A computational approach to investigate constitutive activation of NF-κB.

Nuclear factor kappa B (NF-κB) signaling is the master regulator of inflammatory pathways; therefore, its regulation has been the subject of investigation since last two decades. Multiple models have been published that describes the dynamics of NF-κB activity by stimulated activation and feedback loops. However, there is also paramount evidence of the critical role of posttranslational modifications (PTMs) in the regulation of NF-κB pathway. With the premise that PTMs present alternate routes for activation or repression of the NF-κB pathway, we have developed a model including all PTMs known so far describing the system behavior. We present a pathway network model consisting of 171 proteins forming 315 molecular species and consisting of 482 reactions that describe the NF-κB activity regulation in totality. The overexpression or knockdown of interacting molecular partners that regulate NF-κB transcriptional activity by PTMs is used to infer the dynamics of NF-κB activity and offers qualitative agreement between model predictions and the experimental results heuristically. Finally, we have demonstrated an instance of NF-κB constitutive activation through positive upregulation of cytokines (the stimuli) and IKK complex (NF-κB activator), the characteristic features in several cancer types and metabolic disorders, and its reversal by employing combinatorial activation of PPARG, PIAS3, and P50-homodimer. For the first time, we have presented a NF-κB model that includes transcriptional regulation by PTMs and presented a theoretical strategy for the reversal of NF-κB constitutive activation. The presented model would be important in understanding the NF-κB system, and the described method can be used for other pathways as well.

Exploration of potential inhibitors for autophagy-related protein 8 as antileishmanial agents.

Leishmaniasis is considered a tropical neglected disease, which is caused by an intramacrophagic parasite, Leishmania. It is endemic in 89 different countries. Autophagy-related protein 8 (Ldatg8) is responsible for the transformation of parasites from promastigote to amastigote differentiation. Ldatg8 is one of the key drug targets of Leishmania donovani (L. donovani) responsible for the defense of parasites during stress conditions. Virtual screening of natural ligand library had been performed against Ldatg8 to identify novel and potent inhibitors. Molecular docking and molecular dynamics simulation studies showed that urolithin A stably blocked Ldatg8. Urolithins are combinations of coumarin and isocoumarin. Further, we evaluated the antileishmanial effects of urolithin A by antileishmanial assays. Urolithin A inhibited the growth and proliferation of L. donovani promastigotes with an IC50  value of 90.3 ± 6.014 µM. It also inhibited the intramacrophagic parasite significantly with an IC50  value of 78.67 ± 4.62 µM. It showed limited cytotoxicity to the human THP-1 differentiated macrophages with a CC50  value of 190.80 ± 16.89 µM. Further, we assayed reactive oxygen species (ROS) generation and annexin V/PI staining upon urolithin A treatment of parasites to have an insight into the mechanism of its action. It induced ROS significantly in a dose-dependent manner, which caused apoptosis partially in parasites. The potential inhibitors for Ldatg8, identified in this study, would provide the platform for the development of an effective and affordable antileishmanial drug.

Differential regulation of miR-21-5p delays wound healing of melanocyte-deprived vitiligo skin by modulating the expression of tumor-suppressors PDCD4 and Maspin.

The loss of melanocytes in vitiligo is associated with architectural, transcriptional, and cellular perturbations of keratinocytes and manifests as a reduced proliferation potential in vitro and delayed re-epithelialization in vivo. To understand the molecular mechanisms underlying this delay, microRNA (miRNA) profiling was performed on split skin biopsies collected on Day 1 (basal level) and Day 14 (wound re-epithelialization) from nonlesional (NL) and lesional (L) skin of five subjects with stable nonsegmental vitiligo and 129 miRNAs were found to be differentially regulated between the NL and L healed epidermis. miR-21-5p, expressed at comparable levels on NL and L Day 1 samples, demonstrated significant upregulation during re-epithelialization. However, the extent of its upregulation was relatively lower in L (10 times compared to Day 1) as compared to NL skin (17 times compared to Day 1). The overexpression of miR-21 in keratinocytes led to a significant increase in the expression of proliferation markers (Ki67 and MCM6 messenger RNA, Ki67 positivity), along with an increase in keratinocyte migration. Using a small interfering RNA mediated knockdown approach, we further demonstrated that miR-21-5p mediates its effects by suppressing the expression of programmed cell death 4 (PDCD4) and mammary serine protease inhibitor (Maspin), both tumor-suppressor genes. Investigation of clinical samples corroborated the lower miR-21 levels and a higher expression of PDCD4 and Maspin in L Day 14 compared to the NL Day 14 epidermis. In conclusion, this study revealed that a relatively lower upregulation of miR-21-5p in L skin leads to significantly higher levels of PDCD4 and Maspin, delaying wound re-epithelialization by reducing the proliferation and migration of keratinocytes.

