Network Of Dynamic Interactions Research Articles

Network organization paradigm

Fervent communication on social networking sites provides opportunities for potential issues to trigger individuals into individual action as well as the attraction and mobilization of like-minded individuals into an organization that is both physically and virtually emergent. Examples are the rapid pace of Arab Spring and the diffusion rate of the Occupy Movement. We intend to view this as a complex adaptive system where diverse agents perform various actions without adherence to a predefined structure. The achievement of joint actions will be a result of continual interactions between them that shape a dynamic network. Agents may form an ad hoc organization based on a dynamic network of interactions for the purpose of achieving a long-term objective, which we termed as a Network Organization (NO).

Preliminary Studies on the Activity of Mixed Polyphenol-Heterocyclic Systems Against B16-F10 Melanoma Cancer Cells.

The Bcl-2 family includes 26 proteins involved in apoptosis. Cancer cells can develop the ability to avoid apoptosis through the upregulation and/or down regulation of such proteins Bax, Bcl-xL or Mcl-1, especially during chemoresistance progress. These proteins engaged in a network of dynamic interactions that control apoptosis triggering have become attractive therapeutic targets in cancers including melanoma. Among them, the Bax/Bcl-xL interaction appears critical in maintaining mitochondria integrity. Therefore a series of mixed polyphenol-heterocyclic molecules, were rationally designed by molecular docking as Bax/Bcl-xL inhibitors. It has been screened against B16-F10 melanoma cancer cells for a preliminary investigation of their cytotoxicity. All these compounds exhibited a significant cytotoxicity against these cancer cells, in the 0.3-6 .M range. A pyrazole-type molecule, which had a submicromolar IC50 value with an excellent selectivity index (14), is the most promising derivative for further development.

An urgent need for sustainable thinking in agriculture – An Indian scenario

This article emphasizes on the present urgent need to think in “Holistic Dimensions” to achieve a sustainable agro-ecosystem. In this respect, the complex network of dynamic interactions in the agro-ecosystem soil at spatiotemporal dimensions holds crucial importance. It reflects the inherent tendency of dynamic ecosystems to achieve a more efficient state successively through improved interactions. The short-sighted and inefficient agro-management during Green Revolution decades has been detrimental to these interactions in agricultural soils, which is widely evident by its boomerang effects (i.e. declining efficiency, productivity and multi-functionality). It jeopardized the internal regulation in our agro-ecosystem's functioning by erosion of efficiency building interactions among biotic and abiotic components. Therefore, a bottom-up as well as top-down approach in the soil management is required to restore and sustain the unaccounted but indispensible ecological subsidies for sustainable agriculture and development, globally. We propose a “commercial ecological agriculture” which should be an amalgamation of sustainable agricultural practices and supported by a progressive co-ordination among all the stakeholders via participatory learning and adaptation with time. It should be least-disturbing, resilience-building, resource (i.e. energy and nutrient) use efficient, site-specific, labor and skill-intensive, low-input, diversified and integrated, and intimately harmonized with nature. It may potentially provide us agricultural sustainability with time in real sense. It would be primarily based on management of interactions indirectly through identification of integrative variables as surrogate, which may help to achieve internal regulation or self-reliance in agroecosystems. Further, it would be helpful to eliminate the widening socio-economic divide and in mitigation of global change in environment (i.e. air, water and soil) and climate. Additionally, it would improve and restore the multifaceted potential of soil, thus quality and productivity, through improved internal regulation on resource-use efficiency.

A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2.

Protein O-fucosyltransferase 2 (POFUT2) is an essential enzyme that fucosylates serine and threonine residues of folded thrombospondin type 1 repeats (TSRs). To date, the mechanism by which this enzyme recognizes very dissimilar TSRs has been unclear. By engineering a fusion protein, we report the crystal structure of Caenorhabditis elegans POFUT2 (CePOFUT2) in complex with GDP and human TSR1 that suggests an inverting mechanism for fucose transfer assisted by a catalytic base and shows that nearly half of the TSR1 is embraced by CePOFUT2. A small number of direct interactions and a large network of water molecules maintain the complex. Site-directed mutagenesis demonstrates that POFUT2 fucosylates threonine preferentially over serine and relies on folded TSRs containing the minimal consensus sequence C-X-X-S/T-C. Crystallographic and mutagenesis data, together with atomic-level simulations, uncover a binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions.

