Mapping transcription factor interactome networks using HaloTag protein arrays.

Proc Natl Acad Sci U S A. 2016 Jun 29;

Authors: Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SC, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR

Abstract
Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

PMID: 27357687 [PubMed - as supplied by publisher]

Quantitative deep-mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation.

Am J Physiol Cell Physiol. 2016 Jun 29;:ajpcell.00121.2016

Authors: Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT

Abstract
The renal filtration barrier is maintained by the renal podocyte, an epithelial postmitotic cell. Immortalized mouse podocyte cell lines - both in the differentiated and undifferentiated state - are widely utilized tools to estimate podocyte injury and cytoskeletal rearrangement processes in vitro. Here, we mapped the cultured podocyte proteome at a depth of more than 8800 proteins and quantified 7240 proteins. Copy numbers of proteins mutated in forms of hereditary nephrotic syndrome or focal segmental glomerulosclerosis (FSGS) were assessed. We found that cultured podocytes express abundant copy numbers of endogenous receptors such as tyrosine kinase membrane receptors, the G-protein coupled receptor (GPCR), NPR3 (ANP receptor) and several poorly characterized GPCRs. The dataset was correlated with deep mapping mRNA sequencing ("mRNAseq") data from the native mouse podocyte, the native mouse podocyte proteome and staining intensities from the human protein atlas. The generated dataset was similar to these previously published resources, but several native and high-abundant podocyte-specific proteins were not identified in the dataset. Notably, this dataset detected general perturbations in proteostatic mechanisms as a dominant alteration during podocyte differentiation, with high proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. Phosphoproteomics analysis of mouse podocytes at a resolution of more than 3000 sites suggested a preference of phosphorylation of actin-filament associated proteins in the differentiated state. The dataset obtained here provides a resource and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.

PMID: 27357545 [PubMed - as supplied by publisher]

Unified pre- and postsynaptic long-term plasticity enables reliable and flexible learning.

Elife. 2015;4

Authors: Costa RP, Froemke RC, Sjöström PJ, van Rossum MC

Abstract
Although it is well known that long-term synaptic plasticity can be expressed both pre- and postsynaptically, the functional consequences of this arrangement have remained elusive. We show that spike-timing-dependent plasticity with both pre- and postsynaptic expression develops receptive fields with reduced variability and improved discriminability compared to postsynaptic plasticity alone. These long-term modifications in receptive field statistics match recent sensory perception experiments. Moreover, learning with this form of plasticity leaves a hidden postsynaptic memory trace that enables fast relearning of previously stored information, providing a cellular substrate for memory savings. Our results reveal essential roles for presynaptic plasticity that are missed when only postsynaptic expression of long-term plasticity is considered, and suggest an experience-dependent distribution of pre- and postsynaptic strength changes.

PMID: 26308579 [PubMed - indexed for MEDLINE]

Systems Biology Approaches to a Rational Drug Discovery Paradigm.

Curr Top Med Chem. 2016;16(9):1009-25

Authors: Prathipati P, Mizuguchi K

Abstract
Ligand- and structure-based drug design approaches complement phenotypic and target screens, respectively, and are the two major frameworks for guiding early-stage drug discovery efforts. Since the beginning of this century, the advent of the genomic era has presented researchers with a myriad of high throughput biological data (parts lists and their interaction networks) to address efficacy and toxicity, augmenting the traditional ligand- and structure-based approaches. This data rich era has also presented us with challenges related to integrating and analyzing these multi-platform and multi-dimensional datasets and translating them into viable hypotheses. Hence in the present paper, we review these existing approaches to drug discovery research and argue the case for a new systems biology based approach. We present the basic principles and the foundational arguments/underlying assumptions of the systems biology based approaches to drug design. Also discussed are systems biology data types (key entities, their attributes and their relationships with each other, and data models/representations), software and tools used for both retrospective and prospective analysis, and the hypotheses that can be inferred. In addition, we summarize some of the existing resources for a systems biology based drug discovery paradigm (open TG-GATEs, DrugMatrix, CMap and LINCs) in terms of their strengths and limitations.

PMID: 26306988 [PubMed - indexed for MEDLINE]

The Next Generation of Dietitians: Implementing Dietetics Education and Practice in Integrative Medicine.

