Free energy calculations for membrane morphological transformations and insights to physical biology and oncology.

In this chapter, we aim to bridge basic molecular and cellular principles surrounding membrane curvature generation with rewiring of cellular signals in cancer through multiscale models. We describe a general framework that integrates signaling with other cellular functions like trafficking, cell-cell and cell-matrix adhesion, and motility. The guiding question in our approach is: how does a physical change in cell membrane configuration caused by external stimuli (including those by the extracellular microenvironment) alter trafficking, signaling and subsequent cell fate? We answer this question by constructing a modeling framework based on stochastic spatial continuum models of cell membrane deformations. We apply this framework to explore the link between trafficking, signaling in the tumor microenvironment, and cell fate. At each stage, we aim to connect the results of our predictions with cellular experiments.

Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology.

A definitive understanding of the interplay between protein binding/migration and membrane curvature evolution is emerging but needs further study. The mechanisms defining such phenomena are critical to intracellular transport and trafficking of proteins. Among trafficking modalities, exosomes have drawn attention in cancer research as these nano-sized naturally occurring vehicles are implicated in intercellular communication in the tumor microenvironment, suppressing anti-tumor immunity and preparing the metastatic niche for progression. A significant question in the field is how the release and composition of tumor exosomes are regulated. In this perspective article, we explore how physical factors such as geometry and tissue mechanics regulate cell cortical tension to influence exosome production by co-opting the biophysics as well as the signaling dynamics of intracellular trafficking pathways and how these exosomes contribute to the suppression of anti-tumor immunity and promote metastasis. We describe a multiscale modeling approach whose impact goes beyond the fundamental investigation of specific cellular processes toward actual clinical translation. Exosomal mechanisms are critical to developing and approving liquid biopsy technologies, poised to transform future non-invasive, longitudinal profiling of evolving tumors and resistance to cancer therapies to bring us one step closer to the promise of personalized medicine.

Digital Technology in Hospital Administration: A Strategic Choice.

Digital technology has encompassed all aspects of healthcare. There are many international and national organizations, guidelines, and formats available in health information systems (HIS), but many are presently still not being used in India. The aim is to give a flawless, secure, and user-friendly health information technology (IT) system for Indian healthcare. We discuss the timeline of digital technology in hospital administration, administrative applications, and the importance of clinical quality in health. Clinical perspectives of clinical information systems (CIS), both in acute as well as chronic clinical care models. Cross-integration of healthcare in IT (HIT) in electronic health records (EHR) or electronic medical records (EMRs), in chronic disease management (CDM) systems, and in clinical decision support systems (CDSS) are elaborated. Also, practical strategic application methods are discussed. The limitations of the current HIS software in India are mostly used for transaction reporting, prescription, and administrative tools. They lack CIS and strategic business applications as compared to mature multinational company (MNC) HIS software. Along with this, various features and levels of HIS Software, challenges of HIT adoption, Indian health IT standards, and the future framework of IT in health in India are systematically analyzed. We aim at all physicians in India and at all levels of practice, from individuals, group practices, health institutes, or corporate hospitals, and to encourage them to make strategic use of CIS and strategic IT applications in their individual practice and hospital management. This will improve clinical outcomes, patient safety, practitioner performance, adherence to treatment guidelines, and reduction in medical errors, along with efficiency improvements and cost reductions. How to cite this article: Taneja D, Kulkarni SV, Sinha S, et al. Digital Technology in Hospital Administration: A Strategic Choice. J Assoc Physicians India 2023;71(10):83-88.

Approach to Management of Cerebrospinal Fluid Rhinorrhea: Institutional Based Protocol.

