (P = 0.004), a history of surgery (P < 0.001), and subtotal resection (P = 0.009) were associated with worse progression-free survival. Male gender (P = 0.039), tumor size (per-centimeter increase) (P = 0.043), bone invasion (P = 0.030), and a history of surgery (P = 0.007) were associated with poor overall survival. CONCLUSIONS: This study showed that gross total resection should be achieved in grade II meningiomas. Patients with larger tumors and/or surgical histories had worse outcomes.

Prognostic factors and the management of anaplastic meningioma.

OBJECTIVES: Anaplastic meningiomas (AMs)tend to have a higher local recurrence rate and metastasize. but few studies have reported on the prognosis and management of patients with AM, this study aimed to increase the understanding of the prognosis, management and history of AM. PATIENTS AND METHODS: All patients (n = 56) underwent surgeries in our hospital between December 2008 and January 2016. Postoperative pathology reports confirmed the diagnosis of AM. Prognostic factors and the management were analysed in this study. AM was then divided into two groups. One group was primary AM, the other group was secondary AM. RESULTS: Of all the 56 AM patients, 31 were male and 25 were female (male to female ratio of 1.24:1). The 1-, 3-, and 5-year progression-free survival (PFS) rates were 78.6%, 41.1% and 29.7%, respectively, and the corresponding overall survival (OS) rates were 82.1%, 50.1% and 45.0%, respectively. Homogeneous contrast might be a potential better prognostic factor for PFS (HR = 1.824, P = 0.083). Treatment with postoperative radiotherapy (PRT) was significantly associated with longer PFS (HR = 0.390, P = 0.007) and OS (HR = 0.376, P = 0.008) according to univariate analysis. Gross-total resection (GTR) was a favourable factor for PFS (HR = 2.059, P = 0.035) and OS (HR = 2.802, P = 0.004). CONCLUSION: Achieving GTR is a favourable treatment strategy for patients with AM in our study and patients receiving PRT after resection is essential.

World Health Organization Grade III (Nonanaplastic) Meningioma: Experience in a Series of 23 Cases.

OBJECTIVE: Rhabdoid meningioma (RM) and papillary meningioma (PM) are rare variants of World Health Organization grade III meningiomas. In this study, we presented a series of 23 cases from our institution to investigate adverse factors of and appropriate treatment for RM and PM. METHODS: Clinical data from 23 cases of PM and RM between January 2011 and December 2015 were retrospectively reviewed. RESULTS: The median follow-up was 38.0 months for World Health Organization grade III meningiomas. The mean progression-free survival (PFS) was 37.6 months, with 1-year, 3-year, and 5-year PFS of 78.3%, 50.8%, and 43.6%, respectively. The mean overall survival (OS) was 48.8 months, with 1-year, 3-year, and 5-year OS of 95.7%, 82.6%, and 44.0%, respectively. Univariate analysis showed that a ki-67 proliferation index >20% (hazard ratio [HR], 4.190; 95% confidence interval [CI], 1.033-17.001; P = 0.045) and PM (HR, 3.375; 95% CI, 0.998-11.408; P = 0.005) were related to worse PFS. Patients administered postoperative radiotherapy (PRT) after surgery had longer OS than did patients who did not receive PRT (median, 60.7 vs. 35.1 months; P = 0.029). Multivariate analysis showed that PRT was an independent factor for PFS (HR, 0.147; 95% CI, 0.033-0.657; P = 0.012) and OS (HR, 0.130; 95% CI, 0.025-0.691; P = 0.017) and that RM was an independent factor for PFS (HR, 7.312; 95% CI, 1.587-33.688; P = 0.011) and OS (HR, 6.447; 95% CI, 1.310-31.740; P = 0.022). CONCLUSIONS: We recommended adjuvant radiation regardless of the extent of resection. Individuals with PM or RM were at increased risk of recurrence and death; appropriate treatment for these patients should be further studied, and close follow-up is needed.

Gene expression profiling in Pekin duck embryonic breast muscle.

