New preparation techniques for molecular and in‐situ analysis of ancient organic micro‐ and nanostructures

Organic microfossils preserved in three dimensions in transparent mineral matrices such as cherts/quartzites, phosphates, or carbonates are best studied in petrographic thin sections. Moreover, microscale mass spectrometry techniques commonly require flat, polished surfaces to minimize analytical bias. However, contamination by epoxy resin in traditional petrographic sections is problematic for the geochemical study of the kerogen in these microfossils and more generally for the in situ analysis of fossil organic matter. Here, we show that epoxy contamination has a molecular signature that is difficult to distinguish from kerogen with time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). This contamination appears pervasive in organic microstructures embedded in micro‐ to nano‐crystalline carbonate. To solve this problem, a new semi‐thin section preparation protocol without resin medium was developed for micro‐ to nanoscale in situ investigation of insoluble organic matter. We show that these sections are suited for microscopic observation of Proterozoic microfossils in cherts. ToF‐SIMS reveals that these sections are free of pollution after final removal of a <10 nm layer of contamination using low‐dose ion sputtering. ToF‐SIMS maps of fragments from aliphatic and aromatic molecules and organic sulfur are correlated with the spatial distribution of organic microlaminae in a Jurassic stromatolite. Hydrocarbon‐derived ions also appeared correlated with kerogenous microstructures in Archean cherts. These developments in analytical procedures should help future investigations of organic matter and in particular, microfossils, by allowing the spatial correlation of microscopy, spectroscopy, precise isotopic microanalyses, and novel molecular microanalyses such as ToF‐SIMS.     

New Approaches for Absolute Quantification of Stable‐Isotope‐Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag

Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re‐quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.     

A genome‐wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (N_e) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome.     

复合菌剂M5对红螯螯虾(Cherax quadricarinatus)高密度养殖系统水质及其肠道微生物群落影响的初步研究

应用自制复合菌剂M5于红螯螯虾(Cherax quadricarinatus)的高密度养殖系统中,通过分析肠道菌群并监测养殖水质,研究了复合菌剂作用的效果及潜在的机理。结果显示,复合菌剂M5的使用可显著降低养殖水环境的pH值,降低污染物NH⁺₄、NO^-₂和COD的浓度,抑制弧菌属（Vibrio）中某些条件致病菌的生长。基于PICRUSt与KEGG数据库的功能预测及肠道菌群的群落分析,复合菌剂既可作为额外的营养补充物,缓解肠道群落之间对营养源的竞争,又可提高虾的消化能力、免疫力。新型复合菌剂M5可显著改善养殖水质并影响肠道菌群的组成与功能,从而提高养殖存活率。     

微生态制剂在早期结直肠癌根治术后的作用

目的探讨微生态制剂在早期结直肠癌(CRC)根治术后的作用,并为此类患者提供一种术后康复支持疗法。方法选取2017年6月-2019年6月于本院接受早期CRC根治术术后97例患者作为研究对象,采用随机数字表分为观察组50例和对照组47例。两组术后均接受常规治疗,观察组在对照组基础上接受双歧杆菌三联活菌胶囊治疗,比较两组治疗前后细胞免疫指标、肠道微生态复杂度及属水平相对丰度、肠道菌群OTU数量、肠道黏膜屏障功能。结果治疗后观察组NK细胞、CD3~+T、CD4~+T、CD4~+/CD8~+T均提高(P0.05),观察组CD8~+T治疗前后相近(P0.05);治疗后对照组上述指标与治疗前差异均无统计学意义(P0.05),观察组NK细胞、CD3~+T、CD4~+T、CD4~+/CD8~+T均高于对照组(P0.05);治疗后观察组Chao1指数、Shannon指数、肠道菌群OTU数均升高(P0.05),对照组Chao1指数、Shannon指数、肠道菌群OTU数量治疗前后差异均无统计学意义(P0.05);治疗后观察组Chao1指数、Shannon指数、肠道菌群OTU数量均高于对照组(P0.05);治疗后观察组大肠杆菌、肠球菌、葡萄球菌属水平相对丰度均下降(P0.05),对照组均升高(P0.05),且观察组均低于对照组(P0.05);治疗后观察组乳杆菌、双歧杆菌、梭菌、类杆菌、链球菌属水平相对丰度均升高(P0.05),对照组均下降(P0.05),且观察组均高于对照组(P0.05);治疗后观察组血浆D-乳酸、DAO、I-FABP、内毒素水平分别为(6.94±1.23)mg/L、(3.45±0.65)U/L、(43.95±7.99)μg/L、(4.48±0.85)U/L,均较治疗前下降(P0.05),对照组各项指标水平分别为(15.59±2.79)mg/L、(7.74±1.35)U/L、(74.21±13.82)μg/L、(8.68±1.65)U/L,均较治疗前升高(P0.05),治疗后观察组血浆D-乳酸、DAO、I-FABP、内毒素水平均降低(P0.05)。结论微生态制剂可有效改善早期CRC患者根治术后的细胞免疫水平,有效纠正早期CRC术后患者肠道菌群失调,增强早期CRC根治术后患者肠黏膜屏障功能。     

