Identification of sika deer and red deer using partial cytochrome b and 12s ribosomal RNA genes

A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.

Nematode Diversity of Qingdao Coast Inferred from the 18S Ribosomal RNA Gene Sequence Analysis

The 18S ribosomal DNA gene （18S rDNA） sequences （approxtmately 1300 bp in length） were amplified from the DNA extracted from the free-living marine nematodes collected from the inter-tidal sediment of Qingdao coast in bulk with nematode specific primers. The PCR products were cloned, re-amplified, digested with Rsa I and Hin61 restriction endonucleases and separated in agarose gel. Among 17 restriction fragment length types, types 1, 2 and 6 covered 61.2%, 14.4% and 9.3% of the clones analyzed, respectively, while the remaining 14 only covered 21 clones, which accounted for 15.1% of the total. Twenty-four representative clones were sequenced and phylogenetically analyzed by referring to those currently available in RDP and GenBank databases. Although it was hard to assign these sequences to known species or genera due to the lack of the 18S rDNA sequence data of known marine free-living nematodes, the obtained sequences were assigned to the nematodes of Adenophorea. Among them, twelve sequences were close to Pontonema vulgate and Adoncholaimus sp., four to Daptonema procerus and two （identical） to Enoplus brews. Our results showed that free-living marine nematode diversities could be determined by PCR retrieving and analysis of the 18S rDNA sequences and an 18S rDNA sequence could be assigned to a species or a genus only if the 18S rDNA sequences of the free-living marine nematodes were accumulated to some extent.

某院儿童肺炎支原体感染情况及23S rRNA基因位点突变与抗生素耐药的相关关系

目的分析某院儿童肺炎支原体感染情况及23S rRNA基因位点突变与抗生素耐药的相关性。方法选取2021年2月至2023年1月在浙江省长兴县中医院就诊的100例疑似肺炎支原体感染患儿,对比不同性别、年龄儿童肺炎支原体的感染情况。根据基因检测结果,将患儿分为突变组和非突变组,并对比2组患儿的临床资料,采用多因素Logistic回归分析影响耐药突变的相关因素。结果100例疑似肺炎支原体感染患儿中,92例(92.0%)PCR检测结果为阳性;其中23S rRNA基因位点突变36例(39.1%),未突变56例(60.9%)。女性患儿的肺炎支原体阳性率(93.2%)稍高于男性(91.1%),且23S rRNA基因位点突变率(41.5%)稍高于男性(37.2%),但差异无统计学意义(P>0.05)。>3岁患儿的肺炎支原体阳性率(96.8%)高于1~3岁患儿(83.8%),且23S rRNA基因位点突变率(47.5%)高于1~3岁患儿(22.6%)(P<0.05)。突变组和未突变组患儿的白细胞计数、嗜中性粒细胞百分比、降钙素原、红细胞沉降率、发热持续时间、咳嗽持续时间、住院时间、本次病程大环内酯类药物应用时间、本次病程肺炎支原体-DNA载量等相比,差异有统计学意义(P<0.05)。多因素Logistic回归分析显示,本次病程肺炎支原体-DNA载量与耐药突变相关(P<0.05)。结论肺炎支原体23S rRNA基因位点突变风险随着肺炎支原体肺炎患儿年龄的增加而逐渐升高。此外,本次病程肺炎支原体-DNA载量与V区A2063G和A2064G耐药突变相关。

A phylogeny of the Passerida(Aves: Passeriformes)based on mitochondrial 12S ribosomal RNA gene

Background: Passerida is the largest avian radiation within the order Passeriformes. Current understanding of the high-level relationships within Passerida is based on DNA–DNA hybridizations; however, the phylogenetic relationships within this assemblage have been the subject of many debates.Methods: We analyzed the 12 S ribosomal RNA gene from 49 species of Passerida, representing 14 currently recognized families, to outline the phylogenetic relationships within this group.Results: Our results identified the monophyly of the three superfamilies in Passerida: Sylvioidea, Muscicapoidea and Passeroidea. However, current delimitation of some species is at variance with our phylogeny estimate. First, the Parus major, which had been placed as a distinct clade sister to Sylvioidea was identified as a member of the super family;second, the genus Regulus was united with the Sturnidae and nested in the Muscicapoidea clade instead of being a clade of Passerida.Conclusion: Our results were consistent with Johansson's study of the three superfamilies except for the al ocation of two families, Paridae and Regulidae.

