Genes for the high life： New genetic variants point to positive selection for high altitude hypoxia in Tibetans

People living on the high plateaus of the world have long fascinated biological anthropologists and geneticists because they live in ＂thin air＂ and epitomize an extreme of human biological adaptation.

Positively selected genes of the Chinese tree shrew （Tupaia belangeri chinensis） locomotion system

While the recent release of the Chinese tree shrew(Tupaia belangeri chinensis) genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals(human, rhesus monkey, mouse, rat and dog) and the Chinese tree shrew. Our analyses identified 29 genes with significantly high ω(Ka/Ks ratio) values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6(homeobox A6) and AVP(arginine vasopressin), play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew.

Development of "Multi-Resistance Rice" by Pyramiding of Insect (Cry1C) and Blast Resistance (Pi1 and Pi2) Genes

[Objective] The paper was to improve the blast resistance of insect-resistant transgenic rice. [Method] The Japonica rice variety Jikang10, a new transgenic variety with exogenous insect-resistant gene Cry1C, was used as the receptor, and Kongyu 131, a traditional breeding variety with broad-spectrum high blast resistance genes Pi1 and Pi2, was used as the donor to breeding new rice varieties. The genes were polymerized by hybridization and multi-generation backcrossing, and the offspring of each generation was screened by molecular marker assisted selection, field identification of multi-resistance against insect pests and diseases and agronomic trait selection. [Result] Four lines SK01, SK02, SK03 and SK04 with better resistances to insect pests and blast and outstanding agronomic traits in field were selected. [Conclusion] The results will lay foundations for breeding new multi-resistance rice varieties in Huanghuai rice region.

Genetic mechanism of body size variation in groupers:Insights from phylotranscriptomics

Animal body size variation is of particular interest in evolutionary biology,but the genetic basis remains largely unknown.Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size,providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates.Herein,we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea.Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size,respectively.A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups.Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups.These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks.Based on our results,we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection,leading to genetic variations in metabolic patterns,organ development,and lifespan,resulting in body size divergence between the two locally adapted populations.These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

A DNA-binding protein factor in K562 nuclear extract interacts with positive control region (PCR) in the 5'flanking sequence of human β-globin gene

It has been known that there are at least three regulatory regions (NCR1. NCR2 and PCR) in the 5'-flanking sequence (from -610 bp to +1 bp) of human β-glohin geneand that the function of PCR is unique to the human erythroleukemia (Ksfi2) ceils. Here we have detected a DNA-binding protein factor (termed NFEa) in K562 ceils. which can bind specifically to the PCR of human β-globin gene. The sequence of the binding site is 5'ACTGATG3' (between -222 bp and -216 bp). The NFEa is erythroidspecific and perhaps specific for K562 cells. It seemed that this factor differed from the erythroid-specific transcriptional factor (NFE-1) ,nsing competition assay. The presence of the NFEa further supported that the funciton of the cis-acting element PCR was specitic for K562 cells. and helps us to understand the mechauism of the regulation of the expression of lmman β-globin gene in the human K562 cells.

Impact of noninvasive positive pressure ventilation on the gene expression of ubiquitin system of skeletal muscle in patients with acute exacerbation of chronic obstructive pulmonary disease

Objective:To investigate the change and relativity of noninvasive positive pressure ventilation(NIPPV)on the gene expression of ubiquitin system of skeletal muscle in patient with acute exacerbation of chronic obstructive pulmonary disease(AECOPD).Methods:80 patients with AECOPD were divided into two groups based on whether the NIPPV treatment was given or not,38 cases in the study group and 42 in the control group.The blood gas analysis and pulmonary function were monitored and recorded before and 14 days after treatment.A skeletal muscle biopsy was performed 14 days after therapy.The mRNA expression of ribosomal protein S21(RPS21)and ubiquitin in skeletal muscle cell were measured by RT-PCR.Results:After 14 days treatment,the levels of PaCO_(2),PaO_(2),PH and FEV_(1)% in the NIPPV group improved much better than in the control group(p<.05).The gene expression of RPS21 and ubiquitin was obviously lower in the study group than in the control group(p<.05).The level of RPS21 was negatively related with PaO_(2),PH and FEV1%,and the level of ubiquitin was negatively related with PaO_(2) and FEV1%,but positively correlated with PaCO_(2).The area under the ROC curves of RPS21,ubiquitin,PaCO_(2) and FEV_(1)% were 0.771,0.885,0.821 and 0.734 respectively in the study group.The cut-off points were 103.978,8.128,45.350 and 51.350 respectively.The sensitivity evaluation of acid poisoning was 90.9%,and the specificities for each were 75%,75%,50% and 50%.Conclusions:NIPPV is effective for AECOPD patients through the gene expression of ubiquitin system of skeletal muscle.

