Regulation of interferon stimulated gene expression levels at homeostasis.

Interferon stimulated genes (ISGs), a collection of genes important in the early innate immune response, are upregulated in response to stimulation by extracellular type I interferons. The regulation of ISGs has been extensively studied in cells exposed to significant interferon stimulation, but less is known about ISG regulation in homeostatic regimes in which extracellular interferon levels are low. Using a collection of pre-existing, publicly available microarray datasets, we investigated ISG regulation at homeostasis in CD4, pulmonary epithelial, fibroblast and macrophage cells. We used a linear regression model to predict ISG expression levels from regulator expression levels. Our results suggest significant regulation of ISG expression at homeostasis, both through the ISGF3 molecule and through IRF7 and IRF8 associated pathways. We find that roughly 50% of ISGs have expression levels significantly correlated with ISGF3 expression levels at homeostasis, supporting previous results suggesting that homeostatic IFN levels have broad functional consequences. We find that ISG expression levels varied in their correlation with ISGF3, with epithelial and macrophage cells showing more correlation than CD4 and fibroblast cells. Our analysis provides a novel approach for decomposing and quantifying ISG regulation.

Investigating Functional Roles for Positive Feedback and Cellular Heterogeneity in the Type I Interferon Response to Viral Infection.

Secretion of type I interferons (IFN) by infected cells mediates protection against many viruses, but prolonged or excessive type I IFN secretion can lead to immune pathology. A proper type I IFN response must therefore maintain a balance between protection and excessive IFN secretion. It has been widely noted that the type I IFN response is driven by positive feedback and is heterogeneous, with only a fraction of infected cells upregulating IFN expression even in clonal cell lines, but the functional roles of feedback and heterogeneity in balancing protection and excessive IFN secretion are not clear. To investigate the functional roles for feedback and heterogeneity, we constructed a mathematical model coupling IFN and viral dynamics that extends existing mathematical models by accounting for feedback and heterogeneity. We fit our model to five existing datasets, reflecting different experimental systems. Fitting across datasets allowed us to compare the IFN response across the systems and suggested different signatures of feedback and heterogeneity in the different systems. Further, through numerical experiments, we generated hypotheses of functional roles for IFN feedback and heterogeneity consistent with our mathematical model. We hypothesize an inherent tradeoff in the IFN response: a positive feedback loop prevents excessive IFN secretion, but also makes the IFN response vulnerable to viral antagonism. We hypothesize that cellular heterogeneity of the IFN response functions to protect the feedback loop from viral antagonism. Verification of our hypotheses will require further experimental studies. Our work provides a basis for analyzing the type I IFN response across systems.

Internal Redox Polarity of an Individual G. sulfurreducens Bacterial Cell Attached to an Inorganic Substrate.

Bacterial cell polarity is an internal asymmetric distribution of subcellular components, including proteins, lipids, and other molecules that correlates with the cell ability to sense energy and metabolite sources, chemical signals, quorum signals, toxins, and movement in the desired directions. This ability also plays central role in cell attachment to various surfaces and biofilm formation. Mechanisms and factors controlling formation of this cell internal asymmetry are not completely understood. As a step in this direction, in the present work, we develop an approach for analyzing how information about inorganic substrate can be non-genetically coded inside an individual bacterial cell. As a model system, we use G. sulfurreducens cells attached to an inorganic mineral, mica. The approach utilizes confocal Raman microscopy, Gaussian deconvolution, and Principal Component Analysis (PCA) and allows for quick label-free identification of the molecular signature of cytochrome intracellular location and the cell to substrate binding down to the level of individual bacterial cells. Our results describe a spectroscopic signature of cell adhesion and how the information about cell adhesion can be coded inside individual bacterial cells.

Effect of iron doping on protein molecular conductance.