The role of otolaryngologist in the management of CSF rhinorrhea is expanding. It is prudent to evaluate all cases of CSF leak, understand the etiological causes and formalize a working approach to management of such cases to yield better outcome. A retrospective descriptive study of 39 cases of proven CSF rhinorrhea treated at a tertiary care center between January 2014 to August 2019. The data retrieved were analyzed for age, gender, weight, etiology, recurrence of the disease, history of meningitis, nasal or neurosurgical intervention in past, imaging inform of CT and MR cisternography as and when required. This was aimed at understanding the various etiological types of CSF rhinorrhea and work out a management approach. The patients with skullbase tumors who presented with CSF Rhinorrhea were excluded from the study sample. There were 18 cases of spontaneous CSF rhinorrhea and 20 cases of traumatic CSF rhinorrhea. The mean BMI of spontaneous gp was 32.9 ± 2.46 kg/m2 while in traumatic group was 25.7 ± 2.94 kg/m2 and difference was statistically significant. None of the spontaneous CSF rhinorrhea cases showed features of raised ICP preoperatively either clinically or on imaging except empty sella in 14 of 18 cases. 6 of 18 cases of spontaneous category while 01 of 20 cases in traumatic had recurrence and the recurrence rate was significantly (p < 0.05) higher in spontaneous group. In traumatic group 7 were iatrogenic, 8 were occult traumatic and rest were acute traumatic. 4 of traumatic and 1 spontaneous group had history of meningitis and the incidence was 12.8% in our study group. Early identification and localization of CSF fistula is necessary to reduce morbidity and mortality associated with it. Risk of meningitis is high in CSF rhinorrhea especially in traumatic group. The etiology of CSF rhinorrhea has a bearing on the management and spontaneous CSF rhinorrhea has higher rate of recurrence.

Quantification of Curvature Sensing Behavior of Curvature-Inducing Proteins on Model Wavy Substrates.

Curvature-inducing proteins are involved in a variety of membrane remodeling processes in the cell. Several in vitro experiments have quantified the curvature sensing behavior of these proteins in model lipid systems. One such system consists of a membrane bilayer laid atop a wavy substrate (Hsieh in Langmuir 28:12838-12843, 2012). In these experiments, the bilayer conforms to the wavy substrate, and curvature-inducing proteins show preferential segregation on the wavy membrane. Using a mesoscale computational membrane model based on the Helfrich Hamiltonian, here we present a study which analyzes the curvature sensing characteristics of this membrane-protein system, and elucidates key physical principles governing protein segregation on the wavy substrate and other in vitro systems. In this article we compute the local protein densities from the free energy landscape associated with membrane remodeling by curvature-inducing proteins. In specific, we use the Widom insertion technique to compute the free energy landscape for an inhomogeneous system with spatially varying density and the results obtained with this minimal model show excellent agreement with experimental studies that demonstrate the association between membrane curvature and local protein density. The free energy-based framework employed in this study can be used for different membrane morphologies and varied protein characteristics to gain mechanistic insights into protein sorting on membranes.

Late blight in tomato: insights into the pathogenesis of the aggressive pathogen Phytophthora infestans and future research priorities.

MAIN CONCLUSION: This review provides insights into the molecular interactions between Phytophthora infestans and tomato and highlights research gaps that need further attention. Late blight in tomato is caused by the oomycota hemibiotroph Phytophthora infestans, and this disease represents a global threat to tomato farming. The pathogen is cumbersome to control because of its fast-evolving nature, ability to overcome host resistance and inefficient natural resistance obtained from the available tomato germplasm. To achieve successful control over this pathogen, the molecular pathogenicity of P. infestans and key points of vulnerability in the host plant immune system must be understood. This review primarily focuses on efforts to better understand the molecular interaction between host pathogens from both perspectives, as well as the resistance genes, metabolomic changes, quantitative trait loci with potential for improvement in disease resistance and host genome manipulation via transgenic approaches, and it further identifies research gaps and provides suggestions for future research priorities.

SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches.

SUMMARY: Bistable biochemical switches are key motifs in cellular state decisions and long-term storage of cellular 'memory'. There are a few known biological switches that have been well characterized, however, these examples are insufficient for systematic surveys of properties of these important systems. Here we present a resource of all possible bistable biochemical reaction networks with up to six reactions between three molecules, and three reactions between four molecules. Over 35 000 reaction topologies were constructed by identifying unique combinations of reactions between a fixed number of molecules. Then, these topologies were populated with rates within a biologically realistic range. The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over seven million models from this systematic survey of chemical reaction space. This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at https://switches.ncbs.res.in. Website implemented in PHP, MariaDB, Graphviz and Apache, with all major browsers supported.

