Myxococcus xanthus: an approach to phenotyping complex biofilms

The genotype-to-phenotype (G2P) problem is a fundamental challenge in understanding how genetic information controls the collective phenotypic outputs of multicellular organisms. To address this problem, this thesis focuses on Myxococcus xanthus, a model organism widely used for studying social behavior and morphological differentiation in bacteria. The social behaviors of M. xanthus are mediated by complex gene regulatory networks, making it an excellent model organism for studying the G2P problem. This thesis presents two studies that provide valuable insights into the G2P problem in M. xanthus. The first study investigates the dynamics of biofilm morphogenesis, an essential process for bacteria survival, using image capture and analysis techniques from custom-designed microscopes. Biofilms are complex structures composed of different cell types and gene expression patterns. The study produced a topological map of the process of biofilm formation in wild-type M. xanthus, which allowed the identification and characterization of even subtle mutations associated with different mutations with statistical significance. Stochastic variation was mapped, and this methodology allowed us to distinguish previously non-distinguishable genotypes of M. xanthus using phenotype data. The approach used in this study has the potential to enhance our understanding of the genetic and environmental factors that contribute to the development of M. xanthus and other organisms. The second study employs a common garden approach to investigate the impact of transcriptional regulators on development in M. xanthus. By recording subtle differences in traditional phenotype assays across a library of mutant transcriptional regulators, the study shows there are uncharacterized regulatory genes that play significant roles in regulating biofilm dynamics and gene expression during development. The study identified sigma factors that have an impact on sporulation fitness and characterized the effects of these regulators on the development pathways. The findings of this study supply a deeper understanding of the G2P problem in M. xanthus and could have broader implications for understanding the development of other organisms. By investigating the complex interplay between genotype and phenotype, this thesis aims to shed light on fundamental mechanisms underlying multicellular development, and the potential for these findings to be applied in the fields of biotechnology and medicine

SAM-SoS: A stochastic software architecture modeling and verification approach for complex System-of-Systems

A System-of-Systems (SoS) is a complex, dynamic system whose Constituent Systems (CSs) are not known precisely at design time, and the environment in which they operate is uncertain. SoS behavior is unpredictable due to underlying architectural characteristics such as autonomy and independence. Although the stochastic composition of CSs is vital to achieving SoS missions, their unknown behaviors and impact on system properties are unavoidable. Moreover, unknown conditions and volatility have significant effects on crucial Quality Attributes (QAs) such as performance, reliability and security. Hence, the structure and behavior of a SoS must be modeled and validated quantitatively to foresee any potential impact on the properties critical for achieving the missions. Current modeling approaches lack the essential syntax and semantics required to model and verify SoS behaviors at design time and cannot offer alternative design choices for better design decisions. Therefore, the majority of existing techniques fail to provide qualitative and quantitative verification of SoS architecture models. Consequently, we have proposed an approach to model and verify Non-Deterministic (ND) SoS in advance by extending the current algebraic notations for the formal models as a hybrid stochastic formalism to specify and reason architectural elements with the required semantics. A formal stochastic model is developed using a hybrid approach for architectural descriptions of SoS with behavioral constraints. Through a model-driven approach, stochastic models are then translated into PRISM using formal verification rules. The effectiveness of the approach has been tested with an end-to-end case study design of an emergency response SoS for dealing with a fire situation. Architectural analysis is conducted on the stochastic model, using various qualitative and quantitative measures for SoS missions. Experimental results reveal critical aspects of SoS architecture model that facilitate better achievement of missions and QAs with improved design, using the proposed approach

Aeronautical engineering: A special bibliography with indexes, supplement 80

This bibliography lists 277 reports, articles, and other documents introduced into the NASA scientific and technical information system in January 1977

A proof of convergence of a finite volume scheme for modified steady Richards’ equation describing transport processes in the pressing section of a paper machine

