Revealing mechanisms of infectious disease spread through empirical contact networks

The spread of pathogens fundamentally depends on the underlying contacts between individuals. Modeling the dynamics of infectious disease spread through contact networks, however, can be challenging due to limited knowledge of how an infectious disease spreads and its transmission rate. We developed a novel statistical tool, INoDS (Identifying contact Networks of infectious Disease Spread) that estimates the transmission rate of an infectious disease outbreak, establishes epidemiological relevance of a contact network in explaining the observed pattern of infectious disease spread and enables model comparison between different contact network hypotheses. We show that our tool is robust to incomplete data and can be easily applied to datasets where infection timings of individuals are unknown. We tested the reliability of INoDS using simulation experiments of disease spread on a synthetic contact network and find that it is robust to incomplete data and is reliable under different settings of network dynamics and disease contagiousness compared with previous approaches. We demonstrate the applicability of our method in two host-pathogen systems: Crithidia bombi in bumblebee colonies and Salmonella in wild Australian sleepy lizard populations. INoDS thus provides a novel and reliable statistical tool for identifying transmission pathways of infectious disease spread. In addition, application of INoDS extends to understanding the spread of novel or emerging infectious disease, an alternative approach to laboratory transmission experiments, and overcoming common data-collection constraints.     

Deep learning-based image processing in optical microscopy

Optical microscopy has emerged as a key driver of fundamental research since it provides the ability to probe into imperceptible structures in the biomedical world. For the detailed investigation of samples, a high-resolution image with enhanced contrast and minimal damage is preferred. To achieve this, an automated image analysis method is preferable over manual analysis in terms of both speed of acquisition and reduced error accumulation. In this regard, deep learning (DL)-based image processing can be highly beneficial. The review summarises and critiques the use of DL in image processing for the data collected using various optical microscopic techniques. In tandem with optical microscopy, DL has already found applications in various problems related to image classification and segmentation. It has also performed well in enhancing image resolution in smartphone-based microscopy, which in turn enablse crucial medical assistance in remote places.Graphical abstract     

Plasma microRNA expression and immunoregulatory cytokines in an Indian population occupationally exposed to cadmium

Following its accumulation in the body, cadmium (Cd) exposure is associated with devastating effects on multiple organ system of the human body. The immune system is one of the sensitive targets for Cd-induced toxicity. Recently, studies have demonstrated a significant role of Cd in inducing epigenetic alterations. With this background, the present study was planned to study the changes in candidate microRNA (miRNA) expression associated with immune regulation in occupationally Cd-exposed workers. One hundred individuals involved in welding and metal handicraft manufacturing, while 80 apparently healthy subjects without any prior history of occupational exposure were recruited for the study. Blood Cd level was determined by atomic absorption spectrometry. Serum cytokine levels were measured using an enzyme-linked immunosorbent assay and serum miRNA expression of candidate miRNAs (miR-146a, miR-210, and miR-222) were determined by real-time polymerase chain reaction. The median Cd level (2.40 μg/L) in the occupationally exposed workers was significantly higher than the nonexposed subjects (0.90 μg/L). Among the cytokines, interleukin-4 (IL-4), and tumor necrosis factor-alpha (TNF-α) were significantly higher while IL-2 and IL-10 were significantly lower in the exposed. The expression level of miR-146a and miR-222 were significantly different between the groups with the former showing downregulation and later showing upregulation. Correlation analysis revealed a positive and negative association of miR-222 and miR-146a with blood cadmium level, IL-17 as well as TNF-α, respectively. Furthermore, the in-silico analysis revealed a significant role of the studied miRNAs in various cellular and genetic pathways. The findings of the present study demonstrate significant involvement of Cd-induced alteration in miRNAs in varied immune regulatory changes in exposed individuals.     

Replacement of a conserved proline and the alkaline conformational change in iso-2-cytochrome c

Although point mutations usually lead to minor localized changes in protein structure, replacement of conserved Pro-76 with Gly in iso-2-cytochrome c induces a major conformational change. The change in structure results from mutation-induced depression of the pK for transition to an alkaline conformation with altered heme ligation. To assess the importance of position 76 in stabilizing the native versus the alkaline structure, the equilibrium and kinetic properties of the pH-induced conformational change have been compared for normal and mutant iso-2-cytochrome c. The pKapp for the conformational change is reduced from 8.45 (normal iso-2) to 6.71 in the mutant protein (Gly-76 iso-2), suggesting that conservation of Pro-76 may be required to stabilize the native conformation at physiological pH. The kinetics of the conformational change for both the normal and mutant proteins are well-described by a single kinetic phase throughout most of the pH-induced transition zone. Over this pH range, a minimal mechanism proposed for horse cytochrome c [Davis, L. A., Schejter, A., & Hess, G. P. (1974) J. Biol. Chem. 249, 2624-2632] is consistent with the data for normal and mutant yeast iso-2-cytochromes c: NH KH----N + H+ kcf in equilibrium kcb A NH and N are native forms of cytochrome c with a 695-nm absorbance band, A is an alkaline form that lacks the 695-nm band, KH is a proton dissociation constant, and kcf and kcb are microscopic rate constants for the conformational change. The Gly-76 mutation increases kcf by almost 70-fold, but kcb and KH are unchanged.(ABSTRACT TRUNCATED AT 250 WORDS)     

Electrochemical characterization of Geobacter sulfurreducens cells immobilized on graphite paper electrodes

