Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment

RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.

The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development

ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.

The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming

The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.

Comparison of Serum Zinc in Children of Wilson Disease and Non-Wilsonian Volunteers in Bangladesh

Wilson disease (WD) is an autosomal recessive disorder of copper metabolism with diverse clinical manifestations. Zinc (Zn) has been used for treatment of WD. Recent studies showed low serum zinc level in patients suffering from WD than the normal. This cross-sectional analytical study has been designed to compare the serum zinc level between paediatric patients suffering from WD but yet not started treatment and children who have normal ALT level. This study was carried out at the Department of Pediatric Gastroenterology and Nutrition, BSMMU, Dhaka, Bangladesh from July 2018 to June 2019. Total 51 children were included in this study. Among them 27 were diagnosed case of WD aged between three to eighteen years and 24 children of same ages who were suffering from other than liver disease having normal ALT were included as volunteers. The patients of WD were divided into four groups according to their presentation as acute hepatitis, chronic liver disease (CLD), acute liver failure & neuropsychiatric manifestation. Informed written consent was obtained from all patients and volunteers for participation in this study. Along with other physical findings and laboratory investigations 3 ml of venous blood were collected for estimation of serum zinc level. After estimation of serum zinc level results were analyzed statistically. The difference in serum zinc levels were compared between the groups. Serum zinc level was significantly lower in Wilson disease patients (43.8±19.7μg/dl; range: 13-83) compared to volunteers group (67.8±11.8μg/dl; range: 47-97) p<0.001. Among the diseased group, serum zinc level were significantly lower in 18 CLD (38.4±17.4μg/dl) and in 4 acute liver failure (33.1±3.7μg/dl) compared to 4 acute hepatitis (71.8±4.3μg/dl) (p=0.001) and (p<0.001) respectively. Mean serum zinc level was low in 4 Wilsonian acute liver failure (33.1±3.7μg/dl), which was significant compared to those (23) who presented as Wilson disease non acute liver failure (45.7±20.8μg/dl) (p=0.013). Serum zinc level was significantly lower in Wilson disease children compared to the volunteers. Zinc level was also found significantly low in Wilson disease presented as CLD and acute liver failure in comparison to Wilson disease presented as acute hepatitis.

WWOX P47T partial loss-of-function mutation induces epilepsy, progressive neuroinflammation, and cerebellar degeneration in mice phenocopying human SCAR12

WWOX gene loss-of-function (LoF) has been associated with neuropathologies resulting in developmental, epileptic, and ataxic phenotypes of varying severity based on the level of WWOX dysfunction. WWOX gene biallelic germline variant p.Pro47Thr (P47T) has been causally associated with a new form of autosomal recessive cerebellar ataxia with epilepsy and intellectual disability (SCAR12, MIM:614322). This mutation affecting the WW1 protein binding domain of WWOX, impairs its interaction with canonical proline-proline-X-tyrosine motifs in partner proteins. We generated a mutant knock-in mouse model of Wwox P47T mutation that phenocopies human SCAR12. WwoxP47T/P47T mice displayed epilepsy, profound social behavior and cognition deficits, and poor motor coordination, and unlike KO models that survive only for 1 month, live beyond 1 year of age. These deficits progressed with age and mice became practically immobile, suggesting severe cerebellar dysfunction. WwoxP47T/P47T mice brains revealed signs of progressive neuroinflammation with elevated astro-microgliosis that increased with age. Cerebellar cortex displayed significantly reduced molecular and granular layer thickness and a strikingly reduced number of Purkinje cells with degenerated dendrites. Transcriptome profiling from various brain regions of WW domain LoF mice highlighted widespread changes in neuronal and glial pathways, enrichment of bioprocesses related to neuroinflammation, and severe cerebellar dysfunction. Our results show significant pathobiological effects and potential mechanisms through which WWOX partial LoF leads to epilepsy, cerebellar neurodegeneration, neuroinflammation, and ataxia. Additionally, the mouse model described here will be a useful tool to understand the role of WWOX in common neurodegenerative conditions in which this gene has been identified as a novel risk factor.