Effect of basic fibroblast growth factor and danshen on bcl-2 and p53 mRNA expression in the brain of rats exposed to repeated, high, positive acceleration (+Gz)

BACKGROUND： Both animal experiments and clinical studies have shown that basic fibroblast growth factor （bFGF） and danshen （Salvia miltiorrhiza） can exhibit protective effects on ischemia-reperfusion cerebral injury. OBJECTIVE： To test whether bFGF and danshen can protect cerebral injury induced by exposure to repeated, high, positive acceleration （＋Gz） in an animal model and to analyze the possible mechanisms. DESIGN, TIME AND SETTING： Randomized controlled animal study. The experiment was performed at the Research Center for Molecular Biology, Air-force General Hospital of Chinese PLA from April to August 2000. MATERIALS： A total of 20 clean grade, healthy, Sprague Dawley rats of both genders, weighing （200 ± 15） g, were provided by our experimental animal center. Rats were randomly divided into 5 groups： the control group, ＋Gz exposure group, bFGF group, danshen group, and saline group, with 4 animals per group. bFGF （Beijing Bailuyuan Biotechnology Co. Ltd.） and danshen solution （Shanghai Zhongxi Pharmaceutical Co. Ltd.） were used. METHODS： All rats were fixed on a rotary arm of a centrifugal apparatus （2 m in radius） with their heads oriented towards the center of the apparatus. Except for rats in the control group, the value of ＋Gz exposure was ＋14 Gz with an acceleration rate of 1.5 G/s. The peak force lasted for 45 seconds. ＋Gz exposure was performed three times with intervals of 30 minutes. Rats in the control group received the same ＋Gz procedure, but the G value was ＋1 Gz. Rats in bFGF group and danshen group were intraperitoneally injected with 100 μg/kg bFGF or 15 g/kg danshen solution, respectively, at 30 minutes prior to centrifugation and immediately after centrifugation. Rats in saline group were injected with the same volume of saline. Six hours after exposure, rats were decapitated. One hemisphere was preserved in liquid nitrogen for RNA extraction and the other was processed for apoptosis detection. MAIN OUTCOME MEASURES： mRNA levels of bcl-2 and p53 were measured by semi-quantitative reverse-transcription polymerase chain reaction. Apoptotic cell death was detected by terminal deoxynuleotidyl transferase-mediated dUTP nick end labeling. RESULTS： Changes in mRNA expression of bcl-2 and p53 and apoptotic cells were observed in rat brain six hours after repeated ＋Gz exposures, bFGF and danshen were able block the changes of bcl-2 and p53 expression and inhibit apoptotic cell death. CONCLUSION： The data suggest that apoptosis and changes in bcl-2 and p53 expression in the rat brain can be induced by repeated ＋Gz exposures. Apoptosis is, therefore, one of the molecular mechanisms of brain damage induced by repeated ＋Gz exposures, bFGF and danshen were of the equal potency in preventing brain injury induced by repeated ＋Gz exposures.

Transcriptomic comparison to identify rapidly evolving genes in Braya humilis

The Brassicaceae species Braya humilis shows broad adaptation to different climatic zones and latitudes. However, the molecular adaptation mechanism of B. humilis is poorly understood. In China, B. humilis is mainly distributed on the QinghaiTibetan Plateau(QTP) and in the adjacent arid region. Previous transcriptome analysis of B. humilis has revealed that 39 salt and osmotic stress response genes are subjected to purifying selection during its speciation. To further explore the adaptation mechanism of B. humilis to an arid environment, OrthoMCL program was employed in this study and 6,268 pairs of orthologous gene pairs with high confidence were obtained between B. humilis and Arabidopsis thaliana. A comparative evolutionary analysis based on nonsynonymous to synonymous substitution ratio(Ka/Ks) was then conducted. There were 64 pairs exhibiting a Ka/Ks ratio more than 0.5 and among which, three instrumental candidate genes, T20487,T22576, and T23757, were identified with strong selection signatures(Ka/Ks >1). The corresponding A. thaliana orthologs are double-stranded RNA-binding domain protein, MADS-box family protein, and NADH-dehydrogenase subunit6, which is encoded by mitochondria genome. This report not only demonstrates the adaptation contribution of fast evolving nuclear genes, but also highlights the potential adaptive value of mitochondria gene to the speciation and adaptation of B. humilis toward the extreme environment in an arid region.

