A single structural type in the regular surface layer of Aeromonas salmonicida

The surface protein array of Aeromonas salmonicida (or A-layer) appears, in negatively stained preparations, as two distinct patterns, type I and type II. Type I patterns were restricted to, and predominated in, darkly stained areas, whereas lighter staining regions exclusively displayed type II patterns. The type I morphology was faithfully reproduced in computer-simulated superimpositions of type II patterns, as was the intermediate transition zone frequently seen between the two patterns. Variations in the lattice constant of both patterns, presumably due to artifactual flattening, demonstrated that these patterns could not be distinguished on this basis. The conceptual model presented points to the type II pattern as the only single A-layer structural type. We propose the use of the terms type 1/type II to exclusively describe the morphological patterns that appear upon negative staining and the open/closed nomenclature to describe the conformations that a single structural type can adopt.     

Parameterization and classification of the protein universe via geometric techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.     

On the diffusion theory of phyllotaxis

An inhibitor diffusion theory of phyllotaxis is examined in the steady-state approximation for cylindrical shoot apex models. The model calculations give rise naturally to common patterns of spiral phyllotaxis, as well as to higher whorled patterns. The model also predicts commonly observed subpatterns of axillary organs superimposed on primary phyllotaxis patterns. Application of the model to phyllotaxis patterns in other organisms and in flowers is proposed.     

Distinct mechanisms underlie pattern formation in the skin and skin appendages

Patterns form with the break of homogeneity and lead to the emergence of new structure or arrangement. There are different physiological and pathological mechanisms that lead to the formation of patterns. Here, we first introduce the basics of pattern formation and their possible biological basis. We then discuss different categories of skin patterns and their potential underlying molecular mechanisms. Some patterns, such as the lines of Blaschko and Naevus, are based on cell lineage and genetic mosaicism. Other patterns, such as regionally specific skin appendages, can be set by distinct combinatorial molecular codes, which in turn may be set by morphogenetic gradients. There are also some patterns, such as the arrangement of hair follicles (hair whorls) and fingerprints, which involve genetics as well as stochastic epigenetic events based on physiochemical principles. Many appendage primordia are laid out in developmental waves. In the adult, some patterns, such as those involving cycling hair follicles, may appear as traveling waves in mice. Since skin appendages can renew themselves in regeneration, their size and shape can still change in the adult via regulation by hormones and the environment. Some lesion patterns are based on pathological changes involving the above processes and can be used as diagnostic criteria in medicine. Understanding the different mechanisms that lead to patterns in the skin will help us appreciate their full significance in morphogenesis and medical research. Much remains to be learned about complex pattern formation, if we are to bridge the gap between molecular biology and organism phenotypes.     

Discover 1: a new program to search for unusually represented DNA motifs.

DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, thus generating the diverse patterns of each family. The occurrences of the different patterns are then compared and analysed within each family, assuming that all patterns should have the same probability of occurrence. An extensive use of computer memory, combined with the immediate sorting of counts by address calculation allow a complete counting of all DNA motifs on a single pass on the DNA sequence. This approach offers a very fast way to search for unusually distributed patterns and can identify inexact patterns as well as exact patterns.     

Inferring a District-Based Hierarchical Structure of Social Contacts from Census Data

Researchers have recently paid attention to social contact patterns among individuals due to their useful applications in such areas as epidemic evaluation and control, public health decisions, chronic disease research and social network research. Although some studies have estimated social contact patterns from social networks and surveys, few have considered how to infer the hierarchical structure of social contacts directly from census data. In this paper, we focus on inferring an individual’s social contact patterns from detailed census data, and generate various types of social contact patterns such as hierarchical-district-structure-based, cross-district and age-district-based patterns. We evaluate newly generated contact patterns derived from detailed 2011 Hong Kong census data by incorporating them into a model and simulation of the 2009 Hong Kong H1N1 epidemic. We then compare the newly generated social contact patterns with the mixing patterns that are often used in the literature, and draw the following conclusions. First, the generation of social contact patterns based on a hierarchical district structure allows for simulations at different district levels. Second, the newly generated social contact patterns reflect individuals social contacts. Third, the newly generated social contact patterns improve the accuracy of the SEIR-based epidemic model.     