J Am Coll Nutr. 2015;34(5):430-5

Authors: Wagner LE, Evans RG, Noland D, Barkley R, Sullivan DK, Drisko J

Abstract
Integrative medicine is a quickly expanding field of health care that emphasizes nutrition as a key component. Dietitians and nutritionists have an opportunity to meet workforce demands by practicing dietetics and integrative medicine (DIM). The purpose of this article is to describe a DIM education program and practicum. We report the results of an interprofessional nutrition education and practicum program between the University of Kansas Medical Center (KUMC) Department of Dietetics and Nutrition and KU Integrative Medicine. This partnered program provides training that builds on the strong foundation of the Nutrition Care Process and adds graduate-level educational and practicum experiences in foundational integrative medicine knowledge, including nutritional approaches from a systems biology perspective, nutrigenomics, and biochemistry as the core knowledge to understand the root cause of a chronic disorder and to choose appropriate nutritional tools for interventions. This interprofessional KUMC program provides a dietetic internship, master's degree, and graduate certificate in DIM and fulfills a need for dietitians and nutritionists who seek careers practicing in an integrative medicine setting. The program fulfills expanding workforce needs to provide quality health care for patients with chronic illnesses.

PMID: 25961884 [PubMed - indexed for MEDLINE]

DEVELOPMENT OF AN ANNOTATION SCHEME FOR STANDARDIZED DESCRIPTION OF MATHEMATICAL MODELS IN THE FIELD OF PLANT PROTECTION.

Commun Agric Appl Biol Sci. 2015;80(3):579-82

Authors: Günther T, Büttner C, Käsbohrer A, Filter M

Abstract
Mathematical models on properties and behavior of harmful organisms in the food chain are an increas- ingly relevant approach of the agriculture and food industry. As a consequence, there are many efforts to develop biological models in science, economics and risk assessment nowadays. However, there is a lack of international harmonized standards on model annotation and model formats, which would be neces- sary to set up efficient tools supporting broad model application and information exchange. There are some established standards in the field of systems biology, but there is currently no corresponding provi- sion in the area of plant protection. This work therefore aimed at the development of an annotation scheme using domain-specific metadata. The proposed scheme has been validated in a prototype implementation of a web-database model repository. This prototypic community resource currently contains models on aflatoxin secreting fungal Aspergillus flavus in maize, as these models have a high relevance to food safety and economic impact. Specifically, models describing biological processes of the fungus (growth, Aflatoxin secreting), as well as dose-response- and carry over models were included. Furthermore, phenological models for maize were integrated as well. The developed annotation scheme is based on the well-established data exchange format SBML, which is broadly applied in the field of systems biology. The identified example models were annotated according to the developed scheme and entered into a Web-table (Google Sheets), which was transferred to a web based demonstrator available at https://sites.google.com/site/test782726372685/. By implementation of a software demonstrator it became clear that the proposed annotation scheme can be applied to models on plant pathogens and that broad adoption within the domain could promote communication and application of mathematical models.

PMID: 27141756 [PubMed - indexed for MEDLINE]

KymoRod: A method for automated kinematic analysis of rod-shaped plant organs.

Plant J. 2016 Jun 29;

Authors: Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H

Abstract
A major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well-documented, molecular scale and the organ scale by providing quantitative methods to study within-organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod-shaped organs, which does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio-temporal information on curvature, growth anisotropy and REGR and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth-inhibiting drug or in a mechano-sensing mutant. The method is freely available as an intuitive and user-friendly Matlab application called KymoRod. This article is protected by copyright. All rights reserved.

PMID: 27354251 [PubMed - as supplied by publisher]

A synopsis on Aging - theories, mechanisms and future prospects.

