Fractional models for the migration of biological cells in complex spatial domains

Travelling wave phenomena are observed in many biological applications. Mathematical theory of standard reaction-diffusion problems shows that simple partial differential equations exhibit travelling wave solutions with constant wavespeed and such models are used to describe, for example, waves of chemical concentrations, electrical signals, cell migration, waves of epidemics and population dynamics. However, as in the study of cell motion in complex spatial geometries, experimental data are often not consistent with constant wavespeed. Non-local spatial models have successfully been used to model anomalous diffusion and spatial heterogeneity in different physical contexts. In this paper, we develop a fractional model based on the Fisher-Kolmogoroff equation and analyse it for its wavespeed properties, attempting to relate the numerical results obtained from our simulations to experimental data describing enteric neural crest-derived cells migrating along the intact gut of mouse embryos. The model proposed essentially combines fractional and standard diffusion in different regions of the spatial domain and qualitatively reproduces the behaviour of neural crest-derived cells observed in the caecum and the hindgut of mouse embryos during in vivo experiments.

Proteolytic activation of Chlamydia trachomatis HTRA is mediated by PDZ1 domain interactions with protease domain loops L3 and LC and beta strand β5

Chlamydia trachomatis is a bacterial pathogen responsible for one of the most prevalent sexually transmitted infections worldwide. Its unique development cycle has limited our understanding of its pathogenic mechanisms. However, CtHtrA has recently been identified as a potential C. trachomatis virulence factor. CtHtrA is a tightly regulated quality control protein with a monomeric structural unit comprised of a chymotrypsin-like protease domain and two PDZ domains. Activation of proteolytic activity relies on the C-terminus of the substrate allosterically binding to the PDZ1 domain, which triggers subsequent conformational change and oligomerization of the protein into 24-mers enabling proteolysis. This activation is mediated by a cascade of precise structural arrangements, but the specific CtHtrA residues and structural elements required to facilitate activation are unknown. Using in vitro analysis guided by homology modeling, we show that the mutation of residues Arg362 and Arg224, predicted to disrupt the interaction between the CtHtrA PDZ1 domain and loop L3, and between loop L3 and loop LD, respectively, are critical for the activation of proteolytic activity. We also demonstrate that mutation to residues Arg299 and Lys160, predicted to disrupt PDZ1 domain interactions with protease loop LC and strand β5, are also able to influence proteolysis, implying their involvement in the CtHtrA mechanism of activation. This is the first investigation of protease loop LC and strand β5 with respect to their potential interactions with the PDZ1 domain. Given their high level of conservation in bacterial HtrA, these structural elements may be equally significant in the activation mechanism of DegP and other HtrA family members.

The art of mooting : mooting and the cognitive domain

Mooting is modeled principally on appellate advocacy. However, the skill set developed by participating in a moot program – being that necessary to persuade someone to your preferred position – is indispensible to anyone practising law. Developing effective mooting skills in students necessitates the engagement of coaches with an appropriate understanding of the theories underlying mooting and advocacy practice and their interconnection with each other. This article explains the relevance of the cognitive domain to mooting performance and places it in context with the psychomotor and affective domains.

A sub‒domain smoothed Galerkin method for solid mechanics problems

A sub‒domain smoothed Galerkin method is proposed to integrate the advantages of mesh‒free Galerkin method and FEM. Arbitrarily shaped sub‒domains are predefined in problems domain with mesh‒free nodes. In each sub‒domain, based on mesh‒free Galerkin weak formulation, the local discrete equation can be obtained by using the moving Kriging interpolation, which is similar to the discretization of the high‒order finite elements. Strain smoothing technique is subsequently applied to the nodal integration of sub‒domain by dividing the sub‒domain into several smoothing cells. Moreover, condensation of DOF can also be introduced into the local discrete equations to improve the computational efficiency. The global governing equations of present method are obtained on the basis of the scheme of FEM by assembling all local discrete equations of the sub‒domains. The mesh‒free properties of Galerkin method are retained in each sub‒domain. Several 2D elastic problems have been solved on the basis of this newly proposed method to validate its computational performance. These numerical examples proved that the newly proposed sub‒domain smoothed Galerkin method is a robust technique to solve solid mechanics problems based on its characteristics of high computational efficiency, good accuracy, and convergence.

