Proteomics, nanotechnology and molecular diagnostics

Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.     

Let's Sco1, Oxidase! Let's Sco!

The solution structure of Sco1 from Bacillus subtilis is the first structure of a protein important in the assembly of cytochrome c oxidase (CcO). The assembly of CcO requires the insertion of multiple cofactors. Sco1 is a conserved protein implicated in formation of the binuclear Cu(A) center.     

CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes

Multiple sclerosis (MS) is an immune-mediated, neuro-inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS) with a heterogeneous clinical presentation and course. There is a remarkable phenotypic heterogeneity in MS, and the molecular mechanisms underlying it remain unknown. We aimed to investigate further the etiopathogenesis related molecular pathways in subclinical types of MS using proteomic and bioinformatics approaches in cerebrospinal fluids of patients with clinically isolated syndrome, relapsing remitting MS and progressive MS (n=179). Comparison of disease groups with controls revealed a total of 151 proteins that are differentially expressed in clinically different MS subtypes. KEGG analysis using PANOGA tool revealed the disease related pathways including aldosterone-regulated sodium reabsorption (p=8.02x10^-5) which is important in the immune cell migration, renin-angiotensin (p=6.88x10^-5) system that induces Th17 dependent immunity, notch signaling (p=1.83x10^-10) pathway indicating the activated remyelination and vitamin digestion and absorption pathways (p=1.73x10^-5). An emerging theme from our studies is that whilst all MS clinical forms share common biological pathways, there are also clinical subtypes specific and pathophysiology related pathways which may have further therapeutic implications.     

Specific clinical, epidemiological patterns and laboratory diagnostics of enterovirus infection in the Republic of Belarus

The clinical and epidemiological patterns as well as the results of the laboratory verification of the outbreak of enterovirus infection (EVI) in Minsk during the period of summer-autumn, 2000, are presented. During this outbreak a variety of clinical forms were observed, the serous meningitis being prevalent (57.5%). Practically simultaneous occurrence of infection on the territory of all administrative districts of the city, the predominant involvement of children aged up to 14 years into the outbreak, a high proportion of simultaneous casualities in the multiple foci. A number of circulating enteroviruses (EV)--ECHO 30, ECHO 6 of three serotypes and Coxsackie B5--were simultaneously isolated from clinical material. EV of the same serotypes were isolated from tap drinking water, and neutralizing antibodies to these serotypes were often detected in the patients blood sera. Infectious EV were also present in samples of bottled water and in water reservoirs used for bathing. The routes of EV transmission and the improvement of EVI control are discussed.     

Rhinovirus diseases: pathogenesis, diagnostics and treatment

Contemporary data on human rhinovirus diseases and their pathogenesis are presented. Special attention is paid to complications which may be caused by rhinovirus infections in allergy-susceptible patients. Furthermore, approaches to the diagnostics and treatment of rhinovirus diseases are described. In particular, the advantages of molecular methods for the diagnostics of rhinovirus infection (based on the PCR) in comparison with cultural and immunochemical methods are pointed out. New investigations aimed at the development of specific antirhinovirus preparations--capsid-binding (Pleconaril), blocking the binding of the virus with cell receptors (ICAM, soluble) and inhibiting rhinovirus protease 3C--have been considered.     

Calcium signalling: IP3 rises again...and again

Recent results indicate that 'regulators of G-protein signalling' may contribute to the generation of receptor-specific patterns of cytosolic Ca2+ oscillations by associating with specific receptors, accelerating G-protein inactivation and responding to changes in cytosolic Ca2+.     

Hearing it again and again: on-line subcortical plasticity in humans

Background

Human brainstem activity is sensitive to local sound statistics, as reflected in an enhanced response in repetitive compared to pseudo-random stimulus conditions [1]. Here we probed the short-term time course of this enhancement using a paradigm that assessed how the local sound statistics (i.e., repetition within a five-note melody) interact with more global statistics (i.e., repetition of the melody).

