利用神经网络集成预测MHC-Ⅰ类分子结合肽

目的：利用神经网络集成（NNE）预测MHC-Ⅰ类分子结合肽。 方法： 基于HLA-A*0201编码的MHC-Ⅰ类分子结合肽数据库（含有628个9聚物）及其结合能力分类，利用NNE分别对具有无、低、中和高4类亲合性的结合肽进行分类预测；同时还进一步利用T细胞真实表位集（含50个表位）评估了NNE的预测性能。 结果： 集成数为12的NNE对上述分类的平均预测命中率可达0.8,而且NNE对潜在T细胞表位的预测能力也较高，约84%的真实表位归于高和中等亲合性的潜在抗原肽一类。 结论： 可以利用神经网络集成预测MHC-Ⅰ类分子结合肽，并进而预测相应的T细胞表位。经适当修改，NNE预测工具可扩展为能涵盖任意长度的Ⅰ类分子结合肽甚至可扩展到Ⅱ类分子结合肽的预测。     

Comparison of amplified Q beta replicase and PCR assays for detection of Mycobacterium tuberculosis.

Because of the long time required to isolate Mycobacterium tuberculosis in culture, there is an acute need for simple rapid methods for direct detection of M. tuberculosis from human sputum specimens. We have developed and characterized quantitative manual Q beta replicase and PCR assays for M. tuberculosis. The Q beta replicase assay was based on reversible target capture of M. tuberculosis 23S rRNA followed by amplification of a replicatable detector probe with Q beta replicase. For PCR assays, primers generating a 370-bp amplification product from the IS6110 insertion element were used in combination with a control plasmid containing an internal deletion in the IS6110 amplicon. Serial dilutions of M. tuberculosis were spiked into sputum and subjected to digestion and decontamination with N-acetyl-L-cysteine and NaOH. Assay conditions were optimized for hybridization and sample processing chemistries in order to maximize sample utilization. Following assay optimization, the sensitivities of the Q beta replicase and PCR assays of spiked sputum samples were 0.5 and 5.0 CFU per assay reaction, respectively. The effects of sputum matrix on each assay were examined by testing 20 patient sputum samples which had been cultured for M. tuberculosis. The culture-positive samples included smear-positive and smear-negative samples. The results of the Q beta replicase assay were not inhibited by sputum and were in 100% agreement with those of culture, including detection of 10 culture-positive specimens. However, using an internal control plasmid coamplified with each PCR as an indicator, we detected PCR inhibition in 9 of 20 samples tested.(ABSTRACT TRUNCATED AT 250 WORDS)     

Conversion of highly malignant colon cancer from an aggressive to a controlled disease by oral administration of a metalloproteinase inhibitor

In this study, we describe the activity of CT1746, an orally-active synthetic MMP inhibitor that has a greater specificity for gelatinase A, gelatinase B and stromelysin than for interstitial collagenase and matrilysin, in a nude mouse model that better mimics the clinical development of human colon cancer. The model is constructed by surgical orthotopic implantation (SOI) of histologically-intact tissue of the metastatic human colon tumor cell line Co-3. Animals were gavaged with CT1746 twice a day at 100 mg/kg for 5 days after the SOI of Co-3 for 43 days. In this model CT1746 significantly prolonged the median survival time of the tumor-bearing animals from 51 to 78 days. Significant efficacy of CT1746 was observed on primary tumor growth (32% reduction in mean tumor area at day 36), total spread and metastasis (6/20 treated animals had no detectable spread and metastasis at autopsy compared to 100% incidence of secondaries in control groups). Efficacy of CT1746 could also be seen on reducing tumor spread and metastasis to individual organ sites such as the abdominal wall, cecum and lymph nodes compared to vehicle and untreated controls. We conclude that chronic administration of a peptidomimetic MMP inhibitor via the oral route is feasible and results in inhibition of solid tumor growth, spread and metastasis with increase in survival in this model of human cancer, thus converting aggressive cancer to a more controlled indolent disease.     

