Topology-mediated organization of Escherichia coli chromosome in fast-growth conditions.

The mechanism underlying the spatiotemporal chromosome organization in Escherichia coli cells remains an open question, though experiments have been able to visually see the evolving chromosome organization in fast- and slow-growing cells. We had proposed [D. Mitra et al.

Visualization of Electron Density Changes Along Chemical Reaction Pathways.

We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity S2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds.

Parkin coregulates glutathione metabolism in adult mammalian brain.

We recently discovered that the expression of PRKN, a young-onset Parkinson disease-linked gene, confers redox homeostasis. To further examine the protective effects of parkin in an oxidative stress model, we first combined the loss of prkn with Sod2 haploinsufficiency in mice. Although adult prkn//Sod2 animals did not develop dopamine cell loss in the S.

Topology-driven spatial organization of ring polymers under confinement.

Entropic repulsion between DNA ring polymers under confinement is a key mechanism governing the spatial segregation of bacterial DNA before cell division. Here we establish that "internal" loops within a modified-ring polymer architecture enhance entropic repulsion between two overlapping polymers confined in a cylinder. Interestingly, they also induce entropy-driven spatial organization of polymer segments as seen in vivo.

Polymer architecture orchestrates the segregation and spatial organization of replicating chromosomes in slow growth.

The mechanism of chromosome segregation and organization in the bacterial cell cycle of is one of the least understood aspects in its life cycle. The chromosome is often modelled as a bead spring ring polymer. We introduce cross-links in the DNA-ring polymer, resulting in the formation of loops within each replicating bacterial chromosome.

Glutathione-dependent thioredoxin reduction and lipoamide system support in-vitro mammalian ribonucleotide reductase catalysis: a possible antioxidant redundancy.

Background: The thioredoxin system (Trx), comprising of Trx, Thioredoxin reductase (TrxR) and NADPH aids in donating hydrogen group to support Ribonucleotide reductase (RNR) catalysis during de-novo DNA biosynthesis. However, it has been observed that inhibiting TrxR does not affect the viability of cancer cells that are susceptible to pharmacological glutathione (GSH) depletion. This prompted us to study the potential antioxidant redundancies that might prolong RNR activity.

Decision-making process for esthetic treatment of gummy smile: A surgical perspective.

Gummy smile is a quite frequently found esthetic alteration characterized by excessive display of gingiva during smiling. Several causes have been implicated in the literature, but a dearth of clinical decision-making process has been found in the surgical treatment of excessive gingival display. An external bevel gingivectomy with osseous correction was performed in anterior maxillary region in accordance with the proposed decision-making process.

Rigidity Dictates Spontaneous Helix Formation of Thermoresponsive Colloidal Chains in Poor Solvent.

The formation of helical motifs typically requires specific directional interactions. Here, we demonstrate that isotropic interparticle attraction can drive self-assembly of colloidal chains into thermo-reversible helices, for chains with a critical level of backbone rigidity. We prepare thermoresponsive colloidal chains by cross-linking PNIPAM microgel-coated polystyrene colloids ("monomers"), aligned in an AC electric field.

Experiences and perceptions of school staff regarding the COVID-19 pandemic and racial equity: The role of colorblindness.

As schools physically closed across the country to protect against the spread of the COVID-19 pandemic, it became clear early on that the burden on students will not be equally shared. Structural racism patterns the lives of people of color that, in turn, increases their exposure to the effects of the pandemic further impacting the quality of education the students of color have access to. It is critical to examine the ways in which racial disparities in social emotional and educational outcomes have the potential to increase as a result of the pandemic.

Ribonucleotide reductase: In-vitro S-glutathionylation of R2 and p53R2 subunits of mammalian class I ribonucleotide reductase protein.

Ribonucleotide reductases (RNR) catalyze the rate-limiting step in DNA synthesis during the S-phase of the cell cycle. Its constant activity in order to maintain dNTP homeostasis is a fascinating area of research and an attractive candidate for cancer research and antiviral drugs. Redox modification such as S-glutathionylation of the R1 subunit of mammalian RNR protein has been presumed to regulate the activity of RNR during catalytic cycles.

Stability of S-nitrosothiols and S-nitrosylated proteins: A struggle for cellular existence!

Nitric oxide is a well-known gasotransmitter molecule that covalently docks to sulfhydryl groups of proteins resulting in S-nitrosylation of proteins and nonprotein thiols that serve a variety of cellular processes including cGMP signaling, vasodilatation, neurotransmission, ion-channel modulation, and cardiac signaling. S-nitrosylation is an indispensable modification like phosphorylation that directly regulates the functionality of numerous proteins. However, recently there has been a controversy over the stability of S-nitrosylated proteins (PSNOs) within the cell.

Understanding the role of S-nitrosylation/nitrosative stress in inflammation and the role of cellular denitrosylases in inflammation modulation: Implications in health and diseases.

S-nitrosylation is a very fundamental post-translational modification of protein and non-protein thiols due the involvement of it in a variety of cellular processes including activation/inhibition of several ion channels such as ryanodine receptor in the cardiovascular system; blood vessel dilation; cGMP signaling and neurotransmission. S-nitrosothiol homeostasis in the cell is tightly regulated and perturbations in homeostasis result in an altered redox state leading to a plethora of disease conditions. However, the exact role of S-nitrosylated proteins and nitrosative stress metabolites in inflammation and in inflammation modulation is not well-reviewed.

Cellular S-denitrosylases: Potential role and interplay of Thioredoxin, TRP14, and Glutaredoxin systems in thiol-dependent protein denitrosylation.

