Regulation of nuclear transcription by mitochondrial RNA in endothelial cells

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models

Impaired angiogenesis in diabetes is a key process contributing to ischemic diseases such as peripheral arterial disease. Epigenetic mechanisms, including those mediated by long noncoding RNAs (lncRNAs), are crucial links connecting diabetes and the related chronic tissue ischemia. Here we identify the lncRNA that enhances endothelial nitric oxide synthase (eNOS) expression (LEENE) as a regulator of angiogenesis and ischemic response. LEENE expression was decreased in diabetic conditions in cultured endothelial cells (ECs), mouse hind limb muscles, and human arteries. Inhibition of LEENE in human microvascular ECs reduced their angiogenic capacity with a dysregulated angiogenic gene program. Diabetic mice deficient in Leene demonstrated impaired angiogenesis and perfusion following hind limb ischemia. Importantly, overexpression of human LEENE rescued the impaired ischemic response in Leene-knockout mice at tissue functional and single-cell transcriptomic levels. Mechanistically, LEENE RNA promoted transcription of proangiogenic genes in ECs, such as KDR (encoding VEGFR2) and NOS3 (encoding eNOS), potentially by interacting with LEO1, a key component of the RNA polymerase II-associated factor complex and MYC, a crucial transcription factor for angiogenesis. Taken together, our findings demonstrate an essential role for LEENE in the regulation of angiogenesis and tissue perfusion. Functional enhancement of LEENE to restore angiogenesis for tissue repair and regeneration may represent a potential strategy to tackle ischemic vascular diseases.

Methods to Study RNA-Chromatin Interactions

RNA plays a fundamental role in the organization of chromatin as well as the regulation of gene expression. Although the chromatin is pervasively attached by both coding and noncoding RNAs, the impact of these chromatin-associated RNAs (caRNAs) on gene expression and cellular functions and their underlying mechanisms have just begun to be unraveled. One approach to understand the potential mechanism of gene regulation by caRNAs is to identify the caRNA-associated genomic regions. Several groups have developed methods to capture RNA-chromatin interactions in either one RNA vs the whole genome, i.e., "one-to-all" or all RNAs vs the whole genome, i.e., "all-to-all" manner. In this chapter, we discuss several state-of-the-art methods highlighting the principles behind them, the experimental procedures, the advantages and limitations, and their applications. Our goal is to provide an overview and guide to researchers interested in exploring caRNAs using these techniques.

Correlation of changes in subclonal architecture with progression in the MMRF CoMMpass study

Multiple myeloma (MM) is a heterogeneous plasma cell proliferative disorder that arises from its premalignant precursor stages through a complex cascade of interactions between clonal mutations and co-evolving microenvironment. The temporo-spatial evolutionary trajectories of MM are established early during myelomatogenesis in precursor stages and retained in MM. Such molecular events impact subsequent disease progression and clinical outcomes. Identification of clonal sweeps of actionable gene targets in MM could reveal potential vulnerabilities that may exist in early stages and thus potentiate prognostication and customization of early therapeutic interventions. We have evaluated clonal evolution at multiple time points in 76 MM patients enrolled in the MMRF CoMMpass study. The major findings of this study are (a) MM progresses predominantly through branching evolution, (b) there is a heterogeneous spectrum of mutational landscapes that include unique actionable gene targets at diagnosis compared to progression, (c) unique clonal gains/ losses of mutant driver genes can be identified in patients with different cytogenetic aberrations, (d) there is a significant correlation between co-occurring oncogenic mutations/ co-occurring subclones e.g., with mutated TP53+SYNE1, NRAS+MAGI3, and anticorrelative dependencies between FAT3+FCGBP gene pairs. Such co-trajectories may synchronize molecular events of drug response, myelomatogenesis and warrant future studies to explore their potential for early prognostication and development of risk stratified personalized therapies in MM.

A mathematical model captures the role of adenyl cyclase Cyr1 and guanidine exchange factor Ira2 in creating a growth-to-hyphal bistable switch in Candida albicans

Recent biochemical experiments have indicated that in Candida albicans, a commensal fungal pathogen, the Ras signaling pathway plays a significant role in the yeast-to-hyphal transition; specifically, two enzymes in this pathway, Adenyl Cyclase Cyr1 and GTPase activating protein Ira2, facilitate this transition, in the presence of energy sensor ATP. However, the precise mechanism by which protein interactions between Ira2 and Cyr1 and the energy sensor ATP result in the yeast-to-hyphal transition and create a switch-like process are unknown. We propose a new set of biochemical reaction steps that captures all the essential interactions between Ira2, Cyr1, and ATP in the Ras pathway. With the help of chemical reaction network theory, we demonstrate that this set of biochemical reaction steps results in bistability. Further, bifurcation analysis of the differential equations based on this set of reaction steps supports the existence of a bistable switch, and this switch may act as a checkpoint mechanism for the promotion of growth-to-hyphal transition in C. albicans.