微生态制剂对细菌性痢疾的辅助治疗及对患者血清C反应蛋白水平的影响

目的探讨微生态制剂对细菌性痢疾的辅助治疗及对患者血清C反应蛋白(CRP)水平的影响。方法选取2016年3月至2018年10月在我院门诊接受治疗的86例细菌性痢疾患者为研究对象,入选患者随机分为对照组和观察组,每组43例。对照组患者给予常规药物进行治疗,观察组患者在此基础上加用布拉氏酵母菌散辅助治疗。比较两组患者临床疗效,不良反应发生率及血清CRP水平。结果治疗后观察组患者临床总有效率为90.40%,显著高于对照组的69.77%,差异有统计学意义(χ^2=5.939,P=0.015)。观察组患者不良反应发生率为9.3%,显著低于对照组的34.88%,差异有统计学意义(χ^2=8.174,P=0.004)。同时,观察组患者治疗后血清CRP水平为(4.32±0.43)mg/L,显著低于对照组的(7.03±0.32)mg/L,差异有统计学意义(t=33.154,P<0.001)。结论微生态制剂辅助治疗细菌性痢疾的临床疗效优于常规治疗方法,能降低患者血清CRP水平,减少患者不良反应,安全有效,值得临床推广。     

Aidi injection,a traditional Chinese biomedical preparation for gynecologic tumors: a systematic review and PRISMA-compliant meta-analysis

Aidi injection (ADI), a traditional Chinese biomedical preparation, is a promising adjuvant therapy for gynecologic tumors (GTs), including cervical cancer (CC), endometrial cancer (EC), and ovarian cancer (OC). Although studies have reported positively on ADI therapy, its exact effects and safety in GT patients remain controversial. Therefore, a wide-ranging systematic search of electronic databases was performed for this meta-analysis. Data from 38 trials including 3309 GT patients were analyzed. The results indicated that the combination of conventional treatment and ADI markedly improved the patients’ overall response rate (P<0.00001), disease control rate (P<0.00001), and quality of life (P<0.05) compared with conventional treatment alone. Furthermore, patient immunity was enhanced with combined treatment, as indicated by significantly increased percentages of CD3⁺ (P=0.005) and CD4⁺ (P<0.00001) and increased CD4⁺/CD8⁺ ratio (P=0.001). Most of the adverse events caused by radiochemotherapy such as gastrointestinal issues, leukopenia, thrombocytopenia, and hepatotoxicity, (P<0.05 for all) were significantly alleviated when ADI was used in the GT patients. However, other adverse events such as nephrotoxicity, diarrhea, alopecia, and neurotoxicity did not significantly differ between the two groups. Overall, these results suggest that the combination of conventional and ADI treatment is more effective than conventional treatment alone.     

Assessment of exploited fish species in the Lake Edward System,East Africa

The unknown status of inland fish stocks hinders their sustainable management. Therefore, increasing stock status information is important for sustainable inland fisheries. Fisheries reference points were estimated for five exploited fish species (11 stocks) in the Lake Edward system, East Africa, which is one of the most productive inland water systems. The aim was to ascertain the status of the fisheries and establish reference points for effective management. The reference points were based on four linked stock assessment approaches for data-limited fisheries. Estimates showed poor stock status with the stocks defined as either collapsed, recruitment impaired or overfished. However, higher catches could be obtained under sustainable management. Estimates of maximum sustainable yield (MSY) and supporting biomass (B_msy) are provided for 10 of the stocks as targets for rebuilding plans. The immediate target of management should be rebuilding biomass to B_msy. Applicable measures include shifting length at first capture to the length that maximizes catch without endangering size structure and biomass, and livelihood diversification out of fisheries.     

黄芩苷铝胁迫下产肠毒素大肠杆菌内参基因的筛选

【背景】产肠毒素大肠杆菌(Enterotoxigenic Escherichia coli,ETEC)是导致仔猪腹泻的主要致病菌之一,黄芩苷铝对ETEC诱导的仔猪腹泻具有良好的治疗效果,但作用机制尚不明了。【目的】筛选出黄芩苷铝胁迫下ETEC中表达水平最为稳定的内参基因。【方法】采用qPCR技术测定了12个内参基因16S rRNA、mdh、recA、gapA、gyrA、gyrB、rpoA、rpoB、mdoG、dnaG、secA和fusA在不同浓度(250、500和1 000μg/mL)黄芩苷铝胁迫下培养不同时间后(4.5 h和6 h)的表达水平,并采用比较Ct值法、geNorm、BestKeeper和NormFinder软件4种方法对12个候选内参基因的表达稳定性进行评估。【结果】rpoA表达丰度适中,并在多个分析方法中表达最稳定。【结论】确定了rpoA为ETEC qPCR的最佳内参基因,此研究为后续利用qPCR法研究黄芩苷铝胁迫ETEC后目的基因功能的表达奠定了基础。