Systems-level Approach Research Articles

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.

Recent Advances in Understanding Plant Heterosis

Although heterosis is widely utilized in crop production, its genetic and molecular basis is still elusive. It is arguably that heterosis arises in crosses between genetically and/or epigenetically distinct individuals. Various genetic models have been proposed to explain heterosis, such as dominance and overdominance hypothesis. With the recent advancements in functional genomics, epigenetics, transcriptomics, proteomics, and metabolomics-related technologies, systems-level approaches have been adopted to understand the molecular basis of heterosis. In this review, we gather a brief account of findings from various studies in order to better understand the genetic and molecular basis of heterosis.

Assessing the energy and environmental performance of algae-mediated tertiary treatment of estrogenic compounds.

This study uses a systems-level modeling approach to illustrate a novel synergy between municipal wastewater treatment and large-scale algaculture for production of bio-energy, whereby algae-mediated tertiary treatment provides efficient removal of unregulated, strongly estrogenic steroid hormones from the secondary effluent. Laboratory results from previously published studies suggested that algae-mediated treatment could deliver roughly 75-85% removal of a model estrogen (17β-estradiol) within typical algae pond residence times. As such, experimental results are integrated into a comprehensive life cycle assessment (LCA) framework, to assess the environmental performance of an algae-based tertiary treatment system relative to three conventional tertiary treatments: ozonation, UV irradiation, and adsorption onto granular activated carbon. Results indicate that the algae-mediated tertiary treatment is superior to the selected benchmarks on the basis of raw energy return on investment (EROI) and normalized energy use per mass of estrogenic toxicity removed. It is the only tertiary treatment system that creates more energy than it consumes, and it delivers acceptable effluent quality for nutrient and coliform concentrations while rendering a significant reduction in estrogenic toxicity. These results highlight the dual water and energy sustainability benefits that accrue from the integration of municipal wastewater treatment and large-scale algae farming.

Preparing Doctoral-Level Consultants for Systems Change: Implementing and Supervising Multitiered Practices in Early Childhood Education

Implementing changes that support a preventative approach in early childhood education (ECE) requires the collaboration of skilled professionals. The present case study describes a change effort to implement multitiered systems of support (MTSS) in early childhood settings that included collaboration of agency personnel, school psychology program faculty and trainees, and ECE faculty. It describes a competency-based training initiative that provides applied experiences in consultation, supervision, and change facilitation for systems change efforts. The implementation of a systems-level approach for promoting positive behavior at three ECE agencies is described, with resulting teacher and child outcomes. Implications for future consultation research, training, and practice are discussed in relation to a consultation training model that provides competency-based field experiences to support change in ECE.

Intention tremor and deficits of sensory feedback control in multiple sclerosis: a pilot study.

BackgroundIntention tremor and dysmetria are leading causes of upper extremity disability in Multiple Sclerosis (MS). The development of effective therapies to reduce tremor and dysmetria is hampered by insufficient understanding of how the distributed, multi-focal lesions associated with MS impact sensorimotor control in the brain. Here we describe a systems-level approach to characterizing sensorimotor control and use this approach to examine how sensory and motor processes are differentially impacted by MS.MethodsEight subjects with MS and eight age- and gender-matched healthy control subjects performed visually-guided flexion/extension tasks about the elbow to characterize a sensory feedback control model that includes three sensory feedback pathways (one for vision, another for proprioception and a third providing an internal prediction of the sensory consequences of action). The model allows us to characterize impairments in sensory feedback control that contributed to each MS subject’s tremor.ResultsModels derived from MS subject performance differed from those obtained for control subjects in two ways. First, subjects with MS exhibited markedly increased visual feedback delays, which were uncompensated by internal adaptive mechanisms; stabilization performance in individuals with the longest delays differed most from control subject performance. Second, subjects with MS exhibited misestimates of arm dynamics in a way that was correlated with tremor power. Subject-specific models accurately predicted kinematic performance in a reach and hold task for neurologically-intact control subjects while simulated performance of MS patients had shorter movement intervals and larger endpoint errors than actual subject responses. This difference between simulated and actual performance is consistent with a strategic compensatory trade-off of movement speed for endpoint accuracy.ConclusionsOur results suggest that tremor and dysmetria may be caused by limitations in the brain’s ability to adapt sensory feedback mechanisms to compensate for increases in visual information processing time, as well as by errors in compensatory adaptations of internal estimates of arm dynamics.Electronic supplementary materialThe online version of this article (doi:10.1186/1743-0003-11-170) contains supplementary material, which is available to authorized users.