Ageing Res Rev. 2016 Jun 25;

Authors: da Costa JP, Vitorino R, Silva GM, Vogel C, Duarte AC, Rocha-Santos T

Abstract
Answering the question as to why we age is tantamount to answering the question of what is life itself. There are countless theories as to why and how we age, but, until recently, the very definition of aging - senescence - was still uncertain. Here, we summarize the main views of the different models of senescence, with a special emphasis on the biochemical processes that accompany aging. Though inherently complex, aging is characterized by numerous changes that take place at different levels of the biological hierarchy. We therefore explore some of the most relevant changes that take place during aging and, finally, we overview the current status of emergent aging therapies and what the future holds for this field of research. From this multi-dimensional approach, it becomes clear that an integrative approach that couples aging research with systems biology, capable of providing novel insights into how and why we age, is necessary.

PMID: 27353257 [PubMed - as supplied by publisher]

Cell-to-cell infection by HIV contributes over half of virus infection.

Elife. 2015;4

Authors: Iwami S, Takeuchi JS, Nakaoka S, Mammano F, Clavel F, Inaba H, Kobayashi T, Misawa N, Aihara K, Koyanagi Y, Sato K

Abstract
Cell-to-cell viral infection, in which viruses spread through contact of infected cell with surrounding uninfected cells, has been considered as a critical mode of virus infection. However, since it is technically difficult to experimentally discriminate the two modes of viral infection, namely cell-free infection and cell-to-cell infection, the quantitative information that underlies cell-to-cell infection has yet to be elucidated, and its impact on virus spread remains unclear. To address this fundamental question in virology, we quantitatively analyzed the dynamics of cell-to-cell and cell-free human immunodeficiency virus type 1 (HIV-1) infections through experimental-mathematical investigation. Our analyses demonstrated that the cell-to-cell infection mode accounts for approximately 60% of viral infection, and this infection mode shortens the generation time of viruses by 0.9 times and increases the viral fitness by 3.9 times. Our results suggest that even a complete block of the cell-free infection would provide only a limited impact on HIV-1 spread.

PMID: 26441404 [PubMed - indexed for MEDLINE]

Disease specific modules and hub genes for intervention strategies: A co-expression network based approach for Plasmodium falciparum clinical isolates.

Infect Genet Evol. 2015 Oct;35:96-108

Authors: Subudhi AK, Boopathi PA, Pandey I, Kaur R, Middha S, Acharya J, Kochar SK, Kochar DK, Das A

Abstract
Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, approaches that can provide information about the biological processes that are active in this parasite in vivo during complicated malaria conditions have been scarcely deployed. Here we report the analysis of a weighted gene co-expression based network for P. falciparum, from non-cerebral clinical complications. Gene expression profiles of 20 P. falciparum clinical isolates were utilized to construct the same. A total of 20 highly interacting modules were identified post network creation. In 12 of these modules, at least 10% of the member genes, were found to be differentially regulated in parasites from patient isolates showing complications, when compared with those from patients with uncomplicated disease. Enrichment analysis helped identify biological processes like oxidation-reduction, electron transport chain, protein synthesis, ubiquitin dependent catabolic processes, RNA binding and purine nucleotide metabolic processes as associated with these modules. Additionally, for each module, highly connected hub genes were identified. Detailed functional analysis of many of these, which have known annotated functions underline their importance in parasite development and survival. This suggests, that other hub genes with unknown functions may also be playing crucial roles in parasite biology, and, are potential candidates for intervention strategies.

PMID: 26247716 [PubMed - indexed for MEDLINE]

Network analysis of gene expression in peripheral blood identifies mTOR and NF-κB pathways involved in antipsychotic-induced extrapyramidal symptoms.

Pharmacogenomics J. 2015 Oct;15(5):452-60

Authors: Mas S, Gassó P, Parellada E, Bernardo M, Lafuente A

Abstract
To identify the candidate genes for pharmacogenetic studies of antipsychotic (AP)-induced extrapyramidal symptoms (EPS), we propose a systems biology analytical approach, based on protein-protein interaction network construction and functional annotation analysis, of changes in gene expression (Human Genome U219 Array Plate) induced by treatment with risperidone or paliperidone in peripheral blood. 12 AP-naïve patients with first-episode psychosis participated in the present study. Our analysis revealed that, in response to AP treatment, constructed networks were enriched for different biological processes in patients without EPS (ubiquitination, protein folding and adenosine triphosphate (ATP) metabolism) compared with those presenting EPS (insulin receptor signaling, lipid modification, regulation of autophagy and immune response). Moreover, the observed differences also involved specific pathways, such as anaphase promoting complex /cdc20, prefoldin/CCT/triC and ATP synthesis in no-EPS patients, and mammalian target of rapamycin and NF-κB kinases in patients with EPS. Our results showing different patterns of gene expression in EPS patients, offer new and valuable markers for pharmacogenetic studies.

