The role of Xenopus BRG1, a conserved subunit of SWI/SNF class of remodeling complexes, during early frog development

BRG1 is a conserved subunit of the SWI/SNF family of ATP dependent chromatin remodeling complexes. These complexes play an important role in the transcription of various genes by making promoters accessible to the transcription machinery. Mutations in BRG1 have been connected to various cancers. In addition, a BRG1 knock-out in mice is lethal at the periimplantation stage, while BRG1 heterozygote mice are predisposed to exencephaly and tumors of epithelial origin, showing the importance of BRG1 in normal development and disease. In this study, I used Xenopus laevis to study the role of BRG1 because this system allows manipulation of endogenous protein levels by the use of antisense oligonucleotide mediated knock-down as well as interference analysis at early stages of development by overexpression of wild type and dominant negative protein variants. Since BRG1 is conserved among all vertebrates, I initially studied the role of BRG1 in Xenopus development by overexpression of wild type and dominant negative human BRG1. Overexpression of dominant negative human BRG1 gave a ventralized phenotype suggesting a role of BRG1 in dorsal-ventral patterning. The specificity of phenotypes was confirmed by using wild type human BRG1. On the other hand, overexpression of wild type and dominant negative variants of human BRM showed no developmental phenotypes. Prompted by these results, a frog brg1 cDNA was cloned by searching the Xenopus laevis EST database, using human BRG1 as a query. In addition, monoclonal antibodies specific to xBRG1 were raised and characterized. The expression pattern of Xbrg1 was found to be ubiquitous until gastrula stage and is tissue specific from neurula stage onwards. A Xenopus homologue of INI1, a subunit of SWI/SNF chromatin-remodeling complex, was cloned using database search. The expression pattern of Xini1 was found to be similar to Xbrg1. Using site directed mutagenesis, a dominant negative construct of xBRG1 was made by mutating the conserved lysine into arginine (K770R). Loss and gain of function studies showed that BRG1 is involved in AP axis formation during Xenopus development. The gain of function studies were done by overex-pressing wild type and dominant negative xBRG1, while loss of function studies were done using highly specific antisense morpholino oligos. Specificity of morpholino treatment was further proven by the rescue of ventralized phenotypes of morphant embryos by overexpression of human BRG1. It was found that BRG1 knock-down affects several tissues as assessed by in-situ hybridization using tissue specific markers. To determine the molecular explanation for these pleiotropic effects, several genes involved in early patterning of Xenopus embryo during organizer formation were analyzed. The analysis was done using whole mount in-situ hybridization, revealing the spatial gene expression pattern. This analysis revealed that BRG1 mostly affects WNT signaling dependent genes required for dorsal mesoderm formation while leaving pan-mesodermal genes unaffected. Furthermore the genetic interaction of BRG1 with the WNT pathway was confirmed by epistasis experiments showing that overexpression of β-CATENIN can rescue the xBrg1 antisense morpholino oligos dependent ventralized phenotypes as well as formation of secondary axis by overexpression of β-CATENIN could be prevented by BRG1 knock-down. Since the whole embryo represents a complex situation whereby many signaling pathways interact with each other and influence the outcome, the animal cap system was used to analyze the effect of BRG1 on various signaling pathways by analyzing corresponding direct target genes. Animal cap assays showed that the effect of BRG1 is signal specific. Moreover, among the affected signaling pathways, BRG1 knock-down affected only specific genes. These results showed that the BRG1 effect is gene and signal specific. The importance of WNT signaling has also been shown in cancer as well as in haematopoietic and embryonic stem cell self renewal. Given the importance of the WNT signaling, the role of BRG1 on the WNT signaling pathway was further investigated. Treatment of animal cap cells with various doses of Wnt8 mRNA showed the differential requirement of the WNT signal for maximal stimulation of direct target genes. The direct target genes of the WNT pathway showed various degrees of reduction in their maximal stimulation upon BRG1 protein knock-down. The requirement of BRG1 for proper stimulation of the WNT target genes was further confirmed by overexpression of xBRG1 under sub-optimal conditions of WNT stimulation. A major conclusion from these experiments is that BRG1 protein defines signaling thresholds for WNT-mediated activation of target genes. This implies that chromatin remodeling complexes are part of the machinery, which translates inductive signals into spatial gene expression domains

Managing a Fleet of Autonomous Mobile Robots (AMR) using Cloud Robotics Platform

In this paper, we provide details of implementing a system for managing a fleet of autonomous mobile robots (AMR) operating in a factory or a warehouse premise. While the robots are themselves autonomous in its motion and obstacle avoidance capability, the target destination for each robot is provided by a global planner. The global planner and the ground vehicles (robots) constitute a multi agent system (MAS) which communicate with each other over a wireless network. Three different approaches are explored for implementation. The first two approaches make use of the distributed computing based Networked Robotics architecture and communication framework of Robot Operating System (ROS) itself while the third approach uses Rapyuta Cloud Robotics framework for this implementation. The comparative performance of these approaches are analyzed through simulation as well as real world experiment with actual robots. These analyses provide an in-depth understanding of the inner working of the Cloud Robotics Platform in contrast to the usual ROS framework. The insight gained through this exercise will be valuable for students as well as practicing engineers interested in implementing similar systems else where. In the process, we also identify few critical limitations of the current Rapyuta platform and provide suggestions to overcome them.Comment: 14 pages, 15 figures, journal pape