Evaluation of Fecal Pancreatic Elastase-1 as a Measure of Pancreatic Exocrine Function in Children with Pancreatitis

Pancreatic exocrine insufficiency occurs as a clinical consequence of chronic pancreatitis leading to fat maldigestion, malabsorption and malnutrition. Fecal elastase-1 is a laboratory-based test used for the diagnosis or exclusion of pancreatic exocrine insufficiency. The aim of the study was to observe the value of fecal elastase-1 in children with pancreatitis as an indicator of pancreatic exocrine insufficiency. This was a cross-sectional descriptive study conducted from January 2017 through June 2018. Thirty children with pain abdomen as control and 36 patients with pancreatitis as cases were included. An ELISA technique which recognizes human pancreatic elastase-1 from spot stool sample was employed for the test. Fecal elastase-1 activity in spot stool samples in acute pancreatitis (AP) ranged from 198.2-500μg/g with a mean of 342.1±136.4μg/g, acute recurrent pancreatitis (ARP) ranged from 15-500μg/g with a mean of 332.8±194.5μg/g and chronic pancreatitis (CP) ranged from 15-492.8μg/g with a mean of 222.2±197.1μg/g was obtained. In controls, fecal elastase-1 ranged from 28.4-500μg/g with a mean of 398.8±114.9μg/g. Disease severity was classified as mild to moderate pancreatic insufficiency (fecal elastase-1 100 to 200μg/g stool) was found in AP (14.3%) and CP (6.7%) cases. The severe pancreatic insufficiency (fecal elastase-1<100μg/g stool) was observed in ARP (28.6%) and CP (46.7%) cases. Malnutrition was observed in severe pancreatic insufficiency cases. This study result showed that fecal elastase-1 can be used as a measure of pancreatic exocrine function in children with pancreatitis.

Studies on the behaviour of a passive containment cooling system for the Indian Advanced Heavy Water Reactor

A passive containment cooling system has been proposed for the advanced heavy water reactor being designed in India. This is to provide long term cooling for the reactor containment following a loss of coolant accident. The system removes energy released into the containment through immersed condensers kept in a pool of water. An important aspect of immersed condenser’s working is the potential degradation of immersed condenser’s performance due to the presence of noncondensable gases. An experimental programme to investigate the passive containment cooling system behaviour and performance has been undertaken in a phased manner. In the first phase, system response tests were conducted on a small scale model to under­stand the phenomena involved. Tests were conducted with constant energy input rate and with varying energy input rate simulating decay heat. With constant energy input rate, pressures in volume V1 and V2 reached almost steady value. With varying energy input rate V1 pressure dropped below the pressure in V2. The system could efficiently purge air from V1 to V2. The paper deals with the details of the tests conducted and the results obtained.

Analytical study of flow instability behaviour in a boiling two-phase natural circulation loop under low quality conditions

Analytical investigations have been carried out to study the flow instability behaviour in a boiling two-phase natural circulation loop under low quality conditions. For this purpose, the computer code TINFLO-S has been developed. The code solves the conservation equations of mass, momentum and energy and equation of state for homogeneous equilibrium two-phase flow using linear analytical technique. The results of the code have been validated with the experimental data of the loop for both the steady state and stability. The study reveals that the stability behaviour of low quality flow oscillations is different from that of the high quality flow oscillations. The instability reduces with increase in power and throttling at the inlet of the heater. The instability first increases and then reduces with increase in pressure at any subcooling. The effects of diameter of riser pipe, heater and the height of the riser on this instability are also investigated.

