Mechanism of δ Mediated Transcription Activation in Bacillus subtilis: Interaction with α CTD of RNA Polymerase Stabilizes δ and Successively Facilitates the Open Complex Formation.

The α CTD (C-terminal domain of the α subunit) of RNA polymerase (RNAP) is a target for transcriptional regulators. In the transcription activation at Class I, Class II, and Class III promoters of bacteria, the transcriptional regulator, binds to DNA at different sites and interacts with the α CTD to stabilize the RNAP at the promoter or it binds to the α CTD to form a prerecruitment complex that searches for its cognate binding site. This 'simple recruitment mechanism' of the transcriptional machinery at the promoter is responsible for the activation of transcription. Strikingly, in B. subtilis the binding of RNAP at the promoter stabilizes the transcriptional regulator, δ at the -41 site of the promoter DNA through an interaction with its α CTD and successively facilitates the open complex formation. Two residues R293 and K294 of α CTD (equivalent to K297 and K298 of E. coli) are involved in the interactions with δ and essential for the activation of transcription. R293 is responsible for the stabilization of δ, while K294 is responsible for facilitating the open complex formation. Based on our data we propose a new model of transcription activation by δ of B. subtilis that is similar to (its binding location and interaction with α CTD), but distinct from (the recruitment of transcription factor by RNAP at the DNA, and enhancement of the open complex formation) the model Class II promoters in bacteria.

Phyto-assisted synthesis of CuO/industrial waste derived biochar composite for adsorptive removal of doxycycline hydrochloride and recycling of spent biochar as green energy storage device.

The highest exposure of Endocrine disrupting compounds (EDC) into the water bodies as a result of extensive production and application of Covid-19 related drugs is a growing concern now a days. Herein, a novel nanocomposite material was developed by impregnating green synthesized copper oxide nanoparticles on the porous surface of fabric waste derived biochar to eliminate the concerned EDCs along with a sustainable disposal strategy for the spent adsorbent. Morphological characterizations by Field emission scanning electron microscopy confirmed the formation of hierarchical porous structured material. X-ray analysis revealed presence of both amorphous nature of biochar matrix as well as the crystalline nature attributed from monodispersion of copper oxide nanoparticles onto biochar surface. Batch sorption study showed removal of doxycycline hydrochloride (DOX) of >97% after 2 h at pH 7, 30 mg L-1 initial concentration of DOX and 2 g L-1 of adsorbent dose at room temperature after a two-step optimization process. Spectroscopic study and Raman shift suggested that pore filling, strong complexation and electrostatic interactions maximise the adsorption of DOX in the CuO/biochar composite as compared to the pristine biochar. However disposal of spent adsorbent is a crucial aspect for the environment and therefore, a sustainable recycling strategy for DOX loaded adsorbent as electrode material has been proposed for the first time in this study. Maximum specific capacitance value was observed in the range of 221.9-297.3 F g-1 for the DOX loaded nanocomposite at 1 mV s-1 comparable with other reported heteroatom-doped carbonaceous material as electrode. Therefore the excellent adsorption capacity of green synthesized CuO/biochar composite and its recycling after DOX adsorption can be recommended as a sustainable solution for mitigation of pharmaceuticals from wastewater. A detail study on degradation of DOX into eco-friendly products and its cost-effectiveness would be beneficial to suggest appropriate mitigation strategy for such compounds.

Advancing Electrode Properties through Functionalization for Solid Oxide Cells Application: A Review.

Hydrogen energy has emerged as the only renewable which is capable of sustaining the prevalent energy crisis in conjunction with other intermittent sources. In this connection, solid oxide cell (SOC) is the most sustainable solid-state devices capable of recycling and reproducing green hydrogen fuel. It is operable in reversible modes viz, fuel cell (FC) and electrolysis cell (EC). SOC is capable of engaging multiple fuels thereby promoting carbon neutral planet. The all-solid design further augments the optimization of cost, efficiency, durability and endurance at higher temperature. Electrodes are therefore, an important component which is responsible for electrocatalytic processing of fuel and oxidant for higher recyclability of cell/stack. The present review article embarks a detailed overview on the past and present status of electrode composition, heterointerface engineering applicable for SOC's. Recent trends in electrode engineering and the possibilities for advancement in SOC is also reviewed with respect to both experimental and computational aspects.