Abstract 5472: Systems pharmacogenomics approach identifies synergistic molecular action of combined MTOR/HDAC inhibition on MYC

Abstract Multiple myeloma (MM) and murine plasmacytoma (PCT) are rare mature B-lymphoid malignancies. Allelic variants of Mtor and Cdkn2a affect susceptibility to PCT, and functional alterations in the PI3K/MTOR and CYCLIN/CDK/CDKI/RB (RB) pathways are common to both malignancies. We found that combining sirolimus (rapamycin), an inhibitor of mechanistic target of rapamycin (MTOR), with entinostat (MS-275), a selective class I histone deacytlase (HDAC) inhibitor, was synergistic in controlling 90% of tested cell lines derived from B cell malignancies in vitro, effective in limiting xenograft growth in vivo, and diminished cellular viability in ex vivo patient samples. Similarly, the combination reduced tumor burden and volume and increased survival in a long-term, in-vivo study in C.B6-Bcl2l1 mice. To examine the core synergistic consequence of combining entinostat with sirolimus, an integrated, systems-level approach was used. Weighted gene co-expression analysis (WGCNA) of GEP data from MM cells treated individually and in combination was used to identify a distinct module of 126 genes cooperatively affected by both drugs. Of the cooperatively affected genes, 37 were found to be differentially expressed in MM and predictive of survival (p<0.01). Ingenuity upstream analysis identified MYC as a potential core regulator of the synergistic transcriptional response. MYC protein, but not mRNA, decreased in response to the drug combination when examined by Western blot and NanoString analyses, respectively. Using tet-off, MYC-inducible transformed P493 cells, the necessity of MYC for the drop in cellular viability and response of the gene signature to the combination was evident. Using the translational and proteasomal inhibitors, cycloheximide and MG132, respectively, it was determined that MYC protein half-life decreased with the combination, largely due to proteasomal degradation. Utilizing a systems-level approach and biological filters, an alternative route to MYC inhibition was determined. Biologically relevant, this methodology can be used to define the molecular underpinnings of drug combinations, applicable to many diseases. Citation Format: Benjamin J. Gamache, John K. Simmons, Aleksandra Michalowski, Jyoti Patel, Ke Zhang, Shuling Zhang, Wendy DuBois, Adriana Zingone, Michael Kuehl, Jing Huang, Ola Landgren, Beverly Mock. Systems pharmacogenomics approach identifies synergistic molecular action of combined MTOR/HDAC inhibition on MYC. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5472. doi:10.1158/1538-7445.AM2014-5472

Abstract 1610: MAPK inhibitor resistance leads to ligand-independent Ephrin A2 receptor signaling and the formation of new melanoma metastases