Experimental studies on condensation of steam mixed with noncondensable gas inside the vertical tube in a pool filled with subcooled water

A passive containment cooling system with immersed condensers has been proposed as one of the alternatives for the Advanced Heavy Water Reactor (AHWR) being designed in India. The system removes residual/decay heat released into the containment through the immersed condensers kept in a pool of water following loss of coolant accident. An important aspect of the immersed condensers is the potential degradation of its performance due to the presence of noncondensable gases. Experiments are performed to obtain reliable data on condensation phenomena in presence of air. These experiments are conducted on full-scale tubes of condensers immersed in a pool of water maintaining similar conditions as in the prototype of AHWR. A method has been proposed for the determination of the local heat transfer rate using correlations given in literature. The parametric effects of air mass fraction, pressure, steam flow, etc. on condensation heat transfer in presence of noncondensable gas have been studied. The experimental results are compared with the correlations given in literature.

Population genetic structure and association mapping for iron toxicity tolerance in rice

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

Stochastic point process models for multi-compartment dendritic-tree input-output transformations in spiking neurons

We extend stochastic point-process generalized linear models (PPGLMs) to the estimation of input-output transformations in dendritic trees and their contribution to the generation of soma action potentials in multi-compartmental models of single neurons. We used simulations of a model enthorinal cortex pyramidal neuron, with known dentritic tree and soma spatial organization, including active compartments defined in terms of standard cable and standard Hodgkin-Huxley equations. Each dendritic compartment (391 total) was endowed with either excitatory (E) or inhibitory (I) synaptic inputs whose strength was randomly specified. We examined the cases of both homogeneous and inhomogeneous spatial distributions for E and I synaptic inputs. The times for synaptic inputs followed a Poisson process with different mean rate regimes varying from 50 to 600 inputs/s. The soma membrane potential received also a background noise in the form of an Ornstein-Uhlenbeck process. Our main findings are: (1) Power spectra of soma membrane potentials revealed subthreshold resonances at ~40 Hz and ~80 Hz; (2) The contribution of different dendritic compartments, under the examined input ranges and spatial distributions, depended not only of the dendrite-soma path distance, but also on the number of compartments in the dendritic segment. (3) Estimated conditional intensity functions (CIFs) with PPGLMs successfully predicted spiking activity based on given E-I input times; area under ROC curves computed on test data varied from 0.8 - 0.95. (4) The CIF models identified compartments and regions receiving E-I synaptic inputs; Estimated temporal filters were consistent with dendrite-soma path distances and input weights. We expect this type of PPGLMs to contribute to data-driven identification of input-output transformations in dentritic trees based on single-neuron Ca²⁺ and voltage indicator imaging data.

Telomere repeat-binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters

The role of the telomere repeat-binding factor 2 (TRF2) in telomere maintenance is well-established. However, recent findings suggest that TRF2 also functions outside telomeres, but relatively little is known about this function. Herein, using genome-wide ChIP-Seq assays of TRF2-bound chromatin from HT1080 fibrosarcoma cells, we identified thousands of TRF2-binding sites within the extra-telomeric genome. In light of this observation, we asked how TRF2 occupancy is organized within the genome. Interestingly, we found that extra-telomeric TRF2 sites throughout the genome are enriched in potential G-quadruplex-forming DNA sequences. Furthermore, we validated TRF2 occupancy at several promoter G-quadruplex motifs, which did adopt quadruplex forms in solution. TRF2 binding altered expression and the epigenetic state of several target promoters, indicated by histone modifications resulting in transcriptional repression of eight of nine genes investigated here. Furthermore, TRF2 occupancy and target gene expression were also sensitive to the well-known intracellular G-quadruplex-binding ligand 360A. Together, these results reveal an extensive genome-wide association of TRF2 outside telomeres and that it regulates gene expression in a G-quadruplex-dependent fashion.

Determination of size dependent carrier capture in InGaN/GaN quantum nanowires by femto-second transient absorption spectroscopy: effect of optical phonon, electron-electron scattering and diffusion

Understanding the ultrafast processes corresponding to carrier capture, thermalization and relaxation is essential to design high speed optoelectronic devices. Here, we have investigated a size dependent carrier capture process in InGaN/GaN 20, 50 nm nanowires and quantum well systems. Femto-second transient absorption spectroscopy reveals that the carrier capture is a two-step process. The carriers are captured in the barrier by polar optical phonon (POP) scattering. They further scatter into the active region by electron-electron and POP scatterings. The capture is found to slow down for quantum confined structures. A significant number of carriers are found to disappear from the barrier during the diffusion process. All the experimental observations are explained in a simulation framework depicting various scattering mechanisms.