Supramolecular Arrangement and DFT analysis of Zinc(II) Schiff Bases: An Insight towards the Influence of Compartmental Ligands on Binding Interaction with Protein.

We report, for the first time, a detailed crystallographic study of the supramolecular arrangement for a set of zinc(II) Schiff base complexes containing the ligand 2,6-bis((E)-((2-(dimethylamino)ethyl)imino)methyl)-4-R-phenol], where R=methyl/tert-butyl/chloro. The supramolecular study acts as a pre-screening tool for selecting the compartmental ligand R of the Schiff base for effective binding with a targeted protein, bovine serum albumin (BSA). The most stable hexagonal arrangement of the complex [Zn-Me] (R=Me) stabilises the ligand with the highest FMO energy gap (ΔE=4.22 eV) and lowest number of conformations during binding with BSA. In contrast, formation of unstable 3D columnar vertebra for [Zn-Cl] (R=Cl) tend to activate the system with lowest FMO gap (3.75 eV) with highest spontaneity factor in molecular docking. Molecular docking analyses reported in terms of 2D LigPlot+ identified site A, a cleft of domains IB, IIIA and IIIB, as the most probable protein binding site of BSA. Arg144, Glu424, Ser428, Ile455 and Lys114 form the most probable interactions irrespective of the type of compartmental ligands R of the Schiff base whereas Arg185, Glu519, His145, Ile522 act as the differentiating residues with ΔG=-7.3 kcal mol-1 .

A saponin-polybromophenol antibiotic (CU1) from Cassia fistula Bark Against Multi-Drug Resistant Bacteria Targeting RNA polymerase.

BACKGROUND: Gradual increase of multidrug resistant infections is a threat to the human race as MDR plasmids have acquired.>10 mdr and drug efflux genes to inactivate antibiotics. Plants secret anti-metabolites to retard growth of soil and water bacteria and are ideal source of antibiotics. PURPOSE: Purpose of the study is to discover an alternate phyto-drug from medicinal plants of India that selectively kills MDR bacteria. METHODS: MDR bacteria isolated from Ganga river water, milk, chicken meat and human hair for testing phyto-extracts. Eighty medicinal plants were searched and six phyto-extracts were selected having good antibacterial activities as demonstrated by agar-hole assays giving 15 â€‹mm or greater lysis zone. Phyto-extracts were made in ethanol or methanol (1:5 w/v) for overnight and were concentrated. Preparative TLC and HPLC were performed to purify phytochemical. MASS, NMR, FTIR methods were used for chemical analysis of CU1. In vitro RNA polymerase and DNA polymerase assays were performed for target identification. RESULTS: CU1 belongs to a saponin bromo-polyphenol compound with a large structure that purified on HPLC C18 column at 3min. CU1 is bacteriocidal but three times less active than rifampicin in Agar-hole assay. While in LB medium it shows greater than fifteen times poor inhibitor due to solubility problem. CU1 inhibited transcription from Escherichia coli as well as Mycobacterium tuberculosis RNA Polymerases. Gel shift assays demonstrated that CU1 interferes at the open promoter complex formation step. On the other hand CU1 did not inhibit DNA polymerase. CONCLUSION: Phyto-chemicals from Cassia fistula bark are abundant, less toxic, target specific and may be a safer low cost drug against MDR bacterial diseases.

Design and Development of a Medical Image Databank for Assisting Studies in Radiomics.

CompreHensive Digital ArchiVe of Cancer Imaging - Radiation Oncology (CHAVI-RO) is a multi-tier WEB-based medical image databank. It supports archiving de-identified radiological and clinical datasets in a relational database. A semantic relational database model is designed to accommodate imaging and treatment data of cancer patients. It aims to provide key datasets to investigate and model the use of radiological imaging data in response to radiation. This domain of research area addresses the modeling and analysis of complete treatment data of oncology patient. A DICOM viewer is integrated for reviewing the uploaded de-identified DICOM dataset. In a prototype system we carried out a pilot study with cancer data of four diseased sites, namely breast, head and neck, brain, and lung cancers. The representative dataset is used to estimate the data size of the patient. A role-based access control module is integrated with the image databank to restrict the user access limit. We also perform different types of load tests to analyze and quantify the performance of the CHAVI databank.

Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli.

DevR/DosR response regulator is believed to participate in virulence, dormancy adaptation and antibiotic tolerance mechanisms of Mycobacterium tuberculosis by regulating the expression of the dormancy regulon. We have previously shown that the interaction of DevR with RNA polymerase is essential for the expression of DevR-regulated genes. Here, we developed a M. tuberculosis-specific in vivo transcription system to enrich our understanding of DevR-RNA polymerase interaction. This in vivo assay involves co-transforming E. coli with two plasmids that express α, ß, ß' and σA subunits of M. tuberculosis RNA polymerase and a third plasmid that harbors a DevR expression cassette and a GFP reporter gene under the DevR-regulated fdxA promoter. We show that DevR-dependent transcription is sponsored exclusively by M. tuberculosis RNA polymerase and regulated by α and σA subunits of M. tuberculosis RNA polymerase. Using this E. coli triple plasmid system to express mutant variants of M. tuberculosis RNA polymerase, we identified E280 residue in C-terminal domain of α and K513 and R515 residues of σA to participate in DevR-dependent transcription. In silico modeling of a ternary complex of DevR, σA domain 4 and fdxA promoter suggest an interaction of Q505, R515 and K513 residues of σA with E178 and D172 residues of DevR and E471 of σA, respectively. These findings provide us with new insights into the interactions between DevR and RNA polymerase of M. tuberculosis which can be targeted for intercepting DevR function. Finally, we demonstrate the utility of this system for screening of anti-DevR compounds.

Research Goal-Driven Data Model and Harmonization for De-Identifying Patient Data in Radiomics.

There are various efforts in de-identifying patient's radiation oncology data for their uses in the advancement of research in medicine. Though the task of de-identification needs to be defined in the context of research goals and objectives, existing systems lack the flexibility of modeling data and normalization of names of attributes for accomplishing them. In this work, we describe a de-identification process of radiation and clinical oncology data, which is guided by a data model and a schema of dynamically capturing domain ontology and normalization of terminologies, defined in tune with the research goals in this area. The radiological images are obtained in DICOM format. It consists of diagnostic, radiation therapy (RT) treatment planning, RT verification, and RT response images. During the DICOM de-identification, a few crucial pieces of information are taken about the dataset. The proposed model is generic in organizing information modeling in sync with the de-identification of a patient's clinical information. The treatment and clinical data are provided in the comma-separated values (CSV) format, which follows a predefined data structure. The de-identified data is harmonized throughout the entire process. We have presented four specific case studies on four different types of cancers, namely glioblastoma multiforme, head-neck, breast, and lung. We also present experimental validation on a few patients' data in these four areas. A few aspects are taken care of during de-identification, such as preservation of longitudinal date changes (LDC), incremental de-identification, referential data integrity between the clinical and image data, de-identified data harmonization, and transformation of the data to an underlined database schema.

Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response.

AtHMGB15 belongs to a group of ARID-HMG proteins which are plant specific. The presence of two known DNA binding domains: AT rich interacting domain (ARID) and High Mobility Group (HMG)-box, in one polypeptide, makes this protein intriguing. Although proteins containing individual HMG and ARID domains have been characterized, not much is known about the role of ARID-HMG proteins. Promoter analysis of AtHMGB15 showed the presence of various stress responsive cis regulatory elements along with MADS-box containing transcription factors. Our result shows that the expression of AtHMGB15 increased significantly upon application of cold stress. Using ChIP-chip approach, we have identified 6128 and 4689 significantly enriched loci having AtHMGB15 occupancy under control and cold stressed condition respectively. GO analysis shows genes belonging to abiotic stress response, cold response and root development were AtHMGB15 targets during cold stress. DNA binding and footprinting assays further identified A(A/C)--ATA---(A/T)(A/T) as AtHMGB15 binding motif. The enriched probe distribution in both control and cold condition shows a bias of AtHMGB15 binding towards the transcribed (gene body) region. Further, the expression of cold stress responsive genes decreased in athmgb15 knockout plants compared to wild-type. Taken together, binding enrichment of AtHMGB15 to the promoter and upstream to stress loci suggest an unexplored role of the protein in stress induced transcription regulation.

BIOINTMED: integrated biomedical knowledge base with ontologies and clinical trials.

