Variation in EMG activity: a hierarchical approach

Recordings of naturally occurring Electromyographic (EMG) signalsare variable. One of the first formal and successful attemptsto quantify variation in EMG signals was Shaffer and Lauder's(1985) study examining several levels of variation but not withinmuscle. The goal of the current study was to quantify the variationthat exists at different levels, using more detailed measuresof EMG activity than did Shaffer and Lauder (1985). The importanceof accounting for different levels of variation in an EMG studyis both biological and statistical. Signal variation withinthe same muscle for a stereotyped action suggests that eachrecording represents a sample drawn from a pool of a large numberof motor units that, while biologically functioning in an integratedfashion, showed statistical variation. Different levels of variationfor different muscles could be related to different functionsor different tasks of those muscles. The statistical impactof unaccounted or inappropriately analyzed variation can leadto false rejection (type I error) or false acceptance (typeII error) of the null hypothesis. Type II errors occur becausesuch variation will accrue to the error, reducing power, andproducing an artificially low F-value. Type I errors are associatedwith pseudoreplication, in which the replicated units are nottruly independent, thereby leading to inflated degrees of freedom,and an underestimate of the error mean square. To address theseproblems, we used a repeated measures, nested multifactor modelto measure the relative contribution of different hierarchicallevels of variation to the total variation in EMG signals duringswallowing. We found that variation at all levels, among electrodesin the same muscle, in sequences of the same animal, and amongindividuals and between differently named muscles, was significant.These findings suggest that a single intramuscular electrode,recording from a limited sample of the motor units, cannot berelied upon to characterize the activity of an entire muscle.Furthermore, the use of both a repeated-measures model, to avoidpseudoreplication, and a nested model, to account for variation,is critical for a correct testing of biological hypotheses aboutdifferences in EMG signals.     

Developmental genetics and homology: a hierarchical approach

New advances in developmental genetics are providing a bridge to connect the study of development and evolution. The successful integration of these fields, however, is dependent on having a clear understanding of the concept of homology. Therefore, developmental genetic data must be placed within the context of the comparative method to provide insight into the evolutionary and developmental origins of traits. The comparative analysis of traits derived from several hierarchical levels (genes, gene expression patterns, embryonic origins and morphology) can potentially reveal scenarios of developmental integration, opportunity and constraint. Moreover, this approach has implications for resolving modern controversies surrounding the concept of homology.     

Connectivity independent protein-structure alignment: a hierarchical approach

Background  

Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity).     

Multilocus sequence typing as an approach for population analysis of Medicago-nodulating rhizobia

Multilocus sequence typing (MLST), a sequence-based method to characterize bacterial genomes, was used to examine the genetic structure in a large collection of Medicago-nodulating rhizobial strains. This is the first study where MLST has been applied in conjunction with eBURST analysis to determine the population genetic structure of nonpathogenic bacteria recovered from the soil environment. Sequence variation was determined in 10 chromosomal loci of 231 strains that predominantly originated from southwest Asia. Genetic diversity for each locus ranged from 0.351 to 0.819, and the strains examined were allocated to 91 different allelic profiles or sequence types (STs). The genus Medicago is nodulated by at least two groups of rhizobia with divergent chromosomes that have been classified as Sinorhizobium meliloti and Sinorhizobium medicae. Evidence was obtained that the degree of genetic exchange among the chromosomes across these groups is limited. The symbiosis with Medicago polymorpha of nine strains placed in one of these groups, previously identified as S. medicae, ranged from ineffective to fully effective, indicating that there was no strong relationship between symbiotic phenotype and chromosomal genotype.     

Environmental scales on the reproduction of a gypsophyte: a hierarchical approach

BACKGROUND AND AIMS: Environmental variability at several scales can determine plant reproductive success. The main goal of this work was to model the reproductive flexibility of a semi-arid specialist considering different scales of environmental variability. METHODS: A 2-year field study was performed on the determinants of the female reproductive success of Helianthemum squamatum, an Iberian gypsophyte, considering two scales of environmental variability: differences between two contrasting slope aspects; and, on individual scale, the neighbouring microenvironment. Generalized linear mixed models were used to evaluate simultaneously the potential effects of environmental variability at both scales, together with flowering phenology and plant size on the reproductive output of H. squamatum. The following reproductive response variables were considered: number of flowers, fruit-set, number of viable and aborted seeds per fruit, and number of seeds per plant. KEY RESULTS: Contrary to expectations, environmental variability exerted a weak or even absent effect on the reproductive variables considered, while flowering phenology and plant size, which did not vary between slopes, played a major role. Surprisingly, the absolute reproductive variables were even higher in the extremely dry year of 2003, although only on the south-facing slope. The relatively milder conditions of the north-facing slope did not involve any advantage to this species in terms of reproductive output. CONCLUSIONS: The species seemed to be considerably well adapted to the environmental unpredictability characteristic of Mediterranean systems, considering its ability to maintain reproduction across contrasting environments and contrasting climatic conditions. These findings make us face the question of what must be considered stressful conditions in the case of a stress-tolerant specialist.     