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.     

浙江天童常绿阔叶林中11种常绿乔灌木叶片虫食状分析

为探讨昆虫对植物叶片的取食行为和伤害方式,作者选择浙江天童常绿阔叶林内的11种常绿乔灌木为对象,对叶片虫食状类型和格局进行分析。结果如下:(1)共发现16种虫食状类型,每种植物叶片虫食状类型数在10–13种之间,每种虫食状出现频率在0.5–28.7%之间。缘食状出现频率最高(28.7%),虫瘿和泡状出现频率最低(0.5%)。(2)叶片虫食状分布格局可分为3种类型,即一种虫食状占绝对优势的单优格局,如马银花(Rhododendronovatum)和檵木(Loropetalumchinense);两种虫食状(缘食状和顶食状)共占优势的双优格局,仅有木荷(Schimasu-perba);3种及3种以上虫食状占优势的多优格局(其余8种植物)。(3)叶片虫食状多样性指数变化在1.57–2.23之间,最高为苦槠(Castanopsissclerophylla),最低为马银花;乔木的多样性指数(2.040)高于灌木(1.882),优势种多样性指数高于伴生种,但差异均不显著;多样性指数反映了虫食状类型和出现频率的综合差异。(4)16种虫食状类型中有8对显著正相关,4对显著负相关,可能反映出不同类型昆虫取食植物的趋同和差异。     

Traumatic Brain Injury Rehabilitation: QEEG Biofeedback Treatment Protocols

Interventions for improvement of cognitive problems in patients with traumatic brain injury (TBI) include electroencephalography biofeedback, also known as neurofeedback. Quantitative electroencephalography (QEEG) patterns are assessed in TBI patients and then compared to a database obtained from a normative population. Deviations in QEEG patterns from the normative group are the basis for an intervention plan. While QEEG patterns, obtained under an eyes closed, resting condition, provide information about deviations at rest, QEEG patterns obtained while the patient engages in cognitive tasks reflect specific deficiencies in brain functioning. This paper reviews and assesses QEEG patterns collected under both resting conditions as well as cognitive tasks. The article provides a theoretical and empirical base for QEEG interventions with TBI.     

Red cell lactic acid dehydrogenase in the family Macropodidae

Lactic acid dehydrogenase isoenzyme patterns from red cells of members of the family Macropodidae are described as they appear in disc acrylamide gels. The reproducibility of patterns, which are determined by the relative intensities of LDH isoenzymes, is noted. Of the 473 animals tested, 471 had red cell LDH patterns belonging to one of five patterns. The distribution of these five patterns among the different genera and species is discussed, and it is suggested that investigation of LDH patterns by this method might assist in the classification of members of the family Macropodidae.     

Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity

The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.     

Characterization of Staphylococcus species by ribosomal RNA gene restriction patterns

The rRNA gene restriction pattern sof 110 strains belonging to 12 staphylococcal species have been determined. The strains, isolated from various sources, were epidemiologically unrelated. Total DNA was cleaved with restriction enzymes HindIII and EcoRI, electrophoretically separated and probed with radiolabelled 16S rDNA from Bacillus subtilis inserted in a plasmid vector, pBR322. Fourty-four distinct HindIII patterns and 44 distinct EcoRI patterns were observed. Strains belonging to different species had different patterns. Although distinct patterns were also observed with some species, a core of common bands could be discerned within each species or subspecies. Analysis of the patterns revealed two taxa in Staphylococcus xylosus which were not evident using phenotypic characteristics. Of 18 strains which were difficult to identify using phenotypic schemes, 15 showed patterns typical of known species. The three remaining atypical strains showed unusual patterns and may belong either to a known species, not included in the study, or to a new species. Since various patterns were observed within some species (e.g.S.aureus and S. epidermidis), rRNA gene restriction patterns may have epidemiological, as well as taxonomic interest.     

