cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13482369
title: PluriMetNet: A dynamic electronic model decrypting the metabolic variations in human embryonic stem cells (hESCs) at fluctuating oxygen concentrations

description: Stem cells are an excellent resource in translational medicine however much is known only in terms of transcriptional and epigenetic regulation of human embryonic stem cells (hESCs). Metabolic regulation of hESCs is still unexplored in many ways, particularly the role of energy metabolism, which is intrinsic to the maintenance of cell viability, however, is very little explored in the past years. Also, there exists no hESC specific core metabolic model of pluripotency as per our knowledge. Through our work, we establish such a metabolic model of hESC using combinatorial in-silico approach of genome scale model reduction and literature curation. Further, through perturbations taking oxygen as a parameter we propose that under lower levels of oxygen concentration there is a significant dynamic change in the energy metabolism of the hESC. We further investigated energy subsystem pathways and their respective reactions in order to locate the direction of energy production along with the dynamic of nutrient metabolites like glucose and glutamine. The output shows a steep increment/decrement at a certain oxygen range. These sharp increments/decrements under hypoxic conditions are termed here as a critical range for hESC metabolic pathway. The data also resonates with the previous experimental studies on hESC energy metabolism confirming the robustness of our model. The model helps to extract range for different pathways in the energy subsystem, making us a little closer in understanding the metabolism of hESC. We also demonstrated the possible range of pathway changes in hESC's energy metabolism that can serve as the crucial preliminary data for further prospective studies. The model also offers a promise in the prediction of the flux behaviour of various metabolites in hESC. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13482369.v1
title: PluriMetNet: A dynamic electronic model decrypting the metabolic variations in human embryonic stem cells (hESCs) at fluctuating oxygen concentrations

description: Stem cells are an excellent resource in translational medicine however much is known only in terms of transcriptional and epigenetic regulation of human embryonic stem cells (hESCs). Metabolic regulation of hESCs is still unexplored in many ways, particularly the role of energy metabolism, which is intrinsic to the maintenance of cell viability, however, is very little explored in the past years. Also, there exists no hESC specific core metabolic model of pluripotency as per our knowledge. Through our work, we establish such a metabolic model of hESC using combinatorial in-silico approach of genome scale model reduction and literature curation. Further, through perturbations taking oxygen as a parameter we propose that under lower levels of oxygen concentration there is a significant dynamic change in the energy metabolism of the hESC. We further investigated energy subsystem pathways and their respective reactions in order to locate the direction of energy production along with the dynamic of nutrient metabolites like glucose and glutamine. The output shows a steep increment/decrement at a certain oxygen range. These sharp increments/decrements under hypoxic conditions are termed here as a critical range for hESC metabolic pathway. The data also resonates with the previous experimental studies on hESC energy metabolism confirming the robustness of our model. The model helps to extract range for different pathways in the energy subsystem, making us a little closer in understanding the metabolism of hESC. We also demonstrated the possible range of pathway changes in hESC's energy metabolism that can serve as the crucial preliminary data for further prospective studies. The model also offers a promise in the prediction of the flux behaviour of various metabolites in hESC. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13397230
title: Biophysical binding profile with ct-DNA and cytotoxic studies of a modulated nanoconjugate of umbelliferone cobalt oxide loaded on graphene oxide (GO) as drug carrier

