A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem

Pedigree reconstruction using genotypic markers has become an important tool for the study of natural populations. The nonstandard nature of the underlying statistical problems has led to the necessity of developing specialized statistical and computational methods. In this article, a new version of pedigree reconstruction tools (PRT 2.0) is presented. The software implements algorithms proposed in Almudevar & Field (Journal of Agricultural Biological and Environmental Statistics, 4, 1999, 136) and Almudevar (Biometrics, 57, 2001a, 757) for the reconstruction of single generation sibling groups (SG). A wider range of enumeration algorithms is included, permitting improved computational performance. In particular, an iterative version of the algorithm designed for larger samples is included in a fully automated form. The new version also includes expanded simulation utilities, as well as extensive reporting, including half-sibling compatibility, parental genotype estimates and flagging of potential genotype errors. A number of alternative algorithms are described and demonstrated. A comparative discussion of the underlying methodologies is presented. Although important aspects of this problem remain open, we argue that a number of methodologies including maximum likelihood estimation (COLONY 1.2 and 2.0) and the set cover formulation (KINALYZER) exhibit undesirable properties in the sibling reconstruction problem. There is considerable evidence that large sets of individuals not genetically excluded as siblings can be inferred to be a true sibling group, but it is also true that unrelated individuals may be genetically compatible with a true sibling group by chance. Such individuals may be identified on a statistical basis. PRT 2.0, based on these sound statistical principles, is able to efficiently match or exceed the highest reported accuracy rates, particularly for larger SG. The new version is available at http://www.urmc.rochester.edu/biostat/people/faculty/almudevar.cfm.     

Elementary network reconstruction: A framework for the analysis of regulatory networks in biological systems

Complexity of regulatory networks arises from the high degree of interaction between network components such as DNA, RNA, proteins, and metabolites. We have developed a modeling tool, elementary network reconstruction (ENR), to characterize these networks. ENR is a knowledge-driven, steady state, deterministic, quantitative modeling approach based on linear perturbation theory. In ENR we demonstrate a novel means of expressing control mechanisms by way of dimensionless steady state gains relating input and output variables, which are purely in terms of species abundances (extensive variables). As a result of systematic enumeration of network species in n×n matrix, the two properties of linear perturbation are manifested in graphical representations: transitive property is evident in a special L-shape structure, and additive property is evident in multiple L-shape structures arriving at the same matrix cell. Upon imposing mechanistic (lowest-level) gains, network self-assembly through transitive and additive properties results in elucidation of inherent topology and explicit cataloging of higher level gains, which in turn can be used to predict perturbation results. Application of ENR to the regulatory network behind carbon catabolite repression in Escherichia coli is presented. Through incorporation of known molecular mechanisms governing transient and permanent repressions, the ENR model correctly predicts several key features of this regulatory network, including a 50% downshift in intracellular cAMP level upon exposure to glucose. Since functional genomics studies are mainly concerned with redistribution of species abundances in perturbed systems, ENR could be exploited in the system-level analysis of biological systems.     

An in vitro model for the growth and analysis of chronic wound MRSA biofilms

Aims: To develop an in vitro model (Colony/drip‐flow reactor – C/DFR) for the growth and analysis of methicillin‐resistant Staphylococcus aureus (MRSA) biofilms. Methods and Results: Using the C/DFR model, biofilms were grown on the top of polycarbonate filter membranes inoculated with a clinical isolate of MRSA, placed on absorbent pads in the DFR and harvested after 72 h. The biofilms varied from 256 to 308 μm in thickness with a repeatability standard deviation of 0·22. Testing of antimicrobial agents was also performed where C/DFR biofilms were grown in parallel with conventional colony biofilms. A saline solution (control), 1% silver sulfadiazine solution, and 0·25% Dakin’s solution were used to treat the biofilms for 15 min. Microscopic evaluation of biofilm morphology and thickness was conducted. The Dakins solution in both models produced statistically significantly higher log reductions than silver sulfadiazine treatment. Conclusions: The C/DFR biofilms were thick and repeatable and exhibited higher resistance to Dakins solution than the treated colony biofilms. Significance and Impact of the Study: The C/DFR can be used as a tool for examining complex biofilm physiology as well as for performing comparative experiments that test wound care products and novel antimicrobials.     