Design, development and model analysis of lower extremity Exo-skeleton

Over the past few years the growth and development of exo-skeleton has dramatically raised with the development of precise control elements and actuation systems. Many exo-skeleton systems have been designed, developed and tested for performance optimization. In the recent years, the significance of exo-skeleton in medical fields have got increased and are used in providing therapy and rehabilitation to the patients. With this development there comes the importance for analysis and control of the exo-skeleton for precise functioning and to avoid malfunction of the system in the later part. Dynamic analysis of limb joints is essential to better facilitate a deeper understanding of the exo-skeleton limb during various environmental conditions like varied loading. The dynamic model so developed will assist in choosing an apt actuation system based on the torque requirement of the model.This paper focusses on the analysis of a 2DOF lower limb active control exo-skeleton system and makes a torque calculation for actuator selection for the lower limb to provide rehabilitation to the patients as wearable walking aid. The work also makes a trajectory planning for the lower limb to move in sequence for making a walking cycle with angular limitations to avoid damage to the user's limbs. The motion analysis for the developed lower limb Exoskeleton as per the analysis is 52.055 Nm at hip joint 11.677 Nm at knee joint.

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological networks and pathways, both under homeostatic and pathological states like cancer.Despite their immense importance as key regulators of cellular processes, accurate and reliable estimation of miRNAs using Next Generation Sequencing is challenging, largely due to the limited availability of robust computational tools/methods/pipelines. Here, we introduce miRPipe, an end-to-end computational framework for the identification, characterization, and expression estimation of small RNAs, including the known and novel miRNAs and previously annotated pi-RNAs from small-RNA sequencing profiles. Our workflow detects unique novel miRNAs by incorporating the sequence information of seed and non-seed regions, concomitant with clustering analysis. This approach allows reliable and reproducible detection of unique novel miRNAs and functionally same miRNAs (paralogues). We validated the performance of miRPipe with the available state-of-the-art pipelines using both synthetic datasets generated using the newly developed miRSim tool and three cancer datasets (Chronic Lymphocytic Leukemia, Lung cancer, and breast cancer). In the experiment over the synthetic dataset, miRPipe is observed to outperform the existing state-of-the-art pipelines (accuracy: 95.23% and F1-score: 94.17%). Analysis on all the three cancer datasets shows that miRPipe is able to extract more number of known dysregulated miRNAs or piRNAs from the datasets as compared to the existing pipelines.

Abstract 147: Endothelial Regulation By Enhancer Associated Long Non-coding RNA

Lining the critical interface between circulating blood and vascular wall, endothelial cells (ECs) play vital functions in health and disease. The optimal gene expression in ECs is essential to maintain endothelial homeostasis, and its dysregulation can lead to EC dysfunction, a common mechanism underlying many metabolic and cardiovascular diseases, e.g. diabetes and diabetes-associated vasculopathy. We identified an enhancer-associated long non-coding RNA (lncRNA) that enhances endothelial nitric oxide synthase (eNOS) expression, aka LEENE in ECs. LEENE is suppressed in diabetes conditions in ECs in vitro, in vivo, and in human arteries. Knockout of leene homologue in mouse resulted in impaired microvascular function, evident in a diabetic hindlimb ischemia model. Overexpression of human LEENE RNA in the knockout mice rescued the ischemic recovery, resembling that of wildtype animals at tissue function and transcriptome, and single cell gene expression levels. Mechanistically, LEENE binds to the promoters of a set of pro-angiogenic genes to induce their transcription, as revealed by chromatin isolation with RNA pulldown combined with sequencing. Taken together, our work demonstrates an essential role for LEENE in the regulation of angiogenesis and tissue perfusion. Functional enhancement of LEENE to restore angiogenesis and blood flow perfusion may provide a novel strategy to tackle ischemic diseases such as peripheral arterial disease.

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Endothelial cells (ECs) are crucial for vascular and whole-body function through their dynamic response to environmental cues. Elucidating the transcriptome and epigenome of ECs is paramount to understanding their roles in development, health, and disease, but is limited in the availability of isolated primary cells. Recent technologies have enabled the high-throughput profiling of EC transcriptome and epigenome, leading to the identification of previously unknown EC cell subpopulations and developmental trajectories. While EC cultures are a useful tool in the exploration of EC function and dysfunction, the culture conditions and multiple passages can introduce external variables that alter the properties of native EC, including morphology, epigenetic state, and gene expression program. To overcome this limitation, the present paper demonstrates a method of isolating human primary ECs from donor mesenteric arteries aiming to capture their native state. ECs in the intimal layer are dissociated mechanically and biochemically with the use of particular enzymes. The resultant cells can be directly used for bulk RNA or single-cell RNA-sequencing or plated for culture. In addition, a workflow is described for the preparation of human arterial tissue for spatial transcriptomics, specifically for a commercially available platform, although this method is also suitable for other spatial transcriptome profiling techniques. This methodology can be applied to different vessels collected from a variety of donors in health or disease states to gain insights into EC transcriptional and epigenetic regulation, a pivotal aspect of endothelial cell biology.

