Flexibility and specificity of the cohesin–dockerin interaction: implications for cellulosome assembly and functionality

Cellulosomes are highly elaborate multi-enzyme complexes of Carbohydrate Active enZYmes (CAZYmes) secreted by cellulolytic microorganisms, which very effectively degrade the most abundant polymers on Earth, cellulose and hemicelluloses. Cellulosome assembly requires that a non-catalytic dockerin module found in cellulosomal enzymes binds to one of the various cohesin domains located in a large molecular scaffold called Scaffoldin. A diversity of cohesin–dockerin binding specificities have been described, the combination of which may result in complex plant cell wall degrading systems, maximising the synergy between enzymes in order to improve catalytic efficiency. Structural studies have allowed the spatial flexibility inherent to the cellulosomal system to be determined. Recent progress achieved from the study of the fundamental cohesin and dockerin units involved in cellulosome assembly will be reviewed.     

Statistical methods for temporal and space–time analysis of community composition data

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran''s eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.     

Cole–Cole, linear and multivariate modeling of capacitance data for on-line monitoring of biomass

This work evaluates three techniques of calibrating capacitance (dielectric) spectrometers used for on-line monitoring of biomass: modeling of cell properties using the theoretical Cole–Cole equation, linear regression of dual-frequency capacitance measurements on biomass concentration, and multivariate (PLS) modeling of scanning dielectric spectra. The performance and robustness of each technique is assessed during a sequence of validation batches in two experimental settings of differing signal noise. In more noisy conditions, the Cole–Cole model had significantly higher biomass concentration prediction errors than the linear and multivariate models. The PLS model was the most robust in handling signal noise. In less noisy conditions, the three models performed similarly. Estimates of the mean cell size were done additionally using the Cole–Cole and PLS models, the latter technique giving more satisfactory results.     

Scientific data and theories for salmonellosis dose–response assessment

An “expansive” risk assessment approach is illustrated, characterizing dose–response relationships for salmonellosis in light of the full body of evidence for human and murine superorganisms. Risk assessments often require analysis of costs and benefits for supporting public health decisions. Decision-makers and the public need to understand uncertainty in such analyses for two reasons. Uncertainty analyses provide a range of possibilities within a framework of present scientific knowledge, thus helping to avoid undesirable consequences associated with the selected policies. And, it encourages the risk assessors to scrutinize all available data and models, thus helping avoid subjective or systematic errors. Without the full analysis of uncertainty, decisions could be biased by judgments based solely on default assumptions, beliefs, and statistical analyses of selected correlative data. Alternative data and theories that incorporate variability and heterogeneity for the human and murine superorganisms, particularly colonization resistance, are emerging as major influences for microbial risk assessment. Salmonellosis risk assessments are often based on conservative default models derived from selected sets of outbreak data that overestimate illness. Consequently, the full extent of uncertainty of estimates of annual number of illnesses is not incorporated in risk assessments and the presently used models may be incorrect.     

Enzyme–substrate reporters for evaluation of substrate specificity of HIF prolyl hydroxylase isoforms

An organism naturally responds to hypoxia via stabilization of hypoxia-inducible factor (HIF). There are three isoforms of HIFα subunits whose stability is regulated by three isozymes of HIF prolyl hydroxylase (PHD1-3). Despite intense studies on recombinant enzyme isoforms using homogeneous activity assay, there is no consensus on the PHD iso-form preference for the HIF isoform as a substrate. This work provides a new approach to the problem of substrate specificity using cell-based reporters expressing the enzyme and luciferase-labeled substrate pair encoded in the same expression vector. The cell is used as a microbioreactor for running the reaction between the overexpressed enzyme and substrate. Using this novel approach, no PHD3 activity toward HIF3 was demonstrated, indirectly pointing to the hydroxylation of the second proline in 564PYIP567 (HIF1) catalyzed by this isozyme. The use of “paired” enzyme–substrate reporters to evaluate the potency of “branched tail” oxyquinoline inhibitors of HIF PHD allows higher precision in revealing the optimal structural motif for each enzyme isoform.     

Evolutionary physiology by data of publications for 1965–2005

Evolutionary physiology as independent direction of physiology was formed in the XX century and was rapidly developing in its second half. To evaluate some tendencies of this process, we analyzed publications in Journal of Evolutionary Biochemistry and Physiology, one of the leading specialized periodicals on this problem. Analysis of works published for 4 decades has shown that the majority of papers deals with study of evolution of function of the nervous system (40–60 papers per year), less papers concern study of functions of sensory and visceral systems (20–30 per year). Among the used method, the most widely spread is the comparative-physiological method. By the end of the 1990s the number of works with use of methods of embryophysiology decreased. In the performed studies, predominant are physiological methods. Use of biochemical methods decreased, while of methods of molecular biology increased. The most often used objects of studies were mammals. By the end of the XX—beginning of the XXI century, in the greater number of papers the object of study has become human, while the number of publications in which experiments were performed on amphibians, reptiles, and birds decreased. More than a half of all works were carried out in St. Petersburg (Leningrad); the number of papers submitted from Moscow institutions gradually decreased, but the number of works from regions of Russia rose. Most studies were performed at institutes of the Russian Academy of Sciences and universities, while the number of papers from institutes of the Russian Academy of Medical Sciences decreased. For the last few years, several generalizations on evolution of functions and functional evolution have been formulated; handbooks and monographs on problems of evolutional physiology have been published.     