Protein molecular conductance has attracted attention from researchers for the possibility of constructing innovative flexible biocompatible nanoscale electronic devices and smart hybrid materials. Due to protein complexity, most evaluations of protein conductivity are based on the simple estimation of protein's molecular orbital energy levels and spatial distributions without analysing its protein interaction with electrodes and the calculation of the rates of electron transfer (ET). In the present work, we included in our density functional theory (DFT) analysis an approach based on the non-equilibrium Green's function (NEGF) allowing for calculation from the first principles the molecular interaction with electrodes and thus the role of electrode materials, Fermi level, the thermal distribution of electronic energy levels, and the coupling efficiency between the molecule and the electrodes. Compared to proteins studied so far, mainly artificial peptides, heme-containing cytochromes, and bacterial pili, we choose rubredoxin for our calculation. Rubredoxin contains a non-heme iron that, as we have discovered recently, can be involved in extracellular ET in electroactive bacterial biofilms (Yates et al., Energy Environ. Sci., 2016, 9, 3544-3558). Our calculations show that an iron atom incorporated into the protein structure as an iron-sulfur cluster opens a transmission path at the energy corresponding to the Fermi level of the electrodes. This allows the protein to become an extremely efficient conductor at very low bias voltages (<±350 mV). Calculation of the role of protein amino acids based on the local density of states and electron transfer paths reveals that neither aromatic amino acid Tyr nor Phe at any ring orientation participates in coherent ET through the FeS cluster of the protein. Moreover, direct ET through surrounding amino acids, bypassing FeS, is possible only at biases ±1.5 to ±2 V. The polar amino acid Asn might participate in ET at these bias voltages. The conductivity of the protein core substantially depends on the polarity of the applied electric field, allowing for unidirectional ET and operation of the protein as a molecular rectifier. These results can be used for a wise de novo design of proteins for molecular electronics and cellular energy converting devices, particularly for utilization of iron doping in the construction of conductive protein wires.

A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.

MOTIVATION: Next generation sequencing (NGS) has been increasingly applied to characterize viral evolution during HIV and SIV infections. In particular, NGS datasets sampled during the initial months of infection are characterized by relatively low levels of diversity as well as convergent evolution at multiple loci dispersed across the viral genome. Consequently, fully characterizing viral evolution from NGS datasets requires haplotype reconstruction across large regions of the viral genome. Existing haplotype reconstruction algorithms have not been developed with the particular characteristics of early HIV/SIV infection in mind, raising the possibility that better performance could be achieved through a specifically designed algorithm. RESULTS: Here, we introduce a haplotype reconstruction algorithm, RegressHaplo, specifically designed for low diversity and convergent evolution regimes. The algorithm uses a penalized regression that balances a data fitting term with a penalty term that encourages solutions with few haplotypes. The regression covariates are a large set of potential haplotypes and fitting the regression is made computationally feasible by the low diversity setting. Using simulated and in vivo datasets, we compare RegressHaplo to PredictHaplo and QuRe, two existing haplotype reconstruction algorithms. RegressHaplo performs better than these algorithms on simulated datasets with relatively low diversity levels. We suggest RegressHaplo as a novel tool for the investigation of early infection HIV/SIV datasets and, more generally, low diversity viral NGS datasets. CONTACT: sr286@georgetown.edu. AVAILABILITY AND IMPLEMENTATION: https://github.com/SLeviyang/RegressHaplo.

A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor.

Fabrication of nanoscale structures with localized surface plasmons allows for substantial increase in sensitivity of chem/bio sensors. The main challenge for realizing complex nanoplasmonic structures in solution is the high level of precision required at the nanoscale to position metal nanoparticles in 3D. In this study, we report a virus-like particle (VLP) for building a 3D plasmonic nanostructure in solution in which gold nanoparticles are precisely positioned on the VLP by directed self-assembly techniques. These structures allow for concentration of electromagnetic fields in the desired locations between the gold nanoparticles or "hot spots". We measure the efficiency of the optical field spatial concentration for the first time, which results in a ten-fold enhancement of the capsid Raman peaks. Our experimental results agree with our 3D finite element simulations. Furthermore, we demonstrate as a proof-of-principle that the plasmonic nanostructures can be utilized in DNA detection down to 0.25 ng/µl (lowest concentration tested), while the protein peaks from the interior of the nanoplasmonic structures, potentially, can serve as an internal tracer for the biosensors.

Structural reorganizations control intermolecular conductance and charge trapping in paraquat-tetraphenylborate inverse photochemical cell.

