A glimpse into the clinical proteome of human malaria parasites Plasmodium falciparum and Plasmodium vivax

Malaria causes a worldwide annual mortality of about a million people. Rapidly evolving drug-resistant species of the parasite have created a pressing need for the identification of new drug targets and vaccine candidates. By developing fractionation protocols to enrich parasites from low-parasitemia patient samples, we have carried out the first ever proteomics analysis of clinical isolates of early stages of Plasmodium falciparum (Pf) and P. vivax. Patient-derived malarial parasites were directly processed and analyzed using shotgun proteomics approach using high-sensitivity MS for protein identification. Our study revealed about 100 parasite-coded gene products that included many known drug targets such as Pf hypoxanthine guanine phosphoribosyl transferase, Pf L-lactate dehydrogenase, and Plasmepsins. In addition, our study reports the expression of several parasite proteins in clinical ring stages that have never been reported in the ring stages of the laboratory-cultivated parasite strain. This proof-of-principle study represents a noteworthy step forward in our understanding of pathways elaborated by the parasite within the malaria patient and will pave the way towards identification of new drug and vaccine targets that can aid malaria therapy.     

类黄酮化合物抑制恶性疟原虫的预测模型

建立预测类黄酮化合物抑制恶性疟原虫株活性定量的模型,并确定影响类黄酮化合物活性的主要因素。本文选用了38个结构不同的类黄酮化合物作为数据集,采用多元线性同归法及主成分分析法分析每个化合物的220个分子参数,建立最优的预测模型。比较用不同方法建立的模型,结果发现带logP参数的向后筛选法为最优方法,所建模型统计结果良好(训练集相关系数R~2=0.81,标准训练误差SEE=0.27),模型代入检验集数据时结果也令人满意(检验集相关系数R~2=0.83,标准检验误差SEP=0.39),可靠性和预测性较强。脂水分配系数的对数logP为模型重要影响参数。建模和确定影响因素有助于筛选新型类黄酮抗疟疾药物和研发。     

In silico design of knowledge-based Plasmodium falciparum epitope ensemble vaccines

Malaria is a global health burden, and a major cause of mortality and morbidity in Africa. Here we designed a putative malaria epitope ensemble vaccine by selecting an optimal set of pathogen epitopes. From the IEDB database, 584 experimentally-verified CD8+ epitopes and 483 experimentally-verified CD4+ epitopes were collected; 89% of which were found in 8 proteins. Using the PVS server, highly conserved epitopes were identified from variability analysis of multiple alignments of Plasmodium falciparum protein sequences. The allele-dependent binding of epitopes was then assessed using IEDB analysis tools, from which the population protection coverage of single and combined epitopes was estimated. Ten conserved epitopes from four well-studied antigens were found to have a coverage of 97.9% of the world population: 7 CD8+ T cell epitopes (LLMDCSGSI, FLIFFDLFLV, LLACAGLAYK, TPYAGEPAPF, LLACAGLAY, SLKKNSRSL, and NEVVVKEEY) and 3 CD4+ T cell epitopes (MRKLAILSVSSFLFV, KSKYKLATSVLAGLL and GLAYKFVVPGAATPYE). The addition of four heteroclitic peptides − single point mutated epitopes − increased HLA binding affinity and raised the predicted world population coverage above 99%.     

Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations

The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. Bi-lobed catalytic domain of PfCKI shares a high degree of secondary structure topology with CKI domains of rice, human, and mouse indicating co-evolution of these kinases. Molecular docking study revealed that ATP binds to the active site where the glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with few conserved residues plays a crucial role maintaining stability of the complex. Structural superposition of PfCKI with close structural homologs depicted that the location and length of important loops are different, indicating the dynamic properties of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA displayed that the overall global motion of ATP-bound form is comparatively higher than that of apo form. The present study provides insights into the structural features of PfCKI, which could contribute towards further understanding of related protein structures, dynamics of catalysis and phosphorylation mechanism in these important STKs from malarial parasite in near future.     