A meta-analysis of comorbidities in COVID-19: Which diseases increase the susceptibility of SARS-CoV-2 infection?

Comorbidities in COVID-19 patients often lead to more severe outcomes. The disease-specific molecular events, which may induce susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, are being investigated. To assess this, we retrieved array-based gene expression datasets from patients of 30 frequently occurring acute, chronic, or infectious diseases. Comparative analyses of the datasets were performed after quantile normalization and log2 transformation. Among the 78 host genes prominently implicated in COVID-19 infection, ACE2 (receptor for SARS-CoV-2) was positively regulated in several cases, namely, leukemia, psoriasis, lung cancer, non-alcoholic fatty liver disease (NAFLD), breast cancer, and pulmonary arterial hypertension (PAH). FURIN was positively regulated in some cases, such as leukemia, psoriasis, NAFLD, lung cancer, and type II diabetes (T2D), while TMPRSS2 was positively regulated in only 3 cases, namely, leukemia, lung cancer, and T2D. Genes encoding various interferons, cytokines, chemokines, and mediators of JAK-STAT pathway were positively regulated in leukemia, NAFLD, and T2D cases. Among the 161 genes that are positively regulated in the lungs of COVID-19 patients, 99-111 genes in leukemia (including various studied subtypes), 77 genes in NAFLD, and 48 genes in psoriasis were also positively regulated. Because of the high similarity in gene expression patterns, the patients of leukemia, NAFLD, T2D, psoriasis, and PAH may need additional preventive care against acquiring SARS-CoV-2 infections. Further, two genes CARBONIC ANHYDRASE 11 (CA11) and CLUSTERIN (CLU) were positively regulated in the lungs of patients infected with either SARS-CoV-2, or SARS-CoV or Middle East Respiratory Syndrome Coronavirus (MERS-CoV).

T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders.

We performed integrative analysis of genes associated with type 2 Diabetes Mellitus (T2DM) associated complications by automated text mining with manual curation and also gene expression analysis from Gene Expression Omnibus. They were analysed for pathogenic or protective role, trends, interaction with risk factors, Gene Ontology enrichment and tissue wise differential expression. The database T2DiACoD houses 650 genes, and 34 microRNAs associated with T2DM complications. Seven genes AGER, TNFRSF11B, CRK, PON1, ADIPOQ, CRP and NOS3 are associated with all 5 complications. Several genes are studied in multiple years in all complications with high proportion in cardiovascular (75.8%) and atherosclerosis (51.3%). T2DM Patients' skeletal muscle tissues showed high fold change in differentially expressed genes. Among the differentially expressed genes, VEGFA is associated with several complications of T2DM. A few genes ACE2, ADCYAP1, HDAC4, NCF1, NFE2L2, OSM, SMAD1, TGFB1, BDNF, SYVN1, TXNIP, CD36, CYP2J2, NLRP3 with details of protective role are catalogued. Obesity is clearly a dominant risk factor interacting with the genes of T2DM complications followed by inflammation, diet and stress to variable extents. This information emerging from the integrative approach used in this work could benefit further therapeutic approaches. The T2DiACoD is available at www.http://t2diacod.igib.res.in/ .

Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis.