Nitric Oxide is a very well known gaseous second messenger molecule and vasorelaxant agent involved in a variety of signaling in the body such as neurotransmission, ion channel modulation, and inflammation modulation. However, it's reversible covalent attachment to thiol groups of cysteine residues under nitrosative stress leading to aberrant protein S-nitrosylation (PSNO) has been reported in several pathological conditions in the body stemming from neurodegenerative diseases, cancer, cardiovascular system, and immune system disorders. In the cell, PSNOs are partly unstable and transit to a more stable disulfide state serving as an intermediate step towards disulfide formation thus eliciting the biological response.

Neuron-glia: understanding cellular copper homeostasis, its cross-talk and their contribution towards neurodegenerative diseases.

Over the years, the mechanism of copper homeostasis in various organ systems has gained importance. This is owing to the involvement of copper in a wide range of genetic disorders, most of them involving neurological symptoms. This highlights the importance of copper and its tight regulation in a complex organ system like the brain.

Structural Characterization and Antioxidant Potential of Chitosan by γ-Irradiation from the Carapace of Horseshoe Crab.

Natural product extraction is ingenuity that permits the mass manufacturing of specific products in a cost-effective manner. With the aim of obtaining an alternative chitosan supply, the carapace of dead horseshoe crabs seemed feasible. This sparked an investigation of the structural changes and antioxidant capacity of horseshoe crab chitosan (HCH) by γ-irradiation using Co source.

Transient helix formation in charged semiflexible polymers without confinement effects.

Switching on generic interactions e.g. the Coulomb potential or other long ranged spherically symmetric repulsive interactions between monomers of bead-spring model of a semi-flexible polymer induce instabilities in a semiflexible polymer chain to form transient helical structures.

Differential tissue stiffness of body column facilitates locomotion of on solid substrates.

The bell-shaped members of the Cnidaria typically move around by swimming, whereas the polyp can perform locomotion on solid substrates in an aquatic environment. To address the biomechanics of locomotion on rigid substrates, we studied the 'somersaulting' locomotion in We applied atomic force microscopy to measure the local mechanical properties of 's body column and identified the existence of differential Young's modulus between the shoulder region versus rest of the body column at 3:1 ratio. We show that somersaulting primarily depends on differential tissue stiffness of the body column and is explained by computational models that accurately recapitulate the mechanics involved in this process.

Characterization dataset for pre- and post-irradiated shrimp waste chitosan.

This dataset presents morphological features, elemental composition and functional groups of different pre- and post-gamma (γ)-irradiated chitosan (10kGy & 20kGy) prepared from shrimp waste. The γ-irradiated chitosan was characterized using Fourier transfer infrared (FTIR) spectroscopy and X-ray diffraction (XRD) analyses. Thermogravimetry/differential thermal analysis (TG/DTA) were performed using Perkin Elmer Pyris Diamond DSC with a heating rate of 10 °C/minute and dynamic synthetic atmospheric air set at flow rate of 100 ml/minute.

Environmental effects on the oxygen consumption rate in juvenile Epinephelus fuscoguttatus (Forsskal, 1775).

This study was designed to optimize the culture conditions of juvenile Epinephelus fuscoguttatus (Forsskål, 1775) under laboratory conditions. To this effect, the rate of oxygen consumption was monitored as an index of stress under different temperature, salinity, pH, photoperiod, and urea concentrations. The result obtained after 12 h of exposure suggests the preference of the juvenile E.

Three-Component Approach to Pyridine-Stabilized Ketenimines for the Synthesis of Diverse Heterocycles.

Ketenimines are versatile synthetic intermediates capable of performing novel transformations in organic synthesis. They are normally generated in situ due to their inherent instability and high level of reactivity. Herein, we report pyridine-stabilized ketenimine zwitterionic salts, which are prepared through click chemistry from readily accessible alkynes and sulfonyl azides.

Hierarchical and synergistic self-assembly in composites of model wormlike micellar-polymers and nanoparticles results in nanostructures with diverse morphologies.

Using Monte Carlo simulations, we investigate the self-assembly of model nanoparticles inside a matrix of model equilibrium polymers (or matrix of wormlike micelles) as a function of the polymeric matrix density and the excluded volume parameter between polymers and nanoparticles. In this paper, we show morphological transitions in the system architecture via synergistic self-assembly of nanoparticles and the equilibrium polymers. In a synergistic self-assembly, the resulting morphology of the system is a result of the interaction between the nanoparticles and the polymers and corresponding re-organization of both the assemblies.

Bacterial chromosome organization. II. Few special cross-links, cell confinement, and molecular crowders play the pivotal roles.

Using a coarse-grained bead-spring model of bacterial chromosomes of Caulobacter crescentus and Escherichia coli, we show that just 33 and 38 effective cross-links in 4017 and 4642 monomer chains at special positions along the chain contour can lead to the large-scale organization of the DNA polymer, where confinement effects of the cell walls play a key role in the organization. The positions of the 33/38 cross-links along the chain contour are chosen from the Hi-C contact map of bacteria C. crescentus and E.

Bacterial chromosome organization. I. Crucial role of release of topological constraints and molecular crowders.

We showed in our previous studies that just 3% cross-links (CLs), at special points along the contour of the bacterial DNA, help the DNA-polymer to get organized at micron length scales [T. Agarwal et al., J.

Stereoselective Synthesis of Diverse Lactones through a Cascade Reaction of Rhodium Carbenoids with Ketoacids.

A convergent cascade approach for the stereoselective synthesis of diverse lactones is described. The Rh(TFA)-catalyzed cascade reaction proceeds via a carboxylic acid O-H insertion/aldol cyclization with high chemo-, regio-, and diastereoselectivity. The cascade reaction provides quick access to highly functionalized γ-butyro- and δ-valerolactones from readily accessible ketoacid and diazo synthons.