EP300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production

The genetic adaptation of Tibetans to high altitude hypoxia likely involves a group of genes in the hypoxic pathway,as suggested by earlier studies.To test the adaptive role of the previously reported candidate gene EP300 (histone acetyltransferase p300),we conducted resequencing of a 108.9 kb gene region of EP300 in 80 unrelated Tibetans.The allele-frequency and haplotype-based neutrality tests detected signals of positive Darwinian selection on EP300 in Tibetans,with a group of variants showing allelic divergence between Tibetans and lowland reference populations,including Han Chinese,Europeans,and Africans.Functional prediction suggested the involvement of multiple EP300 variants in gene expression regulation.More importantly,genetic association tests in 226 Tibetans indicated significant correlation of the adaptive EP300 variants with blood nitric oxide (NO) concentration.Collectively,we propose that EP300 harbors adaptive variants in Tibetans,which might contribute to high-altitude adaptation through regulating NO production.     

Rare allele of HvLox-1 associated with lipoxygenase activity in barley (Hordeum vulgare L.)

Key message

Identification and allele-specific marker development of a functional SNP of HvLox - 1 which associated with barley lipoxygenase activity.

Abstract

Improving the stability of the flavor of beer is one of the main objectives in breeding barley for malting, and lipoxygenase-1 (LOX-1) is a key enzyme controlling this trait. In this study, a modified LOX activity assay was used for null LOX-1 mutant screening. Four barley landraces with no detected level of LOX-1 activity were screened from 1,083 barley germplasm accessions from China. The genomic sequence diversity of the HvLox-1 gene of the four null LOX-1 Chinese landraces was compared with that of a further 76 accessions. A total of 104 nucleotide polymorphisms were found, which contained 83 single-nucleotide polymorphisms (SNPs), 7 multiple-nucleotide polymorphisms, and 14 insertions and deletions. Most notably, we found a rare C/G mutation (SNP-61) in the second intron which led to null LOX-1 activity through an altered splicing acceptor site. In addition, an allele-specific polymerase chain reaction marker was developed for the genotyping of SNP-61, which could be used in breeding programs for barley to be used for malting. The objective was to improve beer quality.     

Relationships between Head Circumference,Brain Volume and Cognition in Children with Prenatal Alcohol Exposure

Head circumference is used together with other measures as a proxy for central nervous system damage in the diagnosis of fetal alcohol spectrum disorders, yet the relationship between head circumference and brain volume has not been investigated in this population. The objective of this study is to characterize the relationship between head circumference, brain volume and cognitive performance in a large sample of children with prenatal alcohol exposure (n = 144) and healthy controls (n = 145), aged 5–19 years. All participants underwent magnetic resonance imaging to yield brain volumes and head circumference, normalized to control for age and sex. Mean head circumference, brain volume, and cognitive scores were significantly reduced in the prenatal alcohol exposure group relative to controls, albeit with considerable overlap between groups. Males with prenatal alcohol exposure had reductions in all three measures, whereas females with prenatal alcohol exposure had reduced brain volumes and cognitive scores, but no difference in head circumference relative to controls. Microcephaly (defined here as head circumference ≤ 3rd percentile) occurred more often in prenatal alcohol exposed participants than controls, but 90% of the exposed sample had head circumferences above this clinical cutoff indicating that head circumference is not a sensitive marker of prenatal alcohol exposure. Normalized head circumference and brain volume were positively correlated in both groups, and subjects with very low head circumference typically had below-average brain volumes. Conversely, over half of the subjects with very low brain volumes had normal head circumferences, which may stem from differential effects of alcohol on the skeletal and nervous systems. There were no significant correlations between head circumference and any cognitive score. These findings confirm group-level reductions in head circumference and increased rates of microcephaly in children with prenatal alcohol exposure, but raise concerns about the predictive value of this metric at an individual-subject level.     

