Synthesis and chemical characterisation of target identification reagents based on an inhibitor of human cell invasion by the parasite Toxoplasma gondii

The use of phenotype-based screens as an approach for identifying novel small molecule tools is reliant on successful protein target identification strategies. Here we report on the synthesis and chemical characterisation of a novel reagent for protein target identification based on a small molecule inhibitor of human cell invasion by the parasite Toxoplasma gondii. A detailed (1)H NMR study and biological testing confirmed that incorporation of an amino-containing functional group into the aryl ring of this inhibitor was possible without loss of biological activity. Interesting chemical reactivity differences were identified resulting from incorporation of the new substituent. The amine functionality was then used to prepare a biotinylated reagent that is central to our current protein target identification studies with this inhibitor.     

Target identification strategies in chemical genetics

Chemical inhibitors have had a profound impact on many diverse fields of biology. The goal of chemical genetics is to use small molecules to perturb biological systems in a manner conceptually similar to traditional genetics. Key to the advancement of the chemical genetic paradigm is the further development of tools and approaches for the identification of the protein targets of active compounds identified in chemical genetic screens. This review will address historic examples in which forward chemical genetics yielded new insight into a biological problem through successful identification of the target of an active molecule. The approaches covered have been grouped into two broad classes: target identification by affinity-based methods and target identification by deduction. Strengths and shortcomings of each approach as it pertains to their application to modern chemical genetics will be discussed. Finally, a series of new genomic and proteomic-based techniques for target identification will be described. Although a truly general approach to target identification has yet to be developed, these examples illustrate that there are many effective strategies for successfully elucidating the biological targets of active small molecules.     

Mass spectrometric identification of toxins of biological origin

The chemical/biological (CB) threat spectrum encompasses a wide range of potential agents including chemical warfare agents, biological warfare agents and toxins of biological origin that fall between these two main agent categories. These proteinaceous and non-proteinaceous toxins, commonly referred to as mid-spectrum agents, range in molecular mass from a few hundred to more than a hundred thousand daltons. The large number of potential candidates as well as the structural diversity of possible mid-spectrum agents makes identification of these compounds a challenge. The NATO defense community has recognized these challenges and has a working group that is developing identification protocols and evaluating methods through a series of international analytical exercises. Identification strategies rely heavily on recent advances that have been made in both mass spectrometry (MS) and liquid chromatography (LC), with LC-MS typically being employed as the primary method for separation/identification. While this paper focuses on the application of these and related instrumental analytical techniques for the identification of mid-spectrum agents, the approach described could be applied in the fields of toxicology, forensic science and environmental analysis. Areas for future research have been identified and application of developed mid-spectrum identification methods to the ongoing biological and toxin weapons convention (BTWC) are anticipated.     

Aplysqualenol A binds to the light chain of dynein type 1 (DYNLL1)

A bidirectional affinity system has been developed for the identification of cancer-related natural products and their biological targets. Aplysqualenol A is thus selectively identified as a ligand of the dynein light chain. The use of forward and reverse affinity methods suggests that both small-molecule isolation and target identification can be conducted using conventional molecular biological methods.     

FINDER: A Fluidly Confined CRISPR-Based DNA Reporter on Living Cell Membranes for Rapid and Sensitive Cancer Cell Identification

The accurate, rapid, and sensitive identification of cancer cells in complex physiological environments is significant in biological studies, personalized medicine, and biomedical engineering. Inspired by the naturally confined enzymes on fluid cell membranes, a f luidly confin ed CRISPR-based D NA reporter (FINDER) was developed on living cell membranes, which was successfully applied for rapid and sensitive cancer cell identification in clinical blood samples. Benefiting from the spatial confinement effect for improved local concentration, and membrane fluidity for higher collision efficiency, the activity of CRISPR-Cas12a was, for the first time, found to be significantly enhanced on living cell membranes. This new phenomenon was then combined with multiple aptamer-based DNA logic gate for cell recognition, thus a FINDER system capable of accurate, rapid and sensitive cancer cell identification was constructed. The FINDER rapidly identified target cells in only 20 min, and achieved over 80 % recognition efficiency with only 0.1 % of target cells presented in clinical blood samples, indicating its potential application in biological studies, personalized medicine, and biomedical engineering.     