Systematics of the amphiatlantic Microphthalmus-listensis-species-group (Polychaeta: Hesionidae): Facts and concepts for reconstruction of phylogeny and speciation

Previous studies established the existence of morphologically highly similar amphiatlantic populations of the predominantly interstitial genus Microphthatmus (European coastline - from the German Bay to the Bay of Biscaya; American coastline - from Maine to Massachusetts and at the coast of North Carolina). Originally these three populations were seen as belonging to a single species. By using a broad spectrum of different methodologies for character investigations (especially through the use of electron microscopy) three, distinct species can now be distinguished: M. listensis Westheide 1967, M. nahantensis n. sp. and M. carolinensis n. sp. While habitat structure and external morphology - generally important in polychaete systematics - were found to be rather similar between the three species, this study uncovered distinct differences between the species in their internal organization. Such sharp differences could even be followed down to the ultrastructure of single cells (e. g. copulatory stylets, position and number of ovaries, sperm and secretory granules of male accessory glands). Within population character variability is significantly lower in several features of M. carolinensis than in the same characters of the other two species. Similarities as well as differences have been noted in behavioural features and population dynamics between the species.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Principles for the virtual reconstruction of hominin crania

Fossils are usually discovered broken or distorted, therefore reconstruction is inevitably the first step towards any comparative analysis. We outline a general methodological framework by which missing information about biological specimens can be estimated using geometric morphometric methods and discuss how this relates to effective paleoanthropological use of incomplete and distorted crania.Combining digital data resources with geometric morphometrics, we go beyond the assembly of fragments on the computer. As in a three-dimensional jigsaw puzzle, we first assemble the virtual pieces manually. Then we use landmarks, several hundred semilandmarks, and information from complete specimens to estimate missing coordinates and correct for distortion simultaneously. One can thus incorporate information from incomplete specimens in a comparative morphometric analysis while keeping track of the uncertainties that result from partial preservation or deformation. We exemplify our approach by reconstructing the fossil crania Arago XXI, Taung, and KNM-WT 15000. As different assumptions and algorithms lead to different estimations, there exists no “all-purpose” reconstruction. Instead one creates multiple reconstructions—a posterior distribution in a Bayesian sense. This distribution reflects uncertainty due to missing data values and sensitivity to prior assumptions. While there will typically be shape differences among equally plausible reconstructions, these different estimates might still support a single conclusion.     

Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules

Membrane proteins play important roles in cell functions such as neurotransmission, muscle contraction, and hormone secretion, but their structures are mostly undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Electron microscopy-based single particle reconstruction, a computer-aided structure determination method, reconstructs a three-dimensional (3D) structure from projections of monodispersed protein. A large number of particle images are picked up from EM films, aligned and classified to generate two-dimensional (2D) averages, and, using the Euler angle of each 2D average, reconstructed into a 3D structure. This method is challenging due to the necessity for close collaboration between classical biochemistry and innovative information technology, including parallel computing. However, recent progress in electron microscopy, mathematical algorithms, and computational ability has greatly increased the subjects that are considered to be primarily addressable using single particle reconstruction. Membrane proteins are one of these targets to which the single particle reconstruction is successfully applied for understanding of their structures. In this paper, we will introduce recently reconstructed channel-related proteins and discuss the applicability of this technique in understanding molecular structures and their roles in pathology.     

The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles

Generating reliable initial models is a critical step in the reconstruction of asymmetric single-particles by 3D electron microscopy. This is particularly difficult to do if heterogeneity is present in the sample. The Random Conical Tilt (RCT) method, arguably the most robust presently to accomplish this task, requires significant user intervention to solve the "missing cone" problem. We present here a novel approach, termed the orthogonal tilt reconstruction method, that eliminates the missing cone altogether, making it possible for single-class volumes to be used directly as initial references in refinement without further processing. The method involves collecting data at +45 degrees and -45 degrees tilts and only requires that particles adopt a relatively large number of orientations on the grid. One tilted data set is used for alignment and classification and the other set--which provides views orthogonal to those in the first--is used for reconstruction, resulting in the absence of a missing cone. We have tested this method with synthetic data and compared its performance to that of the RCT method. We also propose a way of increasing the level of homogeneity in individual 2D classes (and volumes) in a heterogeneous data set and identifying the most homogeneous volumes.     

合成未来：从大肠杆菌的重构看合成生物学的发展

合成生物学（synthetic biology）是伴随着基因工程、系统生物学以及生物信息学的发展而出现的一个新的交叉学科。大肠杆菌（Escherichia coli）作为一种宿主在合成生物学的发展中功不可没。从某种意义上讲,合成生物学的每一次进展都离不开大肠杆菌。从大肠杆菌的角度出发,对合成生物学的发展进行深入分析,并提出了合成生物学在中圉发展的重点。