Graph topological transformations in space-filling cell aggregates.

Cell rearrangements are fundamental mechanisms driving large-scale deformations of living tissues. In three-dimensional (3D) space-filling cell aggregates, cells rearrange through local topological transitions of the network of cell-cell interfaces, which is most conveniently described by the vertex model. Since these transitions are not yet mathematically properly formulated, the 3D vertex model is generally difficult to implement. The few existing implementations rely on highly customized and complex software-engineering solutions, which cannot be transparently delineated and are thus mostly non-reproducible. To solve this outstanding problem, we propose a reformulation of the vertex model. Our approach, called Graph Vertex Model (GVM), is based on storing the topology of the cell network into a knowledge graph with a particular data structure that allows performing cell-rearrangement events by simple graph transformations. Importantly, when these same transformations are applied to a two-dimensional (2D) polygonal cell aggregate, they reduce to a well-known T1 transition, thereby generalizing cell-rearrangements in 2D and 3D space-filling packings. This result suggests that the GVM's graph data structure may be the most natural representation of cell aggregates and tissues. We also develop a Python package that implements GVM, relying on a graph-database-management framework Neo4j. We use this package to characterize an order-disorder transition in 3D cell aggregates, driven by active noise and we find aggregates undergoing efficient ordering close to the transition point. In all, our work showcases knowledge graphs as particularly suitable data models for structured storage, analysis, and manipulation of tissue data.

A Study on Demographic Profile of Patients and Correlation Between Clinical and Radiological Findings in Oral and Oropharyngeal Malignancies.

Oral and Oropharyngeal cancers are on rise year after year and Head and Neck Cancer rank sixth among all cancers worldwide. This study is an institutional based retrospective type of study conducted in a tertiary care hospital for a period of 6 months with an aim to identify the demographic profile of the patients and to correlate between the clinical and radiological findings of the disease using Cohen's Kappa value. Both oral and oropharyngeal cancer was predominant in male population with commonest age being the 5th decade of life. Tongue was the most common site for oral cancer, on the other hand, base of tongue was commonest among oropharyngeal cancer. The disease extension was thoroughly examined clinically by palpation and 70 degree Hopkins Endoscope and also radiologically using appropriate imaging tools. The clinical and radiological T showed moderate degree of agreement for both oral and oropharyngeal cancers whereas clinical and radiological N showed a almost perfect degree of agreement.

Characterizing the heterogeneity of membrane liquid-ordered domains.

We use a lattice model of a ternary mixture containing saturated and unsaturated lipids with cholesterol (Chol), to study the structural properties characterizing the coexistence between the liquid-disordered and liquid-ordered phases. Depending on the affinity of the saturated and unsaturated lipids, the system may exhibit macroscopic (thermodynamic) liquid-liquid phase separation or be divided into small-size liquid-ordered domains surrounded by a liquid-disordered matrix. In both cases, it is found that the nanoscale structure of the liquid-ordered regions is heterogeneous, and that they are partitioned into Chol-rich sub-domains and Chol-free, gel-like, nano-clusters. This emerges as a characteristic feature of the liquid-ordered state, which helps distinguishing between liquid-ordered domains in a two-phase mixture, and similar-looking domains in a one-phase mixture that are rich in saturated lipids and Chol, but are merely thermal density fluctuations. The nano-structure heterogeneity of the liquid-ordered phase can be detected by suitable experimental spectroscopic methods and is observed also in atomistic computer simulations.

A lattice model of ternary mixtures of lipids and cholesterol with tunable domain sizes.

Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary mixtures consisting of saturated and unsaturated lipids, and cholesterol (Chol). To explore the properties of such systems at large spatial scales, we here present a simple ternary mixture lattice model, involving a small number of nearest neighbor interaction terms. Monte Carlo simulations of mixtures with different compositions show excellent agreement with experimental and atomistic simulation observations across multiple scales, ranging from the local distributions of lipids to the phase diagram of the system. The simplicity of the model allows us to identify the roles played by the different interactions between components, and the interplay between them. Importantly, by changing the value of one of the model parameters, we can tune the size of the liquid-ordered domains, thereby simulating both Type II mixtures exhibiting macroscopic phase separation and Type I mixtures with nanoscopic domains. The Type II mixture simulation results fit well to the experimentally determined phase diagram of mixtures containing saturated DPPC/unsaturated DOPC/Chol. When the tunable parameter is changed, we obtain the Type I version of DPPC/DOPC/Chol, i.e., a mixture not showing thermodynamic phase transitions but one that may be fitted to the same phase diagram if local measures are used to distinguish between the different states. Our model results suggest that short range packing is likely to be a key regulator of the stability and size distribution of biological rafts.