39株对克拉霉素耐药的结核分枝杆菌临床分离株23S rRNA检测结果分析

目的分析对克拉霉素耐药的结核分枝杆菌临床分离株23SrRNA的A2058位点的变化。方法选择我院菌株库的结核分枝杆菌临床分离株64株,其中10株为对全部抗结核药物敏感的结核分枝杆菌临床分离株;14株为单耐克拉霉素的结核分枝杆菌临床分离株;15株为耐多药,同时耐克拉霉素的结核分枝杆菌临床分离株;15株为耐多药,同时对克拉霉素敏感的结核分枝杆菌临床分离株;10株为广泛耐药菌株,同时对克拉霉素耐药的结核分枝杆菌临床分离株;此外,还有结核分枝杆菌标准株H37Rv 1株。对结核分枝杆菌23SrRNA行PCR检测和测序。结果经检测,H37Rv标准株没有A2058突变,只有1株广泛耐药临床分离株检测有A2058A-G的突变,其他临床分离株均没有突变,在耐克拉霉素的结核分枝杆菌临床分离株中占2.56%(1/39),在广泛耐药结核分枝杆菌临床分离株中占1/10。结论结核分枝杆菌临床分离株对克拉霉素耐药的机制中,A2058突变可能不是产生对克拉霉素耐药的主要机制。结核分枝杆菌产生对克拉霉素耐药的机制有待进一步研究。

23S核糖体RNA结构域Ⅴ区位点A2063G、A2064G突变与儿童难治性肺炎支原体肺炎的相关性

目的 探讨23S核糖体RNA(rRNA)结构域Ⅴ区位点A2063G、A2064G突变与儿童难治性肺炎支原体肺炎的相关性。方法 将184例肺炎支原体肺炎患儿分为难治性肺炎组56例和非难治性肺炎组128例。比较两组患儿白细胞和中性粒细胞计数,降钙素原、C反应蛋白(CRP)、血沉、ALT、AST、乳酸脱氢酶(LDH)水平,以及23S rRNA结构域Ⅴ区位点A2063G、A2064G突变情况。分析相关指标与难治性肺炎支原体肺炎的相关性,并采用多因素Logistic回归模型分析难治性肺炎支原体肺炎的危险因素。结果 难治性肺炎组的CRP、血沉、LDH水平,中性粒细胞计数,以及A2063G和/或A2064G位点突变的比例均高于非难治性肺炎组(均P<0.05)。CRP、血沉、LDH水平,中性粒细胞计数,以及A2063G和/或A2064G位点突变情况均与难治性肺炎支原体肺炎具有相关性(均P<0.05)。Logistic回归模型分析结果显示,CRP、血沉、LDH水平升高,以及A2063G或/和A2064G位点突变均是难治性肺炎支原体肺炎的危险因素(均P<0.05)。结论 存在23S rRNA结构域Ⅴ区位点A2063G、A2064G突变的肺炎支原体肺炎患儿发展为难治性肺炎支原体肺炎的可能性增大,检测23S rRNA结构域Ⅴ区位点A2063G、A2064G的突变情况对判断肺炎支原体肺炎患儿病情和制定治疗方案具有重要意义。

用组织芯片研究结直肠腺癌组织中nm23mRNA,CD44s和CD44v6的表达意义

目的 研究 nm2 3m RNA,CD44 s和 CD44 v6表达与结直肠腺癌发生、发展及转移的关系 .方法 应用组织芯片技术 ,通过原位杂交和免疫组织化学方法分别检测 40例结直肠腺癌标本和 2 2例正常结直肠组织标本中 nm2 3m RNA,CD44 s和 CD44 v6表达情况 .结果 nm2 3m RNA在结直肠腺癌组织和正常组织中表达无显著性差异 (P>0 .0 5 ) ,且与结直肠腺癌的分化程度无相关性 (P>0 .0 5 ) ,但与癌细胞的侵润及淋巴结转移呈明显负相关 (r=- 0 .49,P<0 .0 1) .CD44 s在结直肠腺癌组织和正常组织中阳性率分别为 42 %(17/ 40 )和 18. 1%(4 / 2 2 ) ,有显著性差异 (P <0 .0 5 ) ,而CD44 v6只在结直肠腺癌组织中表达 ,阳性率为 5 5 . 8%(2 2 / 40 ) ,且与结直肠腺癌淋巴结转移和癌侵润呈明显正相关(r=0 .47,P<0 .0 1) .在高、中分化腺癌组织中 ,CD44 v6阳性率分别为 45 .8%(11/ 2 4)和 6 8.7%(11/ 16 ) ,有显著性差异(P<0 .0 5 ) ,但在直肠腺癌组织与结肠腺癌组织间表达无显著性差别 (P>0 .0 5 ) .结论 CD44 s、CD44 v6在结直肠腺癌组织中过量表达伴随 nm 2 3m RNA表达缺失 ,与结直肠腺癌转移和侵润密切相关 ,联合检测 3种基因能更准确判断结直肠腺癌转移和侵润状态 . CD44 v6表达过量与结直肠腺癌分化程度相关 .