Reaction of β-propiolactone with amino acids and its specificity for methionine

1. The reactions of beta-propiolactone with amino acids were investigated under various conditions of pH and temperature to find those under which the reagent acted with specificity. 2. At pH9.0 and 22 degrees , after 15min. of reaction, at least 85% of each amino acid had reacted, methionine and cystine being the most reactive. 3. At pH7.0 and 22 degrees most amino acids reacted; methionine, cystine and histidine reacted almost entirely, and proline and lysine to a significantly smaller extent. 4. At pH3.0 and 22 degrees further specificity was obtained; methionine and cystine were the only reactive amino acids. 5. Reaction at pH3.0 and 0 degrees was specific for methionine; it was the only amino acid modified even after 145hr. of reaction.     

Susceptibility gene search for nephropathy and related traits in Mexican–Americans

The rising global epidemic of diabetic nephropathy (DN) will likely lead to increase in the prevalence of cardiovascular morbidity and mortality posing a serious burden for public health care. Despite greater understanding of the etiology of diabetes and the development of novel treatment strategies to control blood glucose levels, the prevalence and incidence rate of DN is increasing especially in minority populations including Mexican–Americans. Mexican–Americans with type 2 diabetes (T2DM) are three times more likely to develop microalbuminuria, and four times more likely to develop clinical proteinuria compared to non-Hispanic whites. Furthermore, Mexican–Americans have a sixfold increased risk of developing renal failure secondary to T2DM compared to Caucasians. Prevention and better treatment of DN should be a high priority for both health-care organizations and society at large. Pathogenesis of DN is multi-factorial. Familial clustering of DN-related traits in MAs show that DN and related traits are heritable and that genes play a susceptibility role. While, there has been some progress in identifying genes which when mutated influence an individual’s risk, major gene(s) responsible for DN are yet to be identified. Knowledge of the genetic causes of DN is essential for elucidation of its mechanisms, and for adequate classification, prognosis, and treatment. Self-identification and collaboration among researchers with suitable genomic and clinical data for meta-analyses in Mexican–Americans is critical for progress in replicating/identifying DN risk genes in this population. This paper reviews the approaches and recent efforts made to identify genetic variants contributing to risk for DN and related phenotypes in the Mexican–American population.     

Localized Surface Plasmon Resonance and Refractive Index Sensitivity of Metal–Dielectric–Metal Multilayered Nanostructures

The localized surface plasmon resonances of multilayered nanostructures are studied using finite difference time domain simulations and plasmon hybridization method. Concentric metal–dielectric–metal (MDM) structure with metal core and nanoshell separated by a thin dielectric layer exhibits a strong coupling between the core and nanoshell plasmon resonance modes. The coupled resonance mode wavelengths show dependence on the dielectric layer thickness and composition of core and outer layer metal. The aluminum-based MDM structures show lower plasmon wavelength compared with Ag- and Au-based MDM nanostructures. The calculated refractive index sensitivity (RIS) factor is in the order Ag–Air–Ag>Au–Air–Au>Al–Air–Al for monometallic multilayered nanostructures. Bimetallic multilayered nanostructures support strong and tunable plasmon resonance wavelengths as well as high RIS factor of 510 nm/refractive index unit (RIU) and 470 nm/RIU for Al–Air–Au and Ag-Air-Au, respectively. The MDM structures not only exhibit higher index sensitivity but also cover a wide ultraviolet–near-infrared wavelengths, making these structures very promising for index sensing, biomolecule sensing, and surface-enhanced Raman spectroscopy.     

Structural basis for the affinity of four insolubilized lectins,with a specificity for α-D-mannose,towards various glycopeptides with the N-glycosylamine linkage and related oligosaccharides

Precisions are given on the fine specificity and on the usefulness of immobilized concanavalin A,Lens culinaris, Vicia faba andPisum sativum agglutinins for fractionation of glycopeptides with the N-glycosylamine linkage.While insolubilized concanavalin A represents a very useful tool for the fractionation of both N-acetyllactosaminic and oligomannosidic type glycopeptides or related oligo-saccharides, immobilizedLens culinaris, as well asVicia faba orPisum sativum agglutinins allow the subfractionation of some N-acetyllactosaminic glycopeptide populations on the basis of the presence of an α-L-fucose residue substituting in C-6 position the N-acetylglucosamine residue involved in the N-glycosylamine bond.     

A review of prostate cancer incidence and mortality studies of farmers and non-farmers, 2002–2013

ObjectivesTo review the recent literature on the incidence and mortality of prostate cancer in farmers compared to non-farmers.MethodsSearches were conducted in seven electronic databases for observational studies published from 2002 to 2013. Studies were assessed against eligibility criteria and a narrative summary of findings presented.ResultsEighteen primary research articles were included in the review. Four of ten mortality studies and two of nine incidence studies reported statistically significant increases in prostate cancer risk in farmers. However, nearly half of all studies reported non-significant reductions in farmers’ risk. Additionally, one study reported significantly increased and decreased risk using different outcome measures. Results varied considerably by geographic region, study design and degree of control for confounders, affecting comparability and strength of findings.ConclusionsThe overall evidence for increased prostate cancer risk in farmers was weak.     

Is literature data useful for identifying enzyme catalysts for new substrates? A case study on reduction of 1-aryl-2-alkanoates

The use of literature data to identify catalysts for a novel transformation is a commonly used approach. Herein, we have evaluated if this is a viable strategy in enzyme catalysis, using asymmetric reduction of 1-aryl-2-alkanoates as a model system. The study, which includes data from 24 ketone substrates and 108 enzymes, clearly identifies pitfalls with this approach, but anyhow shows that literature data is highly useful for identification of enantioselective catalysts. By combining data for selectivity and rate useful catalyst for converting different substrates to their corresponding (R)- and (S)-enantiomers are highlighted.