description: In an attempt to identify suitable nano-carriers for drug delivery, natural drug umbelliferone was chosen to synthesize new modulated nanoconjugate of umbelliferone cobalt oxide with cobalt (II) nitrate in one pot assembly in the presence of tannic acid. The synthesized nanoconjugate drug (NCD) was then loaded on graphene oxide (GO) as drug carrier by simple ultrasonication method and thoroughly characterized by various spectroscopic techniques (FT-IR, SEM, TEM, XRD, EPR and thermogravimetric analysis) which revealed the successful loading of the nanoconjugate drug on GO. The UV-visible, fluorescence and electrochemical studies suggested that strong π-π stacking interactions exist between nanoconjugate drug and GO. The binding studies of NCD-GO with ct-DNA were performed by various optical and biophysical methods <i>viz.</i>, UV-visible, fluorescence, circular dichroism (CD) and cyclic voltammetry (CV) which indicated electrostatic mode of binding towards the ct-DNA. Furthermore, condensate of nanoconjugate drug-loaded GO (NCD-GO) with ct-DNA was prepared and analyzed by scanning electron microscopy (SEM) which revealed that the interaction of NCD-GO with ct-DNA had occurred. Cleavage activity of NCD-GO with pBR322 was evaluated by gel electrophoresis and it was found that NCD-GO cleave DNA through hydrolytic pathway involving hydroxyl radical (OH). The cytotoxicity of NCD-GO was evaluated against human liver carcinoma (Huh-7), prostate cancer (Du-145) cell lines along with normal cell line (PNT 2). The results obtained showed selective cytotoxic activity of NCD-GO against Du-145 cell lines. The intracellular uptake was visualized by confocal microscopy which revealed the significant cellular uptake and internalization of nanoparticles by cells. Moreover, the adsorption of cobalt oxide umbelliferone on GO was studied by density functional theory. The process of adsorption was found exothermic in nature and the optimized geometry structure is quite stable. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13397230.v1
title: Biophysical binding profile with ct-DNA and cytotoxic studies of a modulated nanoconjugate of umbelliferone cobalt oxide loaded on graphene oxide (GO) as drug carrier

description: In an attempt to identify suitable nano-carriers for drug delivery, natural drug umbelliferone was chosen to synthesize new modulated nanoconjugate of umbelliferone cobalt oxide with cobalt (II) nitrate in one pot assembly in the presence of tannic acid. The synthesized nanoconjugate drug (NCD) was then loaded on graphene oxide (GO) as drug carrier by simple ultrasonication method and thoroughly characterized by various spectroscopic techniques (FT-IR, SEM, TEM, XRD, EPR and thermogravimetric analysis) which revealed the successful loading of the nanoconjugate drug on GO. The UV-visible, fluorescence and electrochemical studies suggested that strong π-π stacking interactions exist between nanoconjugate drug and GO. The binding studies of NCD-GO with ct-DNA were performed by various optical and biophysical methods <i>viz.</i>, UV-visible, fluorescence, circular dichroism (CD) and cyclic voltammetry (CV) which indicated electrostatic mode of binding towards the ct-DNA. Furthermore, condensate of nanoconjugate drug-loaded GO (NCD-GO) with ct-DNA was prepared and analyzed by scanning electron microscopy (SEM) which revealed that the interaction of NCD-GO with ct-DNA had occurred. Cleavage activity of NCD-GO with pBR322 was evaluated by gel electrophoresis and it was found that NCD-GO cleave DNA through hydrolytic pathway involving hydroxyl radical (OH). The cytotoxicity of NCD-GO was evaluated against human liver carcinoma (Huh-7), prostate cancer (Du-145) cell lines along with normal cell line (PNT 2). The results obtained showed selective cytotoxic activity of NCD-GO against Du-145 cell lines. The intracellular uptake was visualized by confocal microscopy which revealed the significant cellular uptake and internalization of nanoparticles by cells. Moreover, the adsorption of cobalt oxide umbelliferone on GO was studied by density functional theory. The process of adsorption was found exothermic in nature and the optimized geometry structure is quite stable. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13416098.v1
title: Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

description: Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13416098
title: Investigation of nanotubes as the smart carriers for targeted delivery of mercaptopurine anticancer drug

description: Mercaptopurine (MCP) is an anticancer drug that is used to treat acute lymphoblastic leukemia. The therapeutic effect of the mercaptopurine limits its severe side effects like other cytotoxic (anti-cancer) drugs. Nanostructures or nanoparticles can be widely used as potential drug carriers for diagnosis and treatment of cancer. In the current study, the boron nitride nanotube (BNNT) and carbon nanotube (CNT) were studied as the delivery carriers of MCP using the density functional theory (DFT) calculations and molecular dynamics (MDs) simulation studies. To further understand the electronic properties of mercaptopurine, the partial density of states (PDOS) was calculated. The PDOS results depicted that the electronic features of the MCP do not change after the adsorption on the surface of the nanotubes. More stability of the MCP/BNNT complexes may be attributed to the existence of the intermolecular hydrogen bonds (H-bonds) between the hydrogen atoms of the MCP molecule and the N atoms of the BNNT. The results of the quantum theory of atoms in molecules (QTAIM) confirmed the presence of H-bonds in these complexes. Moreover, MD simulation studies were done in the presence of five drug molecules. The results revealed that the strongest van der Waals (vdW) interaction energy was found between the BNNT and MCP among the studied nanotubes, indicating the BNNT is a better nanocarrier than carbon nanotube for delivery of the MCP drug within the biological systems. In general, the obtained results may present helpful information on the nature of the interactions between mercaptopurine anticancer drug with BNNT and/or CNT. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13482388.v1
title: Structure and dynamics of membrane protein in SARS-CoV-2