PMID: 25623440 [PubMed - indexed for MEDLINE]

The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells.

Semin Cell Dev Biol. 2016 Jun 24;

Authors: Fey D, Matallanas D, Rauch J, Rukhlenko OS, Kholodenko BN

Abstract
The intricate dynamic control and plasticity of RAS to ERK mitogenic, survival and apoptotic signalling has mystified researches for more than 30 years. Therapeutics targeting the oncogenic aberrations within this pathway often yield unsatisfactory, even undesired results, as in the case of paradoxical ERK activation in response to RAF inhibition. A direct approach of inhibiting single oncogenic proteins misses the dynamic network context governing the network signal processing. In this review, we discuss the signalling behaviour of RAS and RAF proteins in normal and in cancer cells, and the emerging systems-level properties of the RAS-to-ERK signalling network. We argue that to understand the dynamic complexities of this control system, mathematical models including mechanistic detail are required. Looking into the future, these dynamic models will build the foundation upon which more effective, rational approaches to cancer therapy will be developed.

PMID: 27350026 [PubMed - as supplied by publisher]

Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide.

Clin Exp Metastasis. 2016 Jun 27;

Authors: Jeanne A, Boulagnon-Rombi C, Devy J, Théret L, Fichel C, Bouland N, Diebold MD, Martiny L, Schneider C, Dedieu S

Abstract
Thrombospondin-1 (TSP-1) is a matricellular glycoprotein known for being highly expressed within a tumor microenvironment, where it promotes an aggressive phenotype particularly by interacting with the CD47 cell-surface receptor. While it originates from the stromal compartment in many malignancies, melanoma is an exception as invasive and metastatic melanoma cells overexpress TSP-1. We recently demonstrated that a new molecular agent that selectively prevents TSP-1 binding to CD47, called TAX2, exhibits anti-cancer properties when administered systemically by decreasing viable tumor tissue within subcutaneous B16 melanoma allografts. At the same time, emerging evidence was published suggesting a contribution of TSP-1 in melanoma metastatic dissemination and resistance to treatment. Through a comprehensive systems biology approach based on multiple genomics and proteomics databases analyses, we first identified a TSP-1-centered interaction network that is overexpressed in metastatic melanoma. Then, we investigated the effects of disrupting TSP-1:CD47 interaction in A375 human malignant melanoma xenografts. In this model, TAX2 systemic administrations induce tumor necrosis by decreasing intra-tumoral blood flow, while concomitantly making tumors less infiltrative. Besides, TAX2 treatment also drastically inhibits B16F10 murine melanoma cells metastatic dissemination and growth in a syngeneic experimental model of lung metastasis, as demonstrated by histopathological analyses as well as longitudinal and quantitative µCT follow-up of metastatic progression. Altogether, the results obtained by combining bioinformatics and preclinical studies strongly suggest that targeting TSP-1/CD47 axis may represent a valuable therapeutic alternative for hampering melanoma spreading.

PMID: 27349907 [PubMed - as supplied by publisher]

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma.