An in vitro and computational validation of a novel loss-of-functional mutation in PAX9 associated with non-syndromic tooth agenesis.

Congenital tooth agenesis (CTA) is one of the most common craniofacial anomalies. Its frequency varies among different population depending upon the genetic heterogeneity. CTA could be of familial or sporadic and syndromic or non-syndromic. Five major genes are found to be associated with non-syndromic CTA, namely PAX9, MSX1, EDA1, AXIN2, and WNT10A. Very few studies have been carried out so far on CTA on this Indian population making this study unique and important. This study was initiated to identify potential pathogenic variant associated with congenital tooth agenesis in an India family with molar tooth agenesis. CTA was investigated and a novel c.336C > G variation was identified in the exon 3 of PAX9, leading to substitution of evolutionary conserved Cys with Trp at 112th amino acid position located at the functionally significant DNA-binding paired domain region. Functional analysis revealed that p.Cys112Trp mutation did not prevent the nuclear localization although mutant protein had higher cytoplasmic retention. EMSA using e5 probe revealed that mutant protein was unable to bind with the paired-domain-binding site. Subsequently, GST pull-down assay revealed lower binding activity of the mutant protein with its known interactor MSX1. These in vitro results were consistent with the computational results. The in vitro and computational observations altogether suggest that c.336C > G (p.Cys112Trp) variation leads to loss of function of PAX9 leading to CTA in this family.

Inhibitor of DNA binding proteins revealed as orchestrators of steady state, stress and malignant hematopoiesis.

Adult mammalian hematopoiesis is a dynamic cellular process that provides a continuous supply of myeloid, lymphoid, erythroid/megakaryocyte cells for host survival. This process is sustained by regulating hematopoietic stem cells (HSCs) quiescence, proliferation and activation under homeostasis and stress, and regulating the proliferation and differentiation of downstream multipotent progenitor (MPP) and more committed progenitor cells. Inhibitor of DNA binding (ID) proteins are small helix-loop-helix (HLH) proteins that lack a basic (b) DNA binding domain present in other family members, and function as dominant-negative regulators of other bHLH proteins (E proteins) by inhibiting their transcriptional activity. ID proteins are required for normal T cell, B cell, NK and innate lymphoid cells, dendritic cell, and myeloid cell differentiation and development. However, recent evidence suggests that ID proteins are important regulators of normal and leukemic hematopoietic stem and progenitor cells (HSPCs). This chapter will review our current understanding of the function of ID proteins in HSPC development and highlight future areas of scientific investigation.

ID2 and HIF-1α collaborate to protect quiescent hematopoietic stem cells from activation, differentiation, and exhaustion.

Defining mechanism(s) that maintain tissue stem quiescence is important for improving tissue regeneration, cell therapies, aging, and cancer. We report here that genetic ablation of Id2 in adult hematopoietic stem cells (HSCs) promotes increased HSC activation and differentiation, which results in HSC exhaustion and bone marrow failure over time. Id2Δ/Δ HSCs showed increased cycling, ROS production, mitochondrial activation, ATP production, and DNA damage compared with Id2+/+ HSCs, supporting the conclusion that Id2Δ/Δ HSCs are less quiescent. Mechanistically, HIF-1α expression was decreased in Id2Δ/Δ HSCs, and stabilization of HIF-1α in Id2Δ/Δ HSCs restored HSC quiescence and rescued HSC exhaustion. Inhibitor of DNA binding 2 (ID2) promoted HIF-1α expression by binding to the von Hippel-Lindau (VHL) protein and interfering with proteasomal degradation of HIF-1α. HIF-1α promoted Id2 expression and enforced a positive feedback loop between ID2 and HIF-1α to maintain HSC quiescence. Thus, sustained ID2 expression could protect HSCs during stress and improve HSC expansion for gene editing and cell therapies.

Universal electrode for ambipolar charge injection in organic electronic devices.