Biomedical data are complex and heterogeneous. An ample reliable quantity of data is important for understanding and exploring the domain. The work aims to integrate biomedical data from various heterogeneous sources like dictionaries or corpus and amalgamate them into a uniform format for easier access by the end-user like biologist, pharmacist, and data scientist. The proposed integrated biomedical knowledge base, BIOINTMED, has 11,299, 12,981, 4428, 61,491, 48,663, and 13,146 unique entities for drugs, diseases, targets, genes, biomedical pathways, and adverse events, respectively. The uniform aggregated collection is also explored to study the interaction among these entity pairs. Finally, a complete statistical analysis of the consolidated biomedical entities is provided.

De-Identification of Radiomics Data Retaining Longitudinal Temporal Information.

We propose a de-identification system which runs in a standalone mode. The system takes care of the de-identification of radiation oncology patient's clinical and annotated imaging data including RTSTRUCT, RTPLAN, and RTDOSE. The clinical data consists of diagnosis, stages, outcome, and treatment information of the patient. The imaging data could be the diagnostic, therapy planning, and verification images. Archival of the longitudinal radiation oncology verification images like cone beam CT scans along with the initial imaging and clinical data are preserved in the process. During the de-identification, the system keeps the reference of original data identity in encrypted form. These could be useful for the re-identification if necessary.

Evidence of Robustness in a Two-Component System Using a Synthetic Circuit.

Variation in the concentration of biological components is inescapable for any cell. Robustness in any biological circuit acts as a cushion against such variation and enables the cells to produce homogeneous output despite the fluctuation. The two-component system (TCS) with a bifunctional sensor kinase (that possesses both kinase and phosphatase activities) is proposed to be a robust circuit. Few theoretical models explain the robustness of a TCS, although the criteria and extent of robustness by these models differ. Here, we provide experimental evidence to validate the extent of the robustness of a TCS signaling pathway. We have designed a synthetic circuit in Escherichia coli using a representative TCS of Mycobacterium tuberculosis, MprAB, and monitored the in vivo output signal by systematically varying the concentration of either of the components or both. We observed that the output of the TCS is robust if the concentration of MprA is above a threshold value. This observation is further substantiated by two in vitro assays, in which we estimated the phosphorylated MprA pool or MprA-dependent transcription yield by varying either of the components of the TCS. This synthetic circuit could be used as a model system to analyze the relationship among different components of gene regulatory networks.IMPORTANCE Robustness in essential biological circuits is an important feature of the living organism. A few pieces of evidence support the existence of robustness in vivo in the two-component system (TCS) with a bifunctional sensor kinase (SK). The assays were done under physiological conditions in which the SK was much lower than the response regulator (RR). Here, using a synthetic circuit, we varied the concentrations of the SK and RR of a representative TCS to monitor output robustness in vivo. In vitro assays were also performed under conditions where the concentration of the SK was greater than that of the RR. Our results demonstrate the extent of output robustness in the TCS signaling pathway with respect to the concentrations of the two components.

Development of Objective Evidence in Rorschach Ink Blot Test: An Eye Tracking Study.

The Rorschach inkblot test (RIBT) is a standardized projective technique. It uses a subjective way of collecting and mapping responses of different regions like large (D) and small details (d). In this paper, eye tracking parameters like Initial Fixation Location, SF Ratio, Mean Fixation Duration and Mean Return are used to develop some objective measures which would be helpful in the assessment of the Rorschach responses. The study was conducted on 25 normal subjects who were administered RIBT cards I, II and X. The result shows an initial tendency to fixate in the central regions of the Rorschach cards. Computation of SF ratio helps in understanding most frequently fixated regions leading to popular response. Certain locations of each card have high attentional value where most shifts and fixations occur. The study supplements to the information obtained by the subjective scoring of RIBT and also indicates that specific eye tracking parameters could be an objective marker for personality assessment with RIBT.

Stroke Volume, Ejection Fraction and Cardiac Health Monitoring using Impedance Cardiography.