Isoelectric focusing of human antibody to the Haemophilus influenzae b capsular polysaccharide: restricted and identical spectrotypes in adults

Serum antibody to the capsular polysaccharide of Haemophilus influenzae b of human adults was analyzed by isoelectric focusing. Restricted antibody spectrotype patterns were commonly observed with as few as one spectrotype in some subjects after immunization with the isolated capsular polysaccharide. Some patterns were as restricted as human hybridoma antibody. There was no correlation of antibody titer and heterogeneity of patterns. The dominant spectrotype persisted unchanged for over 2 yr after immunization, and the pattern detected in preimmunization serum samples persisted unchanged after immunization. Indistinguishable patterns were commonly observed in genetically unrelated adults. Adults immunized with conjugate vaccines, which were composed of oligosaccharides prepared from the capsular polysaccharide that were covalently linked to protein carriers, also produced restricted serum antibody spectrotype patterns. Immunization with the cross-reactive polysaccharide of E. coli K100 induced a spectrotype pattern that was restricted but different from that induced by the H. influenzae b capsular polysaccharide.     

Restriction fragment polymorphism in mitochondrial DNA of Cryptococcus neoformans

The restriction patterns of mitochondrial DNA from 20 isolates of the two varieties of Cryptococcus neoformans were compared. The patterns exhibited extensive heterogeneity among the isolates regardless of their serotype or varietal status. Hybridizations with cloned fragments of the conserved cytochrome oxidase gene from Saccharomyces cerevisiae exhibited at least seven patterns among the 20 isolates. There were, however, similarities in the restriction patterns among isolates within the same serotype that were not shared by isolates of other serotypes. Intra-varietal similarities were observed in the restriction patterns among the isolates of C. neoformans var. neoformans which were not present in the restriction patterns among the isolates of C. neoformans var. gattii. Hybridization of some cloned mitochondrial DNA fragments to total DNA digests of various isolates revealed polymorphic as well as variety-specific patterns of homology. These findings agree with the antigenic heterogeneity among the isolates and support the current taxonomic classification of C. neoformans into two varieties.     

Role of biomechanics and muscle activation strategy in the production of endpoint force patterns in the cat hindlimb

We used a musculoskeletal model of the cat hindlimb to compare the patterns of endpoint forces generated by all possible combination of 12 hindlimb muscles under three different muscle activation rules: homogeneous activation of muscles based on uniform activation levels, homogeneous activation of muscles based on uniform (normalized) force production, and activation based on the topography of spinal motoneuron pools. Force patterns were compared with the patterns obtained experimentally by microstimulation of the lumbar spinal cord in spinal intact cats. Magnitude and orientation of the force patterns were compared, as well as the proportion of the types found, and the proportions of patterns exhibiting points of zero force (equilibrium points). The force patterns obtained with the homogenous activation and motoneuron topography models were quite similar to those measured experimentally, with the differences being larger for the patterns from the normalized endpoint forces model. Differences in the proportions of types of force patterns between the three models and the experimental results were significant for each model. Both homogeneous activation and normalized endpoint force models produced similar proportions of equilibrium points as found experimentally. The results suggest that muscle biomechanics play an important role in limiting the number of endpoint force pattern types, and that muscle combinations activated at similar levels reproduced best the experimental results obtained with intraspinal microstimulation.     

Purification of Two Acid-Proteases of Aspergillus oryzae from Takadiastase

Two acid-proteases, shown previously to be present in Takadiastase and tentatively named as SE- and DEAE-protease, were purified. These two enzymes did not differ in enzymatic properties investigated but differed in some physical properties, such as isoelectric points.

Though the SE-protease showed only a single peak in ultracentrifugal sedimentation patterns, it was separated into two or three components in electrophoretic patterns. On the contrary, the DEAE-protease showed only a single peak in either sedimentation patterns or electrophoretic patterns.     