Ambipolar transistors, i.e. transistors with symmetrical n- and p-type performances, open new avenues for the design and integration of high-density, efficient and versatile circuits for advanced technologies. Their performance requires two processes: efficient injection of holes and electrons from the metal electrodes into the semiconductor; and transport of both carriers through the semiconductor. Organic semiconductors (OSCs) support ambipolar transport, but charge injection is strongly asymmetric due to inherent misalignment of the electrode work function with both conducting levels of the OSC. Here we introduce a new electrode concept capable of efficiently injecting both types of charge carriers into OSCs. The electrode has a mosaic-like structure composed of islands of two metals with high and low work functions, in this case Al and Au, respectively. Under suitable applied bias the Au (Al) domains in direct contact with the OSC allow efficient hole (electron) injection into the HOMO (LUMO) level. Implementing this electrode as both the source and drain in an organic field effect transistor (OFET) led to fully balanced ambipolar performance while maintaining high ON/OFF ratios. We then used the ambipolar OFETs to significantly simplify the circuit design and fabricate digital and analogue elements, i.e. a digital inverter and an analogue phase shifter using one type of transistor only. Finally, we demonstrate that a single ambipolar OFET can replace several unipolar transistors to fabricate digital transmission gate circuits. The new electrode design concept can include other metal combinations and compositions to balance ambipolar injection, and the use of the mosaic electrodes can be extended to other electronic devices that require ambipolar charge injection such as light emitting transistors, memory devices etc.

Unraveling hidden rules behind the wet-to-dry transition of bubble array by glass-box physics rule learner.

A liquid-gas foam, here called bubble array, is a ubiquitous phenomenon widely observed in daily lives, food, pharmaceutical and cosmetic products, and even bio- and nano-technologies. This intriguing phenomenon has been often studied in a well-controlled environment in laboratories, computations, or analytical models. Still, real-world bubble undergoes complex nonlinear transitions from wet to dry conditions, which are hard to describe by unified rules as a whole. Here, we show that a few early-phase snapshots of bubble array can be learned by a glass-box physics rule learner (GPRL) leading to prediction rules of future bubble array. Unlike the black-box machine learning approach, the glass-box approach seeks to unravel expressive rules of the phenomenon that can evolve. Without known principles, GPRL identifies plausible rules of bubble prediction with an elongated bubble array data that transitions from wet to dry states. Then, the best-so-far GPRL-identified rule is applied to an independent circular bubble array, demonstrating the potential generality of the rule. We explain how GPRL uses the spatio-temporal convolved information of early bubbles to mimic the scientist's perception of bubble sides, shapes, and inter-bubble influences. This research will help combine foam physics and machine learning to better understand and control bubbles.

A Case Series on Unusual Neck Masses.

Neck masses can be defined as any abnormal swelling or growth from the level of base of skull to clavicle. They can be benign or malignant so a thorough investigation is necessary to reach to a final diagnosis. Here we report a case series of three unusual neck masses presenting to the Out patient Department of Otorhinolaryngology and Head and Neck Surgery in R. G. Kar Medical College, a tertiary care hospital of Kolkata in a span of 1.5 years. The rarity of the etiology behind the neck masses makes this case series unique.

Synovial Fluid Cell Proteomic Analysis Identifies Upregulation of Alpha-Taxilin Proteins in Rheumatoid Arthritis: A Potential Prognostic Marker.

Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease affecting the joints and surrounding tissue. Identification of novel proteins associated with the progression of a disease is a prerequisite for understanding the pathogenesis of RA. The present study was undertaken to identify the potential biomarkers from a less explored biological sample such as synovial fluid (SF) cells which is specific for RA and to analyze their functional aspects using proteomic approach. Two-dimensional gel electrophoresis (2-DE) was performed using synovial fluid cells of RA and osteoarthritis (OA) patients, and 7 differentially expressed proteins were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS). Αlpha-Taxilin (α-Taxilin) has been found as one of the novel, significantly up regulated protein in RA. It has been validated in the synovium, synovial fluid (SF), SF cells, and plasma samples by Western blot, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS), immunohistochemistry (IHC), and real-time PCR. The identification of autoantibody against α-Taxilin and in silico studies has further helped us to understand its involvement in disease mechanism. The present study will therefore provide knowledge towards the etiology of RA that pave the way for suitable prognostic marker identification along with other clinical parameters.

Poiseuille Flow of Soft Polycrystals in 2D Rough Channels.

