Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes

Bacterial diversity of the mucosal biopsies from human jejunum, distal ileum, ascending colon and rectum were compared by analysis of PCR-amplified 16S rDNA clone libraries. A total of 347 clones from the mucosal biopsies were partially sequenced and assigned to six phylogenetic phyla of the domain Bacteria: Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, and Actinobacteria. The jejunum sample had least microbial diversity compared to the other samples and a trend towards highest diversity in ascending colon was observed. The clone libraries of distal ileum, ascending colon and rectum were not significantly different from each other (P>0.0043), but they differed significantly from the jejunum library (P=0.001). The population of sequences retrieved from jejunal biopsies was dominated by sequences closely related to Streptococcus (67%), while the population of sequences derived from distal ileum, ascending colon and rectum were dominated by sequences affiliated with Bacteroidetes (27-49%), and Clostridium clusters XIVa (20-34%) and IV (7-13%). The results indicate that the microbial community in jejunum is different from those in distal ileum, ascending colon and rectum, and that the major phylogenetic groups are similar from distal ileum to rectum.     

Determination of an Optimal Standardized Uptake Value of Fluorodeoxyglucose for Positron Emission Tomography Imaging to Assess Pathological Volumes of Cervical Cancer: A Prospective Study

Purpose

To determine the optimal standardized uptake value (SUV) of ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) for positron emission tomography (PET) imaging, at which the PET-defined gross tumor volume (GTV_PET) best matches with the pathological volume (GTV_PATH) in the cervical cancer.

Materials and Methods

Ten patients with the cervical cancer who underwent surgery were enrolled in this study. The excised specimens were processed for whole-mount serial sections and H-E staining. The tumor borders were outlined in sections under a microscope, histopathological images were scanned and the GTV_PATH calculated. The GTV_PET was delineated automatically by using various percentages relative to the maximal SUV and absolute SUV. The optimal threshold SUV was further obtained as the value at which the GTV_PET best matched with the GTV_PATH.

Results

An average of 85±10% shrinkage of tissue was observed after the formalin fixation. The GTV_PATH was 13.38±2.80 cm³ on average. The optimal threshold on percentile SUV and absolute SUV were 40.50%±3.16% and 7.45±1.10, respectively. The correlation analysis showed that the optimal percentile SUV threshold was inversely correlated with GTV_PATH (p<0.05) and tumor diameter (p<0.05). The absolute SUV was also positively correlated with SUV_max (p<0.05).

Conclusion

The pathological volume could provide the more accurate tumor volume. The optimal SUV of FDG for PET imaging by use of GTV_PATH as standard for cervical cancer target volume delineation was thus determined in this study, and more cases are being evaluated to substantiate this conclusion.     

3，4苯并芘对内皮祖细胞生物学功能的影响

目的研究3,4苯并芘（BaP）对人脐血来源的内皮祖细胞（EPC）生物学功能的影响。方法密度梯度离心法分离获取人脐血单个核细胞,采用贴壁培养法培养MNC中的EPC,通过Dil标记的乙酰化低密度脂蛋白（Dil-ac-LDL）摄取实验和FITC标记的植物凝集素（FITC-UEA-I lectin）结合实验鉴定细胞。消化收集第3代细胞,分别采用细胞计数试剂盒（CCK-8）、黏附能力测定实验、Transwell小室法及Matrigel体外成血管试验观察BaP对EPC增殖能力、粘附能力、迁移能力及成血管能力的影响,并检测各组细胞培养上清液SOD含量。采用单因素方差分析及LSD-t检验进行统计学分析。结果采用贴壁培养法能成功培养出EPC;与正常对照组相比,BaP呈浓度依赖性降低EPC的增殖能力{正常对照组OD（1.02±0.04）显著高于BaP各组[BaP①组OD（0.66±0.04）,BaP②组OD（0.55±0.04）,BaP③组OD（0.35±0.05）,均P〈0.01],BaP染毒组间增殖能力差异亦有统计学意义（两两比较,均P〈0.01）};与正常对照组比较,BaP呈浓度依赖性降低EPC的黏附能力{正常对照组[（117.50±17.16）个/200倍镜]显著高于BaP各组[BaP①组（80.00±14.46）个/200倍镜,BaP②组（66.00±9.06）个/200倍镜,BaP③组（49.80±10.72）个/200倍镜,均P〈0.01],BaP染毒组间黏附能力差异亦有统计学意义（两两比较,均P〈0.05）};与正常对照组相比,EPC的迁移能力亦呈BaP浓度依赖性降低{正常对照组[（46.10±4.51）个/400倍镜]显著高于BaP各组[BaP①组（35.50±4.95）个/400倍镜,BaP②组（26.80±4.08）个/400倍镜,BaP③组（19.50±2.84）个/400倍镜,均P〈0.01],BaP染毒组间迁移能力差异亦有统计学意义（两两比较,均P〈0.01）};与正常对照组比较,EPC的成血管能力亦呈BaP浓度依赖性降低{正常对照组[（33.20±3.70）个/100倍镜]显著高于BaP各组[BaP①组（22.00±3.39）个/100倍镜,BaP②组（16.20±2.59）个/100倍镜,BaP③组（10.80±2.39）个/100倍镜,均P〈0.01],BaP染毒组间成血管能力差异亦有统计学意义（两两比较,均P〈0.05）}。同时细胞培养上清液中SOD的活力也呈BaP浓度依赖性地降低{正常对照组[（22.6±2.19）U/ml]高于BaP各组[BaP①组（15.94±1.68）U/ml,BaP②组（12.5±1.58）U/ml,BaP③组（6.9±1.55）U/ml,均P〈0.01],BaP染毒组间SOD活力差异亦有统计学意义（两两比较,均P〈0.01）}。结论 BaP体外诱导显著影响EPC的多种生物学功能,其机制可能与氧化损伤有关。     