Abstract Melanoma is the deadliest form of skin cancer with the worst prognosis in patients with metastasis to distant sites such as brain, liver and bone. Studies have shown that MAPK reactivation is a key signaling event leading to BRAF inhibitor resistance. As such, clinical investigations are now underway to evaluate the efficacy of combining frontline BRAF plus MEK inhibitors. Though this approach appears to have meaningful clinical benefit, there are a number of patients who do not respond to therapy, or who through unknown mechanisms, succumb to refractory disease. In order to identify the dynamic changes that drive MAPK inhibitor resistance, we have developed a systems level approach combining mass spectrometry based phosphoproteomic and bioinformatics methodologies. Based on significant changes in tyrosine, threonine and serine phosphorylation events between naive and vemurafenib resistant melanoma cell lines, we have mapped a resistance interactome of ∼550 nodes. This resistance network was significantly enriched for pathways associated with metastatic disease where changes in network connectivity resulted in the appearance of new signaling hubs such as EGFR, EphA2, EphB4, STAT3, FAK1 and HDAC1. The clinical relevance of these findings was demonstrated in a retrospective study showing that 65% of BRAFV600E patients on vemurafenib therapy developed metastases at new sites, with 25% of these new metastases involving the brain. Consistent with our bioinformatics prediction, resistant lines had greater metastatic potential as seen by increased migration and invasion across matrigel and endothelial cell barriers. Extending our findings to a panel of BRAF and BRAF plus MEK inhibitor resistant cell lines, we found compelling evidence that EphA2 is essential for maintaining a resistance phenotype. This phenotype was associated with AKT activation and uncoupled Eph-ephrin signaling resulting in S897 phosphorylation and overexpression of EphA2. In vivo analysis of matched primary and metastatic tumors from vemurafenib resistant xenografts showed that EphA2 expression is increased in metastatic but not primary lesions. Importantly, analysis of clinical specimens from melanoma patients undergoing or failing vemurafenib therapy confirmed that EphA2 receptor expression is significantly upregulated in metastatic but not primary tumors. Functionally, EphA2 S897 phosphorylation was increased at the tumor leading edge of metastatic lesions while absent in primary lesions. Our results show that MAPK resistant melanomas can adaptively rewire their signaling leading to a more malignant phenotype and that through proteomics based approaches we can reliably identify resistance pathways that will translate into rational therapeutic strategies for disseminated disease. Citation Format: Kim H. T. Paraiso, Meghna Das Thakur, Jobin K. John, Bin Fang, John M. Koomen, Inna V. Fedorenko, Hensin Tsao, Keith T. Flaherty, Jane L. Messina, Elena M. Pasquale, Alejandro Villagra, John M. Kirkwood, Friedegund Meier, Sarah Sloot, Geoffrey T. Gibney, Darrin Stuart, Hussein Tawbi, Keiran S.M. Smalley. MAPK inhibitor resistance leads to ligand-independent Ephrin A2 receptor signaling and the formation of new melanoma metastases. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1610. doi:10.1158/1538-7445.AM2014-1610

Pharmacogenomics in asthma therapy: where are we and where do we go?

The response to drug treatment in asthma is a complex trait and is markedly variable even in patients with apparently similar clinical features. Pharmaco-genomics, which is the study of variations of human genome characteristics as related to drug response, can play a role in asthma therapy. Both a traditional candidate-gene approach to conducting genetic association studies and genome-wide association studies have provided an increasing list of genes and variants associated with the three major classes of asthma medications: β2-agonists, inhaled corticosteroids, and leukotriene modifiers. Moreover, a recent integrative, systems-level approach has offered a promising opportunity to identify important pharmacogenomics loci in asthma treatment. However, we are still a long way away from making this discipline directly relevant to patients. The combination of network modeling, functional validation, and integrative omics technologies will likely be needed to move asthma pharmacogenomics closer to clinical relevance.

Allele-specific network reveals combinatorial interaction that transcends small effects in psoriasis GWAS.

Hundreds of genetic markers have shown associations with various complex diseases, yet the “missing heritability” remains alarmingly elusive. Combinatorial interactions may account for a substantial portion of this missing heritability, but their discoveries have been impeded by computational complexity and genetic heterogeneity. We present BlocBuster, a novel systems-level approach that efficiently constructs genome-wide, allele-specific networks that accurately segregate homogenous combinations of genetic factors, tests the associations of these combinations with the given phenotype, and rigorously validates the results using a series of unbiased validation methods. BlocBuster employs a correlation measure that is customized for single nucleotide polymorphisms and returns a multi-faceted collection of values that captures genetic heterogeneity. We applied BlocBuster to analyze psoriasis, discovering a combinatorial pattern with an odds ratio of 3.64 and Bonferroni-corrected p-value of 5.01×10−16. This pattern was replicated in independent data, reflecting robustness of the method. In addition to improving prediction of disease susceptibility and broadening our understanding of the pathogenesis underlying psoriasis, these results demonstrate BlocBuster's potential for discovering combinatorial genetic associations within heterogeneous genome-wide data, thereby transcending the limiting “small effects” produced by individual markers examined in isolation.