Study to determine serum vitamin D levels in patients with congestive heart failure

Background: It was to evaluate the association of serum levels of vitamin D in patients with congestive heart failure.Methods: The present study was conducted in the department of Medicine at Chattrapati Shivaji Subharti Hospital among 100 patients, aged 18 years and above diagnosed as congestive heart failure on the basis of clinical and echocardiographic evidence. Clinical manifestations looked for CHF were: Dyspnea, orthopnea, acute pulmonary edema, cerebral symptoms, cheyne-stokes respiration, cyanosis, sinus tachycardia, raised jugular venous pressure, congestive hepatomegaly and pedal edema. In the present study deficiency/ insufficiency of vitamin D was considered when the presence of levels of 25-hydroxyvitamin D was 30 respectively with statistically significant difference. The Mean±SD scores of CPK MB (IU/L) was found to be 33.1±20.8 and 18.6±13.3 among the subjects having vitamin D levels 30 respectively with statistically significant difference.Conclusions: The results of the present study suggest that low levels of vitamin D may adversely affect the cardiovascular system

Pleomorphic Lobular Carcinoma in a Male Breast: A Rare Occurrence

Carcinoma of male breast is uncommon as it accounts for 0.7% of total breast cancer. The pathology of male breast cancer is remarkably similar to that of cancers seen in women. The same histological subtypes of invasive cancer are present, although papillary carcinomas (both invasive and in situ) are more common and lobular carcinomas are less common. The predominant histological type, in males, as in females, reported in large series has been infiltrating ductal carcinoma with scattered reports of infiltrating lobular carcinoma, all of them of classical type except for a single case of pleomorphic infiltrating lobular carcinoma. Herein, we describe a case of pleomorphic lobular carcinoma occurring in male breast

Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming

SummaryReprogramming of somatic cells achieved by combination of the four transcription factors Oct4, Sox2, Klf4, and c-Myc has very low efficiency. To increase the reprogramming efficiency and better understand the process, we sought to identify factors that mediate reprogramming with higher efficiency. We established an assay to screen nuclear fractions from extracts of pluripotent mouse cells based on Oct4 reactivation. Using proteomics, we identified components of the ATP-dependent BAF chromatin-remodeling complex, which significantly increases reprogramming efficiency when used together with the four factors. The reprogrammed cells could transmit to the germline and exhibited pluripotency. Reprogramming remained highly efficient when c-Myc was not present but BAF components were overexpressed. BAF complex components mediate this effect by facilitating enhanced Oct4 binding to target promoters during reprogramming. Thus, somatic cell reprogramming using chromatin-remodeling molecules represents an efficient method of generating reprogrammed cells

Electroencephalographic Abnormalities in Clozapine-Treated Patients: A Cross-Sectional Study

The objective of our study was to examine the electroencephalogram (EEG) abnormalities associated with clozapine treatment. It was a cross-sectional study on 87 psychiatric patients on clozapine treatment. 32 channel digital EEG was recorded and analysed visually for abnormalities. EEG abnormalities were observed in 63.2% of patients. Both slowing and epileptiform activities were noted in 41.4% of patients. The EEG abnormalities were not associated with dose or duration of clozapine exposure

Daksha: On Alert for High Energy Transients

We present Daksha, a proposed high energy transients mission for the study of electromagnetic counterparts of gravitational wave sources, and gamma ray bursts. Daksha will comprise of two satellites in low earth equatorial orbits, on opposite sides of earth. Each satellite will carry three types of detectors to cover the entire sky in an energy range from 1 keV to >1 MeV. Any transients detected on-board will be announced publicly within minutes of discovery. All photon data will be downloaded in ground station passes to obtain source positions, spectra, and light curves. In addition, Daksha will address a wide range of science cases including monitoring X-ray pulsars, studies of magnetars, solar flares, searches for fast radio burst counterparts, routine monitoring of bright persistent high energy sources, terrestrial gamma-ray flashes, and probing primordial black hole abundances through lensing. In this paper, we discuss the technical capabilities of Daksha, while the detailed science case is discussed in a separate paper.Comment: 9 pages, 3 figures, 1 table. Additional information about the mission is available at https://www.dakshasat.in

Bronchiectasis in India:results from the European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) and Respiratory Research Network of India Registry

