Reconstruction of Cellular Signal Transduction Networks Using Perturbation Assays and Linear Programming

Perturbation experiments for example using RNA interference (RNAi) offer an attractive way to elucidate gene function in a high throughput fashion. The placement of hit genes in their functional context and the inference of underlying networks from such data, however, are challenging tasks. One of the problems in network inference is the exponential number of possible network topologies for a given number of genes. Here, we introduce a novel mathematical approach to address this question. We formulate network inference as a linear optimization problem, which can be solved efficiently even for large-scale systems. We use simulated data to evaluate our approach, and show improved performance in particular on larger networks over state-of-the art methods. We achieve increased sensitivity and specificity, as well as a significant reduction in computing time. Furthermore, we show superior performance on noisy data. We then apply our approach to study the intracellular signaling of human primary nave CD4⁺ T-cells, as well as ErbB signaling in trastuzumab resistant breast cancer cells. In both cases, our approach recovers known interactions and points to additional relevant processes. In ErbB signaling, our results predict an important role of negative and positive feedback in controlling the cell cycle progression.     

Field Studies Using European Starlings to Establish Causality between PCB Exposure and Reproductive Effects

Accumulation and effects of polychlorinated biphenyls (PCBs) in avian species were evaluated at a Superfund site located at Crab Orchard National Wildlife Refuge, Illinois, and seven criteria were used to assess whether there was a causal relationship between PCB exposure and observed reproductive effects. European starlings (Sturnus vulgaris) were monitored at nest boxes constructed at each of two exposed and two reference sites. During the breeding season, starling productivity (number of chicks produced per nest) and adult nest attentiveness behavior (provisioning behavior) were monitored. At 15 days post-hatch, chicks were collected for contaminant and biomarker analyses. Chicks were necropsied, ethoxyresorufin-O-deethylase (EROD) activity measured in liver tissue, and PCB (Aroclor 1254) and 34 chlorinated biphenyl (CB) congener concentrations measured in carcasses using gas chromatography. PCB and CB concentrations also were measured in eggs that failed to hatch. Mean Aroclor 1254 and quantified CB concentrations were greater (P<0.001) in eggs that failed to hatch and 15-day-old chicks collected from PCB sites compared to those collected from reference sites. EROD activity was greater (P=0.005) in 15-day-old chicks collected from PCB sites and was correlated with carcass PCB concentrations. Reduced adult nest attentiveness behavior and decreased chick survival were observed at PCB sites. Six of the seven causal criteria evaluated provided evidence that observed reproductive effects resulted from exposure to PCBs. Using this weight-of-evidence approach provided a means for establishing the likely cause of effects and thus provided managers with information needed in decision-making processes.     

Relations between Computational and Experimental Engineering Approaches to Molecules from Molecular Fragments

Computational techniques have become important tools in the preliminary stages of the design of new molecules. The mutual arrangements of interacting molecular parts and the required accessibility of important reactive groups on the peripheral regions of possible new molecules can be tested by computational means before the expensive and often complex synthetic methods are used to the actual construction of these molecules. There are some common features involved in the computational representation of molecular fragments and the synthetic methodologies used in the process of incorporating actual molecular fragments in such engineered molecules. One trend that appears to link these two approaches is based on the following observation: the greater local autonomy is shown by the calculated electron density contribution of a given molecular fragment, the more likely that this fragment can be regarded as a suitable building block of the molecule, and it is also more likely that there are convenient synthetic methods for the delivery of this fragment to its desired target location in the new molecule to be synthesized. For a precise formulation of this statement, a new concept, the degree of molecular fragment autonomy is introduced, using the inherent properties of molecular electron densities.     

Loss of Cardiolipin Leads to Perturbation of Mitochondrial and Cellular Iron Homeostasis

Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays a critical role in mitochondrial bioenergetic functions. The importance of CL in human health is underscored by the observation that perturbation of CL biosynthesis causes the severe genetic disorder Barth syndrome. To fully understand the cellular response to the loss of CL, we carried out genome-wide expression profiling of the yeast CL mutant crd1Δ. Our results show that the loss of CL in this mutant leads to increased expression of iron uptake genes accompanied by elevated levels of mitochondrial iron and increased sensitivity to iron and hydrogen peroxide. Previous studies have shown that increased mitochondrial iron levels result from perturbations in iron-sulfur (Fe-S) cluster biogenesis. Consistent with an Fe-S defect, deletion of ISU1, one of two ISU genes that encode the mitochondrial Fe-S scaffolding protein essential for the synthesis of Fe-S clusters, led to synthetic growth defects with the crd1Δ mutant. We further show that crd1Δ cells have reduced activities of mitochondrial Fe-S enzymes (aconitase, succinate dehydrogenase, and ubiquinol-cytochrome c oxidoreductase), as well as cytosolic Fe-S enzymes (sulfite reductase and isopropylmalate isomerase). Increased expression of ATM1 or YAP1 did not rescue the Fe-S defects in crd1Δ. These findings show for the first time that CL is required for Fe-S biogenesis to maintain mitochondrial and cellular iron homeostasis.     

The Causal Effect of Market Priming on Trust: An Experimental Investigation Using Randomized Control

We report data from laboratory experiments where participants were primed using phrases related to markets and trade. Participants then participated in trust games with anonymous strangers. The decisions of primed participants are compared to those of a control group. We find evidence that priming for market participation affects positively the beliefs regarding the trustworthiness of anonymous strangers and increases trusting decisions.     

A Cellular Screening Assay Using Analysis of Metal-Modified Fluorescence Lifetime

Current methods for screening cell receptor internalization often require complex image analysis with limited sensitivity. Here we describe a novel bioassay based on detection of changes in global fluorescence lifetime above a gold substrate, with superresolution axial sensitivity and no need for image analysis. We show that the lifetime of enhanced green fluorescent protein expressed in a cellular membrane is greatly reduced in close proximity to the gold, resulting in a distance-dependent lifetime distribution throughout the cell. We demonstrate the application of this phenomenon in a screening assay by comparing the efficacies of two small molecule inhibitors interfering with the internalization process of a G protein-coupled receptor.     

Using Multivariable Mendelian Randomization to Disentangle the Causal Effects of Lipid Fractions

Background

Previous Mendelian randomization studies have suggested that, while low-density lipoprotein cholesterol (LDL-c) and triglycerides are causally implicated in coronary artery disease (CAD) risk, high-density lipoprotein cholesterol (HDL-c) may not be, with causal effect estimates compatible with the null.

Principal Findings

The causal effects of these three lipid fractions can be better identified using the extended methods of ‘multivariable Mendelian randomization’. We employ this approach using published data on 185 lipid-related genetic variants and their associations with lipid fractions in 188,578 participants, and with CAD risk in 22,233 cases and 64,762 controls. Our results suggest that HDL-c may be causally protective of CAD risk, independently of the effects of LDL-c and triglycerides. Estimated causal odds ratios per standard deviation increase, based on 162 variants not having pleiotropic associations with either blood pressure or body mass index, are 1.57 (95% credible interval 1.45 to 1.70) for LDL-c, 0.91 (0.83 to 0.99, p-value  = 0.028) for HDL-c, and 1.29 (1.16 to 1.43) for triglycerides.

Significance

Some interventions on HDL-c concentrations may influence risk of CAD, but to a lesser extent than interventions on LDL-c. A causal interpretation of these estimates relies on the assumption that the genetic variants do not have pleiotropic associations with risk factors on other pathways to CAD. If they do, a weaker conclusion is that genetic predictors of LDL-c, HDL-c and triglycerides each have independent associations with CAD risk.     

High-Dimensional Mediation Analysis with Applications to Causal Gene Identification

Statistics in Biosciences - Mediation analysis has been a popular framework for elucidating the mediating mechanism of the exposure effect on the outcome in many disciplines including genetic...     

Using Trust to Establish a Secure Routing Model in Cognitive Radio Network

Specific to the selective forwarding attack on routing in cognitive radio network, this paper proposes a trust-based secure routing model. Through monitoring nodes’ forwarding behaviors, trusts of nodes are constructed to identify malicious nodes. In consideration of that routing selection-based model must be closely collaborative with spectrum allocation, a route request piggybacking available spectrum opportunities is sent to non-malicious nodes. In the routing decision phase, nodes’ trusts are used to construct available path trusts and delay measurement is combined for making routing decisions. At the same time, according to the trust classification, different responses are made specific to their service requests. By adopting stricter punishment on malicious behaviors from non-trusted nodes, the cooperation of nodes in routing can be stimulated. Simulation results and analysis indicate that this model has good performance in network throughput and end-to-end delay under the selective forwarding attack.     