MolCraft: a hierarchical approach to the synthesis of artificial proteins

The modular structures of extant proteins and genes suggest that modern genes developed hierarchically from combinatorial assemblages of smaller primordial genetic units (microgenes). The MolCraft system described in this review is the new type of in vitro protein evolution system whose underlying concept is the hierarchical evolution of genes. In MolCraft, a microgene is initially evolved in silico and then tandemly polymerized with insertion or deletion mutations at the junctions between microgene units. Because of the junctional perturbations, proteins translated from a single microgene polymer are molecularly diverse, originating from the combinatorics of three reading frames, and are thus combinatorial polymers of three peptides. Notably, repetitiousness retained in the overall structure of proteins contributes to the formation of ordered structures, and enhances the chances of reconstituting biological activity rationally encrypted in the microgene unit. Applications of this new technology are discussed.     

Statistical analyses of enzyme inhibitor kinetics: a hierarchical model-dependent approach.

Inference of the nature of an enzyme inhibitor and calculations of inhibitor constants from linear plots are prone to be unreliable when experimental error is significant. This may be minimised by a method of statistical analysis using nonlinear regression methods and modelling using the variance ratio test of a hierarchy of models of inhibitor behaviour.     

口腔螺旋体新种Treponema putidum的多位点序列分析

目的应用多位点序列分析方法鉴定一种与齿垢密螺旋体(Treponema denticola,T.denticola)近似的新种口腔螺旋体细菌Treponema putidum(T.putidum)。方法选用16S r RNA,rec A和pyr H基因构建5种T.putidum菌株和7种T.denticola菌株以及其他相关临床分离株之间的最大似然进化树和贝叶斯进化树。通过分析两种进化树的拓扑结构,鉴定它们之间的亲缘关系。结果从最大似然进化树和贝叶斯进化树可见,T.putidum和T.denticola菌种几乎为同一系统来源,但是它们又能被彻底分开。结论 T.putidum是一种与口腔致病菌T.denticola相似而又不同的新型菌种。     

Multilocus phylogenetic analysis of the genus Aeromonas

A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several “bona fide” strains representing all described species.     

Multilocus analysis of the fragile X syndrome

Summary A multilocus analysis of the fragile X (fra(X)) syndrome was conducted with 147 families. Two proximal loci, DXS51 and F9, and two distal loci, DXS52 and DXS15, were studied. Overall, the best multipoint distances were found to be DXS51-F9, 6.9%, F9-fra(X), 22.4%; fra(X)-DXS52, 12.7%; DXS52-DXS15, 2.2%. These distances can be used for multipoint mapping of new probes, carrier testing and counseling of fra(X) families. Consistent with several previous studies, the families as a whole showed genetic heterogeneity for linkage between F9 and fra(X).     

Multilocus enzyme electrophoresis: a practical guide

Multilocus enzyme electrophoresis (MEE) uses the relative electrophoretic mobilities of intracellular enzymes to characterize and differentiate organisms by generating an electromorph type (ET). This article presents the chemical conditions that may be useful, a guide to the successful practice of the electrophoretic technique, and analysis of the results.     

Multilocus linkage analysis of affected sib pairs

OBJECTIVE: The conventional affected sib pair methods evaluate the linkage information at a locus by considering only marginal information. We describe a multilocus linkage method that uses both the marginal information and information derived from the possible interactions among several disease loci, thereby increasing the significance of loci with modest effects. METHODS: Our method is based on a statistic that quantifies the linkage information contained in a set of markers. By a marker selection-reduction process, we screen a set of polymorphisms and select a few that seem linked to disease. RESULTS: We test our approach on genome scan data for inflammatory bowel disease (InfBD) and on simulated data. On real data we detect 6 of the 8 known InfBD loci; on simulated data we obtain improvements in power of up to 40% compared to a conventional single-locus method. CONCLUSION: Our extensive simulations and the results on real data show that our method is in general more powerful than single-locus methods in detecting disease loci responsible for complex traits. A further advantage of our approach is that it can be extended to make use of both the linkage and the linkage disequilibrium between disease loci and nearby markers.     

