Biophysical and functional characterization of N-terminal domain of Human Interferon Regulatory Factor 6.

BACKGROUND: Interferon regulatory factor 6 (IRF6) has a key function in palate fusion during palatogenesis during embryonic development, and mutations in IRF6 cause orofacial clefting disorders. METHODS AND RESULTS: The in silico analysis of IRF6 is done to obtain leads for the domain boundaries and subsequently the sub-cloning of the N-terminal domain of IRF6 into the pGEX-2TK expression vector and successfully optimized the overexpression and purification of recombinant glutathione S-transferase-fused NTD-IRF6 protein under native conditions. After cleavage of the GST tag, NTD-IRF6 was subjected to protein folding studies employing Circular Dichroism and Intrinsic fluorescence spectroscopy at variable pH, temperature, and denaturant. CD studies showed predominantly alpha-helical content and the highest stability of NTD-IRF6 at pH 9.0. A comparison of native and renatured protein depicts loss in the secondary structural content. Intrinsic fluorescence and quenching studies have identified that tryptophan residues are majorly present in the buried areas of the protein and a small fraction was on or near the protein surface. Upon the protein unfolding with a higher concentration of denaturant urea, the peak of fluorescence intensity decreased and red shifted, confirming that tryptophan residues are majorly present in a more polar environment. While regulating IFNß gene expression during viral infection, the N-terminal domain binds to the promoter region of Virus Response Element-Interferon beta (VRE-IFNß). Along with the protein folding analysis, this study also aimed to identify the DNA-binding activity and determine the binding affinities of NTD-IRF6 with the VRE-IFNß promoter region. The protein-DNA interaction is specific as demonstrated by gel retardation assay and the kinetics of molecular interactions as quantified by Biolayer Interferometry showed a strong affinity with an affinity constant (KD) value of 7.96 × 10-10 M. CONCLUSION: NTD-IRF6 consists of a mix of α-helix and ß-sheets that show temperature-dependent cooperative unfolding between 40 °C and 55 °C. Urea-induced unfolding shows moderate tolerance to urea as the mid-transition concentration of urea (Cm) is 3.2 M. The tryptophan residues are majorly buried as depicted by fluorescence quenching studies. NTD-IRF6 has a specific and high affinity toward the promoter region of VRE-IFNß.

Alleviation of arsenic-induced neurobehavioral defects with selenium in the larvae of Zaprionus indianus.

Selenium is an essential antioxidative micronutrient. This study was conducted to characterize the arsenic toxicity induced on the African fig fly, Zaprionus indianus, and its possible amelioration by selenium. We used computational tools and in vivo experiments to elucidate the mechanism of action of arsenic and selenium on Z. indianus larvae. We conducted experiments to study neurobehavioral parameters including learning and memory ability test and crawling and contraction assays. Our in silico study revealed twelve primary targets of arsenic trioxide. The gene ontology annotation of primary and secondary targets of arsenic trioxide revealed selenocysteine metabolic processes as one of the most reliable targets. To validate our in silico data, we analyzed the effect of arsenic trioxide on larvae of Z. indianus and tested the possible amelioration by sodium selenite supplementation. Our data demonstrated that the arsenic trioxide deteriorated the learning and memory ability of 2nd instar larvae of Z. indianus and such effect was reversed by sodium selenite supplementation. Furthermore, crawling and contraction assay done on 3rd instar larvae showed that there was reduction in both parameters upon arsenic trioxide exposure, which was restored with sodium selenite supplementation. Altogether, our computational and in vivo results strongly indicated that the neurobehavioral defects induced by arsenic trioxide on the larvae of Z. indianus can be successfully alleviated in the presence of sodium selenite.

Chylous ascites following retroperitoneal lymphadenectomy in a patient with recurrent dysgerminoma of ovary: A case report.

Chylous ascites is an uncommon condition of accumulation of milky fluid rich in lymph and chylomicrons in the peritoneal cavity. Post-surgical complications following dissection near the base of the mesentery, retroperitoneum, or near the cisterna chyli, malignancies (e.g., pancreatic adenocarcinomas, lymphoma, gastric carcinoma), cirrhosis, and trauma are the prime causes of chylous ascites. Here we report a rare case of chylous ascites following clearance of isolated paraaortic nodal recurrence in a 28-year-old female with dysgerminoma of ovary. The patient developed chylous ascites on the fifth day following surgery, which was confirmed by an increased drain fluid triglyceride level. She was managed conservatively with dietary modification including a high-protein and carbohydrate but low-fat-based diet mainly containing medium-chain fatty acids. Subsequently, she recovered from chylous ascites on the sixteenth day, completed second line chemotherapy, and is now doing well.

A Pilot Study on Blood Components in COVID-19 Affected Subjects: A Correlation to UPR Signalling and ER-Stress.

