Simultaneous separation of lysophospholipids from the total lipid fraction of crude biological samples using two-dimensional thin-layer chromatography

A novel solvent system for two-dimensional thin-layer chromatography was shown to simultaneously separate lysophospholipid standards, including lysophosphatidylcholine, lysophosphatidylethanolamine, lysophosphatidylserine, lysophosphatidylinositol, lysophosphatidylglycerol, lysophosphatidic acid, lysosphingomyelin (sphingosylphosphorylcholine), and sphingosine-1-phosphate from diradylphospholipids, glycosphingolipids, and neutral lipids. Lysophospholipids contained in the total lipid fraction of activated platelets were also well separated by the same system. The present system is a useful tool for the metabolic and structural analysis of lysophospholipids in biological samples.     

Application of green analytical chemistry to a green chemistry process: Magnetic resonance and Raman spectroscopic process monitoring of continuous ethanolic fermentation

Compact ¹H NMR and Raman spectrometers were used for real-time process monitoring of alcoholic fermentation in a continuous flow reactor. Yeast cells catalyzing the sucrose conversion were immobilized in alginate beads floating in the reactor. The spectrometers proved to be robust and could be easily attached to the reaction apparatus. As environmentally friendly analysis methods, ¹H NMR and Raman spectroscopy were selected to match the resource- and energy-saving process. Analyses took only a few seconds to minutes compared to chromatographic procedures and were, therefore, suitable for real-time control realized as a feedback loop. Both compact spectrometers were successfully implemented online. Raman spectroscopy allowed for faster spectral acquisition and higher quantitative precision, NMR yielded more resolved signals thus higher specificity. By using the software Matlab for automated data loading and processing, relevant parameters such as the ethanol, glycerol, and sugar content could be easily obtained. The subsequent multivariate data analysis using partial linear least-squares regression type 2 enabled the quantitative monitoring of all reactants within a single model in real time.     

Fish gut content from biological collections as a tool for long-term environmental impact studies

Most of the world’s fish fauna is suffering from different types of human impacts and new conservation tools are required. The fish diet analysis is a tool that has been used to evaluate degradation processes of aquatic environments, however, few long-term studies are performed by several reasons (e.g., lack of funding, opportunity). Our aim was to test whether the fish gut content from biological collections can be used for comparisons with current data and, consequently, be used as a tool for long-term environmental impact studies. We compared the gut content of fish preserved for fifteen years in a biological collection with recently sampled fish, considering the factors size of the specimen, preservation time and preservation form. We did not find differences in the gut content percentage of preservation between fish size classes and preservation time. However, we found differences between preservation form, in which the fish fixed in formalin kept the digestive content preserved while the fish preserved directly in alcohol did not. Thus, we encourage the use of fish gut content from biological collections fixed in formalin for long-term ecological studies. Our findings may help elucidate some long-term effects of human impacts on fish fauna.     

MAAP: a versatile and universal tool for genome analysis

Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonucleotide primers (5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either directly or as sequence-characterized amplified regions (SCARs). MAAP profiles can be tailored in the number of monomorphic and/or polymorphic products. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphic DNA. Comparison of the expected and actual number of amplification products produced with primers differing in length, sequence and GC content from templates of varying complexity reveal severe departures from theoretical formulations with interesting implications in primer-template interaction. Extensive primer-template mismatching can occur when using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3-terminal primer domain, requires sites with perfect homology to the first 5–6 nt fom the 3 terminus, and involves direct physical interaction between amplicon annealing sites.     

Electrospray-ionization mass spectrometry as a tool for fast screening of protein structural properties

Since the early 1990s, electrospray-ionization mass spectrometry (ESI-MS) has encountered growing interest as a complementary tool to established biochemical and biophysical methods for investigating protein structure and conformation. Nowadays, applications of ESI-MS to protein investigation span from the area of analytical biochemistry to that of structural biology. This review focuses on applications of this technique to the analysis of protein conformational properties and molecular interactions, underscoring their possible relevance for molecular biotechnology, although representing a still very young field. An introductive section presents the major issues related to theoretical and technical aspects of ESI-MS under non-denaturing conditions. Examples from our work and from the literature illustrate which kind of information can be obtained concerning key issues in biotechnology such as stability and aggregation of proteins under both near-native and challenging conditions, and interactions with other proteins, ligands and cofactors.     

Interaction of sex steroids with proteins from the soluble fraction of swine and cattle liver (a preliminary analysis)]

The interactions of [3H]estradiol, [3H]testosterone and [3H]progesterone with soluble proteins from porcine and calf liver were studied. The specific binding of [3H]progesterone and [3H]testosterone in calf liver cytosol seems to be due to serum transcortin or its intracellular precursor (analog). Contrariwise, the specific binding of [3H]progesterone observed in porcine liver cytosol was absent in the serum. This binding was characterized by slow association and dissociation dynamics, moderate affinity for the [3H]-ligand and a high binding capacity. The structural determinants of the ligands were studied by competitive inhibition of the [3H]-ligand binding. The delta 4-3-keto group in the steroid A-ring was found to be the most important determinant. An intensive metabolism of [3H]progesterone was observed during its incubation with cytosol (data from thin-layer chromatography). A 3H-metabolite (presumably, 20 beta-dihydroprogesterone) was predominant in the bound ligand fraction. The data obtained suggest that proteins of a steromodulin type are widely distributed in the mammalian liver.     