The effect of RANTES chemokine genetic variants on early HIV-1 plasma RNA among African American injection drug users

HIV-1 plasma RNA is a prognostic indicator of HIV-1, and increased levels of HIV-1 plasma RNA are associated with rapid progression to AIDS. Because chemokines and chemokine receptors are involved in the binding and entry of HIV-1, possible effects of host genetics on viral RNA levels should be visible in early infection. HIV-1 plasma RNA was measured within 2 years of seroconversion in 198 seroincident injection drug users followed in the AIDS Link to Intravenous Experience cohort. Genetic variants were identified in the chemokine receptors (CCR2, CCR5, and CCR5 promoter) and the chemokine RANTES using TaqMan and restriction fragment length polymorphism assays. Linear regression of RANTES haplotypes on early HIV-1 plasma RNA identified individuals homozygous for the RANTES R1 haplotype as having a lower viral load by almost one-half log10 unit compared with those bearing non-RANTES R1 haplotypes (-0.43, 95% confidence interval: -0.74, -0.12). Genetic variants in RANTES may downregulate RANTES gene expression and increase early HIV-1 plasma RNA. Because RANTES is a critical chemokine and competitively inhibits HIV-1 by binding to its receptor CCR5, treatment to enhance RANTES expression may assist in delaying the progression of AIDS by decreasing the initial viral load.     

The relationship of vascularity and water content to tensile strength in a patellar tendon replacement of the anterior cruciate in dogs

The methods and materials for ACL reconstruction are important issues for the practicing orthopaedic surgeon. In this study a model was developed to study the biological and biomechanical characteristics of a patellar tendon autograft used for ACL reconstruction. Specifically it was hypothesized that since vascularity of these grafts reflects their "healthiness," strength and vascularity should be inversely related in the early period after implantation. Using an over the top technique, a patellar tendon graft was placed in three groups of dogs and studied at 37, 57, and 120 days. Vascularity of the grafts was measured using technetium-tagged red blood cells, and percent water by weight was determined by dessication. Tensile testing to failure was performed using an MTS machine. The grafts became more vascular, more hydrated, less stiff, and less strong (by 4 weeks) than controls. By 16 weeks the vascular response was subsiding but the grafts remained only 40% as strong as controls. Percent water increased significantly over controls for all time periods. Decrease in strength correlated poorly with vascularity but correlated well with increase in percent water. These findings suggest that the change in strength of an intraarticular ACL replacement relates more to a basic rearrangement of its collagen-ground substance relationships, and that vascularity may reflect the inflammatory response bringing about these changes. The model developed in this study serves as a basis for further studies, and the findings reveal important information about the behavior of ACL grafting materials.     

痛泻要方水煎液化学成分的UPLC-LTQ-Orbitrap-MS分析

目的：采用超高效液相色谱-线性离子阱-静电场轨道阱高分辨质谱法(UPLC-LTQ-Orbitrap-MS)快速鉴定痛泻要方水煎液中的化学成分。方法：色谱条件为ACQUITY UPLC BEH C₁₈色谱柱(2.1 mm×100 mm,1.7μm),流动相0.1%甲酸水溶液(A)-乙腈(B)梯度洗脱(0～4 min,5%～15%B;4～10 min,15%～25%B;10～15 min,25%～60%B;15～20 min,60%～90%B;20～25 min,90%～100%B;25～27 min,100%B;27～30 min,100%～5%B;30～32 min,5%B),流速0.3 m L·min^-1,进样量3μL,柱温35℃。质谱条件为电喷雾离子源(ESI),扫描范围m/z 100～1 250,正、负离子模式下分别采集MS、MS/MS数据。结合对照品、数据库和文献信息,运用Trace Finder 4.1和Xcalibur 2.1软件对痛泻要方水煎液进行化学成分鉴定。结果：在正、负离子模式下,从痛泻要方水煎液中共鉴定出90个化合物,主...     

