Combined genetic effects of EGLN1 and VWF modulate thrombotic outcome in hypoxia revealed by Ayurgenomics approach.

BACKGROUND: Extreme constitution "Prakriti" types of Ayurveda exhibit systemic physiological attributes. Our earlier genetic study has revealed differences in EGLN1, key modulator of hypoxia axis between Prakriti types. This was associated with differences in high altitude adaptation and susceptibility to high altitude pulmonary edema (HAPE). In this study we investigate other molecular differences that contribute to systemic attributes of Prakriti that would be relevant in predictive marker discovery. METHODS: Genotyping of 96 individuals of the earlier cohort was carried out in a panel of 2,800 common genic SNPs represented in Indian Genomic Variation Consortium (IGVC) panel from 24 diverse populations. Frequency distribution patterns of Prakriti differentiating variations (FDR correction P < 0.05) was studied in IGVC and 55 global populations (HGDP-CEPH) panels. Genotypic interactions between VWF, identified from the present analysis, and EGLN1 was analyzed using multinomial logistic regression in Prakriti and Indian populations from contrasting altitudes. Spearman's Rank correlation was used to study this genotypic interaction with respect to altitude in HGDP-CEPH panel. Validation of functional link between EGLN1 and VWF was carried out in a mouse model using chemical inhibition and siRNA studies. RESULT: Significant differences in allele frequencies were observed in seven genes (SPTA1, VWF, OLR1, UCP2, OR6K3, LEPR, and OR10Z1) after FDR correction (P < 0.05). A non synonymous variation (C/T, rs1063856) associated with thrombosis/bleeding susceptibility respectively, differed significantly between Kapha (C-allele) and Pitta (T-allele) constitution types. A combination of derived EGLN1 allele (HAPE associated) and ancestral VWF allele (thrombosis associated) was significantly high in Kapha group compared to Pitta (p < 10(-5)). The combination of risk-associated Kapha alleles was nearly absent in natives of high altitude. Inhibition of EGLN1 using (DHB) and an EGLN1 specific siRNA in a mouse model lead to a marked increase in vWF levels as well as pro-thrombotic phenotype viz. reduced bleeding time and enhanced platelet count and activation. CONCLUSION: We demonstrate for the first time a genetic link between EGLN1 and VWF in a constitution specific manner which could modulate thrombosis/bleeding susceptibility and outcomes of hypoxia. Integration of Prakriti in population stratification may help assemble common variations in key physiological axes that confers differences in disease occurrence and patho-phenotypic outcomes.

Recurrent pustular eruption masquerading as pustular psoriasis in Netherton syndrome.

We report a unique presentation of Netherton syndrome with recurrent pustular eruptions leading to an erroneous diagnosis of infantile pustular psoriasis. Light microscopy of eyebrow hair showed trichorrhexis invaginata, consistent with Netherton syndrome.

Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27.

BACKGROUND: Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. Thus, it is highly required to consider systems biological approaches where T. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological characteristics under such harsh conditions. RESULTS: We reconstructed a genome-scale metabolic model of T. thermophilus, iTT548, the first ever large-scale network of a thermophilic bacterium, accounting for 548 unique genes, 796 reactions and 635 unique metabolites. Our initial comparative analysis of the model with Escherichia coli has revealed several distinctive metabolic reactions, mainly in amino acid metabolism and carotenoid biosynthesis, producing relevant compounds to retain the cellular membrane for withstanding high temperature. Constraints-based flux analysis was, then, applied to simulate the metabolic state in glucose minimal and amino acid rich media. Remarkably, resulting growth predictions were highly consistent with the experimental observations. The subsequent comparative flux analysis under different environmental conditions highlighted that the cells consumed branched chain amino acids preferably and utilized them directly in the relevant anabolic pathways for the fatty acid synthesis. Finally, gene essentiality study was also conducted via single gene deletion analysis, to identify the conditional essential genes in glucose minimal and complex media. CONCLUSIONS: The reconstructed genome-scale metabolic model elucidates the phenotypes of T. thermophilus, thus allowing us to gain valuable insights into its cellular metabolism through in silico simulations. The information obtained from such analysis would not only shed light on the understanding of physiology of thermophiles but also helps us to devise metabolic engineering strategies to develop T. thermophilus as a thermostable microbial cell factory.

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.

It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P < 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema.

Hypoxia response in asthma: differential modulation on inflammation and epithelial injury.