Vascular Regulation by Super Enhancer-Derived LINC00607

Vascular endothelial cells (ECs) play a pivotal role in whole body homeostasis. Recent advances have revealed enhancer-associated long non-coding RNAs (lncRNAs) as essential regulators in EC function. We investigated LINC00607, a super enhancer-derived lncRNA (SE-lncRNA) in human arteries with an emphasis on ECs. Based on public databases and our single cell RNA-sequencing (scRNA-seq) data from human arteries collected from healthy and diabetic donors, we found that LINC00607 is abundantly expressed in the arteries and its level is increased in diabetic humans. Using RNA-sequencing, we characterized the transcriptomes regulated by LINC00607 in ECs and vascular smooth muscle cells (VSMCs) and in basal and diabetic conditions in ECs. Furthermore, through transcriptomic and promoter analysis, we identified c-Myc as an upstream transcription factor of LINC00607. Finally, using scRNA-seq, we demonstrated that modified antisense oligonucleotide inhibitor of LINC00607 can reverse dysfunctional changes induced by high glucose and TNFα in ECs. Collectively, our study demonstrates a multi-pronged approach to characterize LINC00607 in vascular cells and its gene regulatory networks in ECs and VSMCs. Our findings provide new insights into the regulation and function of SE-derived lncRNAs in both vascular homeostasis and dysfunction in a cell-type and context-dependent manner, which could have a significant impact on our understanding of epigenetic regulation implicated in cardiovascular health and diseases like diabetes.

Effect of seed layer thickness on the Ta crystalline phase and spin Hall angle

Heavy metal-ferromagnet bilayer structures have attracted great research interest for charge-to-spin interconversion. In this work, we investigated the effect of the permalloy (Py) seed layer on the tantalum (Ta) polycrystalline phase and its spin Hall angle. Interestingly, for the same deposition rates the crystalline phase of Ta deposited on the Py seed layer strongly depends on the thickness of the seed layer. We observed a phase transition from α-Ta to (α + β)-Ta while increasing the Py seed layer thickness. The observed phase transition is attributed to the strain at the interface between the Py and Ta layers. Ferromagnetic resonance-based spin pumping studies reveal that the spin-mixing conductance in the (α + β)-Ta is relatively higher as compared to the α-Ta. Spin Hall angles of α-Ta and (α + β)-Ta are obtained from the inverse spin Hall effect (ISHE) measurements. The spin Hall angle of (α + β)-Ta is estimated to be θ_SH = -0.15 ± 0.009 which is relatively higher than that of the α-Ta. Our systematic results connecting the phase of Ta with the seed layer and its effect on the efficiency of spin to charge conversion might resolve ambiguities across various literature and open up new functionalities based on the growth process for emerging spintronic devices.

Revealing protein-protein interactions at the transcriptome scale by sequencing

We describe PROPER-seq (protein-protein interaction sequencing) to map protein-protein interactions (PPIs) en masse. PROPER-seq first converts transcriptomes of input cells into RNA-barcoded protein libraries, in which all interacting protein pairs are captured through nucleotide barcode ligation, recorded as chimeric DNA sequences, and decoded at once by sequencing and mapping. We applied PROPER-seq to human embryonic kidney cells, T lymphocytes, and endothelial cells and identified 210,518 human PPIs (collected in the PROPER v.1.0 database). Among these, 1,365 and 2,480 PPIs are supported by published co-immunoprecipitation (coIP) and affinity purification-mass spectrometry (AP-MS) data, 17,638 PPIs are predicted by the prePPI algorithm without previous experimental validation, and 100 PPIs overlap human synthetic lethal gene pairs. In addition, four previously uncharacterized interaction partners with poly(ADP-ribose) polymerase 1 (PARP1) (a critical protein in DNA repair) known as XPO1, MATR3, IPO5, and LEO1 are validated in vivo. PROPER-seq presents a time-effective technology to map PPIs at the transcriptome scale, and PROPER v.1.0 provides a rich resource for studying PPIs.

RAMP2-AS1 Regulates Endothelial Homeostasis and Aging

The homeostasis of vascular endothelium is crucial for cardiovascular health and endothelial cell (EC) aging and dysfunction could negatively impact vascular function. Leveraging transcriptome profiles from ECs subjected to various stimuli, including time-series data obtained from ECs under physiological pulsatile flow vs. pathophysiological oscillatory flow, we performed principal component analysis (PCA) to identify key genes contributing to divergent transcriptional states of ECs. Through bioinformatics analysis, we identified that a long non-coding RNA (lncRNA) RAMP2-AS1 encoded on the antisense of RAMP2, a determinant of endothelial homeostasis and vascular integrity, is a novel regulator essential for EC homeostasis and function. Knockdown of RAMP2-AS1 suppressed RAMP2 expression and caused EC functional changes promoting aging, including impaired angiogenesis and increased senescence. Our study demonstrates an integrative approach to quantifying EC aging based on transcriptome changes, which also identified a number of novel regulators, including protein-coding genes and many lncRNAs involved EC functional modulation, exemplified by RAMP2-AS1.

Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction

BACKGROUND

Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth factor-vascular endothelial growth factor receptor-mediated angiogenic signaling, little is known about the EC-derived signals in adipose tissue regulation. We previously identified Argonaute 1 (AGO1; a key component of microRNA-induced silencing complex) as a crucial regulator in hypoxia-induced angiogenesis. In this study, we intend to determine the AGO1-mediated EC transcriptome, the functional importance of AGO1-regulated endothelial function in vivo, and the relevance to adipose tissue function and obesity.

METHODS

We generated and subjected mice with EC-AGO1 deletion (EC-AGO1-knockout [KO]) and their wild-type littermates to a fast food-mimicking, high-fat high-sucrose diet and profiled the metabolic phenotypes. We used crosslinking immunoprecipitation- and RNA-sequencing to identify the AGO1-mediated mechanisms underlying the observed metabolic phenotype of EC-AGO1-KO. We further leveraged cell cultures and mouse models to validate the functional importance of the identified molecular pathway, for which the translational relevance was explored using human endothelium isolated from healthy donors and donors with obesity/type 2 diabetes mellitus.

RESULTS

We identified an antiobesity phenotype of EC-AGO1-KO, evident by lower body weight and body fat, improved insulin sensitivity, and enhanced energy expenditure. At the organ level, we observed the most significant phenotype in the subcutaneous and brown adipose tissues of KO mice, with greater vascularity and enhanced browning and thermogenesis. Mechanistically, EC-AGO1 suppression results in inhibition of thrombospondin-1 (THBS1/TSP1), an antiangiogenic and proinflammatory cytokine that promotes insulin resistance. In EC-AGO1-KO mice, overexpression of TSP1 substantially attenuated the beneficial phenotype. In human endothelium isolated from donors with obesity or type 2 diabetes mellitus, AGO1 and THBS1 are expressed at higher levels than the healthy controls, supporting a pathological role of this pathway.

CONCLUSIONS

Our study suggests a novel mechanism by which ECs, through the AGO1-TSP1 pathway, control vascularization and function of adipose tissues, insulin sensitivity, and whole-body metabolic state.

Hilbert transform-based time-series analysis of the circadian gene regulatory network

In this work, the authors propose the Hilbert transform (HT)‐based numerical method to analyse the time series of the circadian rhythms. They demonstrate the application of HT by taking both deterministic and stochastic time series that they get from the simulation of the fruit fly model Drosophila melanogaster and show how to extract the period, construct phase response curves, determine period sensitivity of the parameters to perturbations and build Arnold tongues to identify the regions of entrainment. They also derive a phase model that they numerically simulate to capture whether the circadian time series entrains to the forcing period completely (phase locking) or only partially (phase slips) or neither. They validate the phase model, and numerics with the experimental time series forced under different temperature cycles. Application of HT to the circadian time series appears to be a promising tool to extract the characteristic information about circadian rhythms.

Hydrothermal synthesized magnetically separable mesostructured H2Ti3O7/γ-Fe2O3 nanocomposite for organic dye removal via adsorption and its regeneration/reuse through synergistic non-radiation driven H2O2 activation

Hydrogen titanate (H₂Ti₃O₇) nanotubes/nanosheets (HTN) are emerging class of adsorbent material which possess unique property of activating hydrogen peroxide (H₂O₂) to generate the reactive oxygen species (ROS), such as superoxide radical ions (O₂^.-) and hydroxyl radicals (·OH), effective in the decomposition of surface-adsorbed dye. However, HTN are non-magnetic which create hurdle in their effective separation from the treated aqueous solution. To overcome this issue, magnetic nanocomposites (HTNF) composed of HTN and maghemite (γ-Fe₂O₃) nanoparticles have been processed by subjecting the core-shell magnetic photocatalyst consisting of γ-Fe₂O₃/silica (SiO₂)/titania (TiO₂), having varying amounts of TiO₂ in the shell to the hydrothermal conditions. HTNF-5 magnetic nanocomposite consisting of 31 wt% H₂Ti₃O₇, typically having nanotube morphology with the highest specific surface area (133 m² g^-1) and pore-volume (0.22 cm³ g^-1), exhibits the highest capacity (74 mg g^-1) for the adsorption of cationic methylene blue (MB) dye from an aqueous solution involving the electrostatic attraction mechanism and pseudo-second-order kinetics. Very fast magnetic separation followed by regeneration of HTNF-5 magnetic nanocomposite has been demonstrated via non-radiation driven H₂O₂ activation. It has been ascertained for the first time that the underlying mechanism of dye decomposition involves the synergy effect between the constituents of HTNF magnetic nanocomposite.

Periodontal health status and implication of periodic acid-Schiff diastase - a key in exfoliative cytology among diabetics mellitus patients: A case-control study

Objectives:

The objectives of the study are: (i) To determine if periodic acid–Schiff (PAS)-Diastase is an effective tool to diagnose DM noninvasively, (ii) to use three different types of staining procedures to identify the staining pattern over the exfoliated cells of normal and diabetic patients, (iii) to study the periodontal health status of DM and normal subjects.