Major component analysis of dynamic networks of physiologic organ interactions

The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and nonlinear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions. We analyze a large database of continuously recorded multi-channel physiologic signals from healthy young subjects during night-time sleep. We identify a network of dynamic interactions between key physiologic systems in the human organism. Further, we find that each physiologic state is characterized by a distinct network structure with different relative contribution from individual organ systems to the global network dynamics. Specifically, we observe a gradual decrease in the strength of coupling of heart and respiration to the rest of the network with transition from wake to deep sleep, and in contrast, an increased relative contribution to network dynamics from chin and leg muscle tone and eye movement, demonstrating a robust association between network topology and physiologic function.

HTLV Tax repress nonsense mediated mRNA decay by inhibiting the ATPase activity of UPF1

The Nonsense Mediated mRNA Decay (NMD) is a mRNA quality surveillance pathway that regulates the stability of mRNAs harboring a premature termination codon, avoiding the production of truncated proteins with potential oncogenic properties. NMD regulates also the expression levels of 10 to 15% of human genes such as those regulating the hematopoietic cell differentiation, the maintenance of chromosome structure and function and retroviral RNA. Due to its role in the control of expression of gene involved in the immune response, and the targeting of viral RNA, NMD is now also considered as a viral restriction mechanism. Describing the details of the interplay between HTLV and the NMD is then important to better understand how the virus evades this surveillance and to determine a role of the NMD in the associated pathologies. At the center of the NMD pathway, UPF1 orchestrates a dynamic network of interactions leading to its own structural rearrangement as well as the ribonucleoprotein (RNP) remodeling. In particular, its N-terminal domain (CH domain) repress its ATPase and helicase acitvities held by the central domain (HD domain) until it interacts with the other core factor UPF2 in the early steps of NMD. We showed for the first time that the retrovirus HTLV-1 was able to protect its RNA and modulate some of its transcriptional activators by inhibiting NMD. Now we focuse our attention in deciphering the mechanistics of this inhibition. Thus we demonstrate that HTLV-1 Tax protein targets the RNA helicase UPF1. We found that in cells transfected with a complete provirus, Tax is associated to the NMD sensitive mRNA in an UPF1 dependent manner. This interaction between Tax and the HD domain of UPF1 inhibits the ATPase acivity of UPF1. The homology in amine acid sequence as well as competition assays lead us to the conclusion that Tax could mimics the CH domain in order to maintain a repressive effect even in the latter steps of the pathway. This conclusion is supported in vivo by the accumulation of intermediary complexes stalled on an NMD target. Finally we identified the Tax binding site necessary for this inhibition. Then those data provide structural insights on the regulation of the RNA helicase UPF1 functionning as well as a precise mechanistic of Tax inhibitory effect during NMD.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes.

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

Conformational ensembles explored dynamically from disordered peptides targeting chemokine receptor CXCR4.

This work reports on the design and the synthesis of two short linear peptides both containing a few amino acids with disorder propensity and an allylic ester group at the C-terminal end. Their structural properties were firstly analyzed by means of experimental techniques in solution such as CD and NMR methods that highlighted peptide flexibility. These results were further confirmed by MD simulations that demonstrated the ability of the peptides to assume conformational ensembles. They revealed a network of transient and dynamic H-bonds and interactions with water molecules. Binding assays with a well-known drug-target, i.e., the CXCR4 receptor, were also carried out in an attempt to verify their biological function and the possibility to use the assays to develop new specific targets for CXCR4. Moreover, our data indicate that these peptides represent useful tools for molecular recognition processes in which a flexible conformation is required in order to obtain an interaction with a specific target.

Our Mutual Friend and Network Form

This essay demonstrates how Charles Dickens used the form of serial fiction to experiment with a uniquely Victorian idea of life as a dynamic network of interactions. Reading Our Mutual Friend alongside nineteenth-century physiological and evolutionary writing, I show how Dickens shaped novel form around the attractions and reactions that organized social and psychological life in his city. Victorian sciences—particularly the work of George Henry Lewes and Charles Darwin—were turning to “net-work” to describe the plastic processes underpinning biological life. Dickens's fiction used the same dynamic potential of network form to put in motion the mechanisms of social life. Taking a novel form traditionally organized around the story of a self, Dickens used serial publication to incorporate variety, change, and new combinations of radically heterogeneous characters into each new installment, turning novel form into an ongoing formation. The resulting model of character psychology is one that replaces interiority with interaction and individuated desire with physiological affect.