Oxygen-sensing prolyl-hydroxylase (PHD)-2 negatively regulates hypoxia-inducible factor (HIF)1-α and suppresses the hypoxic response. Hypoxia signaling is thought to be proinflammatory but also attenuates cellular injury and apoptosis. Although increased hypoxic response has been noted in asthma, its functional relevance is unknown. The objectives of this study were to dissect the mechanisms and role of the hypoxic response in asthma pathophysiology. Experimental studies were conducted in mice using acute and chronic allergic models of asthma. The hypoxic response in allergically inflamed lungs was modulated by using pharmacologic PHD inhibitors (ethyl-3-4-dihydroxybenzoic acid [DHB], 1-10 mg/kg) or siRNA-mediated genetic knockdowns. Increased hypoxia response led to exacerbation of the asthma phenotype, with HIF-1α knockdown being beneficial. Chronically inflamed lungs from mice treated with 10 mg/kg DHB showed diffuse up-regulation of the hypoxia response, severe airway remodeling, and inflammation. Fatal asphyxiation during methacholine challenge was noted. However, bronchial epithelium restricted up-regulation of the hypoxia response seen with low-dose DHB (1 mg/kg) reduced epithelial injury and attenuated the asthmatic phenotype. Up-regulation of the hypoxia response was associated with increased expression of CX3CR1, a lymphocyte survival factor, and increased inflammatory cell infiltrate. This study shows that an exaggerated hypoxia response may contribute to airway inflammation, remodeling, and the development of asthma. However, the hypoxia response may also be protective of epithelial apoptosis at lower levels, and the net effects of modulating the hypoxia response may vary based on the context.

Primary Pure Large-Cell Neuroendocrine Carcinoma of the Ovary: A Rare Case Report.

Primary pure large-cell neuroendocrine carcinoma is a rare entity with 17 cases reported till now. A 48-year-old, Para6 Live4, postmenopausal woman presented with complaints of pain abdomen, constipation for 6 months, and postmenopausal bleeding for 1 month. On per abdominal examination, an irregular, hard, fixed, and tender mass was felt in the pelvis corresponding to 32 weeks size gravid uterus. Her magnetic resonance imaging findings were suggestive of a large abdominopelvic mass of size 10.2 cm × 12.7 cm × 14.2 cm with inferior extension into the left adnexa and 3.1 cm × 2.2 cm × 2.1 cm right adnexal mass. Debulking surgery was done. The intraoperative findings were of a large abdominopelvic mass adhered to the sigmoid colon and retroperitoneal space. Histopathological and immunohistochemistry findings were suggestive of bilateral large-cell neuroendocrine carcinoma of ovaries with strong positive for Bcl2, CD56, NSE, PR, and P53. The patient was started on tablet etoposide as adjuvant treatment. After 5 months of primary surgery, contrast-enhanced computed tomography of the chest, abdomen, and pelvis revealed recurrence. She succumbed to her illness 6 months after primary surgery. Owing to its rarity and difficulty in diagnosis, it is suggested that all such cases should be registered at national level and critically analyzed to find the high risk and associated prognostic factors.

Disseminated lupus vulgaris.

A 28-year-old woman presented with reddish raised, shiny lesions over the face and ears present for the past 3 years. Four years ago, she developed in her left axilla a nodule that became fluctuant and tender, which ruptured to discharge seropurulent material. It subsided after the patient had received antibiotics for 6 months, leaving puckered scarring. There was no history of antituberculous treatment. After 1 year, she developed papulonodular lesions on her face, nose, and ears. There was now a history of malaise, fever, dry cough, and anorexia and weight loss for the past 2 months. The patient was fully vaccinated in childhood, including against varicella infection. The general physical examination revealed lymphadenopathy involving cervical, axillary, and inguinal lymph nodes 0.5 x 0.5 cm to 1 x 1.5 cm, firm in consistency, and nontender. They were discrete except in the left axilla where multiple matted lymph nodes were present with overlying scarring and a papule. Her systemic examination was normal. Cutaneous examination showed a shiny erythematous plaque 3x2 cm with central atrophy and scarring on the face (Figure). It was comprised of multiple shiny nontender soft papules arranged in annular configuration. Similar discrete papules and nodules with adherent fine scaling were seen bilaterally on the alar prominence of the nose, lower lip, and post-auricular area. On diascopy, apple jelly nodules were seen. The hemogram, liver function tests, and renal function tests were normal, except for an elevated erythrocyte sedimentation rate. The Mantoux test showed erythema and an induration of 20 x 20 cm. A posteroanterior view on the chest x-ray showed fibrotic changes suggestive of pulmonary tuberculosis. Ultrasonography of the abdomen and pelvis showed no tubercular foci. Human immunodeficiency virus serology by enzyme-linked immunosorbent assay with 3 different kits was nonreactive. Histopathology from a nodule showed a focally thinned-out epidermis with follicular plugging and multiple epithelioid cell granulomas, rimmed by lymphocytes in the deeper portion of the dermis, mainly peri-appendageal. Stain for acid-fast bacteria was negative. Cultures from the skin lesions were negative. The patient was diagnosed as having lupus vulgaris with multiple lesions of varying morphology at different sites with pulmonary tuberculosis and healed lymph node involvement.