Materials and Methods:

Basic questions regarding the demographic data were asked, following which community periodontal index (CPI) was recorded. Oral smears were collected from clinically normal buccal mucosa of 150 patients using wooden tongue spatulas. The subjects were asked to gargle their mouth with water and the wooden spatula was scraped at the site from buccal mucosa. The smears were spread evenly on a dry clean glass slide and fixed immediately with absolute ethyl alcohol. Three slides were prepared for each of the patients. PAS, PAS with diastase digestion, and Papanicolaou staining were performed and examined under a microscope.

Results:

Average CPI for study subjects was 3.2 and control subjects was 2.1. The average loss of attachment was 1.1 in the study group and 0.2 in the control group (P - 0.00) and the result are statistically highly significant. All the 150 cases (100%) were positive for PAS staining, while PAS-diastase (PAS-D) staining showed positivity only for normal subjects and was negative (100%) in the diabetic group (P - 0.00) and the result are statistically highly significant.

Conclusions:

Results of our study showed that exfoliative cytology of the oral cavity, when stained with PAS and PAS-D, can be used as an effective screening and diagnostic tool for DM patients.

Effects of pulmonary exposure to chemically-distinct welding fumes on neuroendocrine markers of toxicity

Exposure to welding fumes may result in disorders of the pulmonary, cardiovascular, and reproductive systems. Welders are also at a greater risk of developing symptoms similar to those seen in individuals with idiopathic Parkinson's disease. In welders, there are studies that suggest that alterations in circulating prolactin concentrations may be indicative of injury to the dopamine (DA) neurons in the substantia nigra. The goal of these studies was to use an established model of welding particulate exposure to mimic the effects of welding fume inhalation on reproductive functions. Since previous investigators suggested that changes in circulating prolactin may be an early marker of DA neuron injury, movement disorders, and reproductive dysfunction, prolactin, hypothalamic tyrosine hydroxylase (TH) levels (a marker of DA synthesis), and other measures of hypothalamic-pituitary-gonadal (HPG) function were measured after repetitive instillation of welding fume particulates generated by flux core arc-hard surfacing (FCA-HS), manual metal arc-hard surfacing (MMA-HS) or gas metal arc-mild steel (GMA-MS) welding, or manganese chloride (MnCl₂). Exposure to welding fume particulate resulted in the accumulation of various metals in the pituitary and testes of rats, along with changes in hypothalamic TH and serum prolactin levels. Exposure to particulates with high concentrations of soluble manganese (Mn) appeared to exert the greatest influence on TH activity levels and serum prolactin concentrations. Thus, circulating prolactin levels may serve as a biomarker for welding fume/Mn-induced neurotoxicity. Other reproductive measures were collected, and these data were consistent with epidemiological findings that prolactin and testosterone may serve as biomarkers of welding particulate induced DA neuron and reproductive dysfunction.

Ion-exchange bonded H2Ti3O7 nanosheets-based magnetic nanocomposite for dye removal via adsorption and its regeneration via synergistic activation of persulfate

Magnetic nanocomposite consisting of H₂Ti₃O₇ nanosheets and γ-Fe₂O₃ nanoparticles has been synthesized via ion-exchange bond formation and utilized for dye-removal application involving its regeneration through synergistic persulfate activation.

Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis

Prion diseases are transmissible neurodegenerative diseases that arise due to conformational change of normal, cellular prion protein (PrPC) to protease-resistant isofrom (rPrPSc). Deposition of misfolded PrpSc proteins leads to an alteration of many signaling pathways that includes immunological and apoptotic pathways. As a result, this culminates in the dysfunction and death of neuronal cells. Earlier works on transcriptomic studies have revealed some affected pathways, but it is not clear which is (are) the prime network pathway(s) that change during the disease progression and how these pathways are involved in crosstalks with each other from the time of incubation to clinical death. We perform network analysis on large-scale transcriptomic data of differentially expressed genes obtained from whole brain in six different mouse strain-prion strain combination models to determine the pathways involved in prion diseases, and to understand the role of crosstalks in disease propagation. We employ a notion of differential network centrality measures on protein interaction networks to identify the potential biological pathways involved. We also propose a crosstalk ranking method based on dynamic protein interaction networks to identify the core network elements involved in crosstalk with different pathways. We identify 148 DEGs (differentially expressed genes) potentially related to the prion disease progression. Functional association of the identified genes implicates a strong involvement of immunological pathways. We extract a bow-tie structure that is potentially dysregulated in prion disease. We also propose an ODE model for the bow-tie network. Predictions related to diseased condition suggests the downregulation of the core signaling elements (PI3Ks and AKTs) of the bow-tie network. In this work, we show using transcriptomic data that the neuronal dysfunction in prion disease is strongly related to the immunological pathways. We conclude that these immunological pathways occupy influential positions in the PFNs (protein functional networks) that are related to prion disease. Importantly, this functional network involvement is prevalent in all the five different mouse strain-prion strain combinations that we studied. We also conclude that the dysregulation of the core elements of the bow-tie structure, which belongs to PI3K-Akt signaling pathway, leads to dysregulation of the downstream components corresponding to other biological pathways.