description: SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (&gt;30% sequence identities) leads us to construct the membrane protein models using template-free modeling (<i>de novo</i> or <i>ab initio</i>) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13378817
title: The cytoplasmic tail of influenza A/H1N1 virus hemagglutinin is β-structural

description: Influenza A/H1N1 virus hemagglutinin (HA) is an integral type I glycoprotein that contains a large glycosylated ectodomain, a transmembrane domain, and a cytoplasmic tail (CT) of 10-14 amino acid residues. There are absolutely no data on the secondary or tertiary structure of the HA CT, which is important for virus pathogenesis. Three highly conserved cysteines are post-translationally modified by the attachment of fatty acid residues that pin the CT to the lipid membrane inside the virion. We applied circular dichroism (CD) and fluorescence spectroscopy analysis to examine four synthetic peptides corresponding to 14-15 C-terminal residues of H1 subtype HA (NH<sub>2</sub>-WMCSNGSLQCRICI-COOH; NH<sub>2</sub>-FWMCSNGSLQCRICI-COOH), with free or acetaminomethylated cysteines, in the reduced or non-reduced state, at various pH values and temperatures. The CD analysis detected the formation of a β-structure (30–65% according to the new BeStSel algorithm), in addition to an unstructured random coil, in every peptide in various conditions. It was completely or partially recognized as an antiparallel β-structure that was also confirmed by the multi-bounce Horizontal Attenuated Total Reflectance Fourier Transformed Infrared (HATR-FTIR) spectroscopy analysis. According to the experimental data, as well as 3 D modeling, we assume that the amino acid sequence corresponding to the HA CT may form a short antiparallel β-structure under the lipid membrane within a virion. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13378817.v1
title: The cytoplasmic tail of influenza A/H1N1 virus hemagglutinin is β-structural

description: Influenza A/H1N1 virus hemagglutinin (HA) is an integral type I glycoprotein that contains a large glycosylated ectodomain, a transmembrane domain, and a cytoplasmic tail (CT) of 10-14 amino acid residues. There are absolutely no data on the secondary or tertiary structure of the HA CT, which is important for virus pathogenesis. Three highly conserved cysteines are post-translationally modified by the attachment of fatty acid residues that pin the CT to the lipid membrane inside the virion. We applied circular dichroism (CD) and fluorescence spectroscopy analysis to examine four synthetic peptides corresponding to 14-15 C-terminal residues of H1 subtype HA (NH<sub>2</sub>-WMCSNGSLQCRICI-COOH; NH<sub>2</sub>-FWMCSNGSLQCRICI-COOH), with free or acetaminomethylated cysteines, in the reduced or non-reduced state, at various pH values and temperatures. The CD analysis detected the formation of a β-structure (30–65% according to the new BeStSel algorithm), in addition to an unstructured random coil, in every peptide in various conditions. It was completely or partially recognized as an antiparallel β-structure that was also confirmed by the multi-bounce Horizontal Attenuated Total Reflectance Fourier Transformed Infrared (HATR-FTIR) spectroscopy analysis. According to the experimental data, as well as 3 D modeling, we assume that the amino acid sequence corresponding to the HA CT may form a short antiparallel β-structure under the lipid membrane within a virion. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13482388
title: Structure and dynamics of membrane protein in SARS-CoV-2