Polycrystals are partially ordered solids where crystalline order extends over mesoscopic length scales, namely, the grain size. We study the Poisuielle flow of such materials in a rough channel. In general, similar to yield stress fluids, three distinct dynamical states, namely, flowing, stick-slip, and jammed can be observed, with a yield threshold dependent on channel width. Importantly, the interplay between the finite channel width, and the intrinsic ordering scale (the grain size) leads to a new type of spatiotemporal heterogeneity. In wide channels, although the average flow profile remains pluglike, at the underlying granular level, there is vigorous grain remodeling activity resulting from the velocity heterogeneity among the grains. As the channel width approaches typical grain size, the flowing polycrystalline state breaks up into a spatially heterogeneous mixture of flowing liquid like patches and chunks of nearly static grains. Despite these static grains, the average velocity still shows a parabolic profile, dominated by the moving liquidlike patches. However, the solid-liquid front moves at nearly constant speed in the opposite direction of the external drive.

Id1 and Id3 Maintain Steady-State Hematopoiesis by Promoting Sinusoidal Endothelial Cell Survival and Regeneration.

Investigating mechanisms that regulate endothelial cell (EC) growth and survival is important for understanding EC homeostasis and how ECs maintain stem cell niches. We report here that targeted loss of Id genes in adult ECs results in dilated, leaky sinusoids and a pro-inflammatory state that increases in severity over time. Disruption in sinusoidal integrity leads to increased hematopoietic stem cell (HSC) proliferation, differentiation, migration, and exhaustion. Mechanistically, sinusoidal ECs (SECs) show increased apoptosis because of reduced Bcl2-family gene expression following Id gene ablation. Furthermore, Id1-/-Id3-/- SECs and upstream type H vessels show increased expression of cyclin-dependent kinase inhibitors p21 and p27 and impaired ability to proliferate, which is rescued by reducing E2-2 expression. Id1-/-Id3-/- mice do not survive sublethal irradiation because of impaired vessel regeneration and hematopoietic failure. Thus, Id genes are required for the survival and regeneration of BM SECs during homeostasis and stress to maintain HSC development.

Advances in the development and use of DREB for improved abiotic stress tolerance in transgenic crop plants.

Abiotic stresses negatively influence the survival, biomass production, and yield of crops. Tolerance to diverse abiotic stresses in plants is regulated by multiple genes responding differently to various stress conditions. Genetic engineering approaches have helped develop transgenic crops with improved abiotic stress tolerance including yields. The dehydration-responsive element binding protein (DREB) is a stress-responsive transcription factor that modulates the expression of downstream stress-inducible genes, which confer simultaneous tolerance to multiple stresses. This review focuses on advances in the development of DREB transgenic crops and their characterization under various abiotic stress conditions. It further discusses the mechanistic aspects of abiotic stress tolerance, yield gain, the fate of transgenic plants under controlled and field conditions and future research directions toward commercialization of DREB transgenic crops.

Layered Double Hydroxide Nanoparticles for Efficient Gene Delivery for Cancer Treatment.

The use of cationic polymer based gene delivery vectors has several limitations such as low transfection efficiency, high toxicity, and inactivation by serum. The present work provides an inorganic based nanocarrier for efficient gene delivery and a method for preparing the same through a facile coprecipitation technique. The vehicle showed high loading capacity of DNA and can release the loaded DNA in a controlled pH-responsive manner. The developed gene delivery vehicle offers remarkable protection against DNase I and also provides protection against thermal damage. This vehicle also demonstrated efficient cellular uptake performance. Transfection and expression of plasmid gene encoding GFP proteins is achieved successfully by this LDH based vehicle. More interestingly, the developed Li-Al LDH efficiently induces GFP-p53 mediated apoptosis in HeLa cells exclusively sparing the normal tissue cells like NIH-3T3. The study demonstrates the potential of the developed inorganic based nanocarrier as a promising nonviral gene vector for tumor treatment.

Regulation of antioxidant mechanisms by AtDREB1A improves soil-moisture deficit stress tolerance in transgenic peanut (Arachis hypogaea L.).

The present study evaluated the soil-moisture deficit stress tolerance of AtDREB1A transgenic peanut lines during reproductive stages using lysimetric system under controlled glasshouse conditions. The antioxidant activities of AtDREB1A transgenic lines were measured by biochemical assays. The transgenic peanut lines recorded significantly lower accumulation of malondialdehyde and hydrogen peroxide than the wild-type. Whereas, specific activity of catalase, guaiacol peroxidase, ascorbate peroxidase, glutathione reductase and ascorbic acid were found to be significantly higher in transgenic lines than in the wild-type line under drought stress. The results showed that the transgenic lines expressed lower oxidative damage than wild-type and could protect themselves from the elevated levels of reactive oxygen species under drought stress. This could be attributed to the regulation of various stress-inducible genes by AtDREB1A transcription factor. Improved photosynthetic and growth parameters were also recorded in transgenic lines over wild-type under drought stress. Improved physio-biochemical mechanisms in transgenic peanut lines might have resulted in improved growth-related traits as significant correlations were observed between physio-biochemical parameters and growth-related traits under drought stress. The potential target genes of AtDREB1A transcription factor in transgenic peanut lines during drought stress were identified, which helped in understanding the molecular mechanisms of DREB-regulated stress responses. The transgenic line D6 reported the best physio-biochemical mechanisms and growth-related parameters under drought stress over other transgenic lines and wild-type, suggesting it may be used to develop high yielding and terminal drought-tolerant peanut varieties.