宁夏地区奶牛源隐孢子虫分子鉴定与分析

为了明确宁夏地区奶牛隐孢子虫的流行情况及其优势基因型,采集宁夏4个地区10个规模化奶牛养殖场中1174份奶牛粪便样品,基于核糖体小亚基RNA(SSU rRNA)基因通过套式PCR进行检测和分析。结果显示,宁夏地区奶牛隐孢子虫阳性率为28.5%(335/1174);共鉴定出4种虫种,即微小隐孢子虫、牛隐孢子虫、瑞氏隐孢子虫和安氏隐孢子虫,阳性率分别为40.6%(136/335)、36.1%(121/335)、19.4%(65/335)和3.9%(13/335);微小隐孢子虫共鉴定出4种基因亚型,分别为ⅡdA15G1(n=70)、ⅡdA18G1(n=26)、ⅡdA19G1(n=23)和ⅡdA20G1(n=17)。统计学分析显示,在宁夏地区,0~2月龄的犊牛隐孢子虫感染率最高,且奶牛隐孢子虫的感染率与月龄差异显著相关(P<0.001)。表明宁夏地区奶牛存在隐孢子虫感染且存在人畜共患虫种,ⅡdA15G1微小隐孢子虫是宁夏地区奶牛感染的优势亚型。

3例抗MDA5抗体阳性皮肌炎合并快速进展型间质性肺病患者的临床特点附文献复习

目的探讨抗MDA5阳性皮肌炎合并快速进展型间质性肺病的临床特点、治疗及预后。方法回顾性分析2020年7月至2021年10月在攀枝花学院附属医院呼吸与危重症医学科住院的3例抗MDA5抗体阳性皮肌炎合并快速进展型间质性肺病患者的临床资料、治疗经过、预后特点,结合文献复习进行研讨。结果3例患者中男1例,女2例,年龄(55.7±2.1)岁,病程(3.8±0.2)月。临床主要表现为典型的皮疹,进行性呼吸困难;血清肌酶均增高,血清抗MDA5抗体、抗组氨酰合成酶抗体(Jo-1)、抗Ro-52抗体均阳性;皮疹部位皮肤肌肉活检均提示炎性改变;短期内影像学呈进行性加重的肺间质纤维化。3例患者均使用了激素冲击+丙种球蛋白+环磷酰胺治疗,1例使用了利妥昔单抗治疗。3例患者分别在住院治疗后27、37、48天死亡,2例死于急性呼吸衰竭,1例死于脓毒性休克。结论抗MDA5阳性皮肌炎合并快速进展型间质性肺病是一种病情进展快、疗效差、死亡率高的疾病。其临床主要表现是典型的皮疹和进行性呼吸困难,血清肌酶增高,抗MDA5抗体阳性(3例患者同时合并抗组氨酰合成酶抗体Jo-1、抗Ro-52抗体阳性)。影像学均短期内呈进行性加重的肺间质纤维化。以激素冲击、免疫调节、靶向阻断等为主的药物治疗,未能成功挽救患者的生命。治疗后免疫低下所导致的严重感染,也是死亡的重要原因。早期识别,早期干预,以及疾病后期的ECMO支持、肺移植,可能是降低死亡率的有效手段。

Alloy Gene Gibbs Energy Partition Function and Equilibrium Holographic Network Phase Diagrams of AuCu-Type Sublattice System

Taking AuCu-sublattice system as an example, we present two discoveries and a method. First, the alloy gene sequences are the central characteristic atom sequences in the basic coordination cluster sequences. Second, the transmission mode of the information about structures and properties of the alloy genes is described by the alloy gene Gibbs energy partition function. The most valuable method in the system sciences is “the whole obtained from a few parts”. We have established the alloy gene database and holographic alloy positioning system of the Au-Cu system, as well as alloy gene Gibbs energy partition function and equilibrium holographic network phase diagrams of the AuCu-type sublattice system. It means that a standard way for researchers to share predictive algorithms and computational methods may be produced during designing advanced alloys.