Lean-type Pekin duck is a breed gained through long-term selection and great effort has been exerted to understand the mechanisms underlying increased muscle yields. However, the genes involved in Pekin duck embryonic breast muscle development have not been explored to date. In this study, we investigated gene expression profiles in Pekin Duck embryonic breast muscle at hatched day 13 (E13), E19, and E27 using RNA-seq. In total, we produced 519,312,178 raw reads resulting in 497,348,158 high-quality reads after filtering. The mapping, distribution of reads along annotated genes, and consistency across replicates demonstrates the high quality of the RNA-seq data used in this study, allowing us to continue with the downstream analysis. Significantly fewer differentially expressed genes (DEGs) were identified between E13 and E19 (203 DEGs) compared to E27 and E19 (2,797 DEGs). Many DEGs highly expressed in E19 are involved in metabolic processes and cell division. KEGG analysis showed many pathways associated with fat development were significantly enriched for DEGs highly expressed in E27. These results provide a basis for the further investigation of the mechanisms involved in Pekin duck embryonic breast muscle development.

[Expression of Myogenin and MCK genes regulated by PI3K/AKT pathway].

Many intracellular signaling pathways regulate skeletal muscle differentiation. Among them, PI3K/AKT pathway plays an important role. But the mechanisms of chromatin regulation remain unclear. In this study, the murine C2C12 myoblast cell line was used to investigate the expression of Myogenin and MCK genes during the skeletal muscle differentiation. Western blotting analysis showed that the expression of Myogenin and MCK protein was increased significantly after PI3K/AKT activator treatment for 24 h during the C2C12 cell differentiation and the expression of H3K27me3 demethylase UTX was also increased. Chromatin immunoprecipitation (ChIP) and quantitative PCR (Q-PCR) analysis showed that the enrichment of H3K27me3 on the promoter regions of Myogenin and MCK genes and the enhancer region of MCK gene were decreased. It was opposite to the PI3K/AKT inhibitor treatment. We concluded that the PI3K/AKT pathway maybe regulate skeletal muscle differentiation by regulating the expression of UTX gene to change the enrichment of H3K27me3 on the target genes.

The fear gene stathmin alleles generated heterosis on feed efficiency parameters in Peking ducks.

Stathmin is an inhibitor of microtubule formation, as highly expressed in the lateral nucleus (LA) of the amygdala as well as in the thalamic and cortical structures that send information to the LA about the learned and innate fear. So we assume that STMN1 genetic variation may also affect the physical activity so as to influence the Residual Feed Intake (RFI) of duck. The Single Nucleotide Polymorphisms (SNPs) in duck Stathmin gene were screened by sequencing and genotyped by restriction endonuclease Msp I, EcoR I, Xho I, Taq I, EcoR II. A total of five SNPs (c.187 -15G > A, c.187 -110T > C, c.379 -95G > A, c.379 -318C > T, c.426 C > T) were detected in duck STMN1 gene. The c.187 -15G > A is near the 3' splice site of intron 2, which has a putative effect on the STMN1 pre-mRNA secondary structures. The c.187 -15G > A genotypes had significant effect on RFI of Peking drakes (P < 0.01). Individuals with heterozygous genotypes were more productive than that with homozygous genotypes, which suggested a molecular heterosis in c.187 -15 alleles on RFI. The current study is the first step to confirm the relationship between STMN1 gene polymorphisms and RFI. Supplemental material is available for this article. Go to the publisher's online edition of Animal Biotechnology for a figure of linkage disequilibrium between SNPs and table about frequencies of haploype.

Cytochrome b genetic diversity and maternal origin of Chinese domestic donkey.

To clarify the origin of Chinese domestic donkeys, we investigated the mitochondrial Cytb gene from 244 animals from 13 native breeds. We found 55 variable sites in the Cytb gene sequence and subsequently defined 58 haplotypes. Analysis of haplotypes in combination with Cytb sequences revealed two mitochondrial origins in Chinese domestic donkeys, phenotypically expressed by the Somalian and Nubian lineages. The Somalian lineage predominated in Chinese domestic donkey breeds. Five specific Cytb gene SNPs diagnostic of each of the lineages were found in this study: 225(T-C), 237(C-T), 915(C-T), 1014(C-T), and 1134(A-G) mutations. They effectively distinguish the Nubian from the Somalian lineage in the mtDNA Cytb gene. Both lineages are from Africa and thus support the African maternal origins of Chinese domestic donkeys. No obvious geographic structure was found in Chinese domestic donkey breeds, but the population showed abundant genetic diversity.