In recent years occurrence of cardiac ailments have seen an exponential rise. In view of this it is highly important to monitor one's cardiac health. Currently employed methods for cardiac health monitoring are costly, require expert supervision and are available only at central hospitals. In order to overcome these obstacles, we have proposed a novel, non-invasive, cardiac health monitoring mechanism based on Impedance Cardiography (ICG). In this work we have proposed a methodolgy for determination of stroke volume (SV), left ventricular ejection fraction (LVEF), left ventricular end systolic volume (LVESV), and iso-volumetric relaxation time (IVRT), based on ICG. The proposed models report $\mathrm{r}^{2}$ values of 0.86, 0.97, 0.99, and 0.96 for SV, LVESV, LVEF, and IVRT, respectively. The proposed methodology also provides us an insight into the use of ICG for cardiac health monitoring, and diagnosis of critical cardiac ailments.

A transcriptomic analysis of the mycobacteriophage D29 genome reveals the presence of novel stoperator-associated promoters in its right arm.

Mycobacteriophage D29 is a lytic phage that infects various species of Mycobacterium including M. tuberculosis. Its genome has 77 genes distributed almost evenly between two converging operons designated as left and right. Transcription of the phage genome is negatively regulated by multiple copies of an operator-like element known as stoperator that acts by binding the phage repressor Gp71. The function of the D29 genes and their expression status are poorly understood and therefore we undertook a transcriptome analysis approach to address these issues. The results indicate that the average transcript intensity of the right arm genes was higher than of those on the left, at the early stage of infection. Moreover, the fold increase from early to the late stage was found to be less for the right arm genes than for the left. Both observations support the prediction that the right arm genes are expressed early whereas the left arm ones are expressed late. The analysis further revealed a break in the continuity of the right arm operon between 89, the first gene in it, and 88, the next. Gene 88 was found to be expressed from a newly identified promoter located between 88 and 89. Another new promoter was found upstream of 89. Thus, the promoter Pleft, identified earlier, is not the only one that drives expression of the right arm genes. All these promoters overlap with stoperators, with which they share a conserved sequence motif, TTGACA, commonly known as the -35 promoter element. We demonstrate mutually exclusive binding of RNA polymerase and Gp71 to the stoperator-promoters and conclude that stoperators can function as -35 promoter elements and that they can control gene expression not only negatively as was believed earlier but in many cases positively as well.

Mode of Action of a Designed Antimicrobial Peptide: High Potency against Cryptococcus neoformans.

There is a significant need for developing compounds that kill Cryptococcus neoformans, the fungal pathogen that causes meningoencephalitis in immunocompromised individuals. Here, we report the mode of action of a designed antifungal peptide, VG16KRKP (VARGWKRKCPLFGKGG) against C. neoformans. It is shown that VG16KRKP kills fungal cells mainly through membrane compromise leading to efflux of ions and cell metabolites. Intracellular localization, inhibition of in vitro transcription, and DNA binding suggest a secondary mode of action for the peptide, hinting at possible intracellular targets. Atomistic structure of the peptide determined by NMR experiments on live C. neoformans cells reveals an amphipathic arrangement stabilized by hydrophobic interactions among A2, W5, and F12, a conventional folding pattern also known to play a major role in peptide-mediated Gram-negative bacterial killing, revealing the importance of this motif. These structural details in the context of live cell provide valuable insights into the design of potent peptides for effective treatment of human and plant fungal infections.

A Novel Function of δ Factor from Bacillus subtilis as a Transcriptional Repressor.

δ, a small protein found in most Gram-positive bacteria was, for a long time, thought to be a subunit of RNA polymerase (RNAP) and was shown to be involved in recycling of RNAP at the end of each round of transcription. However, how δ participates in both up-regulation and down-regulation of genes in vivo remains unclear. We have recently shown, in addition to the recycling of RNAP, δ functions as a transcriptional activator by binding to an A-rich sequence located immediately upstream of the -35 element, consequently facilitating the open complex formation. The result had explained the mechanism of up-regulation of the genes by δ. Here, we show that Bacillus subtilis δ could also function as a transcriptional repressor. Our results demonstrate that δ binds to an A-rich sequence located near the -35 element of the spo0B promoter, the gene involved in the regulatory cascade of bacterial sporulation and inhibits the open complex formation due to steric clash with σ region 4.2. We observed a significant increase in the mRNA level of the spo0B gene in a δ-knock-out strain of B. subtilis compared with the wild-type. Thus, the results report a novel function of δ, and suggest the mechanism of down-regulation of genes in vivo by the protein.