Perspectives on Culture and Concepts

The well-respected tradition of research on concepts uses cross-cultural comparisons to explore which aspects of conceptual behavior are universal versus culturally variable. This work continues, but it is being supplemented by intensified efforts to study how conceptual systems and cultural systems interact to modify and support each other. For example, cultural studies within the framework of domain specificity (e.g., folkphysics, folkpsychology, folkbiology) are beginning to query the domains themselves and offer alternative organizing principles (e.g., folksociology, folkecology). Findings highlight the multifaceted nature of both concepts and culture: Individuals adopt distinct conceptual construals in accordance with culturally infused systems such as language and discourse, knowledge and beliefs, and epistemological orientations. This picture complicates questions about cognitive universality or variability, suggesting that researchers may productively adopt a systems-level approach to conceptual organization and cultural epistemologies. Related implications for diversity in cognitive science are discussed.

School meal programs and their potential to operate as school-based obesity prevention and nutrition interventions: case studies from France and Japan

Case studies of government-funded school meal programs in France and Japan are presented as potential school-based child obesity prevention and nutrition intervention programs. It is argued that this type of intervention takes a wider systems-level approach to obesity prevention by addressing the multiple dimensions of child obesity including: socioeconomic status and household food insecurity, and the need for experiential education about healthy eating and nutrition. These programs provide models of financially accessible school meal provision for all children without the social stigma that is sometimes associated with subsidized meal programs. We argue that these school meal programs are potential models for long-term and sustainable child nutrition interventions.

A systems-level approach to understanding transcriptional regulation by p53 during mammalian hibernation.

Presumably to conserve energy, many mammals enter into hibernation during the winter. Homeostatic processes such as transcription and translation are virtually arrested. To further elucidate transcriptional regulation during hibernation, we studied the transcription factor p53. Here, we demonstrate that changes in liver mRNA and protein concentrations of known regulators of p53 are consistent with activation. p53 mRNA and protein concentrations are unrelated. Importantly, p53 protein concentration is increased ~2-fold during the interbout arousal that punctuates bouts of torpor. As a result, both the interbout arousal and the torpid state are characterized by high levels of nuclear-localized p53. Chromatin immunoprecipitation assays indicate that p53 binds DNA during the winter. Furthermore, p53 recruits RNA polymerase II, as indicated by nuclear run-on data. However, and consistent with previous data indicating an arrest of transcriptional elongation during torpor, p53 'activity' does not result in expected changes in target gene transcripts. These data demonstrate the importance of using a systems level-approach in understanding a complex phenotype such as mammalian hibernation. Relying on interpretations of data that are based on steady-state regulation in other systems may be misleading in the context of non-steady-state conditions such as torpor.

Biochemical and Spatial Coincidence in the Provisional Ser/Thr Protein Kinase Interaction Network of Mycobacterium tuberculosis*♦

Many Gram-positive bacteria coordinate cellular processes by signaling through Ser/Thr protein kinases (STPKs), but the architecture of these phosphosignaling cascades is unknown. To investigate the network structure of a prokaryotic STPK system, we comprehensively explored the pattern of signal transduction in the Mycobacterium tuberculosis Ser/Thr kinome. Autophosphorylation is the dominant mode of STPK activation, but the 11 M. tuberculosis STPKs also show a specific pattern of efficient cross-phosphorylation in vitro. The biochemical specificity intrinsic to each kinase domain was used to map the provisional signaling network, revealing a three-layer architecture that includes master regulators, signal transducers, and terminal substrates. Fluorescence microscopy revealed that the STPKs are specifically localized in the cell. Master STPKs are concentrated at the same subcellular sites as their substrates, providing additional support for the biochemically defined network. Together, these studies imply a branched functional architecture of the M. tuberculosis Ser/Thr kinome that could enable horizontal signal spreading. This systems-level approach provides a biochemical and spatial framework for understanding Ser/Thr phospho-signaling in M. tuberculosis, which differs fundamentally from previously defined linear histidine kinase cascades.