A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information

In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.     

Using Conformational Analysis to Identify Structurally Conserved Regions of MAP Peptides that Exhibit Cellular Attachment Ability

A natural bioadhesive obtained from Mytilus edulis , mussel adhesive protein, MAP or mefp-1, is frequently used for cellular attachment. MAP is approximately 114 kD, and generally composed of repeating decapeptide units, A-K-P-S-Y-Hyp-Hyp-T-DOPA-K, MAP-RD. Prior nuclear magnetic resonance (NMR) spectroscopy and molecular modeling of MAP-RD revealed an overall bent-helix. NMR spectroscopy and molecular modeling of a MAP fourteen residue peptide, P-S-Y-Hyp-Hyp-T-Y-K-A-K-P-S-Y-Hyp, MAP-14, are presented. Additionally, a molecular model built and minimized from MAP-RD and MAP-14 produced a twenty-six-residue MAP peptide, (MAP-26), that maintained regional structural consistency with both MAP-RD and MAP-14. Multiple attenuated internal reflection infrared (MAIR-IR) spectroscopy and ellipsometry of the MAP-14 as well as that of L-DOPA-containing MAP-14, (MAP-14(D)), showed uniform film formation near a monolayer in thickness was L-DOPA dependent. Significantly more undifferentiated leukocyte cells (MOLT-4) attached to and spread on MAP-14 (D) films (applied at 2 w g cm m 2 ) compared with intact MAP, MAP-RD or tissue culture treated polystyrene, indicating a cellular binding domain presence in the MAP-14 sequence. The culmination of biophysical data indicate the lysine-alanine-lysine (K-A-K) sequence as structurally conserved and responsible for the cellular attachment ability noted for MAP14(D) and ultimately MAP.     

Automatic Prediction of Cardiovascular and Cerebrovascular Events Using Heart Rate Variability Analysis

Background

There is consensus that Heart Rate Variability is associated with the risk of vascular events. However, Heart Rate Variability predictive value for vascular events is not completely clear. The aim of this study is to develop novel predictive models based on data-mining algorithms to provide an automatic risk stratification tool for hypertensive patients.

Methods

A database of 139 Holter recordings with clinical data of hypertensive patients followed up for at least 12 months were collected ad hoc. Subjects who experienced a vascular event (i.e., myocardial infarction, stroke, syncopal event) were considered as high-risk subjects. Several data-mining algorithms (such as support vector machine, tree-based classifier, artificial neural network) were used to develop automatic classifiers and their accuracy was tested by assessing the receiver-operator characteristics curve. Moreover, we tested the echographic parameters, which have been showed as powerful predictors of future vascular events.

Results

The best predictive model was based on random forest and enabled to identify high-risk hypertensive patients with sensitivity and specificity rates of 71.4% and 87.8%, respectively. The Heart Rate Variability based classifier showed higher predictive values than the conventional echographic parameters, which are considered as significant cardiovascular risk factors.

Conclusions

Combination of Heart Rate Variability measures, analyzed with data-mining algorithm, could be a reliable tool for identifying hypertensive patients at high risk to develop future vascular events.     

新方法建立大鼠不完全性肠梗阻模型的实验研究

目的探讨一种建立不完全性肠梗阻模型的新方法,以寻求一种稳定可靠的动物模型。方法 SD大鼠随机分为正常组(n=24)、丝线组(n=30)和套环组(n=30)。分别用丝线和套环造成回肠末端梗阻,造模后观测大鼠体重和排便情况,分别于造模后12h、24h、48h和72h开腹腔进行肠道大体形态评分,测量梗阻部位以上肠管周径;取肠组织制作常规石蜡切片,HE染色后观察肠粘膜损伤程度。结果与正常组相比两模型组的粪便颗数和干重在12h和72h均显著下降,梗阻大鼠体重减轻、进食量减少,梗阻上段肠周径逐渐增粗;两模型组的肠道大体形态损伤评分值和肠粘膜损伤评分值均随时间而增高且高于正常组,72h时套环组的两类损伤评分值均显著低于丝线组;套环组的存活率高于丝线组。结论两种方法均建立了不完全性肠梗阻模型,套环法对大鼠肠道损伤更小、安全性高,且适合研究早期不完全性肠梗阻。     