Enhanced luminescence from InGaN/GaN nano-disk in a wire array caused by surface potential modulation during wet treatment

Here we have demonstrated the profound impact of surface potential on the luminescence of an array of InGaN/GaN nano-disk in a wire heterostructure. The change in surface potential is brought about by a combination of dry and successive wet-processing treatments. The photoluminescence (PL) properties are determined as a function of size and height of this array of nano-disks. The observed characteristics are coherently explained by considering a change in quantum confinement induced by the change in surface potential, quantum-confined Stark effect, exciton binding energy and strain relaxation for varying surface potential. The change in hole bound state energy due to parabolic potential well near the side-wall is found to be the dominating factor. The PL peak position, full width at half-maximum, strain relaxation and integrated PL intensity are studied as a function of incident power and temperature. The devices demonstrate higher integrated PL intensity and slope efficiency.

Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends

Telomere-binding proteins constituting the shelterin complex have been studied primarily for telomeric functions. However, mounting evidence shows non-telomeric binding and gene regulation by shelterin factors. This raises a key question—do telomeres impact binding of shelterin proteins at distal non-telomeric sites? Here we show that binding of the telomere-repeat-binding-factor-2 (TRF2) at promoters ~60 Mb from telomeres depends on telomere length in human cells. Promoter TRF2 occupancy was depleted in cells with elongated telomeres resulting in altered TRF2-mediated transcription of distal genes. In addition, histone modifications—activation (H3K4me1 and H3K4me3) as well as silencing marks (H3K27me3)—at distal promoters were telomere length-dependent. These demonstrate that transcription, and the epigenetic state, of telomere-distal promoters can be influenced by telomere length. Molecular links between telomeres and the extra-telomeric genome, emerging from findings here, might have important implications in telomere-related physiology, particularly ageing and cancer.

Telomeres (special DNA-protein assemblies that protect chromosome ends) affect ageing and diseases such as cancer. Although this has been recognized for many years, biological processes that connect telomeres to ageing, cancer and other cellular functions remain to be fully understood. Certain proteins, believed to be only telomere-associated, engage DNA outside telomeres. This raises an interesting question. Does telomere length influence how telomere-binding proteins associate with DNA at regions distal from telomeres. If so, how does this impact function? Motivated by these questions, in the present studies we tested if extra-telomeric binding of the well-known telomere-repeat-binding-actor-2 (TRF2) depends on telomere length. Our results show that the level of DNA-bound TRF2 at telomere-distal sites changes as telomeres shorten or elongate. Consequently, TRF2-mediated gene regulation affects many genes. Notably, histone modifications that dictate chromatin compaction and access to regulatory factors, at sites distant from telomere ends also depended on telomere length. Together, this links the state of telomeres to gene regulation and epigenetics directly in ways not previously appreciated that might impact a more complete understanding of molecular processes underlying ageing and cancer.

Geochemical signatures and isotopic systematics constraining dynamics of fluoride contamination in groundwater across Jamui district, Indo-Gangetic alluvial plains, India

