Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers

Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.     

Genomic characterization of a bovine viral diarrhea virus 1 isolate from swine

The SD0803 strain of the bovine viral diarrhea virus (BVDV) was isolated from a piglet in China in 2008 and has been classified as a novel subgenotype of BVDV-1. To describe the molecular features of this novel subgenotype, we sequenced and characterized the complete genome of the SD0803 virus. The genome is 12,271 bp in length and contains 5′ and 3′ untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a 3,898-amino-acid polypeptide. The full-length genome of the SD0803 strain shares 78.8 % to 83.3 % identity with those of other BVDV-1 strains, 70.0 % to 70.7 % identity with those of BVDV-2 strains, and less than 67.6 % identity with those of other pestiviruses. The highest level of shared identity was 83.3 % between the complete SD0803 genome and that of the ZM-95 strain of BVDV-1. Phylogenetic analysis of the 5′ UTR and the coding sequence for the N-terminal protease fragment of the SD0803 polyprotein indicated that the SD0803 virus is a member of the novel subgenotype BVDV-1q, isolates of which have been identified recently in dairy cattle and camels in China.     

The effect of temperature on the extrinsic incubation period and infection rate of dengue virus serotype 2 infection in Aedes albopictus

Dengue fever is an acute mosquito-borne viral disease caused by dengue virus (DENV). Temperature may affect the efficiency of the mosquito vectors in spreading DENV. Aedes albopictus mosquitoes were infected orally with a DENV2 suspension and incubated at different temperatures. Subsequently, DENV2 antigen was collected from salivary gland and thorax-abdomen samples on different days postinfection and tested using an immunofluorescence assay to determine the extrinsic incubation period and infection rate. As the temperature increased, the extrinsic DENV2 incubation period in Ae. albopictus gradually shortened, and infection rates showed a tendency to initially increase, followed by a subsequent decrease.     

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs. Comparison of the breeds from different altitudes reveals strong signals of population differentiation at the locus of hypoxia-related genes including endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) and beta hemoglobin cluster. Notably, four novel nonsynonymous mutations specific to high-altitude dogs are identified at EPAS1, one of which occurred at a quite conserved site in the PAS domain. The association testing between EPAS1 genotypes and blood-related phenotypes on additional high-altitude dogs reveals that the homozygous mutation is associated with decreased blood flow resistance, which may help to improve hemorheologic fitness. Interestingly, EPAS1 was also identified as a selective target in Tibetan highlanders, though no amino acid changes were found. Thus, our results not only indicate parallel evolution of humans and dogs in adaptation to high-altitude hypoxia, but also provide a new opportunity to study the role of EPAS1 in the adaptive processes.The mechanisms of organismal adaptation to high-altitude hypoxia are of great interest during recent years. Highland wild animals have a long life history at high altitude, and the whole genomes of yak (descendants of wild yak) (Qiu et al. 2012), Tibetan antelope (Ge et al. 2013), snow leopard (Cho et al. 2013), and wild boar (Li et al. 2013) have been sequenced. In contrast, the human settlement history on highland is rather short, which dates from ∼25,000 yr ago (Zhao et al. 2009). Whole-genome genotyping and re-sequencing have been performed for three typical highland populations including Tibetans (Beall et al. 2010; Bigham et al. 2010; Simonson et al. 2010; Yi et al. 2010; Peng et al. 2011; Xu et al. 2011), Andeans (Bigham et al. 2009, 2010), and Ethiopians (Alkorta-Aranburu et al. 2012; Scheinfeldt et al. 2012).The increased oxygen uptake and delivery are physiological hallmarks of high-altitude adaptation. On one hand, the capacity of oxygen uptake is determined by hemoglobin concentration and oxygen affinity. For example, the Andean highlanders display a high level of hemoglobin concentration (Beall et al. 2002; Beall 2007). The high oxygen affinity of hemoglobin is found in many highland animals such as yak (Weber et al. 1988), alpaca (Piccinini et al. 1990), deer mice (Storz et al. 2007; Storz et al. 2009), bar-headed goose (Zhang et al. 1996; Liang et al. 2001), and Andean goose (Jessen et al. 1991). On the other hand, the rate of oxygen delivery is determined by blood flow. For example, although Tibetans maintain a nearly normal level of hemoglobin concentration and a low level of oxygen saturation, they display a high level of blood flow, resulting in the increase of oxygen delivery (Beall et al. 2001; Erzurum et al. 2007).Whole-genome scans revealed that positive selection for human high-altitude adaptation occurred in the hypoxia-inducible factor (HIF) pathway (Bigham et al. 2009; Beall et al. 2010; Bigham et al. 2010; Simonson et al. 2010; Yi et al. 2010; Peng et al. 2011; Xu et al. 2011; Alkorta-Aranburu et al. 2012; Scheinfeldt et al. 2012), which regulates genes associated with blood physiology. In addition, metabolic pathways may also be involved in the adaptive process of yak (Qiu et al. 2012) and Tibetan antelope (Ge et al. 2013).Although a lot of studies focused on wildlife and human highlanders, no research was performed on domesticated animals that migrated to the plateau with humans, which represent an adaptation pattern on a short evolutionary time scale of thousands of years. For example, the Tibetan Mastiff is a native dog living in the Tibetan Plateau with an altitude of 3000–6000 m. It is also an ancient dog in the world (Li and Zhang 2012). However, the genetic and physiological mechanisms of its adaptation to high-altitude environments remain elusive.In this study, we sampled five dog breeds including the Tibetan Mastiff from continuous altitudes along the Ancient Tea Horse Road in southwestern China as well as one European breed. We performed whole-genome sequencing for the dogs and identified candidate genes for high-altitude adaptation using selective sweep mapping. We also measured the hematologic and hemorheologic parameters of the dogs and tested the association between the candidate alleles and blood physiology.     