Bacteria able to transfer electrons to conductive surfaces are of interest as catalysts in microbial fuel cells, as well as in bioprocessing, bioremediation, and corrosion. New procedures for immobilization of Geobacter sulfurreducens on graphite electrodes are described that allow routine, repeatable electrochemical analysis of cell-electrode interactions. Immediately after immobilizing G. sulfurreducens on electrodes, electrical current was obtained without addition of exogenous electron shuttles or electroactive polymers. Voltammetry and impedance analysis of pectin-immobilized bacteria transferring electrons to electrode surfaces could also be performed. Cyclic voltammetry of immobilized cells revealed voltage-dependent catalytic current similar to what is commonly observed with adsorbed enzymes, with catalytic waves centered at -0.15 V (vs. SHE). Electrodes maintained at +0.25 V (vs. SHE) initially produced 0.52 A/m(2) in the presence of acetate as the electron donor. Electrical Impedance Spectroscopy of coatings was also consistent with a catalytic mechanism, controlled by charge transfer rate. When electrodes were maintained at an oxidizing potential for 24 h, electron transfer to electrodes increased to 1.75 A/m(2). These observations of electron transfer by pectin-entrapped G. sulfurreducens appear to reflect native mechanisms used for respiration. The ability of washed G. sulfurreducens cells to immediately produce electrical current was consistent with the external surface of this bacterium possessing a pathway linking oxidative metabolism to extracellular electron transfer. This electrochemical activity of pectin-immobilized bacteria illustrates a strategy for preparation of catalytic electrodes and study of Geobacter under defined conditions.     

Cloning, expression, purification and characterization of the alternate splice Src variants for drug discovery

Protein tyrosine kinases (PTKs) are key members of intra- and extra-cellular signaling pathways. Aberrant signaling pathways are responsible for many human diseases, making these enzymes targets for drug development programs. The difficulty in PCR-amplification of Src due to the high G-C content was overcome using a commercial “G-C melt” reagent. The N06 Src was cloned along with the N12 and N23 neuronal variants. Neuronal variants of Src occur due to splicing within the N-loop of the SH3 domain. These variants have greater catalytic activity. Affinity purification methodologies were established that takes advantage of binding sites within the SH1 and SH2 domains. The purified enzyme is stable, without loss of activity for >1 year when frozen and more than 1 week at 4°C. A 96-well solution phase assay was developed and validated that overcomes many of the false positives and negatives generated by other assays. Studies of the catalytic mechanism have indicated that a second metal ion is essential for catalysis. Some transition metals can be substituted for the second metal ion and maintain activity while others act as dead-end inhibitors with binding constants in the sub-micromolar range. The precise role of this second metal ion is being studied.     

B cells from patients with Graves' disease aberrantly express the IGF-1 receptor: implications for disease pathogenesis

Graves' disease (GD) is an autoimmune process involving the thyroid and connective tissues in the orbit and pretibial skin. Activating anti-thyrotropin receptor Abs are responsible for hyperthyroidism in GD. However, neither these autoAbs nor the receptor they are directed against have been convincingly implicated in the connective tissue manifestations. Insulin-like growth factor-1 receptor (IGF-1R)-bearing fibroblasts overpopulate connective tissues in GD and when ligated with IgGs from these patients, express the T cell chemoattractants, IL-16, and RANTES. Disproportionately large fractions of peripheral blood T cells also express IGF-1R in patients with GD and may account, at least in part, for expansion of IGF-1R(+) memory T cells. We now report a similarly skewed B cell population exhibiting the IGF-1R(+) phenotype from the blood, orbit, and bone marrow of patients with GD. This expression profile exhibits durability in culture and is maintained or increased with CpG activation. Moreover, IGF-1R(+) B cells produce pathogenic Abs against the thyrotropin receptor. In lymphocytes from patients with GD, IGF-1 enhanced IgG production (p < 0.05) and increased B cell expansion (p < 0.02) in vitro while those from control donors failed to respond. These findings suggest a potentially important role for IGF-1R display by B lymphocytes in patients with GD in supporting their expansion and abnormal Ig production.     

KIT associated intracellular tyrosines play an essential role in EpoR co-signaling

KIT and erythropoietin receptor (EpoR) mediated co-signaling is essential for normal erythroid cell expansion, however the intracellular signals that contribute to cooperative signaling are poorly understood. Here, we examined the role of intracellular tyrosine residues in KIT and EpoR cooperation by co-expressing tyrosine (Y) to phenylalanine (F) and deletion mutants of KIT and EpoR in 32D cells. Of the four EpoR mutants examined, only EpoR-Y343 induced proliferation to near wildtype EpoR levels. A modest increase in the growth was also observed in 32D cells expressing the EpoR-Y343F; however neither EpoR-W282R nor EpoR-F8 showed any increase in growth over baseline. Biochemical analysis revealed that EpoR-Y343 induced the activation of Stat5, PI-3Kinase/Akt and MAP kinase Erk1/2 to near wildtype EpoR levels, while the remaining mutants failed to activate any of these signals. Interestingly, none of the EpoR mutants cooperated with WT KIT, although EpoR-Y343 showed a modest increase in co-signaling. Loss of seven tyrosine residues in KIT (KIT-F7) completely abrogated EpoR induced co-signaling. Restoring the Src kinase binding sites in KIT-F7 alone or together with the PI3Kinase binding site restored KIT induced signals as well as co-signals with WT EpoR, although restoring the Src kinase binding sites along with the PLC-gamma binding site repressed both KIT induced signaling as well as co-signaling with WT EpoR. Taken together, these results suggest that KIT and EpoR mediated co-signaling requires intracellular tyrosine residues and tyrosine residues that bind Src kinases in the KIT receptor appear to be sufficient for restoring both KIT signaling as well as co-signaling with EpoR. In contrast, restoration of the PLC-gamma binding site in the context of Src binding sites appears to antagonize the positive signals induced via the Src kinase binding sites in the KIT receptor.