基于18 S rRNA的鸡组织滴虫病PCR诊断方法的建立

河南某鸡场约4周龄鸡疑似发生鸡组织滴虫病。根据鸡组织滴虫18 S rRNA序列设计引物,提取肝脏、盲肠内容物寄生虫DNA,采用PCR方法检测。结果表明,PCR扩增到与预期大小一致的产物,经测序比对,证实为鸡组织滴虫感染。所建立的PCR方法具有灵敏、特异、快速等优点,不仅能用于鸡组织滴虫病临床诊断,还能用于开展流行病学研究。

Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification

AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into eight diarrhoea-predominant (IBS-D),eight constipation-predominant(IBS-C)and four mixed symptom-subtype(IBS-M)IBS patients,and fifteen control subjects,were analysed at three time-points with a set of fourteen quantitative real-timepolymerase chain reaction assays.All assays targeted 16S rRNA gene phylotypes putatively associated with IBS,based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobac-teria,Bacteroidetes and Firmicutes.Eight of the target phylotypes had less than 95%similarity to cultured bacterial species according to their 16S rRNA gene sequence.The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis(PCA)with linear mixed-effects models applied to the principal component scores. RESULTS:Bacterial phylotypes Clostridium cocleatum 88%,Clostridium thermosuccinogenes 85%,Coprobacillus catenaformis 91%,Ruminococcus bromii-like, Ruminococcus torques 91%,and R.torques 93%were detected from all samples analysed.A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups.The PCA on the first principal component(PC1),explaining 30.36%of the observed variation in the IBS-D patient group,was significantly altered from all other sample groups(IBS-D vs control, P=0.01;IBS-D vs IBS-M,P=0.00;IBS-D vs IBS-C, P=0.05).Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria.A phy- lotype with 85%similarity to C.thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects(-4.08±0.90 vs -3.33±1.16,P=0.04)and IBS-D and IBS-M subjects (-4.08±0.90 vs-3.08±1.38,P=0.05).Furthermore,a phylotype with 94%similarity to R.torques was more prevalent in IBS-D patients'intestinal micro- biota than in that of control subjects(-2.43±1.49 vs -4.02±1.63,P=0.01).A phylotype with 93%simi- larity to R.torques was associated with control sam- ples when compared with IBS-M(-2.41±0.53 vs -2.92±0.56,P=0.00).Additionally,a R.bromii-like phylotype was associated with IBS-C patients in com- parison to control subjects(-1.61±1.83 vs-3.69± 2.42,P=0.01).All of the above mentioned phylotype specific alterations were independent of the effect of time. CONCLUSION:Significant phylotype level alterationsin the intestinal microbiotas of IBS patients were observed,further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.

Correlation analysis of breast fibroadenoma and the intestinal flora based on 16S rRNA sequencing

Objective To analyze the characteristics of the intestinal microflora in patients with breast fibroadenoma using 16S ribosomal RNA(rRNA)high-throughput sequencing.Methods Fecal samples from 20 patients with breast fibroadenoma and 36 healthy subjects were randomly collected and analyzed using high-throughput sequencing technology for 16S rRNA V4 region sequencing,and the alpha diversity(Chao index,Shannon index)was calculated using Mothur(v.1.39.5)software.Beta diversity was analyzed using QIIME(v1.80).SPSS software(version 23.0)and the t-test of two independent samples were used to analyze differences in the abundance of bacteria between the two groups.Results Compared with that in the healthy control group,theαdiversity of the intestinal microflora in breast fibroadenoma patients increased,but the difference was not statistically significant(P>0.05).At the phylum level,significant differences were observed between the two groups.The abundance of Firmicutes was higher in the breast fibroadenoma group(P<0.05),whereas the abundance of Synergistetes was higher in the healthy control group(P<0.005).A total of five bacterial genera showed significant differences between the two groups:the breast fibroadenoma group showed higher levels of Bautia(P<0.005),Coprococcus(P<0.005),Roseburia(P<0.05),and Ruminococcus(P<0.005),whereas Sutterella was more abundant in the healthy control group than in the breast fibroadenoma group(P<0.05).Conclusion The diversity and abundance of the intestinal flora in patients with breast fibroadenoma are significantly different from those in healthy subjects,suggesting that an imbalance in the intestinal flora is correlated with the occurrence of breast fibroadenoma.