Scattering Matrix Approach to Design of One-Port Surface Acoustic Wave Resonator Sensors Utilizing Reflectors as Sensing Element.

It has been recently demonstrated that one-port surface acoustic wave (SAW) resonators known for their high Q value and relatively small device footprint could be utilized for in-liquid mass loading sensing applications where only the reflectors of the device are coated with the sensing film, while the interdigital transducer (IDT) is isolated from the sensing environment. The sensor relies on changes induced in reflectivity and phase velocity of SAW in the region of the reflectors upon detection of the measurand and is particularly advantageous for SAW resonator-type sensors as any contact of the sensing film with the IDT could change its static capacitance during sensing and thereby introduce serious instability in the sensor response. Accordingly, in the present work, the existing scattering matrix approach to the design of one-port SAW resonator filters, which does not cater to the integration of sensing film on the resonator surface, is adapted to develop a method to design one-port SAW resonator sensors utilizing reflectors as sensing element. The reflector block of the one-port SAW resonator is readily split into sensing-active and sensing-inactive parts using the SAW grating transmission matrix in order to study the changes introduced in input admittance of the device for varying level of coverage of the sensing film. The theoretical design approach presented in this work could be used to fabricate high-performance one-port SAW resonator sensors operating at its point of highest sensitivity while utilizing one of the device reflectors as sensing element, without the use of additional impedance matching circuit elements.

Tracheostomy: Open Surgical or Percutaneous? An Effort to Solve the Continued Dilemma.

Due to lack of globally standardized guidelines and clarity on indications, patient selection, intra-operative preparations, technique, complications, postoperative care and decannulation protocols, percutaneous tracheostomy (PT) has come in vogue as compared to standard open surgical tracheostomy (OST). PercuTwist and guide wire dilatational method (GWDF), techniques of PT, offer lesser operative time and ease of surgery being a bedside procedure. There seems to be paucity of Indian literature on rising trend of increasing indications, post-operative care, management of complications and outcomes of tracheostomy. And thus, there arises a felt need to envisage a study in tertiary care setup targeting these issues and to question the so far unchallenged acceptance of new techniques and technology. Our aim is to study the recent trend of indications, complications, and outcomes of both OST and PT in a cohort of Indian patients who underwent tracheostomy. 80 patients with mean age of 59.0 ± 15 years underwent tracheostomy (OST: 48 (60%), PT: 32 (40%), and among PT, PercuTwist: 16 (50%), GWDF: 16 (50%)) for various indications with objectives to compare operative time, complications and decannulation rates of tracheostomy surgery, within the follow up period of 3 months. Most common indication of elective tracheostomy was prolonged ventilation, and for emergency ones, upper airway obstruction. Mean operative time taken by all the three techniques was comparable, i.e., 16.3 v/s 15 v/s 15.3 min (Open v/s PT GWDF v/s PT PercuTwist). Most common intra-operative complication of OST was haemorrhage (16.3%) and that of PT was false passage (8.8%). Early post-operative complications were haemorrhage (OST: 3.75%, PT: 1.25%) and tube blockage and dislodgement (equal distribution among OST and PT). Late post-operative complications were stomal granulations in PT: 7.5%. Outcomes of tracheostomy were significantly better with OST (36 (45%)) than PT (14 (17.5%)). In PT group, PercuTwist fared better than GWDF in terms of lesser complications (PercuTwist: 10%, GWDF: 18.6%) and better decannulation rates (PercuTwist: 13.6%, GWDF: 3.75%). Most common indication for tracheostomy remains prolonged intubation; complication of OST is intra and early post-operative haemorrhage and that of PT being tube dislodgement and blockage. Outcomes in form of successful decannulation are with OST.

Nanofluid Dynamics of Flexible Polymeric Nanoparticles Under Wall Confinement.