Miniaturization of electronic devices to the level of single molecules requires detailed understanding of the mechanisms of their operation. One of the questions here is the identification of the role of structural alterations in charge separation and stabilization in photoactive complexes. To address this question, we calculate optimized molecular and electronic structures, and optical and vibrational spectra of l,l'-dimethyl 4,4'-bipyridinium-bis tetraphenylborate PQ(BPh(4))(2) complex ab initio using density functional theory approach and compare them with the experimentally observed UV-Vis and Raman spectra of the molecules in solid-state films. The results indicate that the association of PQ and BPh(4) leads to the formation of an internally ionized structure that is accompanied by the structural reorganization of both PQ (the twisting of pyridinium rings) and BPh(4) (phenyl rings rotation) moieties. The quanta of light do not seem to be directly involved in the formation of this ionized structure, but provide energy for fast recombination of the separated charges between BPh(4)(-) and PQ(2+). The high efficiency of the dark charge separation and the stabilization of separated charges in the complex permit the using of PQ(BPh(4))(2) in various charge-transfer devices like molecular probes, photovoltaic devices or chemical memory units.

Observation of two discrete conductivity states in quinone-oligo(phenylene vinylene).

The single-molecule conductivity of quinone-oligo(phenylene vinylene) (Q-OPV) attached to a gold substrate was studied using electrochemical scanning tunnelling microscopy. The results show that the molecule has two discrete conductivity states: a low-conductivity state, when it is oxidized, and a high-conductivity state, when reduced. The electron transport through the molecule in both states occurs via coherent tunnelling. The molecular conductivity in either oxidation state is independent from the electrochemical gate potential; however, the gate potential can be used to switch the oxidation state of the molecule. Numerical calculations suggest that the highest occupied molecular orbital (HOMO) of Q-OPV controls tunnelling through the molecule and that the independence of conductivity from the electrochemical gate in either oxidation state originates from strong penetration of HOMO into the substrate. In addition, the greater delocalization of HOMO in the reduced state than in the oxidized state explains the greater conductivity of Q-OPV in the former than in the latter.

Improved Statistical Methods are Needed to Advance Personalized Medicine.

Common methods of statistical analysis, e.g. Analysis of Variance and Discriminant Analysis, are not necessarily optimal in selecting therapy for an individual patient. These methods rely on group differences to identify markers for disease or successful interventions and ignore sub-group differences when the number of sub-groups is large. In these circumstances, they provide the same advice to an individual as the average patient. Personalized medicine needs new statistical methods that allow treatment efficacy to be tailored to a specific patient, based on a large number of patient characteristics. One such approach is the sequential k-nearest neighbor analysis (patients-like-me algorithm). In this approach, the k most similar patients are examined sequentially until a statistically significant conclusion about the efficacy of treatment for the patient-at-hand can be arrived at. For some patients, the algorithm stops before the entire set of data is examined and provides beneficial advice that may contradict recommendations made to the average patient. Many problems remain in creating statistical tools that can help individual patients but this is an important area in which progress in statistical thinking is helpful.

Electrochemically controlled conductance switching in a single molecule: quinone-modified oligo(phenylene vinylene).

Reversible conductance switching in single quinone-oligo(phenylene vinylene) (Q-OPV) molecules was demonstrated using electrochemical STM. The switching was achieved by application of electrochemical potential to the substrate supporting the molecule. The ratio of conductances between the high- and low-conductivity states is over 40. The high-conductivity state is ascribed to strong electron delocalization of the fully conjugated hydroquinone-OPV structure, whereas the low-conductivity state is characterized by disruption of electron delocalization in the quinone-OPV structure.

Conductive wiring of immobilized photosynthetic reaction center to electrode by cytochrome C.

The photosynthetic reaction center (RC) found in photosynthetic bacteria is one of the most advanced photoelectronic devices developed by nature. However, after immobilization on the electrode surface, the efficiency of electron transfer (ET) between the RC and the electrode is relatively low. This inefficiency has limited the possibility of using the RC for technological applications. Here we show that photoinduced electron transfer between the immobilized RC and a gold electrode can be increased by several tens-fold by incorporation of cytochrome c into the RC-self-assembled monolayer (SAM)-electrode complex. The effect does not depend on the initial redox state of the cytochrome and seems to be the result of the formation of a complex between the RC and the cytochrome c serving as an ET wire. This observation opens the possibility for electrochemical analysis of the special pair in the RC protein that is deeply buried inside the protein globe and is barely electrically addressable from the electrode surface.