Antibiotic overuse and Clostridium difficile infections: the Indian paradox and the possible role of dietary practices

Antibiotic abuse is rampant in India, such that one may expect to see an increase of Clostridium difficile infections (CDI). However, we found that the incidence of CDI in India (1.67%) is no different from that reported in USA (1.6%) using similar techniques of detection (polymerase chain reaction test). We offer a possible explanation for this paradox. It is likely that a diet rich in fiber, yogurt, and possibly turmeric may have a protective role in decreasing the incidence of CDIs in India.

Retrospective Analysis of Ossifying Fibroma of Jaw Bones Over a Period of 10 Years with Literature Review

OBJECTIVE

The purpose of this retrospective analysis is to document and discuss the features, treatment rendered and result of 25 histologically proven cases of ossifying fibromas of jaw bones operated by a single surgeon over a period of 10 years.

MATERIALS AND METHODS

The records of ossifying fibroma were obtained from the archives of Oral and Maxillofacial Surgery at Maulana Azad Institute of Dental Sciences (MAIDS) from 2001 to 2011. Only those cases were included in the study where definitive surgery was performed based on clinical, radiological & histopathological features.

RESULTS

Twenty-five patients were analyzed with a final diagnosis of ossifying fibroma comprising of 14 males (56 %) and 11 females (44 %). The age range was 11-45 years with a mean of 24.12 years. Mandible was involved in 72 % and maxilla in 28 % cases with a predominance of mandibular posterior [19 (76 %)] cases. The study showed similar findings in regard to clinical, radiographic & histological features of ossifying fibroma as compared to other studies. It also showed that the treatment rendered in the form of eneucleation, curettage or resection of the lesion depending on its stage and extent were adequate, as no recurrence has been reported till date.

CONCLUSION

Enucleation is preferred in small and well demarcated lesions. Curettage should be done in relatively large lesions with ill defined borders, not involving basal bone of mandible or cortical perforation. Resection should be reserved for aggressive and extensive cases with involvement of basal bone or perforation of cortices.

A detailed modular analysis of heat-shock protein dynamics under acute and chronic stress and its implication in anxiety disorders

Physiological and psychological stresses cause anxiety disorders such as depression and post-traumatic stress disorder (PTSD) and induce drastic changes at a molecular level in the brain. To counteract this stress, the heat-shock protein (HSP) network plays a vital role in restoring the homeostasis of the system. To study the stress-induced dynamics of heat-shock network, we analyzed three modules of the HSP90 network—namely trimerization reactions, phosphorylation–dephosphorylation reactions, and the conversion of HSP90 from an open to a closed conformation—and constructed a corresponding nonlinear differential equation model based on mass action kinetics laws. The kinetic parameters of the model were obtained through global optimization, and sensitivity analyses revealed that the most sensitive parameters are the kinase and phosphatase that drive the phosphorylation–dephosphorylation reactions. Bifurcation analysis carried out with the estimated kinetic parameters of the model with stress as bifurcation parameter revealed the occurrence of “mushroom”, a type of complex dynamics in which S-shaped and Z-shaped hysteretic bistable forms are present together. We mapped the molecular events responsible for generating the mushroom dynamics under stress and interpreted the occurrence of the S-shaped hysteresis to a normal level of stress, and the Z-shaped hysteresis to the HSP90 variations under acute and chronic stress in the fear conditioned system, and further, we hypothesized that this can be extended to stress-related disorders such as depression and PTSD in humans. Finally, we studied the effect of parameter variations on the mushroom dynamics to get insight about the role of phosphorylation–dephosphorylation parameters in HSP90 network in bringing about complex dynamics such as isolas, where the stable steady states in a bistable system are isolated and separated from each other and not connected by an unstable steady state.

Modeling cortisol dynamics in the neuro-endocrine axis distinguishes normal, depression, and post-traumatic stress disorder (PTSD) in humans