Sub-cellular localization of suppressor proteins of tomato leaf curl New Delhi virus.

Tomato leaf curl New Delhi virus (ToLCNDV), a bipartite begomovirus, is the most important among the 14 species of begomoviruses infecting tomato in Indian subcontinent. Begomovirus is known to  evade RNA silencing of host plants through suppressor proteins. However, in case of ToLCNDV, the suppressor proteins have not been studied well. The objective of the study is to know the sub-cellular localization of three suppressor proteins encoded by AV2, AC2 and AC4 ORFs of ToLCNDV in Nicotiana benthamiana. AV2, AC2 and AC4 ORFs of ToLCNDV were  cloned and sequenced (accession numbers MW423574, MW423576, MW423575, respectively) from a ToLCNDV isolate characterized earlier (accession number MW429271) and GFP tagged constructs were prepared in a plant expressing binary vector pEarleygate103. Bioinformatics analysis using Peptide 2.0 server predicted that all these proteins have more basic amino acid residues then acidic amino acid and AV2 protein has more hydrophobic amino acid residues. ScanProsite server predicted presence of different fuctional motifs in these proteins amongst which presence of kinase motif was observed in all of them. Virus mPLoc server predicted their subcellular localization. The suppressor gene constructs were agroinfiltrated on to leaves of one month old N. benthamiana plants and their subcellular localization has been studied through confocal microscopy. Results have shown that AV2 localizes in the host cell membrane and nucleus, AC2 in the nucleus and AC4 in the host cell membrane. Earlier reports with other begomoviruses also showed similar localization behaviour of these suppressor protein except AV2, where it was shown to be present in cytoplasm. Such localization study will help understand the mechanism of their suppression activity.

Rosai-Dorfman disease: a case with lymphadenopathy and liver involvement.

Rosai-Dorfman disease (RDD), originally described as sinus histiocytosis with massive lymphadenopathy, is a rare histiocytic proliferative disorder with a distinctive microscopic appearance. Formerly thought to be a disease process limited to lymph nodes, RDD has now been reported in many organ systems like bone, skin and soft tissue, central nervous system, eye and orbit, and upper respiratory tract. Here we report a case of RDD with hepatic involvement, which is even more rare.

Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda.

BACKGROUND: Ayurveda is an ancient system of personalized medicine documented and practiced in India since 1500 B.C. According to this system an individual's basic constitution to a large extent determines predisposition and prognosis to diseases as well as therapy and life-style regime. Ayurveda describes seven broad constitution types (Prakritis) each with a varying degree of predisposition to different diseases. Amongst these, three most contrasting types, Vata, Pitta, Kapha, are the most vulnerable to diseases. In the realm of modern predictive medicine, efforts are being directed towards capturing disease phenotypes with greater precision for successful identification of markers for prospective disease conditions. In this study, we explore whether the different constitution types as described in Ayurveda has molecular correlates. METHODS: Normal individuals of the three most contrasting constitutional types were identified following phenotyping criteria described in Ayurveda in Indian population of Indo-European origin. The peripheral blood samples of these individuals were analysed for genome wide expression levels, biochemical and hematological parameters. Gene Ontology (GO) and pathway based analysis was carried out on differentially expressed genes to explore if there were significant enrichments of functional categories among Prakriti types. RESULTS: Individuals from the three most contrasting constitutional types exhibit striking differences with respect to biochemical and hematological parameters and at genome wide expression levels. Biochemical profiles like liver function tests, lipid profiles, and hematological parameters like haemoglobin exhibited differences between Prakriti types. Functional categories of genes showing differential expression among Prakriti types were significantly enriched in core biological processes like transport, regulation of cyclin dependent protein kinase activity, immune response and regulation of blood coagulation. A significant enrichment of housekeeping, disease related and hub genes were observed in these extreme constitution types. CONCLUSION: Ayurveda based method of phenotypic classification of extreme constitutional types allows us to uncover genes that may contribute to system level differences in normal individuals which could lead to differential disease predisposition. This is a first attempt towards unraveling the clinical phenotyping principle of a traditional system of medicine in terms of modern biology. An integration of Ayurveda with genomics holds potential and promise for future predictive medicine.