Antagonistic Yeasts for Biocontrol of the Banana Postharvest Anthracnose Pathogen Colletotrichum musae

The biocontrol potentials of Candida tropicalis YZ1, C. tropicalis YZ27 and Saccharomyces cerevisiae YZ7 against the postharvest anthracnose pathogen Colletotrichum musae were investigated. Treatments with all the three biocontrol agents (1 × 10⁸ CFU/ml) significantly reduced the natural anthracnose disease severity of harvested banana fruits stored at ambient condition. Germination and survival of C. musae spores were markedly inhibited by all the three yeast strains in in vitro tests. The niche overlap index (NOI) was used to determine the interaction between the antagonists and C. musae, and the results (high NOI values) suggest competitive exclusion of C. musae by the yeast strains. C. tropicalis YZ27 inoculated on banana wounds exhibited rapid colonization and maintenance of its population on the inoculated site. The biocontrol efficacy was also observed as a function of concentration of the antagonist applied. The fruits treated with C. tropicalis YZ27, 36 h before pathogen inoculation, showed the best results with 96.0% disease inhibition followed by those treated 24 h before with 84.0% inhibition. The above results point to competition for nutrients and space as the main mechanism of antagonistic action of C. tropicalis YZ27 against C. musae.     

西双版纳热带雨林林窗空间分布格局及其特征数与林窗下植物多样性的相关性

林窗作为森林群落中一种重要的干扰方式, 对林下物种构成有着重要的影响。开展林窗空间格局及其特征指数与林下植物多样性关系研究对于探讨林窗对林下生物多样性的影响有重要意义, 有助于进一步了解群落动态, 在物种多样性保护方面也具有指导作用。本研究在西双版纳热带雨林地区随机选取3块大小为1 ha的热带雨林为研究样地, 采用轻小型六旋翼无人机搭载Sony ILCE-A7r可见光传感器, 分别获取各个样地的高清数字影像, 结合数字表面高程模型以及各个样地的地形数据用以确定各样区的林窗分布格局, 并进一步提取出各林窗的景观格局指数。结合地面样方基础调查数据, 对各样地各林窗下植物多样性情况进行统计, 旨在分析热带雨林林窗空间分布格局以及林窗下植物多样性对各林窗空间格局特征的响应情况。研究表明, 西双版纳州热带雨林林窗呈大而分散的空间分布, 林窗空间格局特征指数如林窗形状复杂性指数、林窗面积都与林下植物多样性呈显著正相关关系。在面积小的林窗下, 较之林窗形状复杂性因子, 林窗面积大小对林下植物多样性影响更显著; 在面积达到一定程度后, 相对于面积因子, 林窗形状复杂性指数对林下植物多样性影响更显著, 各样地林窗皆趋于向各自所处样地顶极群落发展。     

藏北尼阿木底遗址发现的似阿舍利石器——兼论晚更新世人类向青藏高原的扩张

2013年夏,在藏北那曲地区申扎县羌塘高原旧石器调查中,从规模恢弘的尼阿木底遗址地表暴露的、数以万计的石制品中,分别采集到似阿舍利类型"手斧"9件和"薄刃斧"2件。本文对尼阿木底遗址所见的这类器物进行了细致的观察与分析,认为它们只是旧石器时代晚期勒瓦娄哇技术产品的石核,或偶尔为之的、与手斧和薄刃斧形似的石制品,并非真正意义上的手斧与薄刃斧。尼阿木底遗址不存在从选料、剥片、加工出成品,到使用、损坏和废弃等各个阶段的、明确的阿舍利类型石器工业产品生产体系的工艺链条,换言之,在尼阿木底生活的古人脑海中,并不存在一个加工阿舍利类型手斧和薄刃斧等工具的"概念模板"(Mental template)。联系到青藏高原其他地区以前所报道的同类材料,我们认为在青藏高原腹地目前所见的旧石器遗址中,还没有真正意义上的阿舍利石器工业类型的遗存。晚更新世末期时,来自于印巴次大陆方向的早期占领者,沿着喜马拉雅山脉、冈底斯山脉和昆仑山脉三条东西走向的巨大山系之间的通道,自高原西南方向开始向高原腹地扩张,其间阿舍利石器工业技术在非洲和欧亚大陆早已消弭,当时的青藏高原腹地并不具备重新产生该类石器工业技术的土壤。     

Detection of Multiple Cytochrome P450 in Hepatic Tissue of Heteropneustes fossilis (Bloch) Exposed to Cypermethrin