Supercritical fluid extraction of steroids from biological samples and first experience with solid-phase microextraction-liquid chromatography

Modern extraction techniques, supercritical fluid extraction (SFE) and solid-phase microextraction (SPME) were used for isolation of four corticosteroids from biological matrices. SFE was applied for extraction from solid matrices--hydromatrix and pig muscle. The effects of various extraction conditions were studied. Good recoveries of corticosteroids from hydromatrix were obtained under moderate extraction conditions and without modification of carbon dioxide. On the contrary, the best recoveries from spiked pig muscle were obtained with modified carbon dioxide. SPME was used for extraction from liquid samples--water and urine. The eventuality of the use of this fast solvent-free technique in steroid analysis is demonstrated. Several extraction conditions were optimized. Extracted steroids were analyzed by HPLC-UV and a special SPME-HPLC interface was used for combination with SPME.     

CRISPR: a versatile tool for both forward and reverse genetics research

Human genetics research employs the two opposing approaches of forward and reverse genetics. While forward genetics identifies and links a mutation to an observed disease etiology, reverse genetics induces mutations in model organisms to study their role in disease. In most cases, causality for mutations identified by forward genetics is confirmed by reverse genetics through the development of genetically engineered animal models and an assessment of whether the model can recapitulate the disease. While many technological advances have helped improve these approaches, some gaps still remain. CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated), which has emerged as a revolutionary genetic engineering tool, holds great promise for closing such gaps. By combining the benefits of forward and reverse genetics, it has dramatically expedited human genetics research. We provide a perspective on the power of CRISPR-based forward and reverse genetics tools in human genetics and discuss its applications using some disease examples.     

Differential scanning calorimetry as a complementary diagnostic tool for the evaluation of biological samples

BackgroundDifferential scanning calorimetry (DSC) is a tool for measuring the thermal stability profiles of complex molecular interactions in biological fluids. DSC profiles (thermograms) of biofluids provide specific signatures which are being utilized as a new diagnostic approach for characterizing disease but the development of these approaches is still in its infancy.MethodsThis article evaluates several approaches for the analysis of thermograms which could increase the utility of DSC for clinical application. Thermograms were analyzed using localized thermogram features and principal components (PCs). The performance of these methods was evaluated alongside six models for the classification of a data set comprised of 300 systemic lupus erythematosus (SLE) patients and 300 control subjects obtained from the Lupus Family Registry and Repository (LFRR).ResultsClassification performance was substantially higher using the penalized algorithms relative to localized features/PCs alone. The models were grouped into two sets, the first having smoother solution vectors but lower classification accuracies than the second with seemingly noisier solution vectors.ConclusionsCoupling thermogram technology with modern classification algorithms provides a powerful diagnostic approach for analysis of biological samples. The solution vectors from the models may reflect important information from the thermogram profiles for discriminating between clinical groups.General significanceDSC thermograms show sensitivity to changes in the bulk plasma proteome that correlate with clinical status. To move this technology towards clinical application the development of new approaches is needed to extract discriminatory parameters from DSC profiles for the comparison and diagnostic classification of patients. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

A sensitive analytical method for the detection and quantitation of adenosine in biological samples

A new method for the measurement of adenosine in biological materials has been developed. The method is based on the combined principles of isotope dilution and enzymatic catalysis using a highly specific adenosine kinase isolated from rat heart. By differential centrifugation and gel filtration, this adenosine kinase was obtained free of adenosine deaminase and other enzymes which would have been a source of error in the use of this enzyme in the adenosine assay. The cardiac adenosine kinase was shown to be highly specific and to exhibit an apparent K_m for adenosine of 0.35 μM. Using this enzyme, unknown quantities of adenosine could be detected by measuring the effect of their addition on the conversion of radioisotopic adenosine to 5′-AMP in the kinase reaction. In this procedure, as little as 20 pmoles of adenosine could be detected. To test the applicability of the assay, measurements of the tissue content of this nucleoside were made in samples of dog and rat hearts frozen in situ under control, hypoxic, or ischemic conditions. The assay has several advantageous features when compared to other existing methods used to measure adenosine: a minimum of sample preparation is required before the actual assay procedure; many samples can be processed per day by a single operator; single determinations can be done on as little as 5 μl of sample, and the specificity of the assay can be readily checked by treatment of samples with adenosine deaminase.     