Practical aspects of frequency-domain identification of dynamic models of marine structures from hydrodynamic data

The motion response of marine structures in waves can be studied using finite-dimensional linear-time-invariant approximating models. These models, obtained using system identification with data computed by hydrodynamic codes, find application in offshore training simulators, hardware-in-the-loop simulators for positioning control testing, and also in initial designs of wave-energy conversion devices. Different proposals have appeared in the literature to address the identification problem in both time and frequency domains, and recent work has highlighted the superiority of the frequency-domain methods. This paper summarises practical frequency-domain estimation algorithms that use constraints on model structure and parameters to refine the search of approximating parametric models. Practical issues associated with the identification are discussed, including the influence of radiation model accuracy in force-to-motion models, which are usually the ultimate modelling objective. The illustration examples in the paper are obtained using a freely available MATLAB toolbox developed by the authors, which implements the estimation algorithms described.

Type I collagen abrogates the clathrin-mediated internalization of membrane type 1 matrix metalloproteinase (MT1-MMP) via the MT1-MMP hemopexin domain

Type I collagen (Col I)-stimulated matrix metalloproteinase-2 (MMP-2) activation via membrane type 1 MMP (MT1-MMP) involves both a transcriptional increase in MT1-MMP expression and a nontranscriptional response mediated by preexisting MT1-MMP. In order to identify which MT1-MMP domains were required for the nontranscriptional response, MCF-7 cells that lack endogenous MT1-MMP were transfected with either wild type or domain mutant MT1-MMP constructs. We observed that mutant constructs lacking the MT1-MMP cytoplasmic tail were able to activate MMP-2 in response to Col I but not a construct lacking the MT1-MMP hemopexin domain. Col I did not alter total MT1-MMP protein levels; nor did it appear to directly induce MT1-MMP oligomerization. Col I did, however, redistribute preexisting MT1-MMP to the cell periphery compared with unstimulated cells that displayed amore diffuse staining pattern. In addition, Col I blocked the internalization of MT1-MMP in a dynamin-dependent manner via clathrin-coated pit-mediated endocytosis. This mechanism of impaired internalization is different from that reported for concanavalin A, since it is not mediated by the cytoplasmic tail of MT1-MMP but rather by the hemopexin domain. In summary, upon Col I binding to its cell surface receptor, MT1-MMP internalization via clathrin-coated pit-mediated endocytosis is impaired through interactions with the hemopexin domain, thereby regulating its function and ability to activate MMP-2.

Transmembrane/cytoplasmic domain-mediated membrane type 1-matrix metalloprotease docking to invadopodia is required for cellinvasion

The invasion of human malignant melanoma cells into the extracellular matrix (ECM) involves the accumulation of proteases at sites of ECM degradation where activation of matrix metalloproteases (MMP) occurs. Here, we show that when membrane type 1 MMP (MT-MMP) was overexpressed in RPMI7951 human melanoma cells, the cells made contact with the ECM, activated soluble and ECM-bound MMP-2, and degraded and invaded the ECM. Further experiments demonstrated the importance of localization of the MT-MMP to invadopodia. Overexpression of MT-MMP without invadopodial localization caused activation of soluble MMP-2, but did not facilitate ECM degradation or cell invasiveness. Up-regulation of endogenous MT-MMP with concanavalin A caused activation of MMP-2. However, concanavalin A treatment prevented invadopodial localization of MT-MMP and ECM degradation. Neither a truncated MT-MMP mutant lacking transmembrane (TM) and cytoplasmic domains (ΔTM(MT-MMP)), nor a chimeric MT-MMP containing the interleukin 2 receptor α chain (IL-2R) TM and cytoplasmic domains (ΔTM(MT-MMP)/TM(IL-2R)) were localized to invadopodia or exhibited ECM degradation. Furthermore, a chimera of the TM/cytoplasmic domain of MT-MMP (TM(MT-MMP)) with tissue inhibitor of MMP 1 (TIMP-1/TM(MT- MMP)) directed the TIMP-1 molecule to invadopodia. Thus, the MT-MMP TM/cytoplasmic domain mediates the spatial organization of MT-MMP into invadopodia and subsequent degradation of the ECM.

Nanoscale phase domain structure and associated device performance of organic solar cells based on a diketopyrrolopyrrole polymer

We investigate the blend morphology and performance of bulk heterojunction organic photovoltaic devices comprising the donor polymer, pDPP-TNT (poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]pyrrole-1, 4-dione-alt-naphthalene}) and the fullerene acceptor, [70]PCBM ([6,6]-phenyl C71-butyric acid methyl ester). The blend morphology is heavily dependent upon the solvent system used in the fabrication of thin films. Thin films spin-coated from chloroform possess a cobblestone-like morphology, consisting of thick, round-shaped [70]PCBM-rich mounds separated by thin polymer-rich valleys. The size of the [70]PCBM domains is found to depend on the overall film thickness. Thin films spin-coated from a chloroform:dichlorobenzene mixed solvent system are smooth and consist of a network of pDPP-TNT nanofibers embedded in a [70]PCBM-rich matrix. Rinsing the films in hexane selectively removes [70]PCBM and allows for analysis of domain size and purity. It also provides a means for investigating exciton dissociation efficiency through relative photoluminescence yield measurements. Devices fabricated from chloroform solutions show much poorer performance than the devices fabricated from the mixed solvent system; this disparity in performance is seen to be more pronounced with increasing film thickness. The primary cause for the improved performance of devices fabricated from mixed solvents is attributed to the greater donor-acceptor interfacial area and resulting greater capacity for charge carrier generation.