Impact of incomplete DNase I treatment on human macrophage proteome analysis

The aim of our study was to analyze the proteomic pattern of human macrophages obtained over a 4 year period from blood donors. The purpose was to simulate a long-term clinical study to assess the application of 2-D DIGE technique for differential proteomic analysis of these scarce samples. Bioinformatic analysis of 2-D DIGE gels of 19 different cultures of macrophages assessed whether they did or did not contain at least specific five spots identified by MS as being or containing bovine deoxyribonuclease I (DNase I). Bovine DNase I was used during sample treatment to remove nucleic acids from protein extracts. Macrophages were classified in two groups, which appeared to be differentiated by the completeness of DNase I treatment. Further detailed analysis revealed a different proteomic pattern of macrophage protein samples according to the completeness of this treatment. The major group of proteins affected, accounting for one third of the differentially expressed proteins, included proteins involved in cell motion and actin cytoskeleton reorganization. The use of DNase I for the removal of nucleic acids from protein samples must be avoided in proteomic studies since it can generate bias in the analysis of protein expression patterns.     

应用于食品工业中的生物传感器

对食品及其生产加工过程中的生物传感器进行综述。主要包括食品鲜度测定；蛋白及氨基酸的测定；糖、醇、酸的分析及菌数的测定。     

食品加工高新技术的发展现状及趋势

本文阐述了当今国内外食品加工高新技术应用的发展状况及趋势，重点介绍了食品生物技术、计算机智能化自动化及膨化挤压技术的发展，并对微波技术、食品辐照技术等做了扼要介绍。     

计算机软件在食品营养学教学中的应用

食品营养学是高职院校营养检测和食品类专业重要的课程。营养学教学过程中,多个项目都需要学生在掌握大量数据信息基础上进行数据处理,计算机软件可以使学生更有效的进行信息的整理。应加强职业教育现代教学技术的运用,立足于提高学生的职业能力。     

Characteristics of the Plasmodium falciparum PK5 ATP-binding site: implications for the design of novel antimalarial agents

Increasing worldwide resistance of Plasmodium falciparum (P. falciparum) to traditional chemotherapy strategies such as chloroquine and mefloquine demonstrates the urgent need for the discovery of novel chemotherapeutic agents in the fight against malaria. The recent discovery of P. falciparum Protein Kinase 5 (PfPK5) invites the possibility of selectively targeting the life cycle of P. falciparum in order to prevent cerebral malaria. PfPK5 bears a high degree of sequence identity (>58%) to a structurally conserved family of mammalian kinases known as the cyclin-dependent kinases (CDKs). The CDKs are the key regulatory elements governing the ordered progression of the mammalian cell cycle. With numerous X-ray crystal structures of CDK2 to provide a structural template, here we present a three-dimensional structural model of PfPK5 constructed using computer-based homology modeling techniques. Our model was used to compare the ATP binding site of PfPK5 with that of the mammalian kinase CDK2. Furthermore, kinase-ligand interactions of PfPK5 with known inhibitors were investigated and compared to available crystal structures of CDK2 with inhibitors bound. The focus of the study is to identify similarities and differences between the ATP binding sites of the two kinases that can be exploited for future rational drug design.     

Online analysis of in vitro resistance to antimalarial drugs through nonlinear regression

Malaria remains one of the leading causes of morbidity and mortality worldwide which is partly due to the emergence of the parasite resistance to antimalarial drugs. In vitro testing of drugs allows an early detection of resistance. The common parameter used for the monitoring of resistance is the concentration that inhibits 50% of the parasite's activity (IC₅₀). Various methods of calculation are already used but none of them consider new available tools nor display the precision of IC₅₀ estimation. We proposed an approach based on the inhibitory sigmoid E_max model, which is often used in pharmacology, with estimation of IC₅₀ through nonlinear regression using a standard function of the R software. To facilitate the usage of that tool we have developed an online version available on the website ICEstimator (ICEstimator website http://www.antimalarial-icestimator.net/, 2009) [1]. This website is used by various teams in the world and the user can do the analysis without knowing R using the GUI. This article describes version 2.1 of this website and shows illustration on five different real examples.     