A data set of 76 water samples are obtained from surface and sub-surface water bodies to investigate chemical parameters and stable isotopic signatures in order to drive factors leading to fluoride (F^-) contamination in groundwater of parts of Jamui district, India. Hydrochemical facies reveals that F^- concentration is lower in Ca²⁺-HCO₃^- facies representative of recharge area, while discharge area has a tendency towards Na⁺-HCO₃^- facies with elevated F^- concentration. The ionic ratios Na⁺/Ca²⁺>1, Na⁺/Cl^->1, (Ca²⁺+Mg²⁺)/HCO₃^-<1, Na⁺+K⁺ = 0.5TZ⁺ and Ca²⁺+Mg²⁺ = TZ⁺ witness silicate weathering by water-rock interaction coupled with ion exchange and prolonged residence time, are the principle factors for fluoride contamination (3.6 mg/L to 5.8 mg/L) in 67% of deeper bore wells. Geochemical modelling testifies excess of alkalinity due to the dominance of bicarbonate ion leading to calcite precipitation and dissolution of fluoride in solution contributing to fluoride contamination. The chemometric analysis reveals that the water chemistry of the study area is controlled by both anthropogenic and natural sources, and enrichment of fluoride in groundwater is possibly from geogenic source (fractured granite gneiss). The stable isotope plot shows that most of the samples fall along local meteoric water line indicating that the groundwater is originated from local precipitation with a possibility of evaporative enrichment. Groundwater enriched in δ¹⁸O is positively correlated with F^- suggesting evaporation and longer residence time of water. Spatially elevated F^- prevails in the eastern bank of Kiul River and along the groundwater flow direction, which is attributed to control of dynamics of hydrogeological conditions.

MRN complex-dependent recruitment of ubiquitylated BLM helicase to DSBs negatively regulates DNA repair pathways

Mutations in BLM in Bloom Syndrome patients predispose them to multiple types of cancers. Here we report that BLM is recruited in a biphasic manner to annotated DSBs. BLM recruitment is dependent on the presence of NBS1, MRE11 and ATM. While ATM activity is essential for BLM recruitment in early phase, it is dispensable in late phase when MRE11 exonuclease activity and RNF8-mediated ubiquitylation of BLM are the key determinants. Interaction between polyubiquitylated BLM and NBS1 is essential for the helicase to be retained at the DSBs. The helicase activity of BLM is required for the recruitment of HR and c-NHEJ factors onto the chromatin in S- and G1-phase, respectively. During the repair phase, BLM inhibits HR in S-phase and c-NHEJ in G1-phase. Consequently, inhibition of helicase activity of BLM enhances the rate of DNA alterations. Thus BLM utilizes its pro- and anti-repair functions to maintain genome stability.

Bloom helicase is recruited to double strand breaks in an ATM dependent manner. Here the authors show that Bloom helicase is recruited to double strand breaks in an ATM and MRN dependent manner with HR and NHEJ regulated by the helicase depending on the phase of the cell cycle.

Analysis and Characterization of Alumina Particles Reinforced Ultra High Molecular Weight Polyethylene Composite for Acetabular Cup

Composites of ultra high molecular weight polyethylene (UHMWPE) reinforced with 5, 10 and 15 percent of alumina were prepared by a technique of uniform mixing and moulding. Acetabular cups were produced by compression moulding methods. A new walk simulator was also developed in-house for testing the tribological performances of these cups. The results from walk simulator tests are encouraging. Using a human walk simulator machine we did in vitro wear testing. Characterizations were performed to analyse the microstructure, composition, phase purity and crystalline by using XRD, DSC/TGA. Biocompatibility test was done by cytotoxicity, hemocompatibility and MTT assay methods. Biocompatibility tests gave hemolysis counts with these polymer composites well within the acceptable range and the results indicate a significant improvement in biocompatibility of the polymer composites over the in parent polymers.

Strong Size Dependency on the Carrier and Photon Dynamics in InGaN/GaN Single Nanowalls Determined Using Photoluminescence and Ultrafast Transient Absorption Spectroscopy

Here, we have demonstrated strong size dependency of quasi-equilibrium and nonequilibrium carrier and photon dynamics in InGaN/GaN single nanowalls using photoluminescence and transient absorption spectroscopy. We demonstrate that two-dimensional carrier confinement, strain relaxation, and modified density of states lead to a reduced Stokes shift, smaller full width at half-maxima, increased exciton binding energy, and reduced nonradiative recombination. The ultrafast transient spectroscopy shows that carrier capture is a two-step process dominated by optical phonons and carrier-carrier scattering in succession. The carrier capture is a strongly size-dependent process and becomes slower due to modulation of the density of available states for progressively decreasing nanowall sizes. The slowest process is the electron-hole recombination, which is also extremely size-dependent and the rate increases by almost an order of magnitude in comparison to that of quantum-well structures. Electron-hole wave function overlap and modified density of states are among the key aspects in determining all the properties of these structures.