基于GSK-3β/CREB信号通路探讨加味肾气丸减轻糖尿病小鼠肾间质纤维化的作用机制

目的 观察加味肾气丸对糖尿病肾病小鼠肾功能及纤维化的影响,并基于糖原合成酶激酶-3β（GSK-3β）/环磷腺苷效应原件（CREB）信号通路探讨其可能的作用机制。方法 雄性db/db小鼠50只,db/m小鼠10只。50只db/db小鼠按体质量随机分为模型组、厄贝沙坦组、加味肾气丸低、中、高剂量组。db/m小鼠10只为正常组。加味肾气丸低、中、高剂量组中药颗粒剂混悬液灌胃,厄贝沙坦组给予厄贝沙坦混悬液灌胃,正常组及模型组予等体积蒸馏水灌胃,连续干预12周。分别记录治疗前后小鼠的血糖和尿白蛋白肌酐比（UACR）及小鼠肾脏中GSK-3β、CREB、转化生长因子-β₁（TGF-β₁）、钙黏蛋白E（E-cadherin）、波形蛋白（Vimentin）、纤维粘连蛋白（FN）、纤溶酶原激活物抑制剂-1（PAI-1）、Ⅳ型胶原蛋白（Col Ⅳ）蛋白的表达水平,并观测小鼠肾脏的病理损伤程度。结果 与正常组比较,模型组小鼠血糖、UACR水平及肾脏中GSK-3β、TGF-β₁、E-cadherin、Vimentin、FN、PAI-1、Col Ⅳ蛋白的表达水平明显升高（P<0.05）,CREB蛋白表达水平明显下降（P<0.05）,小鼠肾脏病理损伤严重;与模型组比较,肾气丸低、中、高剂量组和厄贝沙坦组小鼠血糖、UACR水平及肾脏中GSK-3β、TGF-β₁、E-cadherin、Vimentin、FN、PAI-1、Col Ⅳ蛋白的表达水平均有不同程度下降（P<0.05）,CREB蛋白表达水平升高（P<0.05）,小鼠肾脏病理损伤有不同程度的减轻。结论 肾气丸可有效降低血糖、改善肾功能和纤维化,其作用机制与其抑制GSK-3β/CREB信号通路有关。     

健脾益肠散对溃疡性结肠炎大鼠NLRP3/ASC/Caspase-1信号通路的影响

目的 探讨健脾益肠散对溃疡性结肠炎（UC）模型大鼠核苷酸结合寡聚化结构域样受体蛋白3（NLRP3）炎症小体信号通路的影响。方法 从60只SD大鼠中随机取10只为正常组,其余大鼠自由饮用5%硫酸葡聚糖（DSS）溶液7 d复制UC大鼠模型后,再随机分为模型组、柳氮磺吡啶（0.3 g·kg^-1）组和健脾益肠散高、中、低剂量（54.4、27.2、13.6 g·kg^-1）组,连续给药14 d。每日观察记录大鼠的一般状态,给药前后进行疾病活动指数（DAI）评分;采用酶联免疫吸附测定法（ELISA）检测各组大鼠血清中白细胞介素-1β（IL-1β）、白细胞介素-18（IL-18）含量,苏木素-伊红（HE）染色法观察结肠组织病理变化,免疫组化法、蛋白免疫印迹法（Western blot）及实时荧光定量聚合酶链式反应（Real-time PCR）分别检测结肠组织NLRP3、凋亡相关斑点样蛋白（ASC）、胱天蛋白酶-1（Caspase-l）的蛋白阳性表达、蛋白及mRNA的表达水平。结果 与正常组比较,模型组大鼠的一般状态相对较差,DAI评分显著增高（P<0.01）,结肠出现病理学改变,血清IL-1β、IL-18含量显著升高（P<0.01）,结肠组织NLRP3、ASC、Caspase-l的蛋白阳性、蛋白及mRNA的表达均显著增强（P<0.01）。与模型组比较,健脾益肠散各剂量组的一般状态明显好转,DAI评分明显减小（P<0.05,P<0.01）,HE染色显示病理变化明显减轻,结肠NLRP3、Caspase-l的蛋白表达均明显减少（P<0.05,P<0.01）;健脾益肠散高、中剂量组血清IL-1β、IL-18含量、结肠ASC的蛋白表达及NLRP3、ASC、Caspase-l的mRNA表达均明显降低（P<0.05,P<0.01）;健脾益肠散高剂量组NLRP3、ASC、Caspase-l的蛋白阳性表达均显著减少（P<0.01）;健脾益肠散中剂量组ASC、Caspase-l的蛋白阳性表达均明显减少（P<0.05）;健脾益肠散低剂量组ASC的mRNA表达明显降低（P<0.05）。结论 健脾益肠散能通过调节NLRP3炎症小体信号通路,减少结肠免疫炎症损伤发挥治疗UC的效应。     