Neoglycoenzymes: a versatile tool for lectin detection in solid-phase assays and glycohistochemistry

Carbodiimide-mediated coupling of p-aminophenyl glycosides to a naturally nonglycosylated enzyme yields a neoglycoenzyme. This compound combines inherent enzymatic activity with synthetically conferred ligand properties to lectins. Appropriate choice of the ligand allows custom-made synthesis to reliably detect various types of lectins. To exemplify practical applications of this class of compounds, glycosylated bacterial beta-galactosidase has been employed to quantitate plant lectins, immobilized on plastic surfaces as well as on nitrocellulose. Competitive inhibition by specific sugar ascertained the dependence of binding on protein--carbohydrate interactions. In view of lectins as tools, a sandwich lectin-binding assay for high mannose-type glycoprotein detection has been modified to principally facilitate wide application to other lectin-reactive sugar chains by introducing the neoglycoenzyme. In addition to lectin determination in solid-phase assays, neoglycoenzymes allow one to glycohistochemically localize endogenous lectins in tissue prints and tissue sections with a minimum number of steps. This nonradioactive, rapid, sensitive, and convenient assay concept, based on conjugation of a ligand to an enzyme with maintenance of its receptor-binding activity, may find extended application beyond lectinology in receptor analysis.     

Comparisons of protocols for decontamination of environmental ice samples for biological and molecular examinations

Drilling and laboratory manipulations of glacial ice cores introduce contemporary microbes and biomolecules onto the cores. We report herein a systematic comparative study of several decontamination protocols. Only treatment with 5% sodium hypochlorite eliminated all external contaminating microbes and nucleic acids while maintaining the integrity of those within the cores.     

GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples

The interpretation of mass spectrometry data for protein identification has become a vital component of proteomics research. However, since most existing software tools rely on protein databases, their success is limited, especially as the pace of annotation efforts fails to keep pace with sequencing. We present a publicly available, web-based version of a software tool that maps peptide mass fingerprint data directly to their genomic origin, allowing for genome-based, annotation-independent protein identification.     

Extraction and physico-chemical characterization of a versatile biodegradable polysaccharide obtained from green algae

During the last years, considerable attention has been given to different marine organisms, like algae, as potential sources of valuable materials. The continuous demand for novel materials and technologies is high and research on the underexploited marine green algae, including its polysaccharidic part—ulvan, has increased accordingly. In this research work, a novel method for extraction of ulvan from green algae is proposed and demonstrated successfully. Different characterization techniques were employed to characterize the isolated algal polysaccharide, namely, on what concerns its thermal trace and crystallinity. Upon heating, ulvan behaves as a non-meltable polysaccharide that is thermally stable before degradation at 220 °C. Ulvan is semi-crystalline in nature and possesses high hygroscopic features, as revealed in this research work. Due to its properties, ulvan can be considered, pure or modified, as a versatile biodegradable polymer for different applications, including tissue engineering and regenerative medicine.     

BioPP: a tool for web-publication of biological networks

Background  

Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental research teams and communities. No current tool supports web publication or hosting of user-developed large scale annotated pathway diagrams. Sharing via web publication is needed to allow real-time access to the current literature pathway knowledgebase, both privately within a research team or publicly among the outside research community. Web publication also facilitates team and/or community input into the curation process while allowing centralized control of the curation and validation process. We have developed new tool to address these needs. Biological Pathway Publisher (BioPP) is a software suite for converting CellDesigner Systems Biology Markup Language (CD-SBML) formatted pathways into a web viewable format. The BioPP suite is available for private use and for depositing knowledgebases into a newly created public repository.     

AutoDimer: a screening tool for primer-dimer and hairpin structures

The ability to select short DNA oligonucleotide sequences capable of binding solely to their intended target is of great importance in developing nucleic acid based detection technologies. Applications such as multiplex PCR rely on primers binding to unique regions in a genome. Competing side reactions with other primer pairs or template DNA decrease PCR efficiency: Freely available primer design software such as Primer3 screens for potential hairpin and primer-dimer interactions while selecting a single primer pair. The development of multiplex PCR assays (in the range of 5 to 20 loci) requires the screening of all primer pairs for potential cross-reactivity. However, a logistical problem results due to the number of total number of comparisons required. Comparing the primer set for a 10-plex assay (20 total primer sequences) results in 210 primer-primer combinations that must be screened. The ability to screen sets of candidate oligomers rapidly for potential cross-reactivity reduces overall assay devlelopment time. Here we report the application of a familiar sliding algorithm for comparing two strands of DNA in an overlapping fashion. The algorithm has been employed in a software package wherein the user can compare multiple sequences in a single computational run. After the screening is completed, a score is assigned to potential duplex interactions exceeding a user-defined threshold. Additional criteria of predicted melting temperature (Tm) and free energy of melting (deltaG) are included for further ranking. Sodium counterion and total stand concentrations can be adjusted for the Tm and deltaG calculations. The predicted interactions are saved in a text file for further evaluation.