BACKGROUND: Bronchiectasis is a common but neglected chronic lung disease. Most epidemiological data are limited to cohorts from Europe and the USA, with few data from low-income and middle-income countries. We therefore aimed to describe the characteristics, severity of disease, microbiology, and treatment of patients with bronchiectasis in India. METHODS: The Indian bronchiectasis registry is a multicentre, prospective, observational cohort study. Adult patients ( 6518 years) with CT-confirmed bronchiectasis were enrolled from 31 centres across India. Patients with bronchiectasis due to cystic fibrosis or traction bronchiectasis associated with another respiratory disorder were excluded. Data were collected at baseline (recruitment) with follow-up visits taking place once per year. Comprehensive clinical data were collected through the European Multicentre Bronchiectasis Audit and Research Collaboration registry platform. Underlying aetiology of bronchiectasis, as well as treatment and risk factors for bronchiectasis were analysed in the Indian bronchiectasis registry. Comparisons of demographics were made with published European and US registries, and quality of care was benchmarked against the 2017 European Respiratory Society guidelines. FINDINGS: From June 1, 2015, to Sept 1, 2017, 2195 patients were enrolled. Marked differences were observed between India, Europe, and the USA. Patients in India were younger (median age 56 years [IQR 41-66] vs the European and US registries; p<0\ub70001]) and more likely to be men (1249 [56\ub79%] of 2195). Previous tuberculosis (780 [35\ub75%] of 2195) was the most frequent underlying cause of bronchiectasis and Pseudomonas aeruginosa was the most common organism in sputum culture (301 [13\ub77%]) in India. Risk factors for exacerbations included being of the male sex (adjusted incidence rate ratio 1\ub717, 95% CI 1\ub703-1\ub732; p=0\ub7015), P aeruginosa infection (1\ub729, 1\ub710-1\ub750; p=0\ub7001), a history of pulmonary tuberculosis (1\ub720, 1\ub707-1\ub734; p=0\ub7002), modified Medical Research Council Dyspnoea score (1\ub732, 1\ub725-1\ub739; p<0\ub70001), daily sputum production (1\ub716, 1\ub703-1\ub730; p=0\ub7013), and radiological severity of disease (1\ub703, 1\ub701-1\ub704; p<0\ub70001). Low adherence to guideline-recommended care was observed; only 388 patients were tested for allergic bronchopulmonary aspergillosis and 82 patients had been tested for immunoglobulins. INTERPRETATION: Patients with bronchiectasis in India have more severe disease and have distinct characteristics from those reported in other countries. This study provides a benchmark to improve quality of care for patients with bronchiectasis in India. FUNDING: EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium, European Respiratory Society, and the British Lung Foundation

Science with the Daksha High Energy Transients Mission

We present the science case for the proposed Daksha high energy transients mission. Daksha will comprise of two satellites covering the entire sky from 1~keV to $>1$~MeV. The primary objectives of the mission are to discover and characterize electromagnetic counterparts to gravitational wave source; and to study Gamma Ray Bursts (GRBs). Daksha is a versatile all-sky monitor that can address a wide variety of science cases. With its broadband spectral response, high sensitivity, and continuous all-sky coverage, it will discover fainter and rarer sources than any other existing or proposed mission. Daksha can make key strides in GRB research with polarization studies, prompt soft spectroscopy, and fine time-resolved spectral studies. Daksha will provide continuous monitoring of X-ray pulsars. It will detect magnetar outbursts and high energy counterparts to Fast Radio Bursts. Using Earth occultation to measure source fluxes, the two satellites together will obtain daily flux measurements of bright hard X-ray sources including active galactic nuclei, X-ray binaries, and slow transients like Novae. Correlation studies between the two satellites can be used to probe primordial black holes through lensing. Daksha will have a set of detectors continuously pointing towards the Sun, providing excellent hard X-ray monitoring data. Closer to home, the high sensitivity and time resolution of Daksha can be leveraged for the characterization of Terrestrial Gamma-ray Flashes.Comment: 19 pages, 7 figures. Submitted to ApJ. More details about the mission at https://www.dakshasat.in

Constructing Optimal Flow Networks: An Exploration Centered on the U.S. Flight Network

Flow networks play a critical role in various fields including engineering, transportation, logistics, and communications. Efficient network design is essential for addressing complex demands, constraints, and priorities. This thesis presents a series of techniques and models for optimal flow network design via edge selection. The U.S. domestic passenger flight network serves as a case study for applying, testing, and visualizing the results of the proposed methods. Four models are explored: spanning tree construction, optimal hub selection, optimal new hub creation, and a generic edge selection model. Spanning trees are shown to minimize the number of edges while satisfying all demand, with fast algorithms available for finding optimal trees based on various factors. Hub selection and new hub creation models are proposed that allow network planners to account for factors such as total passenger-miles traveled, total edge length, and the number of transfers (or a combination thereof)—with an analysis of the conditions under which one model is superior to the other. Finally, a generic edge selection model is presented with a mixed-integer optimization formulation, and is shown to be powerful, versatile, and adaptive to various network settings based on a network planner's preferences, constraints, and circumstances. The thesis contributes to the fields of operations research, graph theory, and network optimization, and has practical implications for the optimal design of complex networks across a wide range of domains