Hydrogen bonds are related to the thermal stability of 16S rRNA

The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal growth temperature (OGT) rather than with the G + C content. Paired and unpaired nucleotides in mesophiles were compared to those in thermophiles. OGT exhibited a relationship with paired nucleotides but not with unpaired nucleotides. The total number of paired as well as unpaired nucleotides in mesophiles was very similar to that in thermophiles. However, the components in base pairs in mesophiles significantly differed from those in thermophiles. As compared with mesophiles, the number of G·C base pairs in thermophiles was high whereas that of A·U base pairs was low. In this study, we showed that hydrogen bonds are important for stabilizing 16S rRNAs at high temperatures.

解脲脲原体23SrRNA位点突变与大环内酯类药物耐药的关系

目的探讨解脲脲原体（Ureaplasma urealyticum，Uu）对大环内酯类药物的耐药机制。方法临床分离的20株对大环内酯药物不同耐药表型的Uu，其中6株为敏感株，采用PCR、DNA测序方法检测其23SrRNA基因序列，与对大环内酯类药物敏感的标准菌株ATCC27618及基因库中的标准菌株基因序列对比分析查找突变位点，并分析突变位点与耐药表型的关系。结果Uu菌株23SrRNA突变位点与其对大环内酯药物耐药表型对照分析结果表明，5株耐药表型为罗红霉素（R）和阿奇霉素（R）的菌株中均存在C2243N（TorC）变异，其中1株伴有A2149C，A2181T；9株耐药表型为罗红霉素（R）和阿齐霉素（I）的Uu菌株和6株表型为罗红霉素（S）和阿奇霉素（S）的Uu菌株中均存在A2149C，A2181T的变异。结论初步判断Uu23SrRNA C2243N（T或C）变异可能导致其对罗红霉素、阿奇霉素产生耐药，具体的相关性尚需大样本深入研究。

应用巢式聚合酶链反应和测序检测肺炎支原体23S rRNA中点突变

目的建立快速检测肺炎支原体（Mycoplasrna pneumoniae，MP）耐药性的实验方法并应用于临床以了解MP耐药现状。方法应用巢式PCR直接检测咽拭子标本MP-23S rRNA基因并对扩增产物进行电泳检测或DNA测序分析；通过MP培养及体外药物敏感性试验测定临床分离株的红霉素最小抑菌浓度，以验证23S rRNA基因检测结果的可靠性。结果200例临床标本经MP-IgM抗体、咽拭子MP种特异性16S rRNA基因巢式PCR扩增和MP分离培养测定证实为MP64例。应用巢式PCR技术扩增MP-23S rRNA基因，并对扩增产物进行测序，将基因序列与基因库中MP标准株基因序列进行比较，与标准株序列相同的共计26例，其余38例存在23S rRNA点突变：35例在2063位点发生了A到G的点突变，1例在2063位点有A到C的点突变，2例在2064位点有A到G的点突变；耐药率为59．4％。MP耐药基因检测方法灵敏度达10^2ccu／ml，MP培养及药物敏感性试验证实23S rRNA基因检测结果可靠。结论建立的MP耐药基因检测方法能直接检测临床标本中的MP耐药基因。59％的受检标本23S rRNA基因发生点突变。