The hexameric structure of the human mitochondrial replicative helicase Twinkle.

The mitochondrial replicative helicase Twinkle is involved in strand separation at the replication fork of mitochondrial DNA (mtDNA). Twinkle malfunction is associated with rare diseases that include late onset mitochondrial myopathies, neuromuscular disorders and fatal infantile mtDNA depletion syndrome. We examined its 3D structure by electron microscopy (EM) and small angle X-ray scattering (SAXS) and built the corresponding atomic models, which gave insight into the first molecular architecture of a full-length SF4 helicase that includes an N-terminal zinc-binding domain (ZBD), an intermediate RNA polymerase domain (RPD) and a RecA-like hexamerization C-terminal domain (CTD). The EM model of Twinkle reveals a hexameric two-layered ring comprising the ZBDs and RPDs in one layer and the CTDs in another. In the hexamer, contacts in trans with adjacent subunits occur between ZBDs and RPDs, and between RPDs and CTDs. The ZBDs show important structural heterogeneity. In solution, the scattering data are compatible with a mixture of extended hexa- and heptameric models in variable conformations. Overall, our structural data show a complex network of dynamic interactions that reconciles with the structural flexibility required for helicase activity.

Understanding the occupational and organizational boundaries to safe hospital discharge

Safe hospital discharge relies upon communication and coordination across multiple occupational and organizational boundaries. Our aim was to understand how these boundaries can exacerbate health system complexity and represent latent sociocultural threats to safe discharge. An ethnographic study was conducted in two local health and social care systems (health economies) in England, focusing on two clinical areas: stroke and hip fracture patients. Data collection involved 345 hours of observations and 220 semi-structured interviews with health and social care professionals, patients and their lay carers. Hospital discharge involves a dynamic network of interactions between heterogeneous health and social care actors, each characterized by divergent ways of organizing discharge activities; cultures of collaboration and interaction and understanding of what discharge involves and how it contributes to patient recovery. These interrelated dimensions elaborate the occupational and organisational boundaries that can influence communication and coordination in hospital discharge. Hospital discharge relies upon the coordination of multiple actors working across occupational and organizational boundaries. Attention to the sociocultural boundaries that influence communication and coordination can help inform interventions that might support enhanced discharge safety.

Functional connectivity among spike trains in neural assemblies during rat working memory task

Working memory refers to a brain system that provides temporary storage to manipulate information for complex cognitive tasks. As the brain is a more complex, dynamic and interwoven network of connections and interactions, the questions raised here: how to investigate the mechanism of working memory from the view of functional connectivity in brain network? How to present most characteristic features of functional connectivity in a low-dimensional network? To address these questions, we recorded the spike trains in prefrontal cortex with multi-electrodes when rats performed a working memory task in Y-maze. The functional connectivity matrix among spike trains was calculated via maximum likelihood estimation (MLE). The average connectivity value Cc, mean of the matrix, was calculated and used to describe connectivity strength quantitatively. The spike network was constructed by the functional connectivity matrix. The information transfer efficiency Eglob was calculated and used to present the features of the network. In order to establish a low-dimensional spike network, the active neurons with higher firing rates than average rate were selected based on sparse coding. The results show that the connectivity Cc and the network transfer efficiency Eglob vaired with time during the task. The maximum values of Cc and Eglob were prior to the working memory behavior reference point. Comparing with the results in the original network, the feature network could present more characteristic features of functional connectivity.

Interplay between steroid signalling and microRNAs: implications for hormone-dependent cancers.

Hormones are key drivers of cancer development. To date, interest has largely been focussed on the classical model of hormonal gene regulation, but there is increasing evidence for a role of hormone signalling pathways in post-translational regulation of gene expression. In particular, a complex and dynamic network of bi-directional interactions with microRNAs (miRs) at all stages of biogenesis and during target gene repression is emerging. miRs, which act mainly by negatively regulating gene expression through association with 3'-UTRs of mRNA species, are increasingly understood to be important in development, normal physiology and pathogenesis. Given recent demonstrations of altered miR profiles in a diverse range of cancers, their ability to function as oncogenes or tumour suppressors, and hormonal regulation of miRs, understanding mechanisms by which miRs are generated and regulated is vitally important. miRs are transcribed by RNA polymerase II and then processed in the nucleus by the Drosha-containing Microprocessor complex and in the cytoplasm by Dicer, before mature miRs are incorporated into the RNA-induced silencing complex. It is increasingly evident that multiple cellular signalling pathways converge upon the miR biogenesis cascade, adding further layers of regulatory complexity to modulate miR maturation. This review summarises recent advances in identification of novel components and regulators of the Microprocessor and Dicer complexes, with particular emphasis on the role of hormone signalling pathways in regulating their activity. Understanding hormone regulation of miR production and how this is perturbed in cancer are critical for the development of miR-based therapeutics and biomarkers.