Describing the hydrodynamics of nanoparticles in fluid media poses interesting challenges due to the coupling between the Brownian and hydrodynamic forces at the nanoscale. We focus on multiscale formulations of Brownian motion and hydrodynamic interactions (HI) of a single flexible polymeric nanoparticle in confining flows using the Brownian Dynamics method. The nanoparticle is modeled as a self-avoiding freely jointed polymer chain that is subject to Brownian forces, hydrodynamics forces, and repulsive interactions with the confining wall. To accommodate the effect of the wall, the hydrodynamic lift due to the wall is included in the mobility of a bead of the polymer chain which depends on its proximity to the wall. Using the example of a flexible polymeric nanoparticle, we illustrate temporal dynamics pertaining to the colloidal scale as well as the nanoscale.

Tubulation pattern of membrane vesicles coated with biofilaments.

Narrow membrane tubes are commonly pulled out from the surface of phospholipid vesicles using forces applied either through laser or magnetic tweezers or through the action of processive motor proteins. Recent examples have emerged in which an array of such tubes grows spontaneously from vesicles coated with bioactive cytoskeletal filaments (e.g., FtsZ, microtubule) in the presence GTP or ATP. We show how a soft vesicle deforms as a result of the interplay between its topology, local curvature, and the forces due to filament bundles. We present results from dynamically triangulated Monte Carlo simulations of a closed membrane vesicle coated with a nematic field (the filaments), and we show how the intrinsic curvature of the filaments and their bundling interactions drive membrane tubulation. We predict interesting patterns consisting of a large number of nematic defects that accompany tubulation. A common theme emerges: defect locations on vesicle surfaces are hot spots of membrane deformation activity, which could be useful for vesicle origami. Although our equilibrium model is not applicable to the nonequilibrium shape dynamics exhibited by active microtubule-coated vesicles, we show that some of the features, such as the size-dependent vesicle shape and the number of tubes, can still be understood from our equilibrium model.

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales.

At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.

Evaluation of nasal obstruction in lowlander males in high altitude.

BACKGROUND: Nasal symptoms are a major problem affecting the quality of life of lowlanders deployed at high altitude. Study was carried out in fresh male inductees inducted in high altitude of 11,500 ft (3500 m) above sea level to evaluate the nasal obstruction using the subjective Nasal obstruction and symptom evaluation (NOSE) score and rhinomanometry during the stay in high altitude. METHODS: A prospective study was carried out in 100 males inducted into high altitude. The subjects were evaluated using the subjective assessment tool, NOSE scale and rhinomanometry on induction and after 2 months. The data were analysed for NOSE scale in the 1st and 2nd visit by test for equality of proportions and the total nasal airway resistance (Pa) has been expressed as mean ± standard deviation and compared across severity of NOSE score using one way ANOVA and between 1st and 2nd visit using paired t test. RESULTS AND CONCLUSIONS: Out of the 100 subjects, 77 came for the 2nd review after 2 months. There was statistically significant worsening in the subjective feeling of nasal obstruction during the stay in high altitude without any significant change in the nasal airway resistance.

Multivalent Binding of a Ligand-Coated Particle: Role of Shape, Size, and Ligand Heterogeneity.

We utilize a multiscale modeling framework to study the effect of shape, size, and ligand composition on the efficacy of binding of a ligand-coated particle to a substrate functionalized with the target receptors. First, we show how molecular dynamics along with steered molecular dynamics calculations can be used to accurately parameterize the molecular-binding free energy and the effective spring constant for a receptor-ligand pair. We demonstrate this for two ligands that bind to the α5ß1-domain of integrin. Next, we show how these effective potentials can be used to build computational models at the meso- and continuum-scales. These models incorporate the molecular nature of the receptor-ligand interactions and yet provide an inexpensive route to study the multivalent interaction of receptors and ligands through the construction of Bell potentials customized to the molecular identities. We quantify the binding efficacy of the ligand-coated-particle in terms of its multivalency, binding free-energy landscape, and the losses in the configurational entropies. We show that 1) the binding avidity for particle sizes less than 350 nm is set by the competition between the enthalpic and entropic contributions, whereas that for sizes above 350 nm is dominated by the enthalpy of binding; 2) anisotropic particles display higher levels of multivalent binding compared to those of spherical particles; and 3) variations in ligand composition can alter binding avidity without altering the average multivalency. The methods and results presented here have wide applications in the rational design of functionalized carriers and also in understanding cell adhesion.