PLoS One. 2015;10(11):e0142443

Authors: Kaushik A, Bhatia Y, Ali S, Gupta D

Abstract
Metastatic melanoma patients have a poor prognosis, mainly attributable to the underlying heterogeneity in melanoma driver genes and altered gene expression profiles. These characteristics of melanoma also make the development of drugs and identification of novel drug targets for metastatic melanoma a daunting task. Systems biology offers an alternative approach to re-explore the genes or gene sets that display dysregulated behaviour without being differentially expressed. In this study, we have performed systems biology studies to enhance our knowledge about the conserved property of disease genes or gene sets among mutually exclusive datasets representing melanoma progression. We meta-analysed 642 microarray samples to generate melanoma reconstructed networks representing four different stages of melanoma progression to extract genes with altered molecular circuitry wiring as compared to a normal cellular state. Intriguingly, a majority of the melanoma network-rewired genes are not differentially expressed and the disease genes involved in melanoma progression consistently modulate its activity by rewiring network connections. We found that the shortlisted disease genes in the study show strong and abnormal network connectivity, which enhances with the disease progression. Moreover, the deviated network properties of the disease gene sets allow ranking/prioritization of different enriched, dysregulated and conserved pathway terms in metastatic melanoma, in agreement with previous findings. Our analysis also reveals presence of distinct network hubs in different stages of metastasizing tumor for the same set of pathways in the statistically conserved gene sets. The study results are also presented as a freely available database at http://bioinfo.icgeb.res.in/m3db/. The web-based database resource consists of results from the analysis presented here, integrated with cytoscape web and user-friendly tools for visualization, retrieval and further analysis.

PMID: 26558755 [PubMed - indexed for MEDLINE]

Mapping nonlinear receptive field structure in primate retina at single cone resolution.

Elife. 2015;4

Authors: Freeman J, Field GD, Li PH, Greschner M, Gunning DE, Mathieson K, Sher A, Litke AM, Paninski L, Simoncelli EP, Chichilnisky EJ

Abstract
The function of a neural circuit is shaped by the computations performed by its interneurons, which in many cases are not easily accessible to experimental investigation. Here, we elucidate the transformation of visual signals flowing from the input to the output of the primate retina, using a combination of large-scale multi-electrode recordings from an identified ganglion cell type, visual stimulation targeted at individual cone photoreceptors, and a hierarchical computational model. The results reveal nonlinear subunits in the circuity of OFF midget ganglion cells, which subserve high-resolution vision. The model explains light responses to a variety of stimuli more accurately than a linear model, including stimuli targeted to cones within and across subunits. The recovered model components are consistent with known anatomical organization of midget bipolar interneurons. These results reveal the spatial structure of linear and nonlinear encoding, at the resolution of single cells and at the scale of complete circuits.

PMID: 26517879 [PubMed - indexed for MEDLINE]

Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes.

Elife. 2015;4:e07545

Authors: Liepe J, Holzhütter HG, Bellavista E, Kloetzel PM, Stumpf MP, Mishto M

Abstract
Proteasomal protein degradation is a key determinant of protein half-life and hence of cellular processes ranging from basic metabolism to a host of immunological processes. Despite its importance the mechanisms regulating proteasome activity are only incompletely understood. Here we use an iterative and tightly integrated experimental and modelling approach to develop, explore and validate mechanistic models of proteasomal peptide-hydrolysis dynamics. The 20S proteasome is a dynamic enzyme and its activity varies over time because of interactions between substrates and products and the proteolytic and regulatory sites; the locations of these sites and the interactions between them are predicted by the model, and experimentally supported. The analysis suggests that the rate-limiting step of hydrolysis is the transport of the substrates into the proteasome. The transport efficiency varies between human standard- and immuno-proteasomes thereby impinging upon total degradation rate and substrate cleavage-site usage.

PMID: 26393687 [PubMed - indexed for MEDLINE]

A balance of positive and negative regulators determines the pace of the segmentation clock.

Elife. 2015;4:e05842

Authors: Wiedermann G, Bone RA, Silva JC, Bjorklund M, Murray PJ, Dale JK

Abstract
Somitogenesis is regulated by a molecular oscillator that drives dynamic gene expression within the pre-somitic mesoderm. Previous mathematical models of the somitogenesis clock that invoke the mechanism of delayed negative feedback predict that its oscillation period depends on the sum of delays inherent to negative-feedback loops and inhibitor half-lives. We develop a mathematical model that explores the possibility that positive feedback also plays a role in determining the period of clock oscillations. The model predicts that increasing the half-life of the positive regulator, Notch intracellular domain (NICD), can lead to elevated NICD levels and an increase in the oscillation period. To test this hypothesis, we investigate a phenotype induced by various small molecule inhibitors in which the clock is slowed. We observe elevated levels and a prolonged half-life of NICD. Reducing NICD production rescues these effects. These data provide the first indication that tight control of the turnover of positive as well as negative regulators of the clock determines its periodicity.

