Incorporating homologues into sequence embeddings for protein analysis

Statistical and learning techniques are becoming increasingly popular for different tasks in bioinformatics. Many of the most powerful statistical and learning techniques are applicable to points in a Euclidean space but not directly applicable to discrete sequences such as protein sequences. One way to apply these techniques to protein sequences is to embed the sequences into a Euclidean space and then apply these techniques to the embedded points. In this work we introduce a biologically motivated sequence embedding, the homology kernel, which takes into account intuitions from local alignment, sequence homology, and predicted secondary structure. This embedding allows us to directly apply learning techniques to protein sequences. We apply the homology kernel in several ways. We demonstrate how the homology kernel can be used for protein family classification and outperforms state-of-the-art methods for remote homology detection. We show that the homology kernel can be used for secondary structure prediction and is competitive with popular secondary structure prediction methods. Finally, we show how the homology kernel can be used to incorporate information from homologous sequences in local sequence alignment.     

Social Transmission of Feeding Techniques in Tonkean Macaques?

We studied the influence of social partners on food processing and drinking techniques in a semifree-ranging group of Tonkean macaques. In a first study, immature subjects observed their mothers repeateadly eating unfamiliar fruits. They were subsequently allowed to consume the same fruits. We found no evidence for social learning when comparing the technical variants used by the mother and her offspring. In a second study, we recorded the techniques displayed by the monkeys while drinking and eating familiar food. We compared the technical variants used by the members of two different maternal lineages. Whereas a majority of techniques did not differ between lineages, some variants were peculiar to each of them, this effect was independent from age. The results indicate that the possibility of technique transmission should not be excluded among macaques.     

The spikes trains probability distributions: A stochastic calculus approach

We discuss the statistics of spikes trains for different types of integrate-and-fire neurons and different types of synaptic noise models. In contrast with the usual approaches in neuroscience, mainly based on statistical physics methods such as the Fokker-Planck equation or the mean-field theory, we chose the point of the view of the stochastic calculus theory to characterize neurons in noisy environments. We present four stochastic calculus techniques that can be used to find the probability distributions attached to the spikes trains. We illustrate the power of these techniques for four types of widely used neuron models. Despite the fact that these techniques are mathematically intricate we believe that they can be useful for answering questions in neuroscience that naturally arise from the variability of neuronal activity. For each technique we indicate its range of applicability and its limitations.     

Basics of PCR and related techniques applied in veterinary parasitology

We attempte through the following overall review pertaining to the basics of PCR techniques (Polymerase Chain Reaction), to introduce the main applications used in veterinary parasitology. A major problem restricting the application possibilities of molecular biology techniques is of quantitative nature. Amplification techniques represent a real revolution, for it makes possible the production of tens, even hundreds of nanogrammes of sequences when starting from very small quantities. The PCR technique has dramatically transformed the strategies used so far in molecular biology and subsequently research and medical diagnosis.     

Ambiguities in results obtained with 2D gel replicon mapping techniques.

Recently, two 2-dimensional (2D) gel techniques, termed neutral/neutral and neutral/alkaline, have been developed and employed to map replication origins in eukaryotic plasmids and chromosomal DNA (1-11). The neutral/neutral technique, which requires less DNA for analysis, has been preferentially used in recent studies. We show here that the signal predicted for an origin is not detected using the neutral/neutral technique if the origin is located near the end of the analyzed restriction fragment. We also demonstrate that analysis of the same batch of DNA by the two different mapping techniques can generate apparently contradictory results: in some situations where neutral/alkaline 2D analysis indicates that a certain origin is always used, neutral/neutral 2D analysis suggests that the origin is not always used. Several possible explanations for this type of disagreement between the two techniques are discussed, and we conclude that it is important to use both techniques in combination in order to minimize possible misinterpretations.     

New PCR-based methods for yeast identification

AIMS: To characterize reference yeast strains and identify indigenous strains isolated from wine fermentations by PCR methods. METHODS AND RESULTS: We compared several PCR techniques for yeast identification. We used oligonucleotide primers that are complementary to (i) intron splice sites, (ii) REP and (iii) ERIC elements to produce PCR fingerprints that display specific patterns between the different yeast species. These three techniques were used to characterize 41 reference yeast strains belonging to 15 different species and to identify 40 indigenous strains isolated from grape must and wine fermentations. Species-specific banding patterns were obtained with the three PCR-techniques with different degrees of intraspecific differentiation depending on the method. By comparing the PCR fingerprints of unknown isolates with those produced by reference strains, we identified yeast strains isolated from an industrial wine fermentation. CONCLUSIONS: All three PCR techniques are rapid, reliable and simple methods of yeast identification. As far as we know, this is the first time that the primers designed for amplifying repetitive elements in bacteria have been successfully used in yeast. SIGNIFICANCE AND IMPACT OF THE STUDY: Industry needs rapid, reliable and simple methods of yeast identification. The proposed PCR techniques will allow to achieve this objective.     