Abstract: The endoplasmic reticulum (ER) is the site for protein synthesis, its folding and secretion. An intricate set of signalling pathways, called UPR pathways, have been evolved by ER in mammalian cells, to allow the cell to respond the presence of misfolded proteins within the ER. Breaching of these signalling systems by disease oriented accumulation of unfolded proteins may develop cellular stress. The aim of this study is to explore whether COVID-19 infection is responsible for developing this kind of endoplasmic reticulum related stress (ER-stress). ER-stress was evaluated by checking the expression of ER-stress markers e.g. PERK (adapting) and TRAF2 (alarming). ER-stress was correlated to several blood parameters viz. IgG, pro- and anti-inflammatory cytokines, leukocytes, lymphocytes, RBC, haemoglobin and PaO2/FiO2 ratio (ratio of arterial oxygen partial pressure to fractional inspired oxygen) in COVID-19 affected subjects. COVID-19 infection was found to be a state of protein homeostasis (proteostasis) collapse. Changes in IgG levels showed very poor immune response by the infected subjects. At the initial phase of the disease, pro-inflammatory cytokine levels were high and anti-inflammatory cytokines levels were low; though they were partly compromised at later phase of the disease. Total leukocyte concentration increased over the period of time; while percentage of lymphocytes were dropped. No significant changes were observed in cases of RBC counts and haemoglobin (Hb) levels. Both RBC and Hb were maintained at their normal range. In mildly stressed group, PaO2/FiO2 ratio (oxygenation status) was in the higher side of normal range; whereas in other two groups the ratio was in respiratory distress syndrome mode. Virus could induce mild to severe ER-stress, which could be the cause of cellular death and systemic dysfunction introducing fatal consequences. Graphical Abstract: Schematic representation of SARS-CoV-2 infection and related consequences.

Severe Acute Respiratory Syndrome Coronavirus 2 and Dengue Virus Co-infection: Indian Perspectives.

Severe acute respiratory syndrome Coronavirus 2 (SARS CoV-2) and Dengue virus (DENV) Coinfection can be a pertinent issue in a country like India, where Dengue is endemic, and Coronavirus disease 19 (COVID-19) is also reported from all states of the country. The coinfection of these viruses has already been reported in different dengue-endemic countries like Singapore, Thailand, and Bangladesh. The outcome and the dynamics of each of the diseases may be altered in the presence of coinfection. We highlighted the critical characteristic similarities and differences between COVID-19 and Dengue infection & the specific point, which may challenge diagnosing and managing these coinfections. COVID-19 and Dengue coinfection can be deadly in combination with an atypical presentation, providing diagnostic and therapeutic challenges. A high index of suspicion, early recognition of symptoms, and warning signs are vital to prevent double jeopardy.

Methane production and estimation from livestock husbandry: A mechanistic understanding and emerging mitigation options.

Globally, livestock is an important contributor to methane (CH4) emissions. This paper reviewed the various CH4 measurement and estimation techniques and mitigation approaches for the livestock sector. Two approaches for enteric livestock CH4 emission estimation are the top-down and bottom-up. The combination of both could further improve our understanding of enteric CH4 emission and possible mitigation measures. We discuss three mitigation approaches: reducing emissions, avoiding emissions, and enhancing the removal of emissions from livestock. Dietary management, livestock management, and breeding management are viable reducing emissions pathways. Dietary manipulation is easily applicable and can bring an immediate response. Economic incentive policies can help the livestock farmers to opt for diet, breeding, and livestock management mitigation approaches. Carbon pricing creates a better option to achieve reduction targets in a given period. A combination of carbon pricing, feeding management, breeding management, and livestock management is more feasible and sustainable CH4 emissions mitigation strategy rather than a single approach.

Climate change impact of livestock CH4 emission in India: Global temperature change potential (GTP) and surface temperature response.

Two climate metrics, Global surface Temperature Change Potential (GTP) and the Absolute GTP (AGTP) are used for studying the global surface temperature impact of CH4 emission from livestock in India. The impact on global surface temperature is estimated for 20 and 100 year time frames due to CH4 emission. The results show that the CH4 emission from livestock, worked out to 15.3 Tg in 2012. In terms of climate metrics GTP of livestock-related CH4 emission in India in 2012 were 1030 Tg CO2e (GTP20) and 62 Tg CO2e (GTP100) at the 20 and 100 year time horizon, respectively. The study also illustrates that livestock-related CH4 emissions in India can cause a surface temperature increase of up to 0.7mK and 0.036mK over the 20 and 100 year time periods, respectively. The surface temperature response to a year of Indian livestock emission peaks at 0.9mK in the year 2021 (9 years after the time of emission). The AGTP gives important information in terms of temperature change due to annual CH4 emissions, which is useful when comparing policies that address multiple gases.

Emerging role of Geographical Information System (GIS), Life Cycle Assessment (LCA) and spatial LCA (GIS-LCA) in sustainable bioenergy planning.

Sustainability of a bioenergy project depends on precise assessment of biomass resource, planning of cost-effective logistics and evaluation of possible environmental implications. In this context, this paper reviews the role and applications of geo-spatial tool such as Geographical Information System (GIS) for precise agro-residue resource assessment, biomass logistic and power plant design. Further, application of Life Cycle Assessment (LCA) in understanding the potential impact of agro-residue bioenergy generation on different ecosystem services has also been reviewed and limitations associated with LCA variability and uncertainty were discussed. Usefulness of integration of GIS into LCA (i.e. spatial LCA) to overcome the limitations of conventional LCA and to produce a holistic evaluation of the environmental benefits and concerns of bioenergy is also reviewed. Application of GIS, LCA and spatial LCA can help alleviate the challenges faced by ambitious bioenergy projects by addressing both economics and environmental goals.