Systems level approach reveals the correlation of endoderm differentiation of mouse embryonic stem cells with specific microstructural cues of fibrin gels

Stem cells receive numerous cues from their associated substrate that help to govern their behaviour. However, identification of influential substrate characteristics poses difficulties because of their complex nature. In this study, we developed an integrated experimental and systems level modelling approach to investigate and identify specific substrate features influencing differentiation of mouse embryonic stem cells (mESCs) on a model fibrous substrate, fibrin. We synthesized a range of fibrin gels by varying fibrinogen and thrombin concentrations, which led to a range of substrate stiffness and microstructure. mESCs were cultured on each of these gels, and characterization of the differentiated cells revealed a strong influence of substrate modulation on gene expression patterning. To identify specific substrate features influencing differentiation, the substrate microstructure was quantified by image analysis and correlated with stem cell gene expression patterns using a statistical model. Significant correlations were observed between differentiation and microstructure features, specifically fibre alignment. Furthermore, this relationship occurred in a lineage-specific manner towards endoderm. This systems level approach allows for identification of specific substrate features from a complex material which are influential to cellular behaviour. Such analysis may be effective in guiding the design of scaffolds with specific properties for tissue engineering applications.

Small vessel disease and the resting functional architecture of the brain.

Small vessel disease (SVD) is linked to cognitive impairment and dementia, yet little is known regarding functional activation in patients with SVD. Resting fMRI recordings suggest reduced connectivity in prefrontal, parietal and cingulate nodes and reciprocally increased connectivity in cerebellum, alterations which predicted neuropsychological test performance. Together with diffusion tensor tensor imaging studies, these data support of a model of disrupted connectivity as a systems-level approach to the cognitive disturbances seen in SVD.

Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome

The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPARγ). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome.

Modeling the underlying dynamics of the spread of crime.

The spread of crime is a complex, dynamic process that calls for a systems level approach. Here, we build and analyze a series of dynamical systems models of the spread of crime, imprisonment and recidivism, using only abstract transition parameters. To find the general patterns among these parameters—patterns that are independent of the underlying particulars—we compute analytic expressions for the equilibria and for the tipping points between high-crime and low-crime equilibria in these models. We use these expressions to examine, in particular, the effects of longer prison terms and of increased incarceration rates on the prevalence of crime, with a follow-up analysis on the effects of a Three-Strike Policy.

The alluring but misleading analogy between mirror neurons and the motor theory of speech.

Speech is commonly claimed to relate to mirror neurons because of the alluring surface analogy of mirror neurons to the Motor Theory of speech perception, which posits that perception and production draw upon common motor-articulatory representations. We argue that the analogy fails and highlight examples of systems-level developmental approaches that have been more fruitful in revealing perception-production associations.

A Food Policy Council Guide for Extension Professionals

Public interest in food systems and national prevention strategies focusing on cross-sectoral, community and systems level approaches paved the way for growing numbers of food policy councils. These councils function as organizations to discuss food-related problems, foster coordination across sectors, and influence food policies. Extension professionals can serve as "change agents," bring a wealth of experience and knowledge, form cross-sectoral collaborations, take leadership roles, and build community capacity through food policy councils. Based on expert interviews and our experiences in establishing a council, we present practice recommendations to serve as a concise how to guide for Extension professionals.

Re-configuration of sphingolipid metabolism by oncogenic transformation.

The sphingolipids are one of the major lipid families in eukaryotes, incorporating a diverse array of structural variants that exert a powerful influence over cell fate and physiology. Increased expression of sphingosine kinase 1 (SPHK1), which catalyses the synthesis of the pro-survival, pro-angiogenic metabolite sphingosine 1-phosphate (S1P), is well established as a hallmark of multiple cancers. Metabolic alterations that reduce levels of the pro-apoptotic lipid ceramide, particularly its glucosylation by glucosylceramide synthase (GCS), have frequently been associated with cancer drug resistance. However, the simple notion that the balance between ceramide and S1P, often referred to as the sphingolipid rheostat, dictates cell survival contrasts with recent studies showing that highly potent and selective SPHK1 inhibitors do not affect cancer cell proliferation or survival, and studies demonstrating higher ceramide levels in some metastatic cancers. Recent reports have implicated other sphingolipid metabolic enzymes such as acid sphingomyelinase (ASM) more strongly in cancer pathogenesis, and highlight lysosomal sphingolipid metabolism as a possible weak point for therapeutic targeting in cancer. This review describes the evidence implicating different sphingolipid metabolic enzymes and their products in cancer pathogenesis, and suggests how newer systems-level approaches may improve our overall understanding of how oncogenic transformation reconfigures sphingolipid metabolism.