Simulating the vibrational spectra of ionic liquid systems: 1-ethyl-3-methylimidazolium acetate and its mixtures.

The vibrational spectra of the ionic liquid 1-ethyl-3-methylimidazolium acetate and its mixtures with water and carbon dioxide are calculated using ab initio molecular dynamics simulations, and the results are compared to experimental data. The new implementation of a normal coordinate analysis in the trajectory analyzer TRAVIS is used to assign the experimentally observed bands to specific molecular vibrations. The applied computational approaches prove to be particularly suitable for the modeling of bulk phase effects on vibrational spectra, which are highly important for the discussion of the microscopic structure in systems with a strong dynamic network of intermolecular interactions, such as ionic liquids.

Integrated RAS signaling defined by parallel NMR detection of effectors and regulators

The RAS GTPase directs cell proliferation and survival by selectively relaying signals amid a dynamic network of regulatory enzymes and protein interactions. Oncogenic mutation of RAS alters cell growth by deleteriously controlling output to RAS-binding effectors. Mechanisms underlying multieffector interactions for both wild-type and oncogenic RAS are poorly understood owing to challenges in quantifying outputs to multiple pathways in parallel. Using highly selective NMR probes for wild-type and oncogenic (G12V) RAS, we develop a systematic approach that quantitatively measures RAS output in composite mixtures of GEF, GAP and effector RAS-binding domains (RBDs). We derive effector signaling hierarchies and establish how oscillating concentrations generate effector 'switching'. The G12V mutation highly perturbs this system, specifically altering interactions with RAL GTPase-specific GEFs and RAF kinases. We further reveal that RAS-RBD complexes show extensive feedback to full-length regulatory proteins. Our approach quantifies output from signaling hubs, here providing an integrated view of the RAS network.

Studying Weak and Dynamic Interactions of Posttranslationally Modified Proteins using Expressed Protein Ligation

Many cellular processes are regulated by posttranslational modifications that are recognized by specific domains in protein binding partners. These interactions are often weak, thus allowing a highly dynamic and combinatorial regulatory network of protein-protein interactions. We report an efficient strategy that overcomes challenges in structural analysis of such a weak transient interaction between the Tudor domain of the Survival of Motor Neuron (SMN) protein and symmetrically dimethylated arginine (sDMA). The posttranslational modification is chemically introduced and covalently linked to the effector module by a one-pot expressed protein ligation (EPL) procedure also enabling segmental incorporation of NMR-active isotopes for structural analysis. Covalent coupling of the two interacting moieties shifts the equilibrium to the bound state, and stoichiometric interactions are formed even for low affinity interactions. Our approach should enable the structural analysis of weak interactions by NMR or X-ray crystallography to better understand the role of posttranslational modifications in dynamic biological processes.

The third intracellular loop plays a critical role in bitter taste receptor activation

Bitter taste receptors (T2Rs) belong to the superfamily of G protein-coupled receptors (GPCRs). T2Rs are chemosensory receptors with important therapeutic potential. In humans, bitter taste is perceived by 25 T2Rs, which are distinct from the well-studied Class A GPCRs. The activation mechanism of T2Rs is poorly understood and none of the structure–function studies are focused on the role of the important third intracellular loop (ICL3). T2Rs have a unique signature sequence at the cytoplasmic end of fifth transmembrane helix (TM5), a highly conserved LxxSL motif. Here, we pursue an alanine scan mutagenesis of the ICL3 of T2R4 and characterize the functionality of 23 alanine mutants. We identify four mutants, H214A, Q216A, V234A and M237A, that exhibit constitutive activity. To our surprise, the H214A mutant showed very high constitutive activity over wild type T2R4. Interestingly, His214 is highly conserved (96%) in T2Rs and is present two amino acids below the LxxSL motif in TM5. Molecular modeling shows a dynamic network of interactions involving residues in TM5–ICL3–TM6 that restrain the movement of the helices. Changes in this network, as in the case of H214A, Q216A, V234A and M237A mutants, cause the receptor to adopt an active conformation. The conserved LxxSL motif in TM5 performs both structural and functional roles in this process. These results provide insight into the activation mechanism of T2Rs, and emphasize the unique functional role of ICL3 even within the GPCR subfamilies.