利奈唑胺体外诱导粪肠球菌耐药株23S rRNA V区基因突变位点分析

目的阐明体外诱导利奈唑胺耐药粪肠球菌的核糖体23SrRNA V区基因位点变异特征。方法收集1株血流感染的粪肠球菌和1株粪肠球菌质控菌ATCC29212(编号分别为F3和F4菌株,均为利奈唑胺敏感株),通过体外浓度倍增法诱导利奈唑胺耐药;挑取单克隆,经E-test条测定MIC值,获得各菌株的耐药浓度梯度;提取耐药菌株基因组DNA,PCR扩增23SrRNA V区基因,扩增产物经测序后与野生株比较,获得V区的突变位点。结果经体外多步法诱导利奈唑胺耐药的不同MIC值粪肠球菌共13株。PCR测序分析2株母株均无变异位点,23SrRNA V区的突变位点主要是G2576U,此外还有T2504A、G2505A、C2610A、C2424U。结论体外多步法可诱导粪肠球菌利奈唑胺耐药,耐药机制与23SrRNA V区位点突变密切相关,突变位点随着MIC值的增高而增多。

细菌16S-23S rRNA基因特异DNA图谱的分子诊断

目的 应用聚合酶链反应 (PCR)、限制性内切酶片段长度多态性分析 (RFLP)及测序技术 ,建立检测不同属种细菌的 16S 2 3SrRNA基因区间的特异图谱。方法 对临床上常见的细菌进行PCR扩增、RFLP、分子克隆及序列分析 ,同时对临床标本进行培养与PCR RFLP比较。结果 2 7株不同细菌行PCR扩增后 ,得到不同DNA图谱。其中 15种细菌经PCR扩增即可区分 ,另 10种经HinfI或AluI酶切后才能区分。肺炎克雷伯菌与坚韧肠球菌的差异只在第 779位碱基上不同 ,XmaIII酶能区别。 42例临床诊断为新生儿败血症者 ,15例培养阳性 ,阳性率 3 5 7% ;而PCR阳性者则为 2 7例 ,阳性率为 64 2 9% ,明显高于血培养 (P <0 0 1)。 6例脑脊液标本中 ,1例PCR及培养均阳性 (表皮葡萄球菌 ) ;2例培养阴性标本 ,其PCR也阳性 ;经图谱分析为葡萄球菌 ,1例培养为新型隐球菌的脑脊液标本PCR检测为阴性。另 2例PCR及培养均阴性。结论 建立了PCR RFLP技术快速检测细菌 16S 2 3SrRNA基因区间的方法 ,具有特异、敏感、快速、准确的特点 ,为临床细菌感染的病原诊断提供新的科学依据。

沈阳地区肺炎支原体23SrRNA基因突变初步研究

目的:了解沈阳地区的肺炎支原体(Mycoplasma pnemoniae,MP)23SrRNA基因的突变现状,为进一步认识突变MP所致肺炎支原体肺炎(MPP)的临床表现及其治疗打下基础。方法:对180例疑似MPP住院患儿咽拭子标本提取MP-DNA应用荧光探针定量PCR(FQ-PCR)技术进行分子鉴定,并于患儿病程7天后采血,应用颗粒凝胶法(PA)进行肺炎支原体抗体测定;对两者均阳性标本应用巢式PCR扩增23SrRNA基因并进行电泳检测及DNA测序分析,将测得序列与基因库中MP标准株基因序列进行比较。结果:180例临床标本荧光探针定量和肺炎支原体抗体均确定阳性52例,应用巢式PCR技术扩增MP-23SrRNA基因,并对扩增产物进行测序,测出45例,45例23SrRNA中均存在2063位A→G的点突变,其中2例为2063位点A、G碱基共存,考虑为敏感株与耐药株共生,突变率100%。结论:沈阳地区MP23SrRNA基因中普遍存在点突变,突变MP与患儿的临床特点有何联系有待于进一步研究。

Novel mitochondrial 16S rRNA mutation, 3200T→C, associated with adult-onset type 2 diabetes

Objective To investigate the role of a potential diabetes related mitochondrial region, which includes two previously reported mutations, 3243AG and 3316GA, in Chinese patients with adult onset type 2 diabetes Methods A total of 277 patients and 241 normal subjects were recruited for the study Mitochondrial nt 3116-3353, which spans the 16S rRNA, tRNA leu(UUR) and the NADH dehydrogenase 1 gene, were detected using polymerase chain reaction (PCR), direct DNA sequencing, PCR restriction fragment length polymorphism and allele specific PCR Variants were analyzed by two tailed Fisher exact test The function of the variants in 16S rRNA were predicted for minimal free energy secondary structures by RNA folding software mfold version 3 Results Four homoplasmic nucleotide substitutions were observed, 3200TC, 3206CT, 3290TC and 3316GA Only the 3200TC mutation is present in the diabetic population and absent in the control population No statistically significant associations were found between the other three variants and type 2 diabetes The 3200TC and 3206CT nucleotide substitutions located in 16S rRNA are novel variants The 3200TC caused a great alteration in the minimal free energy secondary structure model while the 3206CT altered normal 16S rRNA structure little Conclusions The results suggest that the 3200TC mutation is linked to the development of type 2 diabetes, but that the other observed mutations are neutral In contrast to the Japanese studies, the 3316GA does not appear to be related to type 2 diabetes