Epigenetic suppression of human telomerase (hTERT) is mediated by the metastasis suppressor NME2 in a G-quadruplex-dependent fashion

Transcriptional activation of the human telomerase reverse transcriptase (hTERT) gene, which remains repressed in adult somatic cells, is critical during tumorigenesis. Several transcription factors and the epigenetic state of the hTERT promoter are known to be important for tight control of hTERT in normal tissues, but the molecular mechanisms leading to hTERT reactivation in cancer are not well-understood. Surprisingly, here we found occupancy of the metastasis suppressor non-metastatic 2 (NME2) within the hTERT core promoter in HT1080 fibrosarcoma cells and HCT116 colon cancer cells and NME2-mediated transcriptional repression of hTERT in these cells. We also report that loss of NME2 results in up-regulated hTERT expression. Mechanistically, additional results indicated that the RE1-silencing transcription factor (REST)–lysine-specific histone demethylase 1 (LSD1) co-repressor complex associates with the hTERT promoter in an NME2-dependent way and that this assembly is required for maintaining repressive chromatin at the hTERT promoter. Interestingly, a G-quadruplex motif at the hTERT promoter was essential for occupancy of NME2 and the REST repressor complex on the hTERT promoter. In light of this mechanistic insight, we studied the effects of G-quadruplex–binding ligands on hTERT expression and observed that several of these ligands repressed hTERT expression. Together, our results support a mechanism of hTERT epigenetic control involving a G-quadruplex promoter motif, which potentially can be targeted by tailored small molecules.

Pancreatic stellate cells in pancreatic cancer: In focus

Pancreatic stellate cells are stromal cells that have multiple physiological functions such as the production of extracellular matrix, stimulation of amylase secretion, phagocytosis and immunity. In pancreatic cancer, stellate cells exhibit a different myofibroblastic-like morphology with the expression of alpha-smooth muscle actin, the activated form is engaged in several mechanisms that support tumorigenesis and cancer invasion and progression. In contrast to the aforementioned observations, eliminating the stromal cells that are positive for alpha-smooth muscle actin resulted in immune-evasion of the cancer cells and resulted in worse prognosis in animal models. Understanding the cancer-stromal signaling in pancreatic adenocarcinoma will provide novel strategies for therapy. Here we provide an updated review of studies that handle the topic "pancreatic stellate cells in cancer" and recent experimental approaches that can be the base for future directions in therapy.

Expression of microRNA-155 correlates positively with the expression of Toll-like receptor 7 and modulates hepatitis B virus via C/EBP-β in hepatocytes

Effective recognition of viral infection and successive activation of antiviral innate immune responses are vital for host antiviral defence, which largely depends on multiple regulators, including Toll-like receptors (TLRs) and microRNAs. Several early reports suggest that specific TLR-mediated immune responses can control hepatitis B virus (HBV) replication and express differentially with disease outcome. Considering the versatile function of miR-155 in the TLR-mediated innate immune response, we aimed to study the association between miR-155 and TLRs and their subsequent impact on HBV replication using both a HBV-replicating stable cell line (HepG2.2.15) and HBV-infected liver biopsy and serum samples. Our results showed that miR-155 was suppressed during HBV infection and a subsequent positive correlation of miR-155 with TLR7 activation was noted. Further, ectopic expression of miR-155 in vitro reduced HBV load as evidenced from reduced viral DNA, mRNA and subsequently reduced level of secreted viral antigens (HBsAg and HBeAg). Our results further suggested that CCAAT/enhancer-binding protein-β (C/EBP-β), a positive regulator of HBV transcription, was inhibited by miR-155. Taken together, our study established a correlation between miR-155 and TLR7 during HBV infection and also demonstrated in vitro that increased miR-155 level could help to reduce HBV viral load by targeting C/EBP-β.