Cortisol, secreted in the adrenal cortex in response to stress, is an informative biomarker that distinguishes anxiety disorders such as major depression and post-traumatic stress disorder (PTSD) from normal subjects. Yehuda et al. proposed a hypothesis that, in humans, the hypersensitive hypothalamus-pituitary-adrenal (HPA) axis is responsible for the occurrence of differing levels of cortisol in anxiety disorders. Specifically, PTSD subjects have lower cortisol levels during the late subjective night in comparison to normal subjects, and this was assumed to occur due to strong negative feedback loops in the HPA axis. In the present work, to address this hypothesis, we modeled the cortisol dynamics using nonlinear ordinary differential equations and estimated the kinetic parameters of the model to fit the experimental data of three categories, namely, normal, depressed, and PTSD human subjects. We concatenated the subjects (n = 3) in each category and created a model subject (n = 1) without considering the patient-to-patient variability in each case. The parameters of the model for the three categories were simultaneously obtained through global optimization. Bifurcation analysis carried out with the optimized parameters exhibited two supercritical Hopf points and, for the choice of parameters, the oscillations were found to be circadian in nature. The fitted kinetic parameters indicate that PTSD subjects have a strong negative feedback loop and, as a result, the predicted oscillating cortisol levels are extremely low at the nadir in contrast to normal subjects, albeit within the endocrinologic range. We also simulated the phenotypes for each of the categories and, as observed in the clinical data of PTSD patients, the simulated cortisol levels are consistently low at the nadir, and correspondingly the negative feedback was found to be extremely strong. These results from the model support the hypothesis that high stress intensity and strong negative feedback loop may cause hypersensitive neuro-endocrine axis that results in hypocortisolemia in PTSD.

PTSD is an anxiety disorder that occurs among persons exposed to a traumatic event involving life threat and injury. This is a co-morbid psychiatric disorder that occurs along with depression. Cortisol is an informative endocrine biomarker that can distinguish PTSD from other co-morbid disorders. In comparison to normal subjects, hypocortisolemia was observed during the night in PTSD, while hypercortisolemia was observed in depressed subjects. From analyzing the clinical data, Yehuda et al. hypothesized that hypocortisolemia in PTSD was due to the strong negative feedback loop operating in the neuroendocrine axis under severe stress. We complemented this hypothesis by constructing a mathematical model for cortisol dynamics in HPA axis and estimated the kinetic parameters that fitted the cortisol time series obtained from the clinical data of normal, depressed and PTSD patients. The parameters obtained from the simulated phenotypes also strongly support the hypothesis that, due to disruptive negative feedback loops, cortisol levels are different in normal, PTSD and depressed subjects during the night. Importantly, the model predicted the transitions from normal to various diseased states, and these transitions were shown to occur due to changes in the strength of the negative feedback loop and the stress intensity in the neuro-endocrine axis.

Applications of Self-Organising Map (SOM) for prioritisation of endemic zones of filariasis in Andhra Pradesh, India

Entomological and epidemiological data of Lymphatic Filariasis (LF) was collected from 120 villages of four districts of Andhra Pradesh, India. Self-Organising Maps (SOMs), data-mining techniques, was used to classify and prioritise the endemic zones of filariasis. The results show that, SOMs classified all the villages into three major clusters by considering the data of Microfilaria (MF) rate, infection, infectivity rate and Per Man Hour (PMH). By considering the patterns of cluster, appropriate decision can be drawn for each parameter that is responsible for disease transmission of filariasis. Hence, SOM will certainly be a suitable tool for management of filariasis. The detailed application of SOM is discussed in this paper.

Structural analysis to determine the core of hypoxia response network

The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests that the reversibility of the reactions are not important for the essential functionality. The core network is determined to be the union of the three reduced individual modules. The structural analysis results are confirmed by numerical integration of the differential equations induced by the individual modules as well as their composition. The structural analysis leads also to a coarse network structure highlighting the structural principles inherent in the three functional modules. Importantly, our analysis identifies the fragile node in this robust network without which the switch-like behavior is shown to be completely absent.

Localised retroperitoneal amyloidosis mimicking retroperitoneal fibrosis: a rare cause of obstructive uropathy

Primary localised amyloidosis involving the retroperitoneum is a rare disease. We report a 71-year-old diabetic man who presented with generalised fatigue, malaise and elevated serum creatinine. Investigations confirmed obstructive uropathy secondary to a retroperitoneal mass behind the urinary bladder, causing extrinsic compression of both the ureters, resulting in bilateral hydroureteronephrosis. Following initial bilateral percutaneous nephrostomies to stabilise renal function, a computed tomography-guided biopsy of the pelvic lesion which was done, was suggestive of amyloidosis. We present this case due to the rarity of localised retroperitoneal amyloidosis as a cause of obstructive uropathy.

Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans

The two element mutual activation and inhibitory positive feedback loops are a common motifs that occur in many biological systems in both isolated and interlocked form, as for example, in the cell division cycle and thymus differentiation in eukaryotes. The properties of three element interlocked positive feedback loops that embeds both mutual activation and inhibition are studied in depth for their bistable properties by performing bifurcation and stochastic simulations. Codimension one and two bifurcations reveal important properties like robustness to parameter variations and adaptability under various conditions by its ability to fine tune the threshold to a wide range of values and to maintain a wide bistable regime. Furthermore, we show that in the interlocked circuit, mutual inhibition controls the decision to switch from OFF to ON state, while mutual activation enforces the decision. This view is supported through a concrete biological example Candida albicans, a human fungal pathogen that can exist in two distinctive cell types; one in the default white state and the other in an opaque form. Stochastic switching between these two forms takes place due to the epigenetic alternation induced by the transcriptional regulators in the circuit, albeit without any rearrangement of the nuclear chromosomes. The transcriptional regulators constitute interlocked mutual activation and inhibition feedback circuits that provide adaptable threshold and wide bistable regime. These positive feedback loops are shown to be responsible for robust noise induced transitions without chattering, persistence of particular phenotypes for many generations and selective exhibition of one particular form of phenotype when mutated. Finally, we propose for synthetic biology constructs to use interlocked positive feedback loops instead of two element positive feedback loops because they are better controlled than isolated mutual activation and mutual inhibition feedback circuits.