Intra-abdominal cavernous lymphangiomatosis in Siamese twins: a case report.

Lymphangioma is a benign tumor like condition which is a developmental anomaly, involving any site but rarely involves retroperitoneum and abdomen (< 5%). Intraabdominal lymphangiomatosis is an even rarer entity that too occurring in a siamese twins. No such reports have been found in literature, although other congenital anomalies do coexist in Siamese twins and have been reported such as biliary tract and respiratory tract anomalies.

Recapitulation of Ayurveda constitution types by machine learning of phenotypic traits.

In Ayurveda system of medicine individuals are classified into seven constitution types, "Prakriti", for assessing disease susceptibility and drug responsiveness. Prakriti evaluation involves clinical examination including questions about physiological and behavioural traits. A need was felt to develop models for accurately predicting Prakriti classes that have been shown to exhibit molecular differences. The present study was carried out on data of phenotypic attributes in 147 healthy individuals of three extreme Prakriti types, from a genetically homogeneous population of Western India. Unsupervised and supervised machine learning approaches were used to infer inherent structure of the data, and for feature selection and building classification models for Prakriti respectively. These models were validated in a North Indian population. Unsupervised clustering led to emergence of three natural clusters corresponding to three extreme Prakriti classes. The supervised modelling approaches could classify individuals, with distinct Prakriti types, in the training and validation sets. This study is the first to demonstrate that Prakriti types are distinct verifiable clusters within a multidimensional space of multiple interrelated phenotypic traits. It also provides a computational framework for predicting Prakriti classes from phenotypic attributes. This approach may be useful in precision medicine for stratification of endophenotypes in healthy and diseased populations.

Concurrent nonfunctional paraganglioma of the retroperitoneum and urinary bladder: A case report with literature review.

Paragangliomas are the neuroendocrine tumors which arise from the chromaffin cell. Tumors arising from the adrenal medulla are known as pheochromocytomas, while others originating from the extra-adrenal site are known as extra-adrenal paragangliomas. Paraganglioma can be multifocal which can arise synchronously or metachronously. Paragangliomas are less functionally active than the pheochromocytomas; they secrete noradrenaline and rarely dopamine, while adrenal pheochromocytomas secrete adrenaline or nor-adrenaline. Nonfunctional multifocal paragangliomas are very rare. We report a case of a 45-year-old female with multifocal nonfunctional paragangliomas of the retroperitoneum and urinarybladder which were surgically removed, and the diagnosis was confirmed on histopathology.

Primary tuberculosis of the clavicle.

Tuberculosis of the clavicle is a rare lesion, accounting for less than 1% of all osteoarticular tuberculosis. The lesion has been described in a few case reports. The lesion can have a varied presentation, ranging from dull, aching pain to bony swelling and a draining sinus. The rarity of the lesion, its nonspecific symptoms, and its striking resemblance to common cystic conditions such as bone tumors and metabolic conditions such as rickets make diagnosis difficult. The authors describe a series of 17 patients with primary tuberculosis of the clavicle. Radiographs and magnetic resonance images were obtained for all patients, and a preliminary diagnosis was made on the basis of clinical features and the results of erythrocyte sedimentation rate, C-reactive protein, and Mantoux tests. Erythrocyte sedimentation rate was uniformly elevated. Radiographs showed diffused thickening and honeycombing, eccentric expansile lytic lesions with surrounding osteopenia, or sequestration not unlike pyogenic infection. Magnetic resonance imaging is useful for determining the extent of the lesion and soft tissue involvement. The radiological and laboratory findings provided complementary information. The diagnosis was confirmed on biopsy material that was analyzed with histopathology, pus culture and sensitivities, gram stain, acid-fast stain, and cultures on Löwenstein-Jensen medium. Patients were treated with multidrug antitubercular chemotherapy for 18 months and were assessed on pre- and posttreatment radiology, erythrocyte sedimentation rate, and University of California, Los Angeles (UCLA) shoulder rating scale. The results of conservative management of tubercular osteomyelitis were uniformly good, and all patients recovered well.

In silico modeling and evaluation of Gordonia alkanivorans for biodesulfurization.