Exploring the impact of shared domain knowledge on strategic alignment in the Australian public sector

In this age of ever-increasing information technology (IT) driven environments, governments/or public sector organisations (PSOs) are expected to demonstrate the business value of the investment in IT and take advantage of the opportunities offered by technological advancements. Strategic alignment (SA) emerged as a mechanism to bridge the gap between business and IT missions, objectives, and plans in order to ensure value optimisation from investment in IT and enhance organisational performance. However, achieving and sustaining SA remains a challenge requiring even more agility nowadays to keep up with turbulent organisational environments. The shared domain knowledge (SDK) between the IT department and other diverse organisational groups is considered as one of the factors influencing the successful implementation of SA. However, SDK in PSOs has received relatively little empirical attention. This paper presents findings from a study which investigated the influence of SDK on SA within organisations in the Australian public sector. The developed research model examined the relationship of SDK between business and IT domains with SA using a survey of 56 public sector professionals and executives. A key research contribution is the empirical demonstration that increasing levels of SDK between IT and business groups leads to increased SA.

The development and refinement of the practice domain framework as a conceptual tool for understanding and guiding social care practice

This study identified the common factors that influence social care practice across disciplines (such as social work and psychology), practice fields, and geographical contexts and further developed the Practice Domain Framework as an empirically-based conceptual framework to assist practitioners in understanding practice complexities. The framework has application in critical reflection, professional supervision, interdisciplinary understanding, teamwork, management, teaching and research. A mixed-methods design was used to identify the components and structure of the refined framework. Eighteen influential factors were identified and organised into eight domains: the Societal, Structural, Organisational, Practice Field, Professional Practice, Accountable Practice, Community of Place, and Personal.

Alteration of the C-terminal ligand specificity of the Erbin PDZ domain by allosteric mutational effects

Modulation of protein binding specificity is important for basic biology and for applied science. Here we explore how binding specificity is conveyed in PDZ (postsynaptic density protein-95/discs large/zonula occludens-1) domains, small interaction modules that recognize various proteins by binding to an extended C terminus. Our goal was to engineer variants of the Erbin PDZ domain with altered specificity for the most C-terminal position (position 0) where a Val is strongly preferred by the wild-type domain. We constructed a library of PDZ domains by randomizing residues in direct contact with position 0 and in a loop that is close to but does not contact position 0. We used phage display to select for PDZ variants that bind to 19 peptide ligands differing only at position 0. To verify that each obtained PDZ domain exhibited the correct binding specificity, we selected peptide ligands for each domain. Despite intensive efforts, we were only able to evolve Erbin PDZ domain variants with selectivity for the aliphatic C-terminal side chains Val, Ile and Leu. Interestingly, many PDZ domains with these three distinct specificities contained identical amino acids at positions that directly contact position 0 but differed in the loop that does not contact position 0. Computational modeling of the selected PDZ domains shows how slight conformational changes in the loop region propagate to the binding site and result in different binding specificities. Our results demonstrate that second-sphere residues could be crucial in determining protein binding specificity.

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Background: Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue. Results: Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues. Conclusion: We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.

Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

Unsupervised Domain Adaptation by Domain Invariant Projection

Domain-invariant representations are key to addressing the domain shift problem where the training and test exam- ples follow different distributions. Existing techniques that have attempted to match the distributions of the source and target domains typically compare these distributions in the original feature space. This space, however, may not be di- rectly suitable for such a comparison, since some of the fea- tures may have been distorted by the domain shift, or may be domain specific. In this paper, we introduce a Domain Invariant Projection approach: An unsupervised domain adaptation method that overcomes this issue by extracting the information that is invariant across the source and tar- get domains. More specifically, we learn a projection of the data to a low-dimensional latent space where the distance between the empirical distributions of the source and target examples is minimized. We demonstrate the effectiveness of our approach on the task of visual object recognition and show that it outperforms state-of-the-art methods on a stan- dard domain adaptation benchmark dataset