Changes in the gut microbiota of osteoporosis patients based on 16S rRNA gene sequencing:a systematic review and meta-analysis

Background:Osteoporosis(OP)has become a major public health issue,threatening the bone health of middle-aged and elderly people from all around the world.Changes in the gut microbiota(GM)are correlated with the maintenance of bone mass and bone quality.However,research results in this field remain highly controversial,and no systematic review or meta-analysis of the relationship between GM and OP has been conducted.This paper addresses this shortcoming,focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA(rRNA)gene sequencing results,in order to provide new clinical reference information for future customized prevention and treatment options of OP.Methods:According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA),we comprehensively searched the databases of Pub Med,Web of Science,Embase,Cochrane Library,and China National Knowledge Infrastructure(CNKI).In addition,we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis.We also implemented the Newcastle-Ottawa Scale(NOS),funnel plot analysis,sensitivity analysis,Egger’s test,and Begg’s test to assess the risk of bias.Results:This research ultimately considered 12 studies,which included the fecal GM data of 2033 people(604 with OP and 1429 healthy controls).In the included research papers,it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group,while the relative abundance for Bacteroides of Bacteroidetes increased(except for Ireland).Meanwhile,Firmicutes,Blautia,Alistipes,Megamonas,and Anaerostipes showed reduced relative abundance in Chinese studies.In the linear discriminant analysis Effect Size(LEfSe)analysis,certain bacteria showed statistically significant results consistently across different studies.Conclusions:This observational meta-analysis revealed that changes in the GM were correlated with OP,and variations in some advantageous GM might involve regional differences.

Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40 S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40 S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation(RMSD) value of 3.9 ? relative to the template's crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying thisapproach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

阿尔茨海默病患者肠道菌群改变与认知功能损伤的相关性

目的探讨阿尔茨海默病(Alzheimer′s disease,AD)患者肠道菌群改变及其与认知功能损伤相关性。方法根据临床痴呆评定量表(CDR),将35例AD患者分为轻中度组(n=15)和重度组(n=20),收集两组患者的粪便样本,对粪便标本进行16S rRNA高通量测序分析粪便中微生物群的组成和肠道菌群β多样性。采用调查问卷及量表调查AD患者的一般情况、抑郁状态及认知损伤程度。通过血液检测AD患者白细胞、甘油三酯、胆固醇、高密度脂蛋白(HDL)、低密度脂蛋白(LDL)、载脂蛋白A(ApoA)、载脂蛋白B(ApoB)、载脂蛋白E(ApoE)、脂蛋白a(Lpa)、血糖(Glu)、糖化血红蛋白(HbA1c),采用R软件进行粪便菌群与上述指标的相关性分析。结果AD重度组简易精神状态检查量表(MMSE)、重复性成套神经心理状态测验(RBANS)分值均低于AD轻中度组(P<0.01)。肠道菌群β多样性分析结果提示两组间菌群多样性差异有统计学意义(P<0.05)。重度组和轻中度组肠道菌门相对丰度及属相对丰度差异都有统计学意义(P<0.05)。AD患者大肠杆菌、志贺菌与Lpa呈正相关(P<0.01),与LDL呈负相关(P<0.05);双歧杆菌与RBANS、高脂血症呈正相关(P<0.05),与Lpa呈负相关(P<0.01);克雷伯杆菌与病程、CDR呈正相关(P<0.01);阿克曼菌与HLP呈负相关(P<0.05);肠球菌与CDR呈正相关(P<0.05);乳酸杆菌与年龄呈正相关(P<0.05);粪杆菌与CDR、病程、年龄和MMSE负相关(P<0.05)。结论AD患者伴随肠道菌群的改变,AD患者认知功能的损伤及其严重程度与肠道菌群多样性和相对丰度有关。