DTNBP1 Gene Is Associated with Some Symptom Factors of Schizophrenia in Chinese Han Nationality

Objective To study the association of DTNBP1 gene with some symptom factors of schizophrenia.Methods A total of 285 unrelated schizophrenic individuals were recruited from December 2004 to January 2009 for genetic analysis,and their symptom factors were assessed based on the Positive and Negative Syndrome Scale(PANSS).The quantitative trait test was performed by the UNPHASED program(version 3.0.12) to investigate the association between scored positive and negative symptoms and the single nucleotide polymorphisms(SNPs) in DTNBP1 gene.Results The quantitative trait test showed allelic association of rs909706 with the excitement symptom of schizophrenia(P<0.05,adjusted by 10 000 permutations),while the genotype C/G of rs2619539 with a negative symptom,lack of spontaneity and flow of conversation(P<0.05,adjusted by 10 000 permutations).Conclusion DTNBP1 variations are possibly associated with some symptoms of schizophrenia,which could partly explain the relationship between the susceptibility gene DTNBP1 and that disease.

A Study on the Molecular Switch of Gene Expression of the Mouse Heart Nuclear DNA Fragments

It is observed by in situ stain that LDH (1 5) ...nNAD + can probably enter the nucleopore and can be bound bound specifically with the genes that encode them. During the in vitro expression, the dilution of heart nuclear DNA fragments could enhance the expression activity of LDH/DNA and the amount of expressed LDH (1 5) is in proportion to the amount of dissociable LDH (1 5) on the LDH/DNA. With the integration of 14C Leu to the proteins, it is also observed that the addition of LDH (1 5) ...nNAD + can suppress the in vitro expression activity of LDH/DNA. AFM observation shows that the regulation sequence at the both ends of active genes may be bound with such active factors as proteins encoded by the genes which probably is the main molecular switch of gene expression and regulation we have been always searching for. Our work shows the prospective application of the combination of AFM and isotope labeling in the research of biological reaction.

Alloy Gene Sequence Project and System Science Philosophy

System Science Philosophy is a knowledge system constructed of universal principle and law sequences. Alloy gene is a characteristic atom existing in the center of coordination cluster and occupying the lattice point of a lattice cell, and carries holographic information about valence electron structure, physical and thermodynamic properties obtained by alloy gene theory. Alloy gene potential energy curve function has developed traditional atom pair interaction potential functions into many atoms’ interaction function associated with valence electron structure, bond length, bond energy, which makes alloy gene Gibbs energy function can be established. Alloy gene Gibbs energy transmissive function has developed traditional partition function. Its equilibrium and sub-equilibrium transmissive modes produce alloy holographic network positioning bank, which is operable platform to achieve transformation from “trial and error” method to the “whole obtained from a few part” law for getting advanced alloys. It has become possible to launch alloy gene sequence project.

Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia

The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene,GlTop 2 was identified. It is a single copy gene with a 4476 bp long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a -100 aa longer central domain; a ~200 aa shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the ''amitochondriate'' G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G, lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.

念珠藻类(蓝藻)psb A基因的进化分析

蓝藻psbA基因家族编码不同形式的D1蛋白,该蛋白是光系统II反应中心的重要组成部分.以39条念珠藻属(Nostoc)及与其同源性较高的psbA基因序列为研究对象,构建最大似然树进行系统发育分析,然后运行PAML4.9软件,使用分支模型、位点模型和分支-位点模型估测氨基酸位点ω值,进一步探讨psbA基因所受到的选择压力.结果表明:(1)系统发育树呈现出内类群中念珠藻分为2个大分支.(2)在分支-位点模型和位点模型下检测出13S,42V,75S,152R和255K为统计学上显著的正选择位点,绝大多数为负选择位点.揭示了念珠藻psbA基因所经历的正选择可能在其适应极端环境中起着重要作用.

Detecting positive darwinian selection in brain-expressed genes during human evolution

To understand the genetic basis that underlies the phenotypic divergence between human and non- human primates, we screened a total of 7176 protein-coding genes expressed in the human brain and compared them with the chimpanzee orthologs to identify genes that show evidence of rapid evolution in the human lineage. Our results showed that the nonsynonymous/synonymous substitution (Ka/Ks) ratio for genes expressed in the brain of human and chimpanzee is 0.3854, suggesting that the brain-expressed genes are under functional constraint. The X-linked human brain-expressed genes evolved more rapidly than autosomal ones. We further dissected the molecular evolutionary patterns of 34 candidate genes by sequencing representative primate species to identify lineage-specific adaptive evolution. Fifteen out of the 34 candidate genes showed evidence of positive Darwinian selection in human and/or chimpanzee lineages. These genes are predicted to play diverse functional roles in em- bryonic development, spermatogenesis and male fertility, signal transduction, sensory nociception, and neural function. This study together with others demonstrated the usefulness and power of phy- logenetic comparison of multiple closely related species in detecting lineage-specific adaptive evolu- tion, and the identification of the positively selected brain-expressed genes may add new knowledge to the understanding of molecular mechanism of human origin.