Correct determination of charge transfer state energy from luminescence spectra in organic solar cells.

Generation and recombination of electrons and holes in organic solar cells occurs via charge transfer states located at the donor/acceptor interface. The energy of these charge transfer states is a crucial factor for the attainable open-circuit voltage and its correct determination is thus of utmost importance for a detailed understanding of such devices. This work reports on drastic changes of electroluminescence spectra of bulk heterojunction organic solar cells upon variation of the absorber layer thickness. It is shown that optical thin-film effects have a large impact on optical out-coupling of luminescence radiation for devices made from different photoactive materials, in configurations with and without indium tin oxide. A scattering matrix approach is presented which accurately reproduces the observed effects and thus delivers the radiative recombination spectra corrected for the wavelength-dependent out-coupling. This approach is proven to enable the correct determination of charge transfer state energies.

Interlayers Self-Generated by Additive-Metal Interactions in Organic Electronic Devices.

The fundamental structure of all organic electronic devices is a stack of thin layers sandwiched between electrodes, with precise intralayer morphology and interlayer interactions. Solution processing multilayers with little to no intermixing is, however, technically challenging and often incompatible with continuous roll-to-roll, high-speed manufacturing. Here, an overview of a recently developed methodology for self-generation of interlayers positioned between the active layer and metal contact is presented. The interlayer material is blended as an additive in the active layer and migrates to the organic/metal interface during metal deposition. The driving force for this migration is additive-metal interactions. The generated interlayer positions an interfacial dipole that reduces barriers for charge transfer across the organic/metal interface. This methodology is generic and, as reported here, the self-generated interlayers significantly improve the performance of many devices. Importantly, this approach is compatible with printing and reel-to-reel processing. Directives toward additive selection, processing conditions and integration in future applications are also discussed.

Curvature instability of chiral colloidal membranes on crystallization.

Buckling and wrinkling instabilities are failure modes of elastic sheets that are avoided in the traditional material design. Recently, a new paradigm has appeared where these instabilities are instead being utilized for high-performance applications. Multiple approaches such as heterogeneous gelation, capillary stresses, and confinement have been used to shape thin macroscopic elastic sheets. However, it remains a challenge to shape two-dimensional self-assembled monolayers at colloidal or molecular length scales. Here, we show the existence of a curvature instability that arises during the crystallization of finite-sized monolayer membranes of chiral colloidal rods. While the bulk of the membrane crystallizes, its edge remains fluid like and exhibits chiral ordering. The resulting internal stresses cause the flat membrane to buckle macroscopically and wrinkle locally. Our results demonstrate an alternate pathway based on intrinsic stresses instead of the usual external ones to assemble non-Euclidean sheets at the colloidal length scale.

A novel G to A transition at initiation codon and exon-intron boundary of PAX9 identified in association with familial isolated oligodontia.

Several studies on experimental animals indicate that the process of organogenesis crucially depends upon the spatiotemporal dose of certain critical bio-molecules. Tooth development is also not an exception. While most of the knowledge regarding the molecular mechanism of tooth development comes from the studies on mouse model, pathogenic variations identified in human tooth agenesis also provide valuable information on mammalian tooth development. Until now five major candidate genes have been identified for tooth agenesis in human. Among them, PAX9 plays the crucial role in tooth development and in non-syndromic congenital tooth agenesis. In this study, microsatellite and SNP based genotyping identifies a disease specific haplotype block, which includes PAX9 gene, segregates with autosomal dominant tooth agenesis phenotype. Direct sequencing of PAX9 identifies a novel heterozygous G to A transition at the third base (c.3G>A) of initiation codon leading to ATG to ATA shift in all affected individuals which is absent in all unaffected relatives and 200 control chromosomes. Further, in vitro functional analysis creating PAX9 minigene construct did apparently show no effect on the splice-site migration. It is therefore proposed that haploinsufficiency of PAX9 is the causal factor for tooth agenesis in this family.