PLC在生产膨化食品片材中的应用

本文介绍了PLC在生产膨化食品片材中的应用,控制系统基于SIMATIC S7-200PLC和MD204L文本显示器。论述了生产工艺要求,控制系统的硬件组成和软件设计。     

食品抽检登记助手软件的开发

为了提高食品抽检工作中样品信息的录入速度,本文开发了一个食品抽检登记助手软件。该软件通过调用百度智能云提供的通用文字识别功能,自动识别食品生产经营者证照及食品包装上的文字;利用正则表达式提取和保存识别结果中抽检管理系统需要的相关信息。在测试中,该软件对食品样品相关信息的提取准确率超过了98%。利用这种方式代替传统的人工录入方式,提高了工作效率。     

辽宁蔬菜水果硝酸盐含量及其安全性问题探讨

本文通过对辽宁省主要蔬菜和水果硝酸盐含量的测定,参比国内外硝酸盐含量分级评价标准,分析了目前全省蔬菜和水果食用的安全状况,提出了降低蔬菜水果产品中硝酸盐含量的有效途径.     

Application of proteomic techniques to the study of urine and renal tissue

The increasing application of proteomic methods to biomedical research is providing us with important new information; it holds particular promise in advancing basic and clinical renal research, but whether proteomics can ever become a routine diagnostic tool in nephrology is still uncertain. Currently, proteomic techniques are used by many groups in the search for "biomarkers" of disease, especially kidney disease, because of the ready availability of urine as an "end-product" of renal function. However, the question as to whether any disease-specific biomarkers exist or can be identified by proteomics is also uncertain. A growing application of proteomics in biomedical research is to understand the mechanism(s) of disease. This brief review is selective; in it we consider examples of proteomic studies of human urine for biomarkers, others that have explored renal physiology, and still others that have begun to probe the proteome of organelles. No single approach is sufficiently comprehensive, and the pooled application of proteomics to renal research will undoubtedly improve our understanding of renal function and enable us to explore in more detail subcellular structures, and to characterize cellular processes at the molecular level. When combined with other techniques in renal research, proteomics, and related analytical methods could prove indispensable in modeling renal function, and perhaps also in diagnosis and management of renal disease.     

An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum

The understanding of transition processes, such as chemical reactions, is a central topic in theoretical molecular science. A common approach for investigating such processes is to calculate paths between reactant and product structures that are representative of the transition. Many approaches have been proposed to determine such paths but, in this paper, we examine the nudged elastic band algorithm which was recently introduced by Jónsson and co-workers and has been used to study a wide range of transition problems. We describe our implementation of the method in the simulation program Dynamo and some modifications to the original algorithm that we found improve its efficiency. The use of the method is illustrated by an application to the reaction mechanism of the enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase from Plasmodium falciparum.     

西门子S7-1200的设计与应用 第5讲 食品生产线喷嘴控制的S7-1200设计

PWM是一种周期固定、脉冲宽度可以调节的脉冲输出,是数字量输出。在S7-1200 PLC中,它提供两个输出通道用于高速脉冲输出,分别可以组态为PTO或PWM,本案例则充分利用了PWM功能来实现了食品生产线的喷嘴控制,取得了良好的效果。     

基于物联网的低成本食品跟踪技术的应用研究

目前RFID技术在食品跟踪行业的应用成本过高,在一些普通的低成本行业不太适用;提出了一种基于二维码和Internet的低成本技术的食品跟踪、分析、监测的物联网解决方案。通过分析该物联网中二维码、中间件、手机、电脑终端等组成部件,说明了本方案的可行性,其中使用手机识别二维码更为用户提供了莫大的方便;最后得出结果,本方案适用于目前食品跟踪行业的大量应用。