Methodology/Principal Findings

To test the hypothesis that subcortical repetition enhancement builds over time, we recorded auditory brainstem responses in young adults to a five-note melody containing a repeated note, and monitored how the response changed over the course of 1.5 hrs. By comparing response amplitudes over time, we found a robust time-dependent enhancement to the locally repeating note that was superimposed on a weaker enhancement of the globally repeating pattern.

Conclusions/Significance

We provide the first demonstration of on-line subcortical plasticity in humans. This complements previous findings that experience-dependent subcortical plasticity can occur on a number of time scales, including life-long experiences with music and language, and short-term auditory training. Our results suggest that the incoming stimulus stream is constantly being monitored, even when the stimulus is physically invariant and attention is directed elsewhere, to augment the neural response to the most statistically salient features of the ongoing stimulus stream. These real-time transformations, which may subserve humans'' strong disposition for grouping auditory objects, likely reflect a mix of local processes and corticofugal modulation arising from statistical regularities and the influences of expectation. Our results contribute to our understanding of the biological basis of statistical learning and initiate a new investigational approach relating to the time-course of subcortical plasticity. Although the reported time-dependent enhancements are believed to reflect universal neurophysiological processes, future experiments utilizing a larger array of stimuli are needed to establish the generalizability of our findings.     

Rethinking heredity, again

The refutation of 'soft' inheritance and establishment of Mendelian genetics as the exclusive model of heredity is widely portrayed as an iconic success story of scientific progress. Yet, we are witnessing a re-emergence of debate on the role of soft inheritance in heredity and evolution. I argue that this reversal reflects not only the weight of new evidence but also an important conceptual change. I show that the concept of soft inheritance rejected by 20th-century genetics differs fundamentally from the current concept of 'nongenetic inheritance'. Moreover, whereas it has long been assumed that heredity is mediated by a single, universal mechanism, a pluralistic model of heredity is now emerging, based on a recognition of multiple, parallel mechanisms of inheritance.     

Proteomics, networks and connectivity indices

Describing the connectivity of chemical and/or biological systems using networks is a straight gate for the introduction of mathematical tools in proteomics. Networks, in some cases even very large ones, are simple objects that are composed at least by nodes and edges. The nodes represent the parts of the system and the edges geometric and/or functional relationships between parts. In proteomics, amino acids, proteins, electrophoresis spots, polypeptidic fragments, or more complex objects can play the role of nodes. All of these networks can be numerically described using the so-called Connectivity Indices (CIs). The transformation of graphs (a picture) into CIs (numbers) facilitates the manipulation of information and the search for structure-function relationships in Proteomics. In this work, we review and comment on the challenges and new trends in the definition and applications of CIs in Proteomics. Emphasis is placed on 1-D-CIs for DNA and protein sequences, 2-D-CIs for RNA secondary structures, 3-D-topographic indices (TPGIs) for protein function annotation without alignment, 2-D-CIs and 3-D-TPGIs for the study of drug-protein or drug-RNA quantitative structure-binding relationships, and pseudo 3-D-CIs for protein surface molecular recognition. We also focus on CIs to describe Protein Interaction Networks or RNA co-expression networks. 2-D-CIs for patient blood proteome 2-DE maps or mass spectra are also covered.     

Rethinking inheritance,yet again: inheritomes,contextomes and dynamic phenotypes

Journal of Genetics -     

Proteomics: a link between genomics,genetics and physiology

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant biology. In the study of pleiotropic effects of mutants and in the analysis of responses to hormones and to environmental changes, the identification of involved metabolic pathways can be deduced from the function of affected proteins. In molecular quantitative genetics, proteomics can be used to map translated genes and loci controlling their expression, which can be used to identify proteins accounting for the variation of complex phenotypic traits. Linking gene expression to cell metabolism on the one hand and to genetic maps on the other, proteomics is a central tool for functional genomics.