A Discussion of Molecular Biology Methods for Protein Engineering

A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. We discuss the basic principles of these methods in a repertoire that may be used to achieve the elemental steps in protein engineering. These include site-directed, deletion and insertion mutagenesis. We provide detailed case studies, drawn from our own experiences, packaged together with conceptual discussions and include an analysis of the techniques presented with regards to their uses in protein engineering.     

Morphing methods to parameterize specimen-specific finite element model geometries

Shape plays an important role in determining the biomechanical response of a structure. Specimen-specific finite element (FE) models have been developed to capture the details of the shape of biological structures and predict their biomechanics. Shape, however, can vary considerably across individuals or change due to aging or disease, and analysis of the sensitivity of specimen-specific models to these variations has proven challenging. An alternative to specimen-specific representation has been to develop generic models with simplified geometries whose shape is relatively easy to parameterize, and can therefore be readily used in sensitivity studies. Despite many successful applications, generic models are limited in that they cannot make predictions for individual specimens.We propose that it is possible to harness the detail available in specimen-specific models while leveraging the power of the parameterization techniques common in generic models. In this work we show that this can be accomplished by using morphing techniques to parameterize the geometry of specimen-specific FE models such that the model shape can be varied in a controlled and systematic way suitable for sensitivity analysis. We demonstrate three morphing techniques by using them on a model of the load-bearing tissues of the posterior pole of the eye. We show that using relatively straightforward procedures these morphing techniques can be combined, which allows the study of factor interactions. Finally, we illustrate that the techniques can be used in other systems by applying them to morph a femur. Morphing techniques provide an exciting new possibility for the analysis of the biomechanical role of shape, independently or in interaction with loading and material properties.     

Sequence alterations can mask each other's presence during screening with SSCP or heteroduplex analysis: BRCA genes as examples

For mutation detection, various screening techniques are widely used because DNA sequencing, the gold-standard method, is still considered to be expensive and laborious for high-throughput screening. Single-strand conformation polymorphism (SSCP) analysis, heteroduplex analysis (HA) and their variant techniques are popular and frequently used for this purpose. It is widely accepted that when searching for unknown sequence variations, any revealed distinct pattern should always be sequenced. We give examples here of the BRCA1 and BRCA2 genes where the SSCP/HA techniques can produce ambiguous predictions if used to detect known genetic variants compared to positive controls. Using direct DNA sequencing, we provide evidence that in such cases, mutations or polymorphisms can mask each other's presence. This phenomenon can often influence the results of any DNA testing because genetic variations such as single-nucleotide polymorphisms occur frequently in the human genome. We suggest that even in the case of known electrophoretic patterns of well-characterized genetic alterations, every sequence alteration should be confirmed by direct DNA sequencing, especially if genetic testing is carried out for diagnostic purposes.     

Comparison of selected analytical techniques for protein sizing, quantitation and molecular weight determination

Protein analysis techniques are developing fast due to the growing number of proteins obtained by recombinant DNA techniques. In the present paper we compare selected techniques, which are used for protein sizing, quantitation and molecular weight determination: sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip or microfluidics technology (LoaC), size exclusion chromatography (SEC) and mass spectrometry (MS). We compare advantages and limitations of each technique in respect to different application areas, analysis time, protein sizing and quantitation performance.     

Methods for the detection and analysis of protein-protein interactions

A large number of methods have been developed over the years to study protein-protein interactions. Many of these techniques are now available to the nonspecialist researcher thanks to new affordable instruments and/or resource centres. A typical protein-protein interaction study usually starts with an initial screen for novel binding partners. We start this review by describing three techniques that can be used for this purpose: (i) affinity-tagged proteins (ii) the two-hybrid system and (iii) some quantitative proteomic techniques that can be used in combination with, e.g., affinity chromatography and coimmunoprecipitation for screening of protein-protein interactions. We then describe some public protein-protein interaction databases that can be searched to identify previously reported interactions for a given bait protein. Four strategies for validation of protein-protein interactions are presented: confocal microscopy for intracellular colocalization of proteins, coimmunoprecipitation, surface plasmon resonance (SPR) and spectroscopic studies. Throughout the review we focus particularly on the advantages and limitations of each method.     

磁共振功能成像在监测乳腺癌新辅助化疗中的应用和进展

近年来,新辅助化疗在原发乳腺癌治疗中运用越来越广泛。影像学手段在评价新辅助化疗疗效、指导临床治疗方案的制定中发挥重要作用。磁共振功能成像的引入,可以加深对恶性乳腺肿瘤的病理生理活动及分子生物学特性的了解,监测化疗疗效,提高早期预测的准确性。本文总结功能学MRI(磁共振成像)探测乳腺癌患者生物标志物的研究现状及发展情况,描述各种生物学标志物特性,评价其潜在的临床应用价值和局限性。以下将对动态增强磁共振成像、弥散加权成像、血氧水平依赖成像以及波谱成像等几种磁共振功能学成像方法的原理进行描述,重点对其在监测乳腺癌新辅助化疗中的应用进行综述。     

Industrial Production and Quality Control of Two Liposome Gels: Size,Size Distribution and Stability

Abstract

We use the mechanical high-shear homogenization method for large scale production of two cosmetic gels containing a liposome dispersion. To ensure homogeneity, reproducibility and stability, transmission electron-microscope techniques were used to determine particle size and size distribution of vesicles, in addition to other techniques such as flow cytometry fluorescence and Coulter analysis.     