Experimental mapping of soluble protein domains using a hierarchical approach

Exploring the function and 3D space of large multidomain protein targets often requires sophisticated experimentation to obtain the targets in a form suitable for structure determination. Screening methods capable of selecting well-expressed, soluble fragments from DNA libraries exist, but require the use of automation to maximize chances of picking a few good candidates. Here, we describe the use of an insertion dihydrofolate reductase (DHFR) vector to select in-frame fragments and a split-GFP assay technology to filter-out constructs that express insoluble protein fragments. With the incorporation of an IPCR step to create high density, focused sublibraries of fragments, this cost-effective method can be performed manually with no a priori knowledge of domain boundaries while permitting single amino acid resolution boundary mapping. We used it on the well-characterized p85α subunit of the phosphoinositide-3-kinase to demonstrate the robustness and efficiency of our methodology. We then successfully tested it onto the polyketide synthase PpsC from Mycobacterium tuberculosis, a potential drug target involved in the biosynthesis of complex lipids in the cell envelope. X-ray quality crystals from the acyl-transferase (AT), dehydratase (DH) and enoyl-reductase (ER) domains have been obtained.     

Multilocus sequence analysis of Penicillium and Eupenicillium species

Taxonomy of Hyphomycetes has always been a challenging problem, with experts viewing species in different ways and modifying the taxonomy of groups to reflect their best evaluation of species limits and concepts. The advent of phylogenetic analysis, relatively easy DNA sequencing techniques and PCR has provided an opportunity for mycology to move from a strictly morphological analysis of species to phylogenetic analysis of DNA sequences. Phylogenetic theory dictates that data from different loci will produce congruent or at least non-contradictory evolutionary histories of a clonal lineage. Tests of tree congruence such as the index of association can show whether lineages are clonal, and has revealed that some species long thought to be clonal are cryptically recombining. Genealogical concordance phylogenetic species recognition allows unambiguous identification of species boundaries.     

Multilocus sequence analysis of the actinobacterial genus Kribbella

Multilocus sequence analysis (MLSA) was used to refine the phylogenetic analysis of the genus Kribbella, which currently contains 17 species with validly-published names. Sequences were obtained for the 16S rRNA, gyrB, rpoB, recA, relA and atpD genes for 16 of the 17 type strains of the genus plus seven non-type strains. A five-gene concatenated sequence of 4099 nt was used to examine the phylogenetic relationships between the species of the genus Kribbella. Using the concatenated sequence of the gyrB-rpoB-recA-relA and atpD genes, most Kribbella type strains can be distinguished by a genetic distance of >0.04. Each single-gene tree had an overall topology similar to that of the concatenated sequence tree. The single-gene relA tree, used here for the first time in MLSA of actinobacteria, had good bootstrap support, comparable to the rpoB and atpD gene trees, which had topologies closest to that of the concatenated sequence tree. This illustrates that relA is a useful addition in MLSA studies of the genus Kribbella. We propose that concatenated gyrB-rpoB-recA-relA-atpD gene sequences be used for examining the phylogenetic relationships within the genus Kribbella and for determining the closest phylogenetic relatives to be used for taxonomic comparisons.     

Efficiency of the EU regulation on greenhouse gas emissions in Italy: The hierarchical cluster analysis approach

Using both a multivariate technique and a classic convergence analysis, we set out to test in an original way if the European Union (EU) regulation on greenhouse gas (GHG) emissions produced by urban road transport has generated a policy transfer process. By doing so, this paper attempts to fill the gap in research on ex-post analysis to assess whether the decisions taken at the EU level are actually transposed and implemented locally. The results obtained allow to document whether the EU regulation has stimulated the adoption of sustainable mobility policies for a selected group of Italian cities. The findings show that the processes of policy transfer may produce different effects if heterogeneity exists between cities or regions, even if they belong to the same country. Italian evidence demonstrates that northern cities are more actively drawing policy lessons. The study also reveals that large cities choose to look abroad more often than small municipalities. These results indicate that there may be institutional and economic variables that influence the transfer process.