The genus Gordonia is well known for its catabolic diversity and ability to transform several compounds including the various recalcitrant polyaromatic sulfur heterocycles (PASHs) found in the fossil fuels. In fact, some strains offer the unique ability to desulfurize even benzothiophene (BT) and other thiophenic compounds, which most of the commonly studied rhodococci strains cannot. In this work, we present the first genome scale metabolic model for G. alkanivorans, a desulfurizing strain, to enable a holistic study of its metabolism and comparison with R. erythropolis. Our model consists of 881 unique metabolites and 922 reactions associated with 568 ORFs/genes and 544 unique enzymes. It successfully predicts the growth rates from experimental studies and quantitatively elucidates the pathways for the desulfurization of the commonly studied sulfur compounds, namely dibenzothiophene (DBT) and benzothiophene (BT). Using our model, we identify the minimal media for G. alkanivorans, and show the significant effect of carbon sources on desulfurization with ethanol as the best source. Our model shows that the sulfur-containing amino acids such as cysteine and methionine decrease desulfurization activity, and G. alkanivorans prefers BT over DBT as a sulfur source. It also suggests that this preference may be driven by the lower NADH requirements for BT metabolism rather than the higher affinity of the transport system for BT. Our in silico comparison of R. erythropolis and G. alkanivorans suggests the latter to be a better desulfurizing strain due to its versatility for both BT and DBT, higher desulfurization activity, and higher growth rate.

Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis.

Rhodococcus erythropolis has been widely studied for desulfurization. However, activity levels required for commercial application have not been achieved. A major limitation of the current work in biodesulfurization is inadequate information regarding sulfur metabolism generally, and in particular the metabolism of the sulfur obtained from dibenzothiophene (DBT) metabolism via the 4S pathway. In this work, we have investigated the possible routes taken by the sulfur from DBT to convert into biomass or other metabolites. We propose two alternate hypotheses. In the first, we hypothesize that the cell can convert via sulfite reductase (SR) the sulfite from the metabolism of DBT into sulfide that can be assimilated into biomass. However, in the process, it may convert any excess sulfite into extracellular sulfate via sulfite oxidoreductase (SOR) to avoid the toxic effects of sulfite. In the second, we speculate that the cell cannot assimilate the sulfite directly into biomass via SR. It must first use SOR to produce extracellular sulfate, and then recapture that sulfate into biomass via SR. Thus, either way, we propose that SOR and SR activities, in addition to dsz genes and cofactors, may be critical in increasing desulfurization levels significantly. In particular, we suggest that the simultaneous increase in SOR activity and decrease in SR activity can enable increased desulfurization activity.

Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies.

The remarkable catabolic diversity of Rhodococcus erythropolis makes it an interesting organism for bioremediation and fuel desulfurization. However, a model that can describe and explain the combined influence of various intracellular metabolic activities on its desulfurizing capabilities is missing from the literature. Such a model can greatly aid the development of R. erythropolis as an effective desulfurizing biocatalyst. This work reports the reconstruction of the first genome-scale metabolic model for R. erythropolis using the available genomic, experimental, and biochemical information. We have validated our in silico model by successfully predicting cell growth results and explaining several experimental observations in the literature on biodesulfurization using dibenzothiophene. We report several in silico experiments and flux balance analyses to propose minimal media, determine gene and reaction essentiality, and compare effectiveness of carbon, nitrogen, and sulfur sources. We demonstrate the usefulness of our model by studying a few in silico mutants of R. erythropolis for improved biodesulfurization, and comparing the desulfurization abilities of R. erythropolis with an in silico mutant of E. coli.

Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis.

Rhodococcus erythropolis has been studied widely for potential applications in biodesulfurization. Previous works have been largely experimental with an emphasis on the characterization and genetic engineering of desulfurizing strains for improved biocatalysis. A systems modeling approach that can complement these experimental efforts by providing useful insights into the complex interactions of desulfurization reactions with various other metabolic activities is absent in the literature. In this work, we report the first attempt at reconstructing a flux-based model to analyze sulfur utilization by R. erythropolis. The model includes the 4S pathway for dibenzothiophene (DBT) desulfurization. It predicts closely the growth rates reported by two independent experimental studies, and gives a clear and comprehensive picture of the pathways that assimilate the sulfur from DBT into biomass. In addition, it successfully elucidates that sulfate promotes higher cell growth than DBT and its presence in the medium reduces DBT desulfurization rates. A study using eight carbon sources suggests that ethanol and lactate yield higher cell growth and desulfurization rates than citrate, fructose, glucose, gluconate, glutamate, and glycerol.