餐厨垃圾高温好氧生物减量菌种的筛选及特性

【背景】随着餐厨垃圾产生量的逐步提高,如何实现其快速降解,成为餐厨垃圾处理亟待解决的问题。餐厨垃圾的高温好氧生物减量技术是一种可以快速降解餐厨垃圾的有效方法。【目的】筛选能够适应餐厨垃圾环境且具有高效降解餐厨垃圾中有机物能力的菌株,以提高餐厨垃圾的降解效率和减量效果。【方法】采用温度梯度耐受性实验和餐厨垃圾浸出液高油高盐耐受性实验进行菌种初筛,并利用产酶培养基复筛及餐厨垃圾生物减量实验验证。【结果】通过初筛、复筛和功能验证,最终获得4株生物减量效果优良的菌株N3-1、C7、N3-3和G6-1,其对餐厨垃圾挥发性固体(volatile solid,VS)的降解率分别为36.95%、33.23%、32.83%和31.91%,是对照组的3.02、2.71、2.68和2.61倍。经鉴定,这4株菌分别属于热嗜油地芽孢杆菌(Geobacillus thermoleovorans)、史氏芽孢杆菌(Bacillus smithii)、热解木糖地芽孢杆菌(Geobacillus caldoxylosilyticus)和立陶宛地芽孢杆菌(Geobacillus lituanicus)。【结论】筛选出的4株菌均具有较强的餐厨垃圾原料适应性和高效的生物降解能力,为开发餐厨垃圾高温好氧复合菌剂奠定了基础,并为实现餐厨垃圾减量化、无害化处理和资源化利用提供了技术支持。     

宁夏云雾山典型草原灌丛化过程中植被和土壤演变特征

干旱半干旱区灌木、半灌木等木本植物的分布面积持续增加(灌丛化)显著改变了原有植被景观及生态过程,但缺乏对长期封育过程中灌木物种取代草本物种进而影响草地群落组成、结构和功能的研究。为揭示长期封育措施下典型草原灌丛化特征及地上/地下植物群落的响应规律,研究通过对宁夏云雾山典型草原同一封育草地不同时间(2010年、2016年、2021年)植物群落(物种重要值、丰富度、多样性和生物量)和土壤特性(土壤容重、土壤水分及储水量、养分、pH)的定点观测,探讨了长期封育过程中灌木物种矮脚锦鸡儿(Caragana brachypoda)驱动的植被和土壤特性变化。结果表明,(1)灌木矮脚锦鸡儿已经取代草本植物成为封育草地的优势种,群落中灌木生物量、总生物量以及盖度、高度显著增加,但对植物密度的影响较小;(2)灌丛化过程中草地群落Patrick丰富度指数、Simpson优势度指数和Shannon-Wiener多样性指数显著降低,而Pielou均匀度指数显著增加;(3)灌丛化引起土壤深层(60-100 cm)容重显著增大,土层储水量随土层深度的增加呈先减少后增加的趋势;(4)灌丛化使得土壤有机碳含量在浅层(0...     

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Optimization of covalent immobilization of pectinase on sodium alginate support

Pectinase was immobilized on a sodium alginate support using glutaraldehyde and retained 66% activity. The optimal pH for activity shifted from 3.0 to 3.5 after immobilization; however, the optimum temperature remained unchanged at 40°C. The immobilized enzyme also had a higher thermal stability and reusability than the free enzyme, and retained 80% of initial activity after 11 batch reactions.     

持久性有机污染物γ-六六六生物降解研究进展

γ-六六六(γ-Hexachlorocyclohexane,γ-HCH)是一种有机氯杀虫剂,由于它具有持久性和很高的毒性,成为顽固性的世界性污染物。目前从世界上不同的受HCH污染的地区中已经分离出许多能够降解HCH的微生物,其中一些微生物对γ-HCH的降解途径得到了阐明,降解基因/酶也得到了鉴定。综述了γ-HCH降解菌的多样性、降解途径、降解基因和酶,为γ-HCH的生物修复提供了参考。     

萝卜花粉的营养成分研究

萝卜花粉的营养成分测定表明,其蛋白质含量28.38%,总糖含量33.33%,氨基酸总量27.59%,总黄酮含量3.57%,维生素和矿质元素含量亦较丰富。萝卜花粉资源丰富,营养成分齐全,具有很好的开发利用价值。