Association of hypoglycemia, hypocalcemia and hypomagnesemia in neonates with perinatal asphyxia

The clinical evidence of neurological menifestations associated with asphyxia is described as hypoxic ischaemic encephalopathy (HIE). A variety of metabolic problems are present in asphyxiated newborns including hypoglycemia, hypocalcemia, hypomagnesemia and others metabolic abnormalities. Some of these biochemical disturbances may trigger seizure or potentiate further brain damage. This cross sectional case-control study was done in Mymensingh Medical College Hospital, to identify the association of hypoglycemia, hypocalcemia, hypomagnesemia in neonates with perinatal asphyxia. Study period was six months. Sample size was 60. Among total sample 30 term asphyxiated newborns of <24 hours age were case and equal number term healthy newborns <24 hours age were control. The main clinical presentations were delayed cry after birth along with respiratory distress, convulsion and absence of cry in asphyxiated newborns. Major physical findings were cyanosis, convulsion and tachypnoea in asphyxiated group. The mean value of serum calcium level was significantly lower in asphyxiated newborns (7.37 ± 0.10mg/dl) than control value (8.04±0.09mg/dl). Hypocalcemia was found among 23.33% babies in case group. On the contrary, hypocalcemia was found in single baby among control group. The mean value of serum magnesium was significantly lower in asphyxiated newborns (1.83 ± 0.04mg/dl) than control value (1.96 ± 0.05mg/dl). Hypomagnesemia was found among 3(10%) newborns but none was found among control group. Hypoglycemia was found in 7(23.33%) cases though the mean value of blood glucose was higher in case group (5.72 ± 0.62mmol/l) than control group (4.87 ± 0.15mmol/l) difference was not statistically significant. Combined hypoglycemia, hypocalcemia and hypomagnesemia were found in 1(3.33%) case; combined hypoglycemia and hypocalcemia were found in 2(6.67%) cases; and combined hypocalcemia and hypomagnesemia were found in 1(3.33%) case. During the study period, 3(10.0%) cases were expired but no death occurred among control group. This study shows isolated or combined hypoglycemia, hypocalcemia, hypomagnesemia are frequently found in newborns with perinatal asphyxia. So, it is necessary to monitor blood glucose, serum calcium and also serum magnesium among asphyxiated newborns for proper management.

Non-metastatic 2 (NME2)-mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin

Tumor metastasis refers to spread of a tumor from site of its origin to distant organs and causes majority of cancer deaths. Although >30 metastasis suppressor genes (MSGs) that negatively regulate metastasis have been identified so far, two issues are poorly understood: first, which MSGs oppose metastasis in a tumor type, and second, which molecular function of MSG controls metastasis. Herein, integrative analyses of tumor-transcriptomes (n = 382), survival data (n = 530) and lymph node metastases (n = 100) in lung cancer patients identified non-metastatic 2 (NME2) as a key MSG from a pool of >30 metastasis suppressors. Subsequently, we generated a promoter-wide binding map for NME2 using chromatin immunoprecipitation with promoter microarrays (ChIP-chip), and transcriptome profiling. We discovered novel targets of NME2 which are involved in focal adhesion signaling. Importantly, we detected binding of NME2 in promoter of focal adhesion factor, vinculin. Reduced expression of NME2 led to enhanced transcription of vinculin. In comparison, NME1, a close homolog of NME2, did not bind to vinculin promoter nor regulate its expression. In line, enhanced metastasis of NME2-depleted lung cancer cells was found in zebrafish and nude mice tumor models. The metastatic potential of NME2-depleted cells was remarkably diminished upon selective RNA-i-mediated silencing of vinculin. Together, we demonstrate that reduced NME2 levels lead to transcriptional de-repression of vinculin and regulate lung cancer metastasis.