Sequences of symmetry-breaking in phyllotactic transitions

This paper studies the transition of phyllotactic patterns by a group-theoretic approach. Typical phyllotactic patterns are represented here as dotted patterns on a cylinder, where the cylinder is regarded as the stem of a plant and the dots are points where leaves branch from the stem. We can then classify the symmetries of the alternate and opposite phyllotaxis into four types of groups, and clarify sequences of symmetry-breaking among these groups. The sequences turn out to correspond to transition paths of phyllotactic patterns found in the wild. This result shows the usefulness of classification of phyllotactic patterns based on their group symmetries. Moreover, the breaking of reflection symmetry is found to be an important rule for real phyllotactic transitions.     

Structure in plant–animal interaction assemblages

We present a comprehensive approach to detect pattern in assemblages of plant and animal species linked by interactions such as pollination, frugivory or herbivory. Simple structural models produce gradient, compartmented or nested patterns of interaction; intermediate patterns between a gradient and compartments are possible, and nesting within compartments produces a combined model. Interaction patterns can be visualized and analyzed either as matrices, as bipartite networks or as multivariate sets through correspondence analysis. We argue that differences among patterns represent outcomes of distinct evolutionary and ecological processes in these highly diversified assemblages. Instead of choosing one model a priori, assemblages should be probed for a suite of patterns. A plant–pollinator assemblage exemplifies a simple nested pattern, whereas a plant–herbivore assemblage illustrates a compound pattern with nested structures within compartments. Compartmentation should reflect coevolutionary histories and constraints, whereas differences in species abundance or dispersal may generate nestedness.     

Evolutionary origins of novel conchologic growth patterns in tropical American corbulid bivalves

We conducted a combined sclerochronologic and phylogenetic analysis to document patterns and rates of shell accretion in several subclades of related corbulids, and to explore the evolutionary origins of novel conchologic developmental patterns. We found three disparate patterns of valve development in Neogene tropical American corbulid genera. These patterns include growth through primarily radial accretion along the sagittal plane, and two derivative patterns: one characterized by initial deposition of a thin shell followed by valve thickening with little increase in valve height, and another producing a well-defined nepioconch through a marked change in the primary growth direction. We conducted a species-level phylogenetic analysis of the taxa surveyed for growth patterns, focusing on the ([Bothrocorbula+Hexacorbula]+Caryocorbula) clade. The phylogenetic distribution of shell growth patterns suggests that this clade is characterized by derivative patterns of growth. Oxygen-isotope calibrated ontogenetic age estimates of species in the derived Bothrocorbula subclade further suggest that transitions from the ancestral radial (sagittal) growth pattern to a derived pattern of growth are a function of heterochrony (peramorphosis by acceleration). These findings are significant because they link previously observed patterns of morphological constraint with a specific evolutionary process, demonstrate how morphologic constraint and innovation can be interrelated, and serve as a model for understanding the evolution of morphologic diversity in the clade as a whole. Furthermore, this study highlights the utility of sclerochronologic records as an important component of evolutionary developmental research on organisms with accretionary skeletal growth.     

Small-world connectivity, motif composition, and complexity of fractal neuronal connections

Connection patterns of the cerebral cortex consist of pathways linking neuronal populations across multiple levels of scale, from whole brain regions to local minicolumns. This nested interconnectivity suggests the hypothesis that cortical connections are arranged in fractal or self-similar patterns. We describe a simple procedure to generate fractal connection patterns that aim at capturing the potential self-similarity and hierarchical ordering of neuronal connections. We examine these connection patterns by calculating a broad range of structural measures, including small-world attributes and motif composition, as well as some global measures of functional connectivity, including complexity. As we vary fractal patterns by changing a critical control parameter, we find strongly correlated changes in several structural and functional measures, suggesting that they emerge together and are mutually linked. Measures obtained from some modeled fractal patterns closely resemble those of real neuroanatomical data sets, supporting the original hypothesis.