基于人工神经网络的生物组织质谱成像分类与识别方法

生物组织质谱成像技术不仅能够展示组织的生物分子信息,而且能直观地显示分子空间分布,是当今生物质谱的研究热点.如何对生物组织质谱成像的数据进行基于生物分子的有效分类与识别是该领域关注的重要问题,特别对于病变组织与其邻近非病变组织的区分与识别和生物组织功能区域的划分与鉴定具有重要的意义.本研究开发出一种新的分类与识别方法.其流程是,首先进行质谱成像数据预处理,应用无监督的自组织特征映射网络区分组织样品区与非组织区域,提取组织区域的质谱数据,应用有监督的学习向量量化网络对已知类别数据进行学习训练,建立模型;应用模型对未知样品进行识别.应用本方法对6个膀胱癌患者的膀胱癌变组织与邻近非癌变组织的质谱成像数据进行分类与识别,结果显示,癌变组织判错率低于23.38％,而非癌变组织判错率低于9.08％,表现出较高的准确度;对3片邻近的小鼠大脑切片质谱成像数据进行白质与灰质区域划分,将中间的1片用于训练,两边的2片用于验证,结果显示,自组织特征映射网络的分类结果与学习向量量化网络的预测结果不一致率低于4％.本方法基于生物分子的质谱成像组织区域分类与识别,具有较高准确度和操作简便等优点,在临床医学研究领域有大规模的应用潜能.     

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping

We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.     

Capillary electrophoresis and off-line capillary electrophoresis-electrospray ionization quadrupole time-of-flight tandem mass spectrometry of carbohydrates

The use of off-line high-performance capillary electrophoresis in connection with nanospray electrospray ionization quadrupole time-of-flight tandem mass spectrometry for identification of complex carbohydrates of biological origin is presented. The method was applied to the identification of O-glycosylated amino acids and -glycopeptides from the urine of patients suffering from a hereditary disease - N-acetylhexosaminidase deficiency. Structural elements typical for O-glycosylation of proteins, like expression of core 1 and 2 type O-glycans with different numbers of N-acetyllactosaminyl repeats and different degrees of sialylation, can be directly detected.     

A review of advances and new developments in the analysis of biological volatile organic compounds

Biological volatile organic compounds (VOCs) are interlinked to biological metabolism and bacterial populations localized on the surfaces of biological samples. The characteristics of biological VOCs at different physiological status or metabolism phases are various, which contain crucial bio-information. In this review, the significance of the study of biological VOCs was introduced, and crucial techniques greatly influencing the investigation were summarized and reviewed including efficient sampling, suitable analytical and bio-information distillation techniques. From the preliminary identification of biological VOC components to the interpretation of biological VOC characteristics is a great improvement in this field, which would provide more abundant bio-information during biological metabolism. Owing to complicated biological VOC compositions, any single sampling or bio-information distillation method could not obtain complete biological VOCs and interpret the biological VOC characteristics, and would result in the loss of effective bio-information. The combination of some suitable sampling and bio-information distillation techniques for the study of biological VOCs and the related bio-information will be a novel trend in the future.     

Multiple analytical methods for identification and quality evaluation of Fritillariae Thunbergii Bulbus based on biological single molecules by high‐performance liquid chromatography

Quantitative analysis for biological single molecules in Fritillariae Thunbergii Bulbus and identification method by chemometrics was established by using high‐performance liquid chromatography. Amino acids, nucleosides, and nucleobases were quantitatively analyzed, and 11 peaks were selected for species identification. A Common pattern was established for chemometrics, and then similarity analysis, principal component analysis, and hierarchical cluster analysis heatmap were applied, and the results indicated that species were ideally identified from the adulterants as Fritillariae Cirrhosae Bulbus. This evaluation method was valuable for further quality control to select the characteristic components.     

尺寸排阻-反相液相色谱-质谱联用技术在大鼠肾脏翻译后修饰蛋白质鉴定中的应用

LC-MS联用技术在蛋白质组学研究中具有重要的作用,但是在复杂的生物体系中,由于样品的高度复杂性和其中蛋白质含量的巨大差异,执行全面且无倾向的蛋白质组分析是一项挑战。因此,在液相色谱分离中采用基于不同原理的色谱分离方法来降低蛋白质样本的复杂度,并对微量蛋白质进行富集,对后续采用质谱方法进行信息的采集和深入分析至关重要。在这里我们开发了一种基于尺寸排阻色谱(SEC)与反相液相色谱(RPLC)结合的新方法来进行复杂体系蛋白质的分离和鉴定,特别是对于微量蛋白质的分析。首先使用SEC对蛋白质进行分离和富集,并酶解成多肽,再通过RPLC-MS联用的方法对酶解后的多肽进行分离和鉴定。结果显示使用上述方法可以有效降低蛋白质样本的复杂度,并有效提高微量蛋白质的鉴定能力,可从大鼠肾脏鉴定出23621个肽段及1345个蛋白质,比常规的二维强阳离子交换-反相液相色谱法(2D SCX-RPLC)鉴定到的肽段及蛋白质分别多出69%及27%。此外,该方法对肾脏翻译后修饰(PTM)蛋白质的鉴定显示出更多的优势,翻译后修饰的多肽鉴定率显著增加,特别是磷酸化肽段的鉴定效率可达到靶向富集策略的水平。在此展示的SEC-RPLC-MS可以更好地了解蛋白质翻译后修饰对肾脏的影响,最终将有助于增加我们对正常的生理性肾功能以及病理过程机制的理解。     