Comparison of the free and bound phenolic profiles and cellular antioxidant activities of litchi pulp extracts from different solvents

Background

Guizhi Fuling Formula is widely applied for uterine fibroids in China. Many clinical trials are reported. This study assessed the efficacy and safety of Guizhi Fuling Formula for the treatment of uterine fibroids.

Methods

PubMed, Cochrane CENTRAL, EMBASE, and four Chinese databases were searched through May 2013. We included randomised controlled trials (RCTs) that tested Guizhi Fuling Formula for uterine fibroids, compared with no intervention, placebo, pharmaceutical medication, or other Chinese patent medicines approved by the State Food and Drug Administration of China. Authors extracted data and assessed the quality independently. We applied RevMan 5.2.0 software to analyse data of included randomised trials.

Results

A total of 38 RCTs involving 3816 participants were identified. The methodological quality of the included trials was generally poor. Meta-analyses demonstrated that Guizhi Fuling Formula plus mifepristone were more effective than mifepristone alone in reducing the volume of fibroids (in total volume of multiple fibroids, MD ?19.41 cm³, 95% CI ?28.68 to ?10.14; in average volume of multiple fibroids, MD ?1.00 cm³, 95% CI ?1.23 to ?0.76; in average volume of maximum fibroids, MD ?3.35 cm³, 95% CI ?4.84 to ?1.87, I²?=?93%, random effects model). Guizhi Fuling Formula significantly improved symptoms of dysmenorrhea either when it was used alone (RR 2.27, 95% CI 1.04 to 4.97) or in combination with mifepristone (RR 2.35, 95% CI 1.15 to 4.82). No serious adverse events were reported.

Conclusions

Guizhi Fuling Formula appears to have additional benefit based on mifepristone treatment in reducing volume of fibroids. However, due to high risk of bias of the trials, we could not draw confirmative conclusions on its benefit. Future clinical trials should be well-designed and avoid the issues that are identified in this study.     