Complex dynamics in the Oregonator model with linear delayed feedback

The Belousov-Zhabotinsky (BZ) reaction can display a rich dynamics when a delayed feedback is applied. We used the Oregonator model of the oscillating BZ reaction to explore the dynamics brought about by a linear delayed feedback. The time-delayed feedback can generate a succession of complex dynamics: period-doubling bifurcation route to chaos; amplitude death; fat, wrinkled, fractal, and broken tori; and mixed-mode oscillations. We observed that this dynamics arises due to a delay-driven transition, or toggling of the system between large and small amplitude oscillations, through a canard bifurcation. We used a combination of numerical bifurcation continuation techniques and other numerical methods to explore the dynamics in the strength of feedback-delay space. We observed that the period-doubling and quasiperiodic route to chaos span a low-dimensional subspace, perhaps due to the trapping of the trajectories in the small amplitude regime near the canard; and the trapped chaotic trajectories get ejected from the small amplitude regime due to a crowding effect to generate chaotic-excitable spikes. We also qualitatively explained the observed dynamics by projecting a three-dimensional phase portrait of the delayed dynamics on the two-dimensional nullclines. This is the first instance in which it is shown that the interaction of delay and canard can bring about complex dynamics.

Question 7: the first units of life were not simple cells

Five common assumptions about the first cells are challenged by the pre-biotic ecology model and are replaced by the following propositions: firstly, early cells were more complex, more varied and had a greater diversity of constituents than modern cells; secondly, the complexity of a cell is not related to the number of genes it contains, indeed, modern bacteria are as complex as eukaryotes; thirdly, the unit of early life was an 'ecosystem' rather than a 'cell'; fourthly, the early cell needed no genes at all; fifthly, early life depended on non-covalent associations and on catalysts that were not confined to specific reactions. We present here the outlines of a theory that connects findings about modern bacteria with speculations about their origins.

Paecilomyces pyelonephritis in a patient with urolithiasis

Fungal organisms are increasingly implicated in nosocomial urinary tract infections. Although Candida, Mucor and Aspergillus are the most commonly identified species, rare fungi are also occasionally observed to infect humans. Misidentification of the organism could result in treatment with an inappropriate antifungal agent, which could result in a florid fungal pyelonephritis. We report the occurrence of fungal pyelonephritis in a patient with stone disease secondary to Paecilomyces variotii. This case report emphasizes the need for an accurate identification of the organism and early and appropriate treatment.

Compositional complementarity and prebiotic ecology in the origin of life

We hypothesize that life began not with the first self-reproducing molecule or metabolic network, but as a prebiotic ecology of co-evolving populations of macromolecular aggregates (composomes). Each composome species had a particular molecular composition resulting from molecular complementarity among environmentally available prebiotic compounds. Natural selection acted on composomal species that varied in properties and functions such as stability, catalysis, fission, fusion and selective accumulation of molecules from solution. Fission permitted molecular replication based on composition rather than linear structure, while fusion created composomal variability. Catalytic functions provided additional chemical novelty resulting eventually in autocatalytic and mutually catalytic networks within composomal species. Composomal autocatalysis and interdependence allowed the Darwinian co-evolution of content and control (metabolism). The existence of chemical interfaces within complex composomes created linear templates upon which self-reproducing molecules (such as RNA) could be synthesized, permitting the evolution of informational replication by molecular templating. Mathematical and experimental tests are proposed.

Bedside emergency ultrasonographic diagnosis of diaphragmatic rupture in blunt abdominal trauma

Abdominal injury from significant blunt trauma can include injury to bowel, kidneys, liver, and spleen. In approximately 5% of all injuries one of the diaphragms is ruptured. Diaphragmatic rupture may not be easily detected and this can lead to significant morbidity and even mortality. Rupture may be suggested on chest X-ray film especially with abnormal nasogastric tube location but the accuracy of this method is modest only. Abdominal computed tomography is not accurate and magnetic resonance imaging, although very sensitive and specific, is not feasible in most trauma situations. Surgeons have often resorted to exploratory laparotomy or laparoscopy to make the diagnosis. Although not typically part of the basic Focused Abdominal Sonography for Trauma (FAST) examination, ultrasonographic diagnosis of diaphragmatic rupture is possible with little added time to the examination. We present 3 cases of diaphragmatic rupture discovered shortly after the patients' arrival, on initial trauma evaluation with the FAST. A discussion of previous literature and ultrasound technique for diagnosis follows the cases.