Multihyperspectral Microscopic Imaging for the Precise Identification of Pollen

We report a method for precisely identifying and locating the pollen of different species in a microscope based on multihyperspectral imaging. Since pollen species are complicated and difficult to identify by one feature, both fluorescence and transmission spectral images of the samples were obtained and used for the identification together with their morphologic features. Three different species of pollens were used as test samples for investigation. The results showed that the accuracy reached 99.5%, which was a significant improvement comparing with the single spectral detection. Because more information was taken into consideration, this method has great potential for the precise identification of biological specimens.     

Simultaneous identification and verification of Bacillus anthracis

Specific identification of Bacillus anthracis (B. anthracis) is vital for the accurate treatment of afflicted personnel during biological warfare situations and civilian terrorist attacks. In order to accomplish this, we have subjected the lysates from B. anthracis to affinity purification using monoclonal antibodies for the selected antigenic protein present in the bacteria. The bound antigenic protein was identified by multi-dimensional protein identification technology (MudPIT) to be a surface layer protein EA1. The same antigen was identified from the lysates from a few strains of B. anthracis demonstrating the observation to be common for B. anthracis strains. Hence, this presents an effective pathway for the identification of the bacteria present in unknown samples of various origins. Generation of a database containing the EA1 protein has been found to be useful in the database search of unknown samples.     

Application of overpressured layer chromatography combined with digital autoradiography and mass spectrometry in the study of deramciclane metabolism

Overpressured layer chromatography was combined with the highly sensitive and rapid digital autoradiography (DAR) and mass spectrometry to separate, detect, and identify 3H- and 14C-labeled deramciclane metabolites in different biological matrixes. Several minor and major metabolites were separated from plasma and urine samples. The radioactive metabolites localized by DAR were scraped from the thin-layer chromatographic plate and transferred to a mass spectrometer for structure identification. Several metabolites were isolated and characterized, including hydroxy-N-desmethyl deramciclane, which is described in detail. The combination of techniques is efficient and has good sensitivity: about 2 micrograms metabolite from a biological matrix was isolated and identified this way.     

Two-dimensional LC-MS fractioning and cross-matching of mass spectrometric data for rational identification of bioactive compounds in crude extracts

Bioprospecting aims at the identification of biological compounds with novel properties. Identification of such compounds in crude complex biological extracts is a comprehensive challenge. As a large number of extracts must be screened for successful identification of one potential promising lead, rational screening strategies must be developed. Here we report on a novel two stage rational LC-MS strategy of extracts already pre-screened and proven to contain bioactive compound(s). All extracts are initially fractionated using one and the same LC condition with parallel mass spectrometric detection. Fractions containing bioactive compound(s) are then subjected to a second fractional stage using two different chromatographic conditions. Mass detection is also included at this stage, and a cross-matching algorithm for comparison of processed mass chromatograms from the two dimensions was developed. The algorithm reports only masses present in bioactive fractions in both dimensions and enable therefore an efficient identification of potential masses that causes the bioactivity. This mass list can be used to search in natural compound database(s) for a rapid evaluation if the mass belongs to an already identified compound or if it is a potentially new one. This strategy enables thorough screening of several hundred crude extracts in one week on one single instrument.     

Use of correlation between retention indices on low-polarity phases for screening complex mixtures by gas chromatography-mass spectrometry

The reliable identification of numerous compounds in biological fluids by chromatography-mass spectrometry requires the knowledge of their retention on the phase used under specific temperature conditions. A simple method was proposed for calculating retention indices on a 5% phenyl dimethyl polysiloxane phase based on a correlation between the retention values observed for methyl- and phenyl dimethyl polysiloxane phases at different temperatures.     