Cypermethrin (alpha-cyano-3-phenoxybenzyl ester of 2,2-dimethyl-3-(2,2-dichlorovinyl) cyclopropane carboxylic acid) is a synthetic pyrethroid. It is one of the most widely used pesticide in commercial agricultural applications because of its high effectiveness against target species. Beside its target toxicity it is also highly toxic to other non-target species like fish, bees and aquatic insects. The aim of this study was to detect the presence of cytochrome P450 (CYP 450) in the hepatic microsomes of Heteropneustes fossilis upon exposure to cypermethrin. The 96 h LC₅₀ value for each exposure route was calculated and two groups were treated, with one group receiving a single IP (intraperitoneal) injection for 96 h (0.030 mg/kg body weight) and the other group with 1/3 sub-lethal concentration (1.2 μg/l) of the LC₅₀ value in water for 15 days. Activities of the enzymes ethoxyresorufin-o-deethylase (EROD), N,N-dimethylaniline demethylase, aniline hydroxylase and erythromycin demethylase mediated respectively by the isozymes CYP1A, CYP2B, CYP2E1 and CYP3A4 were studied. The liver somatic index (LSI) was also calculated to determine the physiological status of the fish. Activities of CYP1A, CYP2B and CYP2E1 enzymes increased significantly while that of CYP3A4 enzyme inhibited as compared to control. Total CYP 450 content was also significantly induced in both the treated groups. The increase in activities of CYP P450 isozymes could be used as a biomarker to indicate the pollution of an aquatic environment by the pesticide.     

西藏年楚河流域种子植物组成及区系特征

通过野外数据采集和资料整理分析,以年楚河流域种子植物为研究对象,对区域种子植物科、属组成、区系特征和资源型进行分析。年楚河流域共记录到种子植物58科179属339种;生活型以多年生草本为主;资源类型中药用植物最多。科内种水平上大型科为优势科,有菊科(Asteraceae)、禾本科(Poaceae)、豆科(Fabaceae);科内属的数量水平上,大型科、较大型科和小型科是植物科组成的主要成分。科的分布区类型中除世界广布型外,以温带性质为主导,热带性质次之。属的组成以单种属和小型属为主,其分布区类型表现出明显的温带性质;科、属的特有性不高。与邻近区域的植物区系R/T值比较中,本研究区与拉萨河流域、佩枯错地区植物区系的性质较接近;比较这两个区域与研究区域植物属、种的相似性系数,发现拉萨河流域与研究区域植物属、种的相似性均高于佩枯错,本研究区植物区系与拉萨河流域的亲缘关系更为亲近。     

A chromosome‐scale reference genome and genome‐wide genetic variations elucidate adaptation in yak

Yak is an important livestock animal for the people indigenous to the harsh, oxygen‐limited Qinghai‐Tibetan Plateau and Hindu Kush ranges of the Himalayas. The yak genome was sequenced in 2012, but its assembly was fragmented because of the inherent limitations of the Illumina sequencing technology used to analyse it. An accurate and complete reference genome is essential for the study of genetic variations in this species. Long‐read sequences are more complete than their short‐read counterparts and have been successfully applied towards high‐quality genome assembly for various species. In this study, we present a high‐quality chromosome‐scale yak genome assembly (BosGru_PB_v1.0) constructed with long‐read sequencing and chromatin interaction technologies. Compared to an existing yak genome assembly (BosGru_v2.0), BosGru_PB_v1.0 shows substantially improved chromosome sequence continuity, reduced repetitive structure ambiguity, and gene model completeness. To characterize genetic variation in yak, we generated de novo genome assemblies based on Illumina short reads for seven recognized domestic yak breeds in Tibet and Sichuan and one wild yak from Hoh Xil. We compared these eight assemblies to the BosGru_PB_v1.0 genome, obtained a comprehensive map of yak genetic diversity at the whole‐genome level, and identified several protein‐coding genes absent from the BosGru_PB_v1.0 assembly. Despite the genetic bottleneck experienced by wild yak, their diversity was nonetheless higher than that of domestic yak. Here, we identified breed‐specific sequences and genes by whole‐genome alignment, which may facilitate yak breed identification.