A number of water flow problems in porous media are modelled by Richards’ equation [1]. There exist a lot of different applications of this model. We are concerned with the simulation of the pressing section of a paper machine. This part of the industrial process provides the dewatering of the paper layer by the use of clothings, i.e. press felts, which absorb the water during pressing [2]. A system of nips are formed in the simplest case by rolls, which increase sheet dryness by pressing against each other (see Figure 1). A lot of theoretical studies were done for Richards’ equation (see [3], [4] and references therein). Most articles consider the case of x-independent coefficients. This simplifies the system considerably since, after Kirchhoff’s transformation of the problem, the elliptic operator becomes linear. In our case this condition is not satisfied and we have to consider nonlinear operator of second order. Moreover, all these articles are concerned with the nonstationary problem, while we are interested in the stationary case. Due to complexity of the physical process our problem has a specific feature. An additional convective term appears in our model because the porous media moves with the constant velocity through the pressing rolls. This term is zero in immobile porous media. We are not aware of papers, which deal with such kind of modified steady Richards’ problem. The goal of this paper is to obtain the stability results, to show the existence of a solution to the discrete problem, to prove the convergence of the approximate solution to the weak solution of the modified steady Richards’ equation, which describes the transport processes in the pressing section. In Section 2 we present the model which we consider. In Section 3 a numerical scheme obtained by the finite volume method is given. The main part of this paper is theoretical studies, which are given in Section 4. Section 5 presents a numerical experiment. The conclusion of this work is given in Section 6

Using the Sharp Operator for edge detection and nonlinear diffusion

In this paper we investigate the use of the sharp function known from functional analysis in image processing. The sharp function gives a measure of the variations of a function and can be used as an edge detector. We extend the classical notion of the sharp function for measuring anisotropic behaviour and give a fast anisotropic edge detection variant inspired by the sharp function. We show that these edge detection results are useful to steer isotropic and anisotropic nonlinear diffusion filters for image enhancement

Spatial constraints within the chlamydial host cell inclusion predict interrupted development and persistence

Background. The chlamydial developmental cycle involves the alternation between the metabolically inert elementary body (EB) and the replicating reticulate body (RB). The triggers that mediate the interchange between these particle types are unknown and yet this is crucial for understanding basic Chlamydia biology. Presentation of the hypothesis. We have proposed a hypothesis to explain key chlamydial developmental events whereby RBs are replicating strictly whilst in contact with the host cell membrane-derived inclusion via type three secretion (T3S) injectisomes. As the inclusion expands, the contact between each RB and the inclusion membrane decreases, eventually reaching a threshold, beyond which T3S is inactivated upon detachment and this is the signal for RB-to-EB differentiation. Testing the hypothesis. We explore this hypothesis through the development of a detailed mathematical model. The model uses knowledge and data of the biological system wherever available and simulates the chlamydial developmental cycle under the assumptions of the hypothesis in order to predict various outcomes and implications under a number of scenarios. Implications of the hypothesis. We show that the concept of in vitro persistent infection is not only consistent with the hypothesis but in fact an implication of it. We show that increasing the RB radius, and/or the maximum length of T3S needles mediating contact between RBs and the inclusion membrane, and/or the number of inclusions per infected cell, will contribute to the development of persistent infection. The RB radius is the most important determinant of whether persistent infection would ensue, and subsequently, the magnitude of the EB yield. We determine relationships between the length of the T3S needle and the RB radius within an inclusion, and between the RB radius and the number of inclusions per host cell to predict whether persistent infection or normal development would occur within a host cell. These results are all testable experimentally and could lead to significantly greater understanding of one of the most crucial steps in chlamydial development

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

SummaryThe transcriptional activation of one out of ∼2800 olfactory receptor (OR) alleles is a poorly understood process. Here, we identify a plethora of putative OR enhancers and study their in vivo activity in olfactory neurons. Distinguished by an unusual epigenetic signature, candidate OR enhancers are characterized by extensive interchromosomal interactions associated with OR transcription and share a similar pattern of transcription factor footprints. In particular, we establish the role of the transcription factor Bptf as a facilitator of both enhancer interactions and OR transcription. Our observations agree with the model whereby OR transcription occurs in the context of multiple interacting enhancers. Disruption of these interchromosomal interactions results in weak and multigenic OR expression, suggesting that the rare coincidence of numerous enhancers over a stochastically chosen OR may account for the singularity and robustness in OR transcription

Structure and pressure drop of real and virtual metal wire meshes

An efficient mathematical model to virtually generate woven metal wire meshes is presented. The accuracy of this model is verified by the comparison of virtual structures with three-dimensional images of real meshes, which are produced via computer tomography. Virtual structures are generated for three types of metal wire meshes using only easy to measure parameters. For these geometries the velocity-dependent pressure drop is simulated and compared with measurements performed by the GKD - Gebr. Kufferath AG. The simulation results lie within the tolerances of the measurements. The generation of the structures and the numerical simulations were done at GKD using the Fraunhofer GeoDict software

Simulation and analysis of segmental oscillator models for nematode locomotion

Cover title.Includes bibliographical references (p. 23-25).Research was supported by the Army Research Office (Center for Intelligent Control Systems) DAAL-03-86-K-0171by Charles Rockland and Steve Rowley