EGFR wild type antagonizes EGFRvIII-mediated activation of Met in glioblastoma

Epidermal growth factor receptor (EGFR)vIII is the most common EGFR mutant found in glioblastoma (GBM). EGFRvIII does not bind ligand, is highly oncogenic and is usually coexpressed with EGFR wild type (EGFRwt). EGFRvIII activates Met, and Met contributes to EGFRvIII-mediated oncogenicity and resistance to treatment. Here, we report that addition of EGF results in a rapid loss of EGFRvIII-driven Met phosphorylation in glioma cells. Met is associated with EGFRvIII in a physical complex. Addition of EGF results in a dissociation of the EGFRvIII-Met complex with a concomitant loss of Met phosphorylation. Consistent with the abrogation of Met activation, addition of EGF results in the inhibition of EGFRvIII-mediated resistance to chemotherapy. Thus, our study suggests that ligand in the milieu of EGFRvIII-expressing GBM cells is likely to influence the EGFRvIII-Met interaction and resistance to treatment, and highlights a novel antagonistic interaction between EGFRwt and EGFRvIII in glioma cells.

An EGFR wild type-EGFRvIII-HB-EGF feed-forward loop regulates the activation of EGFRvIII

EGFRvIII is a key oncogene in glioblastoma (GBM). EGFRvIII results from an in-frame deletion in the extracellular domain of EGFR, does not bind ligand and is thought to be constitutively active. Although EGFRvIII dimerization is known to activate EGFRvIII, the factors that drive EGFRvIII dimerization and activation are not well understood. Here we present a new model of EGFRvIII activation and propose that oncogenic activation of EGFRvIII in glioma cells is driven by co-expressed activated EGFR wild type (EGFRwt). Increasing EGFRwt leads to a striking increase in EGFRvIII tyrosine phosphorylation and activation while silencing EGFRwt inhibits EGFRvIII activation. Both the dimerization arm and the kinase activity of EGFRwt are required for EGFRvIII activation. EGFRwt activates EGFRvIII by facilitating EGFRvIII dimerization. We have previously identified HB-EGF, a ligand for EGFRwt, as a gene induced specifically by EGFRvIII. In this study, we show that HB-EGF is induced by EGFRvIII only when EGFRwt is present. Remarkably, altering HB-EGF recapitulates the effect of EGFRwt on EGFRvIII activation. Thus, increasing HB-EGF leads to a striking increase in EGFRvIII tyrosine phosphorylation while silencing HB-EGF attenuates EGFRvIII phosphorylation, suggesting that an EGFRvIII-HB-EGF-EGFRwt feed-forward loop regulates EGFRvIII activation. Silencing EGFRwt or HB-EGF leads to a striking inhibition of EGFRvIII-induced tumorigenicity, while increasing EGFRwt or HB-EGF levels resulted in accelerated EGFRvIII-mediated oncogenicity in an orthotopic mouse model. Furthermore, we demonstrate the existence of this loop in human GBM. Thus, our data demonstrate that oncogenic activation of EGFRvIII in GBM is likely maintained by a continuous EGFRwt-EGFRvIII-HB-EGF loop, potentially an attractive target for therapeutic intervention.

Theoretical studies on thermal stratification in a side heated cavity

The Advanced Heavy Water Reactor (AHWR) being designed in India is a vertical pressure tube type boiling water-cooled and heavy water moderated reactor. A key feature of the AHWR is the use of simple passive systems to respond to any postulated accidental condition. Passive Containment Cooling System (PCCS), is one such system, which provides long term cooling for the reactor containment following a Loss Of Coolant Accident (LOCA). The system consists of Immersed Condensers immersed in a gravity driven water pool. One of the important phenomena related to PCCS functioning is the effect of thermal stratification in the water pool. The heat transfer from IC to water pool takes place by natural convection. In this process, the pool water can get stratified. Towards the top of the water pool, the temperature of water may reach almost the boiling point while at the bottom of the pool, the water is likely to remain at the initial temperature. Hence, in order to study the integral system response of PCCS, the phenomenon of stratification requires to be investigated. Towards this objective, the case of a rectangular enclosure heated symmetrically on both the vertical sides was considered and a two-dimensional analysis was done by numerically solving the mass, momentum and energy equations. Theoretical results were generated by the use of a computer code developed for this purpose and the results are then compared with the experimental results available in literature.