Excess area dependent scaling behavior of nano-sized membrane tethers.

Thermal fluctuations in cell membranes manifest as an excess area ([Formula: see text]) which governs a multitude of physical process at the sub-micron scale. We present a theoretical framework, based on an in silico tether pulling method, which may be used to reliably estimate [Formula: see text] in live cells. We perform our simulations in two different thermodynamic ensembles: (i) the constant projected area and (ii) the constant frame tension ensembles and show the equivalence of our results in the two. The tether forces estimated from our simulations compare well with our experimental measurements for tethers extracted from ruptured GUVs and HeLa cells. We demonstrate the significance and validity of our method by showing that all our calculations performed in the initial tether formation regime (i.e. when the length of the tether is comparable to its radius) along with experiments of tether extraction in 15 different cell types collapse onto two unified scaling relationships mapping tether force, tether radius, bending stiffness κ, and membrane tension σ. We show that [Formula: see text] is an important determinant of the radius of the extracted tether, which is equal to the characteristic length [Formula: see text] for [Formula: see text], and is equal to [Formula: see text] for [Formula: see text]. We also find that the estimated excess area follows a linear scaling behavior that only depends on the true value of [Formula: see text] for the membrane, based on which we propose a self-consistent technique to estimate the range of excess membrane areas in a cell.

Motion of a nano-spheroid in a cylindrical vessel flow: Brownian and hydrodynamic interactions.

We study the motion of a buoyant or a nearly neutrally buoyant nano-sized spheroid in a fluid filled tube without or with an imposed pressure gradient (weak Poiseuille flow). The fluctuating hydrodynamics approach and the deterministic method are both employed. We ensure that the fluctuation-dissipation relation and the principle of thermal equipartition of energy are both satisfied. The major focus is on the effect of the confining boundary. Results for the velocity and the angular velocity autocorrelations (VACF and AVACF), the diffusivities and the drag and the lift forces as functions of the shape, the aspect ratio, the inclination angle and the proximity to the wall are presented. For the parameters considered, the boundary modifies the VACF and AVACF such that three distinct regimes are discernible - an initial exponential decay followed by an algebraic decay culminating in a second exponential decay. The first is due to the thermal noise, the algebraic regime is due both to the thermal noise and the hydrodynamic correlations, while the second exponential decay shows the effect of momentum reflection from the confining wall. Our predictions display excellent comparison with published results for the algebraic regime (the only regime for which earlier results exist). We also discuss the role of the off-diagonal elements of the mobility and the diffusivity tensors that enable the quantifications of the degree of lift and margination of the nanocarrier. Our study covers a range of parameters that are of wide applicability in nanotechnology, microrheology and in targeted drug delivery.

Codon usage and codon pair patterns in non-grass monocot genomes.

BACKGROUND AND AIMS: Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. METHODS: First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces. KEY RESULTS: The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots. CONCLUSION: Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.

Numerical insights into the phase diagram of p-atic membranes with spherical topology.

The properties of self-avoiding p-atic membranes restricted to spherical topology have been studied by Monte Carlo simulations of a triangulated random surface model. Spherically shaped p-atic membranes undergo a Kosterlitz-Thouless transition as expected with topology induced mutually repelling disclinations of the p-atic ordered phase. For flexible membranes the phase behaviour bears some resemblance to the spherically shaped case with a p-atic disordered crumpled phase and p-atic ordered, conformationally ordered (crinkled) phase separated by a KT-like transition with proliferation of disclinations. We confirm the proposed buckling of disclinations in the p-atic ordered phase, while the expected associated disordering (crumpling) transition at low bending rigidities is absent in the phase diagram.