description: SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (&gt;30% sequence identities) leads us to construct the membrane protein models using template-free modeling (<i>de novo</i> or <i>ab initio</i>) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.6584574
title: Extended Data for Manuscript titled "Hydrothermal Carbonization (HTC) of Dairy Waste: Effect of Temperature and Initial Acidity on the composition and quality of solid and liquid products"

description: The document includes extended data for the manuscript titled "Hydrothermal Carbonization (HTC) of Dairy Waste: Effect of Temperature and Initial Acidity on the composition and quality of solid and liquid products". The data involved includes tables for the raw data of yield and recovery calculations, in addition to defining analysis methods for the solid and liquid products of the experimental reactions at the heart of the manuscript.
DOI: 10.5281/zenodo.6584573
title: Extended Data for Manuscript titled "Hydrothermal Carbonization (HTC) of Dairy Waste: Effect of Temperature and Initial Acidity on the composition and quality of solid and liquid products"

description: The document includes extended data for the manuscript titled "Hydrothermal Carbonization (HTC) of Dairy Waste: Effect of Temperature and Initial Acidity on the composition and quality of solid and liquid products". The data involved includes tables for the raw data of yield and recovery calculations, in addition to defining analysis methods for the solid and liquid products of the experimental reactions at the heart of the manuscript.
DOI: 10.6084/m9.figshare.14459964
title: Temperature-induced compensatory growth in the nematode C. elegans is regulated by a thermosensitive TRP channel and influences reproductive rate

description: We set to measure compensatory growth and slowed-down plasticity, and its consequences for age-specific reproduction and lifespan in wild-type <i>Caenorhabditis elegans</i> worms as well as worms with a null-mutation in the <i>trpa-1</i> gene. Newly laid eggs of worms were exposed to one of three temperatures: 15°C, 20°C or 25°C until they reached third larval stage whereafter we moved them to standard temperature (20°C). To asses growth rate we photographed worms every 24h for five consecutive days (since switch to 20°C). We analyzed the photographs using ImageJ to calculate the total area of the worms and we calculated growth rate as the size of a worm each day, divided by the number of days since the switch to 20°C. We checked worms every 24h to assess lifespan and if still alive, we moved them to a new plate. We kept the old plates to allow eggs to hatch, and after 48h we counted offspring to asses a daily fecundity.
DOI: 10.6084/m9.figshare.14459964.v4
title: Temperature-induced compensatory growth in the nematode C. elegans is regulated by a thermosensitive TRP channel and influences reproductive rate

description: We set to measure compensatory growth and slowed-down plasticity, and its consequences for age-specific reproduction and lifespan in wild-type <i>Caenorhabditis elegans</i> worms as well as worms with a null-mutation in the <i>trpa-1</i> gene. Newly laid eggs of worms were exposed to one of three temperatures: 15°C, 20°C or 25°C until they reached third larval stage whereafter we moved them to standard temperature (20°C). To asses growth rate we photographed worms every 24h for five consecutive days (since switch to 20°C). We analyzed the photographs using ImageJ to calculate the total area of the worms and we calculated growth rate as the size of a worm each day, divided by the number of days since the switch to 20°C. We checked worms every 24h to assess lifespan and if still alive, we moved them to a new plate. We kept the old plates to allow eggs to hatch, and after 48h we counted offspring to asses a daily fecundity.
DOI: 10.6084/m9.figshare.14459964.v3
title: Temperature-induced compensatory growth in C. elegans is regulated by a thermosensitive TRP channel and influences reproductive rate

description: We set to measure compensatory growth and slowed-down plasticity, and its consequences for age-specific reproduction and lifespan in wild-type <i>Caenorhabditis elegans</i> worms as well as worms with a null-mutation in the <i>trpa-1</i> gene. Newly laid eggs of worms were exposed to one of three temperatures: 15°C, 20°C or 25°C until they reached third larval stage whereafter we moved them to standard temperature (20°C). To asses growth rate we photographed worms every 24h for five consecutive days (since switch to 20°C). We analyzed the photographs using ImageJ to calculate the total area of the worms and we calculated growth rate as the size of a worm each day, divided by the number of days since the switch to 20°C. We checked worms every 24h to assess lifespan and if still alive, we moved them to a new plate. We kept the old plates to allow eggs to hatch, and after 48h we counted offspring to asses a daily fecundity.