Amplification, mutation and selection of catalytic RNA

RNA, by virtue of its genotypic and phenotypic properties, is a suitable substrate for molecular evolution in the laboratory. We have developed techniques for the rapid amplification, mutation and selection of catalytic RNA. By combining these techniques in an iterative fashion, we are attempting to construct an RNA-based evolving system. Such a system could be used to explore the catalytic potential of RNA.     

Current knowledge of the human sperm proteome

The knowledge of the mature sperm proteome is undoubtedly the basis for understanding sperm function, the mechanisms responsible for fertilization, the reasons for infertility and possible treatments. The methods of sperm protein extraction depend mainly on the proteins of interest and the protein separation techniques that will be employed. The isolation of the membrane proteins appears to be most problematic step. Nevertheless, two-dimensional electrophoresis and mass spectrometry have become the main techniques used in human sperm protein analysis. We outline the present techniques used to examine the sperm proteome and data generated from studies on the human sperm and different types of male infertility. We present the most characteristic proteins that are involved in sperm function. Their value as biomarkers for diagnosis and treatment of infertility would require further validation. We focus on selected and critical studies of the human sperm proteome to present our subjective view of this fast-moving field.     

Assays of protein palmitoylation

Protein palmitoylation plays an important role in the structure and function of a wide array of proteins. Unlike other lipid modifications, protein palmitoylation is highly dynamic and cycles of palmitoylation and depalmitoylation can regulate protein function and localization. The dynamic nature of palmitoylation is poorly resolved because of limitations in assay methods. Here, we discuss various methods that can be used to measure protein palmitoylation and identify sites of palmitoylation. We describe new methodology based on "fatty acyl exchange labeling" in which palmitate is removed via hydroxylamine-mediated cleavage of the palmitoyl-thioester bond and then exchanged with a sulfhydryl-specific labeling compound. The techniques are highly sensitive and allow for quantitative estimates of palmitoylation. Unlike other techniques used to assay posttranslational modifications, the techniques we have developed can label all sites of modification with a variety of probes, radiolabeled or non-radioactive, and can be used to assay the palmitoylation of proteins from tissue samples.     

Why and how to objectively evaluate medical gestures?

Junior physicians mainly learn during their observation in the operative room. The senior physicians evaluate them based on the same kind of observation. Knowledge transfer evaluation is thus done without quantitative methods and it mainly lies on a subjective assessment. In this paper, we present some recent techniques used to objectively evaluate medical gestures. The classical techniques used are Hidden Markov Models (HMM) or Dynamic Time Warping (DTW). Both techniques lies on the temporal analysis of the gestures. We proposed here a technique based on the arc length parametrization in order to analyze the gestures in space which is more appropriate because it gives information about the shape of the gestures independently of the chosen coordinate system.     

Age-grading the biting midge Culicoides sonorensis using near-infrared spectroscopy

Age-grading of insects is important in the control and monitoring of both insect populations and vector-borne diseases. Microscopy and morphological techniques exist to age-grade most blood-feeding flies, but these techniques are laborious, often destructive to the insects, and slow. Near-infrared spectroscopy (NIRS) can be automated and is a non-destructive technique for age-grading. We applied NIRS techniques to age-grade females of the biting midge, Culicoides sonorensis Wirth & Jones (Diptera: Ceratopogonidae), the vector of bluetongue and other arboviruses in North America. Female flies of five known age cohorts (1, 3, 6, 9 and 12 days post-emergence) from three laboratory colonies were used. The data indicate that NIRS can be used to differentiate age groups of C. sonorensis .     

Simultaneous visualization of immunodetected antigens and tissue components revealed by non-enzymatic histochemical stains.

We explored the possibility of simultaneous application of histochemical and immunohistochemical staining techniques on the same paraffin-embedded human tissue section. Conventional histological stains (PAS, Alcian, Alcian-PAS, Van Gieson, Gomori silver impregnation, and Giemsa) were used in association with a battery of markers (keratins, leucocyte common antigen, S-100 protein, Factor VIII-related antigen) that are widely employed in diagnostic and experimental studies. We found that the best procedure was to perform immunostaining before the histochemical reaction, as this enables all the other possible combinations to be carried out. In addition, several detection systems, such as peroxidase-anti-peroxidase (PAP), alkaline phosphatase-anti-alkaline phosphatase (APAAP), and avidin-biotin complex (ABC), were tested and all gave consistent results. Some minor modifications of the histological staining methods were necessary, but the current immunohistochemical techniques could be used as established. Preliminary findings indicate that immunohistochemistry can be combined with histochemistry techniques by means of a relatively simple procedure whose only disadvantage is the time required to carry out the double staining.