Robustness of metabolic networks is accomplished by gene regulation, modularity, re-routing of metabolites and plasticity. Here, we probed robustness against perturbations of biochemical reactions of M. tuberculosis in the form of predicting compensatory trends. In order to investigate the transcriptional programming of genes associated with correlated fluxes, we integrated with gene co-expression network. Knock down of the reactions NADH2r and ATPS responsible for producing the hub metabolites, and Central carbon metabolism had the highest proportion of their associated genes under transcriptional co-expression with genes of their flux correlated reactions. Reciprocal gene expression correlations were observed among compensatory routes, fresh activation of alternative routes and in the multi-copy genes of Cysteine synthase and of Phosphate transporter. Knock down of 46 reactions caused the activation of Isocitrate lyase or Malate synthase or both reactions, which are central to the persistent state of M. tuberculosis. A total of 30 new freshly activated routes including Cytochrome c oxidase, Lactate dehydrogenase, and Glycine cleavage system were predicted, which could be responsible for switching into dormant or persistent state. Thus, our integrated approach of exploring transcriptional programming of flux correlated reactions has the potential to unravel features of system architecture conferring robustness.

Development and validation of a high-performance liquid chromatography method with post-column derivatization for the detection of aflatoxins in cereals and grains.

A novel, reliable and rapid high-performance liquid chromatography (HPLC) method with post-column derivatization was developed and validated. The HPLC method was used for the simultaneous determination of aflatoxin B1 (AFB1), B2 (AFB2), G1 (AFG1) and G2 (AFG2) in various cereals and grains. Samples were extracted with 80:20 (v/v) methanol:water and purified using C18 (40-63 µm) solid-phase extraction cartridges. AFs were separated using a LiChroCART-RP-18 (5 µm, 250 × 4.0 mm(2)) column. The mobile phase consisted of methanol:acetonitrile:buffer (17.5:17.5:65 v/v) (pH 7.4) delivered at the flow rate of 1.0 mL min(-1) The fluorescence of each AF was detected at λex = 365 nm and λem = 435 nm. All four AFs were properly resolved within the total run time of 20 min. The established method was extensively validated as a final verification of the method development by the evaluation of selectivity (AFB1, AFB2, AFG1 and AFG2), linearity (R(2) ≥ 0.9994), precision (average SD ≤ 2.79), accuracy (relative mean error ≤ -5.51), robustness (p < 0.0080), ruggedness (p < 0.0100) and average recoveries (89.2-97.8%). The limits of quantification of AFB1, AFB2, AFG1 and AFG2 were 0.080, 0.073, 0.062 and 0.066 ng g(-1), respectively. Finally, the developed method was applied for the analysis of AFs in 45 samples comprising rice (n = 20), wheat (n = 15) and maize (n = 10). The results showed that 65% of rice, 20% of wheat and 80% of maize samples were found contaminated with AFs. Thus, according to the achieved results, it is suggested that the newly developed HPLC method could be effectively applied for the routine analysis of the AFs in different cereals and grains.

Aflatoxins contamination in Pakistani brown rice: a comparison of TLC, HPLC, LC-MS/MS and ELISA techniques.

Advancement in the field of analytical food-chemistry has explored various experimental techniques for aflatoxins (AFs) quantification. The present study was aimed to compare four different techniques; thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), liquid chromatography-tandem mass spectrometry (LC-MS/MS) and enzyme-linked immunosorbent assay (ELISA) for the analysis of aflatoxin B1 (AFB1), B2 (AFB2), G1 (AFG1) and G2 (AFG2) in brown rice (n = 120) being collected from Karachi, Pakistan. All the four assays provide precised, accurate and comparable results. However, some differences were observed. For instance, TLC, HPLC and LC-MS/MS methodologies offered the advantage of the quantification of individual toxins in contrast to ELISA technique. The contamination ranges of AFB1/AFB2 as determined by TLC, HPLC and LC-MS/MS were 1.18-9.97/0.59-1.52, 0.16-10.54/0.26-1.35 and 0.11-10.88/0.38-1.48 µg/kg, respectively. However, AFG1 and AFG2 were not detected in any tested samples. Furthermore, owing to low-detection limit and sensitivity, HPLC and LC-MS/MS methodologies have identified greater number of contaminated samples in comparison to TLC and ELISA techniques. The overall average results of total AFs as provided by HPLC (3.79 µg/kg) and LC-MS/MS (3.89 µg/kg) were found higher in comparison to TLC (3.68 µg/kg) and ELISA (3.70 µg/kg). On the basis of achieved results, it was concluded that TLC, HPLC, LC-MS/MS and ELISA techniques are valuable tool for the quantification of AFs in cereals and grains. Furthermore, HPLC and LC-MS/MS techniques offer an added advantage for the detection of AFs in diminutive levels.