颅中窝脑静脉的显微解剖与影像学观察

目的通过颅中窝脑静脉的显微解剖、影像学观察及其对照研究,为经翼点和经眶颧手术人路中脑静脉的保护提供形态学基础。方法分别对30例（60侧）颈内静脉灌注蓝色乳胶的成人尸头湿标本、36例（60侧）DSA静脉相、25例（50侧）CT静脉造影（CTV）和25例（50侧）MR静脉造影（MRV）图像进行观测。结果以显微解剖观测结果作为评价标准,DSA、CTV和MRV分别能够观察到70％、52％和42％的颅中窝脑静脉;根据颅中窝静脉注入硬脑膜窦处位置的不同,其分为海绵窦型、蝶顶窦型、蝶岩窦型和岩上窦型,各型脑静脉能被影像学手段区分;影像学观测到的大脑中浅静脉数目和分型与显微解剖相比较,差异无统计学意义。结论术前影像学检查有助于经翼点和经眶颧手术入路的设计和术中脑静脉的保护。     

湿疹、血小板减少伴免疫缺陷综合征1例临床表型及基因突变分析

目的:对1例四川籍湿疹、血小板减少伴免疫缺陷综合征儿童(Wiskott-Aldrich syndrome,WAS)临床表现及分子遗传学特征进行分析,为其家系成员提供病因诊断和遗传咨询。方法:收集在我院诊治的1例WAS患儿的临床病例资料,抽取患儿外周静脉血,常规提取基因组DNA,采用聚合酶链反应(PCR)扩增WASP基因,对扩增产物进行测序和序列分析,寻找基因突变位点,进行基因诊断。结果:(1)患儿系1岁4月男性,生后1月即出现血小板减少,伴有湿疹、反复上呼吸道感染史,此次因发热、间断血便入院,血清IgA升高,给予丙种球蛋白及激素治疗效果不佳,临床评分为3分;(2)WASP基因Exon1存在无意义突变c.100CT(p.Arg 34x),编码蛋白质提前终止于氨基酸第34位,导致蛋白缺失;WASP基因Exon11上存在错义突变c.1378CT(P.Pro460Ser)。结论:根据患儿临床表现、实验室检查及分子遗传学检测结果,可临床诊断为WAS患者。     

Role of BAFF in pediatric patients with allergic rhinitis during sublingual immunotherapy

Sublingual immunotherapy (SLIT) is the only therapeutic option for allergic rhinitis (AR) that modifies the immunological process to an allergen, rather than treating symptoms simply. However, its regulatory mechanisms are largely unknown. B-cell-activating factor of the TNF family (BAFF) plays very important roles in the development, differentiation, and proliferation of B cells and T cells. The aim of this study was to identify the role of BAFF during SLIT in pediatric patients with AR. Seventy-two house dust mite (HDM)-sensitized pediatric patients with AR were enrolled in this study. Thirty-six pediatric patients received HDM allergen extract for SLIT and 36 pediatric patients received placebo. Serum and nasal aspirate of different time points during treatment was collected and used for enzyme-linked immunosorbent assay (ELISA) of BAFF and related cytokines, respectively. Peripheral blood mononuclear cells were collected and stimulated by HDM allergen with or without rhBAFF after 12 months of treatment. Our results showed that the expression of BAFF protein decreased during the SLIT treatment compared with that in the placebo group after 6 months of therapy, and this trend lasted for 12 months. The decreased BAFF expression was positively related to Th2 cytokines and increased IL-10 expression. BAFF was also related to local production of IgA. In vitro experiments showed that BAFF can promote Th2 cytokines and inhibit IL-10 expression by PBMCs. Conclusion: During SLIT, BAFF expression was decreased and related to low Th2 cytokine expression and enhanced IL-10 expression. Besides, BAFF may contribute to local production of IgA. Our results suggested that BAFF may be an important biomarker during SLIT. Authors’ summary. Sublingual immunotherapy (SLIT) is the only therapeutic option for allergic rhinitis (AR) that modifies the immunological process to an allergen, rather than simply treating symptoms. However, its regulatory mechanisms are largely unknown. B-cell-activating factor of the TNF family (BAFF) plays very important roles in the development, differentiation, and proliferation of B cells and T cells. Our results showed that during SLIT, BAFF expression was decreased and related to low Th2 cytokine expression and enhanced IL-10 expression. Besides, BAFF may contribute to local production of IgA. Our results suggested that BAFF may be an important biomarker during SLIT.