Dynamic interactions between intermediate neurogenic progenitors and radial glia in embryonic mouse neocortex: potential role in Dll1-Notch signaling.

The mammalian neocortical progenitor cell niche is composed of a diverse repertoire of neuroepithelial cells, radial glia (RG), and intermediate neurogenic progenitors (INPs). Previously, live-cell imaging experiments have proved crucial in identifying these distinct progenitor populations, especially INPs, which amplify neural output by undergoing additional rounds of proliferation before differentiating into new neurons. INPs also provide feedback to the RG pool by serving as a source of Delta-like 1 (Dll1), a key ligand for activating Notch signaling in neighboring cells, a well-known mechanism for maintaining RG identity. While much is known about Dll1-Notch signaling at the molecular level, little is known about how this cell-cell contact dependent feedback is transmitted at the cellular level. To investigate how RG and INPs might interact to convey Notch signals, we used high-resolution live-cell multiphoton microscopy (MPM) to directly observe cellular interactions and dynamics, in conjunction with Notch-pathway specific reporters in the neocortical neural stem cell niche in organotypic brain slices from embryonic mice. We found that INPs and RG interact via dynamic and transient elongate processes, some apparently long-range (extending from the subventricular zone to the ventricular zone), and some short-range (filopodia-like). Gene expression profiling of RG and INPs revealed further progenitor cell diversification, including different subpopulations of Hes1+ and/or Hes5+ RG, and Dll1+ and/or Dll3+ INPs. Thus, the embryonic progenitor niche includes a network of dynamic cell-cell interactions, using different combinations of Notch signaling molecules to maintain and likely diversify progenitor pools.

HMGB1-Facilitated p53 DNA Binding Occurs via HMG-Box/p53 Transactivation Domain Interaction, Regulated by the Acidic Tail

Facilitated binding of p53 to DNA by high mobility group B1 (HMGB1) may involve interaction between the N-terminal region of p53 and the high mobility group (HMG) boxes, as well as HMG-induced bending of the DNA. Intramolecular shielding of the boxes by the HMGB1 acidic tail results in an unstable complex with p53 until the tail is truncated to half its length, at which point the A box, proposed to be the preferred binding site for p53(1-93), is exposed, leaving the B box to bind and bend DNA. The A box interacts with residues 38-61 (TAD2) of the p53 transactivation domain. Residues 19-26 (TAD1) bind weakly, but only in the context of p53(1-93) and not as a free TAD1 peptide. We have solved the structure of the A-box/p53(1-93) complex by nuclear magnetic resonance spectroscopy. The incipient amphipathic helix in TAD2 recognizes the concave DNA-binding face of the A box and may be acting as a single-stranded DNA mimic.

Nonmuscle Myosin II Is Required for Internalization of the Epidermal Growth Factor Receptor and Modulation of Downstream Signaling

Ligand-induced internalization of the epidermal growth factor receptor (EGFR) is an important process for regulating signal transduction, cellular dynamics, and cell-cell communication. Here, we demonstrate that nonmuscle myosin II (NM II) is required for the internalization of the EGFR and to trigger the EGFR-dependent activation of ERK and AKT. The EGFR was identified as a protein that interacts with NM II by co-immunoprecipitation and mass spectrometry analysis. This interaction requires both the regulatory light chain 20 (RLC20) of NM II and the kinase domain of the EGFR. Two paralogs of NM II, NM II-A, and NM II-B can act to internalize the EGFR, depending on the cell type and paralog content of the cell line. Loss (siRNA) or inhibition (25 μm blebbistatin) of NM II attenuates the internalization of the EGFR and impairs EGFR-dependent activation of ERK and AKT. Both internalization of the EGFR and downstream signaling to ERK and AKT can be partially restored in siRNA-treated cells by introduction of wild type (WT) GFP-NM II, but cannot be restored by motor mutant NM II. Taken together, these results suggest that NM II plays a role in the internalization of the EGFR and EGFR-mediated signaling pathways.