Aflatoxin B1 in betel nuts (Areca catechu L.) imported to Pakistan from different regions of South Asia.

Aflatoxin B1 (AFB1) levels were evaluated in betel nuts (Areca catechu L.) being imported to Pakistan during 2010-2011. In total, 278 betel nut samples (India = 21, Indonesia = 51, Sri-Lanka = 34 and Thailand = 172) were received from the Department of Customs and were analysed by thin layer chromatography (TLC). All Indian origin betel nuts showed AFB1 contamination ranging from 11.7-262.0 µg kg(-1) with a mean of 92.5 µg kg(-1). Among Indonesian and Sri Lankan shipments, 80.4% and 73.5% betel nuts were contaminated with AFB1 ranging between 3.3-39.2 and 6.5-103.4 µg kg(-1) with a mean of 11.6 and 35.0 µg kg(-1), respectively. However, only 30.2% of Thailand origin samples showed AFB1 contamination ranging 3.3-77.0 µg kg(-1) with a mean of 6.6 µg kg(-1). The widespread occurrence of AFB1 increases the hazard associated with betel nuts. Thus, strict control is a pre-requisite for the production and import/export of psychoactive substances as betel nuts.

Aflatoxins contamination and prevention in red chillies (Capsicum annuum L.) in Pakistan.

During 2006-2011, 331 red chilli samples (226 whole, 69 powdered and 36 crushed) were collected from all over Pakistan for the estimation of total aflatoxins (AFs = AFB1 + AFB2 + AFG1 + AFG2) contamination by thin layer chromatography (TLC). Mean AFs levels in whole, powdered and crushed chillies were 11.7, 27.8 and 31.2 µg kg(-1), respectively. AFs levels in 62.4% of whole, 26.1% of powdered and 19.4% of crushed chillies were found lower than the maximum limit (ML = 10 µg kg(-1)) as assigned by the European Union. Furthermore, whole (27.9%), powdered (28%) and crushed (27.8%) chillies showed AFs contamination which ranged between 10 and 20 µg kg(-1). However, 9.7% of whole, 46% of powdered and 52.8% of crushed chillies showed AFs levels beyond the ML of 20 µg kg(-1) as assigned by the USDA. It was concluded that AFs contamination in chillies requires further investigation, monitoring and routine analysis. Furthermore, proper harvesting, drying, handling, storage and transport conditions need to be employed.

Occurrence of aflatoxins contamination in brown rice from pakistan.

BACKGROUND: The objective of this study was to determine the distribution of an economically-important class of mycotoxins, the aflatoxins (AFs) in Pakistani Brown Rice. METHODS: A total of 262 of brown rice samples were collected from different vendors during July 2006 to June 2011. Samples were analyzed for the occurrence of aflatoxin B1 (AFB1), B2 (AFB2), G1 (AFG1) and G2 (AFG2) by thin layer chromatography (TLC) technique. RESULTS: AFB1 was detected in 250 (95.4%) samples, whereas AFB2 was detected in 20 (7.6%) samples. Furthermore, AFG1 and AFG2 were not found in any sample. The contamination range of AFB1 and AFB2 was found 1.07-24.65 µg/kg and 0.52-2.62 µg/kg, respectively. Total AFs were quantified in 250 (95.4%) samples with an average of 3.89 µg/kg and contamination range was noted to be between 1.07-27.27 µg/kg. The overall results indicated that in 12 (4.6%) samples, AFs were not found within detectable limits. Furthermore, in 188 (71.7%) samples, AFs level was found below than maximum tolerated levels (MTL) as recommended by the European Union (4 µg/kg). Moreover, in 61 (23.3%) samples, AFs range was found between 4-20 µg/kg, which were fit for human consumption as per MTL (20 µg/kg) assigned by USA (FDA and FAO) and Pakistan (PSQCA). While only one sample (27.27 µg/kg) exceeded the above mention regulation limits. CONCLUSION: Low level of AFs occurs frequently in brown rice, and can be improved using proper harvesting practices, storage and transportation conditions. The small quantities of AFs warrant performing further investigation, monitoring and routine analysis on regular basis.