Studies on DNA-protein interactions in the upstream regulatory region of the human ε-globin gene promoter

The erythroid- and developmental stage-specific expression of the human ε-globin gene is controlled, in part,by the 5’-flanking DNA sequence of this gene. In the present study, we have used DNA-protein binding assays to identify trans-acting factors which regulate the temporal expression of the human ε-globin gene during development. Using gel mobility shift assays and DNasel footprinting assays, a nuclear protein factor (termed ε-SSF1) in the nuclear extracts from mouse haematopoietic tissues at d 11 and d 13 of gestation was identified. It could specifically bind to the positive control region (between -535 and -453bp) of the human ε-globin gene. We speculated that the E-SSF1 might be an erythroid- and developmental stage-specific activator. In addition, we found another nuclear protein factor (termed ε-R1) in the nuclear extract from mouse fetal liver at d 18 of gestation, which could strongly bind to the silencer region (between -392 and -177bp) of this gene. Therefore, we speculated that the ε-R1 might be an erythroid- and developmental stagespecific repressor. Our data suggest that both ε-SSF1 and ε-R1 might play important roles in developmental regulation of the human ε-globin gene expression during the early embryonic life. On the other hand, we observed that the binding patterns of nuclear proteins from three cell lines (K562, HEL and Raji) to these regulatory regions were partially different. These results suggest that different trans-acting factors in K562, HEL and Raji cells might be responsible for activating or silencing the human ε-globin gene in three different cell lines.

TLR10基因多态性与HBeAg阳性慢性乙型肝炎患者PEG-IFNα治疗临床转归的相关性分析

目的:探讨分析TLR10基因多态性与HBeAg阳性慢性乙型肝炎(CHB)患者聚乙二醇化干扰素α(PEG-IFNα)治疗临床归转的相关性。方法:选取2019年8月至2020年8月收治的92例HBeAg阳性CHB患者,均予以PEG-IFNα进行治疗,6个月后根据HBeAg、HBeAb情况将患者分为应答组44例和非应答组48例。提取全血基因组DNA,测定TLR10基因多态性点位(RS10004195位点和RS11096957位点),分析其不同点位基因型和等位基因分布与乙型肝炎病毒感染的关系,进而探讨TLR10基因多态性与临床转归的相关性。结果:TLR10基因RS10004195位点基因型中,应答组AA+AT型基因分布频率为77.27%显著高于非应答组的52.08%,A等位基因频率65.91%显著高于非应答组的41.67%,差异有统计学意义(P<0.05);TLR10基因RS11096957位点基因型中,应答组AC+AA型基因分布频率为70.45%,与非应答组的62.50%差异无统计学意义(P>0.05),应答组A等位基因频率为61.36%显著高于非应答组的39.58%,差异有统计学意义(P<0.05);TLR10基因RS10004195位点中,A型基因、A等位基因频率和RS11096957位点中A等位基因频率是HBeAg阳性CHB患者PEG-IFNα治疗临床转归的独立危险因素(OR>1,P<0.05)。结论:TLR10基因RS10004195位点A型基因携带、A等位基因频率,RS11096957位点A等位基因频率是HBeAg阳性CHB患者PEG-IFNα治疗临床转归的独立危险因素,对CHB患者治疗应答反应具有较好评估作用,可为临床治疗提供指导依据。

Gene X-pert MTB/RIF检测对肺结核病诊断的价值

目的探讨Gene X-pert MTB/RIF检测对肺结核病诊断的价值。方法选取2020年5月—2021年10月期间在张家港市第一人民医院接受治疗的拟诊断为肺结核病患者113例为研究对象,所有患者均接受Gene Xpert MTB/RIF系统分子检测、结核分枝杆菌(MTB)培养和抗酸染色镜检诊断,以Gene X-pert MTB/RIF系统分子检测结果为观察组,以MTB培养检测结果为对照1组,以痰涂片抗酸染色镜检诊断结果为对照2组。对比3组诊断结果。结果结核病患者诊断结果中,以对照1组MTB培养检测结果为金标准,检测阳性39例(34.51%),观察组诊断阳性率(35.40%)高于对照2组(21.24%),差异有统计学意义(χ^(2)=12.250,P<0.05)。观察组诊断结果准确度、灵敏度高于对照2组,差异有统计学意义(P<0.05)。结论在对肺结核病诊断的诊断中,Gene X-pert MTB/RIF检测阳性率显著高于抗酸染色镜检诊断。