Proteomics and peptidomics in neuroscience. Experience of capabilities and limitations in a neurochemical laboratory

The increasing use of proteomics has created a basis for new strategies to develop methodologies for rapid identification of protein patterns in living organisms. It has also become evident that proteomics has other potential applications than protein and peptide identification, e.g. protein characterization, with the aim of revealing their structure, function(s) and interactions of proteins. In comparative proteomics studies, the protein expression of a certain biological system is compared with another system or the same system under perturbed conditions. Global identification of proteins in neuroscience is extremely complex, owing to the limited availability of biological material and very low concentrations of the molecules. Moreover, in addition to proteins, there are number of peptides that must also be considered in global studies on the central nervous system. In this overview, we focus on and discuss problems related to the different sources of biological material and sample handling, which are part of all preparatory and analytical steps. Straightforward protocols are desirable to avoid excessive purification steps, since loss of material at each step is inevitable. We would like to merge the two worlds of proteomics/peptidomics and neuroscience, and finally we consider different practical and technical aspects, illustrated with examples from our laboratory.     

Rapid,simple, and highly sensitive analysis of drugs in biological samples using thin-layer chromatography coupled with matrix-assisted laser desorption/ionization mass spectrometry

Rapid and precise identification of toxic substances is necessary for urgent diagnosis and treatment of poisoning cases and for establishing the cause of death in postmortem examinations. However, identification of compounds in biological samples using gas chromatography and liquid chromatography coupled with mass spectrometry entails time-consuming and labor-intensive sample preparations. In this study, we examined a simple preparation and highly sensitive analysis of drugs in biological samples such as urine, plasma, and organs using thin-layer chromatography coupled with matrix-assisted laser desorption/ionization mass spectrometry (TLC/MALDI/MS). When the urine containing 3,4-methylenedioxymethamphetamine (MDMA) without sample dilution was spotted on a thin-layer chromatography (TLC) plate and was analyzed by TLC/MALDI/MS, the detection limit of the MDMA spot was 0.05 ng/spot. The value was the same as that in aqueous solution spotted on a stainless steel plate. All the 11 psychotropic compounds tested (MDMA, 4-hydroxy-3-methoxymethamphetamine, 3,4-methylenedioxyamphetamine, methamphetamine, p-hydroxymethamphetamine, amphetamine, ketamine, caffeine, chlorpromazine, triazolam, and morphine) on a TLC plate were detected at levels of 0.05 − 5 ng, and the type (layer thickness and fluorescence) of TLC plate did not affect detection sensitivity. In addition, when rat liver homogenate obtained after MDMA administration (10 mg/kg) was spotted on a TLC plate, MDMA and its main metabolites were identified using TLC/MALDI/MS, and the spots on a TLC plate were visualized by MALDI/imaging MS. The total analytical time from spotting of intact biological samples to the output of analytical results was within 30 min. TLC/MALDI/MS enabled rapid, simple, and highly sensitive analysis of drugs from intact biological samples and crude extracts. Accordingly, this method could be applied to rapid drug screening and precise identification of toxic substances in poisoning cases and postmortem examinations.     

Electrochemical Biosensors for Detection of Biological Warfare Agents

This review discusses current development in electrochemical biosensors for detection of biological warfare agents. This could include bacteria, viruses and toxins that are aerosoled deliberately in air, food or water to spread terrorism and cause disease or death to humans, animals or plants. The rapid and unequivocal detection and identification of biological warfare agents is a major challenge for any government including military, health and other government agents. Reliable, specific characterization and identification of the microorganism from sampling location, either air, water, soil or others is required. This review will survey different types of electrochemical biosensors has been developed based on the following: i) Immunosensors ii) PCR (DNA base Sensor) iii) Bacteria or whole cell sensor and iv) Enzyme sensor. This article gives an overview of electrochemical biosensor for detection of biological warfare agents. Electrochemical biosensors have the advantages of sensitivity, selectivity, to operate in turbid media, and amenable to miniaturization. Recent developments in immunofiltration, flow injection, and flow‐through electrochemical biosensors for bacteria, viruses, and toxin detection are reviewed. The current research and development in biosensors for biological warfare agents detection is of interest to the public as well as to the defense is also discussed.     

Determination of phospholipid fatty acids in biological samples by solid-phase extraction and fast gas chromatography

A new method for the determination of phospholipid fatty acids in biological samples, combination of solid-phase extraction (SPE) and fast gas chromatography (GC) was developed. Its application to human plasma and human erythrocytes showed to be robust and reliable for quick and correct identification in routine analysis.