[Investigation of Demodex infection among medical students].

Squeezing and smear method was used to detect Demodex infection for college students, the overall infection rate was 30.81% with Demodex folliculorum as the major one, D. brevis and mixed infection as the second ones. Certain relations were found between facial signs, lipid content and the infection. Prevalence was higher in those students who used to share washing materials (towels, etc.) with family members.

[Cloning, expression and purification of human stem cell growth factor cDNA and its species-specificity in hematopoiesis].

Stem cell growth factor (SCGF) is an early-acting hematopoitic cytokine that has two isoforms including hSCGF with full length molecules and hSCGFbeta, 78 amino acids of which lost in the conserved calcium-dependent carbohydrate-recognition domain (CRD). It has been demonstrated that hSCGFbeta is strictly species-specific in regulating he-matopoiesis. This study was aimed to explore whether human SCGF can exert synergistic stimulatory effect on heterogenous murine CFU-GM progenitor. Firstly, hSCGF cDNA was amplified from human fetal liver cDNA library by using two-step PCR. The hSCGF mature peptide coding sequence was subsequently placed at downstream of glutathione S-transferase (GST) sequence in GST gene fusion expression vector. The results indicated that there existed an additional 60 kD protein compared with mock BL21 when the cells hosting recombinant plasmid were induced with IPTG at 37 degrees C. SDS-PAGE analysis demonstrated that the GST-hSCGF fusion protein mainly existed in insoluble form. When induced at low temperature (28 degrees C), the recombinant protein was mostly soluble. The GST-fusion recombinant protein was subsequently purified by using affinity chromatography. The clonogenic assay revealed that, unlike hSCGFbeta, hSCGF had the granulocyte/macrophage promoting activity (GPA) for murine bone marrow GM progenitor. It is concluded that, in contrast to human SCGFbeta, the intact molecular hSCGF may have no species specificity, implying that CRD domain in human SCGFbeta does not directly bind to corresponding SCGF receptor, but may have certain biological function.

[Construction of a DNA vaccine against human B cell lymphoma].

AIM: To construct a DNA vaccine based on surface Ig V(H) gene of tumor cells in the human B-cell lymphoma biopsy tissue. METHODS: The V(H) gene fragment was amplified by RT-PCR using Ig superfamily primers. Also, the murine monocyte chemotactic protein 3(MCP-3) cDNA was cloned. The fusion gene fragment of MCP-3 gene with V(H) gene was constructed by recombinant PCR and then cloned into the eukaryotic expression vector pcDNA3.1 to construct the DNA vaccine plasmid pcDNA3.1/MCP-V(H). The vaccine plasmid was transiently expressed in the eukaryotic cell line COS-7. RESULTS: The DNA vaccine plasmid was successfully constructed and expressed in COS-7 cells in the form of fusion protein MCP-V(H). CONCLUSION: The DNA vaccine plasmid pcDNA3.1/MCP-V(H) is constructed and expressed successfully, which plays the foundation for further experimental research in animal model.

Optical properties of nanocrystalline Y2O3:Eu depending on its odd structure.

The structure of nanocrystalline Y2O3:Eu prepared by a combustion reaction was analyzed by XRD and high-resolution electron microscopy. Compared with a large-scale particles, 5-nm Y2O3:Eu particles presented as distorted crystallite and rough surfaces. Luminescent and absorption properties of nano-Y2O3:Eu showed remarkably particle size effects. At Y2O3:Eu particle sizes smaller than 10 nm some new results were observed: (a) a red shift of the charge-transfer-state absorption; (b) new emission bands of Eu3+ in the 5D0 --> 7F2 region; (c) luminescent decay of energy level 5D0 of Eu3+ turning to a two-step exponential; and (d) a pronounced increase in quenching concentration and much lower phonon density compared with those of the bulk material. All these phenomena can be attributed to the effect of the softened lattice and surface state of the nanomaterial. The latter was confirmed by stronger excitation by the host absorption after the surface modification.