A Causal Relation between Bioluminescence and Oxygen to Quantify the Cell Niche

Bioluminescence imaging assays have become a widely integrated technique to quantify effectiveness of cell-based therapies by monitoring fate and survival of transplanted cells. To date these assays are still largely qualitative and often erroneous due to the complexity and dynamics of local micro-environments (niches) in which the cells reside. Here, we report, using a combined experimental and computational approach, on oxygen that besides being a critical niche component responsible for cellular energy metabolism and cell-fate commitment, also serves a primary role in regulating bioluminescent light kinetics. We demonstrate the potential of an oxygen dependent Michaelis-Menten relation in quantifying intrinsic bioluminescence intensities by resolving cell-associated oxygen gradients from bioluminescent light that is emitted from three-dimensional (3D) cell-seeded hydrogels. Furthermore, the experimental and computational data indicate a strong causal relation of oxygen concentration with emitted bioluminescence intensities. Altogether our approach demonstrates the importance of oxygen to evolve towards quantitative bioluminescence and holds great potential for future microscale measurement of oxygen tension in an easily accessible manner.     

Non-Invasive Clinical Parameters for the Prediction of Urodynamic Bladder Outlet Obstruction: Analysis Using Causal Bayesian Networks

Purpose

To identify non-invasive clinical parameters to predict urodynamic bladder outlet obstruction (BOO) in patients with benign prostatic hyperplasia (BPH) using causal Bayesian networks (CBN).

Subjects and Methods

From October 2004 to August 2013, 1,381 eligible BPH patients with complete data were selected for analysis. The following clinical variables were considered: age, total prostate volume (TPV), transition zone volume (TZV), prostate specific antigen (PSA), maximum flow rate (Qmax), and post-void residual volume (PVR) on uroflowmetry, and International Prostate Symptom Score (IPSS). Among these variables, the independent predictors of BOO were selected using the CBN model. The predictive performance of the CBN model using the selected variables was verified through a logistic regression (LR) model with the same dataset.

Results

Mean age, TPV, and IPSS were 6.2 (±7.3, SD) years, 48.5 (±25.9) ml, and 17.9 (±7.9), respectively. The mean BOO index was 35.1 (±25.2) and 477 patients (34.5%) had urodynamic BOO (BOO index ≥40). By using the CBN model, we identified TPV, Qmax, and PVR as independent predictors of BOO. With these three variables, the BOO prediction accuracy was 73.5%. The LR model showed a similar accuracy (77.0%). However, the area under the receiver operating characteristic curve of the CBN model was statistically smaller than that of the LR model (0.772 vs. 0.798, p = 0.020).

Conclusions

Our study demonstrated that TPV, Qmax, and PVR are independent predictors of urodynamic BOO.     

Differential Cellular Enrichment of Gangliosides in the Mouse Cerebellum: Analysis Using Neurological Mutants

Abstract: The cellular distribution of gangliosides in the cerebellum was studied in a series of adult mouse mutants that lose specific populations of neurons. The weaver ( wv ) mutation destroys the vast majority of granule cells, whereas the Purkinje cell degeneration mutation ( pcd ) destroys the vast majority of Purkinje cells. The staggerer ( sg ) and lurcher ( Lc ) mutations, on the other hand, destroy the vast majority of both granule and Purkinje cells. A proliferation of reactive glial cells, which occurs as a consequence of neuronal loss, has been reported in the sg/sg and pcd/pcd mutants, but not in the wv/wv mutant. Compared with the normal (+/+) mice, the concentration (μg/100 mg dry weight) of G_D1a was significantly reduced in those mutants that lost granule cells, but was not reduced in the pcd/pcd mutant. The concentration of G_TIa, on the other hand, was significantly reduced in those mutants that lost Purkinje cells, but was not reduced in the wv/wv mutant. A significant elevation in the concentration of G_D3, which may be related to the proliferation of reactive glial cells, was observed in the pcd/pcd, sglsg , and Lc /+ mutants, but was not observed in the wv/wv mutant. Because these ganglioside abnormalities were confined to the cerebellum, they cannot result from genetic defects in ganglioside metabolism. Instead, these abnormalities result from a differential enrichment of gangliosides in neural membranes. Our findings suggest that G_DT1a is more heavily concentrated in granule cells than Purkinje cells, whereas the opposite appears true for G_Tla. It also appears that GD3 is enriched in reactive glial cells and may play an important role during the morphological transformation of neural membranes.