柴胡加龙骨牡蛎汤治疗冠状动脉粥样硬化性心脏病合并焦虑抑郁研究进展

冠状动脉粥样硬化性心脏病（CHD）是全球常见的慢性病之一,焦虑和抑郁是其发生不良预后事件的潜在与关键危险因素。柴胡加龙骨牡蛎汤（CLMT）首见于《伤寒论》,为治疗少阳病兼心神逆乱证的经典名方,具备和解少阳、镇惊安神之功效。目前机制研究表明CLMT能通过调控相关信号通路、抑制相关炎症因子表达、改善氧化应激损伤、调节神经递质水平、抑制下丘脑-垂体-肾上腺轴亢进、促进骨髓间充质干细胞动员、抑制血小板活化等多途径对CHD合并焦虑抑郁发挥作用。临床研究表明CLMT对CHD合并焦虑抑郁导致的心绞痛、失眠等症状具有显著改善作用,可有效减轻患者负性情绪、改善中医证候积分、降低炎症因子水平等,且与西医常规治疗相比不良反应少,安全性较高。该文通过归纳整理近15年来中国知网（CNKI）、万方（Wanfang）、维普（VIP）、PubMed等数据库关于CLMT治疗CHD合并焦虑抑郁的文献,对其进行了机制及临床研究的综述,以期为CLMT指导CHD合并焦虑抑郁的进一步研究提供参考。     

基于网络药理学及分子对接预测安子调冲方中和血中药对免疫相关复发性流产的作用机制

目的：应用网络药理学及分子对接技术探讨安子调冲方（ATF）中起和血作用的鸡血藤–蒲黄炭（JXT–PHT对治疗免疫相关复发性流产（IRRPL）的作用机制,为进一步对ATF的拆方研究奠定基础。方法：利用TCMSP和HERB数据库进行化合物成分检索,在Swiss Target Prediction数据库预测药物作用靶点。使用Genecards和ImmPort数据库获取IRRPL相关靶点。利用jvenn绘制韦恩图,得到潜在作用靶点。在STRING数据库构建蛋白互作（PPI）网络,并分析关键作用靶点。构建“和血作用中药–成分–靶点–疾病”网络,在Cytoscape 3.10.0中可视化,并分析核心成分。应用DAVID(v2023q1)数据库,对潜在作用靶点进行基因本体（GO）和京都基因和基因组数据库（KEGG）功能富集分析。最后通过AutoDock–Vina(v1.2.5)对关键作用靶点和核心成分执行分子对接,在PyMOL 2.5进行可视化。结果：共筛选出ATF中起和血作用的JXT–PHT 31个活性成分,预测靶点586个,IRRPL相关靶点226个,潜在作用靶点38个,构建PPI网络并分析后得...