PMID: 26357015 [PubMed - indexed for MEDLINE]

Hemostasis and thrombosis beyond biochemistry: roles of geometry, flow and diffusion.

Thromb Res. 2015 Oct;136(4):699-711

Authors: Panteleev MA, Dashkevich NM, Ataullakhanov FI

Abstract
An important trend in the modern concept of blood coagulation is the growing agreement that, in order to understand regulation of coagulation in vivo and disorders of its function, it is essential to take into account its spatial heterogeneity, diffusion, and flow. In a way, this suggests that the idea of the "coagulation cascade" itself becomes increasingly misleading because there is no such place in an organism where reactions of this cascade really co-exist: activation, propagation and termination of coagulation are regulated by different subsets of chemical reactions that have different spatial localization and depend on cofactors expressed by different cell types in different tissues, so that only diffusion and flow can link these distinct "compartments" together into the one functional system. Here we review the last two decades of evidence obtained from in vitro, in vivo and computational systems biology approaches. When combined, the data comprise into an adequately comprehensive picture of the spatial regulation and organization of blood coagulation. In addition to the basic insights into the regulatory mechanisms, these approaches provided interesting results in the fields of coagulation diagnostics and other applications. Finally, the remaining unresolved and conflicting issues in the spatiotemporal regulation of coagulation are discussed.

PMID: 26278966 [PubMed - indexed for MEDLINE]

Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing.

Elife. 2015;4:e07090

Authors: Etournay R, Popović M, Merkel M, Nandi A, Blasse C, Aigouy B, Brandl H, Myers G, Salbreux G, Jülicher F, Eaton S

Abstract
How tissue shape emerges from the collective mechanical properties and behavior of individual cells is not understood. We combine experiment and theory to study this problem in the developing wing epithelium of Drosophila. At pupal stages, the wing-hinge contraction contributes to anisotropic tissue flows that reshape the wing blade. Here, we quantitatively account for this wing-blade shape change on the basis of cell divisions, cell rearrangements and cell shape changes. We show that cells both generate and respond to epithelial stresses during this process, and that the nature of this interplay specifies the pattern of junctional network remodeling that changes wing shape. We show that patterned constraints exerted on the tissue by the extracellular matrix are key to force the tissue into the right shape. We present a continuum mechanical model that quantitatively describes the relationship between epithelial stresses and cell dynamics, and how their interplay reshapes the wing.

PMID: 26102528 [PubMed - indexed for MEDLINE]

Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage.

Ann Rheum Dis. 2016 Feb;75(2):449-58

Authors: Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ

Abstract
OBJECTIVE: To use a computational approach to investigate the cellular and extracellular matrix changes that occur with age in the knee joints of mice.
METHODS: Knee joints from an inbred C57/BL1/6 (ICRFa) mouse colony were harvested at 3-30 months of age. Sections were stained with H&E, Safranin-O, Picro-sirius red and antibodies to matrix metalloproteinase-13 (MMP-13), nitrotyrosine, LC-3B, Bcl-2, and cleaved type II collagen used for immunohistochemistry. Based on this and other data from the literature, a computer simulation model was built using the Systems Biology Markup Language using an iterative approach of data analysis and modelling. Individual parameters were subsequently altered to assess their effect on the model.
RESULTS: A progressive loss of cartilage matrix occurred with age. Nitrotyrosine, MMP-13 and activin receptor-like kinase-1 (ALK1) staining in cartilage increased with age with a concomitant decrease in LC-3B and Bcl-2. Stochastic simulations from the computational model showed a good agreement with these data, once transforming growth factor-β signalling via ALK1/ALK5 receptors was included. Oxidative stress and the interleukin 1 pathway were identified as key factors in driving the cartilage breakdown associated with ageing.
CONCLUSIONS: A progressive loss of cartilage matrix and cellularity occurs with age. This is accompanied with increased levels of oxidative stress, apoptosis and MMP-13 and a decrease in chondrocyte autophagy. These changes explain the marked predisposition of joints to develop osteoarthritis with age. Computational modelling provides useful insights into the underlying mechanisms involved in age-related changes in musculoskeletal tissues.

PMID: 25475114 [PubMed - indexed for MEDLINE]