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Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

Binding sites of the chromatin regulator protein CTCF function as important landmarks in the human genome. The recently characterized CTCF-binding sites at LINE-1 repeats depend on another repeat-regulatory protein CGGBP1. These CGGBP1-dependent CTCF-binding sites serve as potential barrier elements for epigenetic marks such as H3K9me3. Such CTCF-binding sites are associated with asymmetric H3K9me3 levels as well as RNA levels in their flanks. The functions of these CGGBP1-dependent CTCF-binding sites remain unknown. By performing targeted studies on candidate CGGBP1-dependent CTCF-binding sites cloned in an SV40 promoter-enhancer episomal system we show that these regions act as inhibitors of ectopic transcription from the SV40 promoter. CGGBP1-dependent CTCF-binding sites that recapitulate their genomic function of loss of CTCF binding upon CGGBP1 depletion and H3K9me3 asymmetry in immediate flanks are also the ones that show the strongest inhibition of ectopic transcription. By performing a series of strand-specific reverse transcription PCRs we demonstrate that this ectopic transcription results in the synthesis of RNA from the SV40 promoter in a direction opposite to the downstream reporter gene in a strand-specific manner. The unleashing of the bidirectionality of the SV40 promoter activity and a breach of the transcription barrier seems to depend on depletion of CGGBP1 and loss of CTCF binding proximal to the SV40 promoter. RNA-sequencing reveals that CGGBP1-regulated CTCF-binding sites act as barriers to transcription at multiple locations genome-wide. These findings suggest a role of CGGBP1-dependent binding sites in restricting ectopic transcription.

This research aims to study structure, functioning and operational mechanism of India’s first gas exchange i.e. Indian Gas Exchange (IGX) which is a subsidiary of Indian Energy Exchange (IEX). Exploratory research is used to study and investigate conceptual framework and operational mechanism of IGX. The results of the study show that IEX has unveiled the nation’s first automated natural gas exchange trading platform called IGX for well organized and hefty Gas market and to stimulate gas trading in the country. IGX would lead India towards Gas Based Economy by designing and providing robust solution for natural gas trading and access. So far as price mechanism at IGX is concerned, it is dynamic and market driven which is based on Double-sided closed auction with uniform price mechanism. IGX plays an extremely important and fundamental role towards capitalizing a free market for gas. Clearing and Settlement system at IGX is structured and transparent. As IGX is purely electronic trading platform for natural gas which is considered as barometer of the India’s progressive policy as it integrates the entire energy value chain from gas production.

Our understanding of DNA G-quadruplexes (G4s) fromin vitrostudies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s. It remains unknown what fraction of G4s formed in human cells are protein-bound. The G4-chromatin immunoprecipitation (G4-ChIP) method hitherto employed to describe G4 landscapes preferentially reports G4s that get crosslinked to proteins in their proximity. Our current understanding of the G4 landscape is biased against representation of G4s which escape crosslinking as they are not stabilized by protein-binding and presumably transient. We report a protocol that captures G4s from the cells efficiently without any bias as well as eliminates the detection of G4s formed artifactually on crosslinked sheared chromatin post-fixation. We discover that G4s form sparingly at SINEs. An application of this method shows that depletion of a repeat-binding protein CGGBP1 enhances net G4 capture at CGGBP1-dependent CTCF-binding sites and regions of sharp interstrand G/C-skew transitions. Thus, we present an improved method for G4 landscape determination and by applying it we show that sequence property-specific constraints of the nuclear environment mitigate G4 formation.

In the present work, we have studied the inactivation of Candida albicans (C. albicans) and lemon (Citrus limon) spoilage fungi using plasma activated water (PAW). Air and N2 are used as plasma forming gases for PAW preparation. Optical emission spectroscopy is used to determine various active radicals and species present in the air and N2 plasma. The present study shows the changes in physicochemical properties and reactive oxygen–nitrogen species formed in PAW. Furthermore, the fungicidal efficacy of PAW is investigated on C. albicans. The role of oxidizing potential of PAW and PAW treatment time with fungi (C. albicans and Citrus limon spoilage fungi) is investigated in the present work. Results showed high oxidizing PAW can achieve 6 + log10 CFU ml−1 reduction in fungi even with low treatment time. Morphology analysis by HR-SEM, leaked nucleic acids and protein measurement by UV–visible spectroscopy, and PI binding red fluorescence of cells showed PAW treatment with C. albicans damaged the membrane of cells due to which leakage of extracellular materials occurred that led to cells death. The present study also reveals the long-term fungicidal efficacy of PAW on C. albicans and Citrus limon spoilage fungi.

Presently, the world is using different types of disinfectants for various applications such as disinfecting instrument surfaces in the medical field, sanitizers in airplanes, wash-rooms, etc. These disinfectants carry various harmful chemicals that harm our ecosystem. Hence in search of more eco-friendly disinfectants, our research leads us to explore plasma activated water (PAW). PAW can be produced with the help of plasma interaction with water. This interaction changes the physicochemical properties of water and makes it reactive to kill pathogens. PAW can be used for a wide variety of applications such as food preservation, fast germination, sterilization agents, etc. In the present work, PAW has been formed using non-thermal plasma and different gas or gas mixture as plasma forming gas. Its physicochemical properties have been studied to identify pH value, oxidation reduction potential, and chemical species formed after plasma interaction with a water surface. Further, the study has been carried out to determine the disinfectant ability of PAW for two types of pathogens named Staphylococcus aureus and Pseudomonas aeruginosa. Different bactericidal methods have been adopted to confirm the results. SEM, fluorescence microscopy, and release of nucleic acids and proteins from raptured cell membrane of pathogens clearly show bactericidal efficacy of PAW. The important finding of the present work is the effective killing of pathogens by PAW in a short span of interaction time (≤ 10 s). The PAW has a strong possibility of using it as a disinfectant to kill a wide variety of pathogens and micro-organisms.

During Aspergillus fumigatus mediated lung inflammation, NLRP3 inflammasome is rapidly activated that aggravates IL-1β production contributing to lung inflammation. Previously, we have shown the protective role of SYK-1 inhibition in inhibiting inflammasome activation during lung inflammation. In the current manuscript, we explored the protective role of direct caspase-1 inhibition during β-glucan-induced lung inflammation. We have mimicked the lung inflammation by administering intranasal β-glucan in mice model. YVAD was used for caspase-1 inhibition. We have shown that caspase-1 inhibition by YVAD did not alter inflammasome independent inflammatory cytokines, while it significantly reduced inflammasome activation and IL-1β secretion. Caspase-1 inhibited bone marrow derived dendritic cells (BMDCs), co-cultured with T cells showed decreased T-cell proliferation and direct them to secrete high TGF-β and IL-10 compared to the T cells co-cultured with β-glucan primed dendritic cells. Caspase-1 inhibition in BMDCs also induced IL-22 secretion from CD4+T cells. Caspase-1 inhibition in intranasal β-glucan administered mice showed decreased tissue damage, immune cell infiltration and IgA secretion compared to control mice. Further, splenocytes challenged with β-glucan show high IL-10 secretion and increased FOXp3 and Ahr indicating an increase in regulatory T cells on caspase-1 inhibition. Caspase-1 inhibition can thus be an attractive target to prevent inflammation mediated tissue damage during Aspergillus fumigatus mouse model and can be explored as an attractive therapeutic strategy.HIGHLIGHTSCaspase-1 inhibition protects lung damage from inflammation during β-glucan exposureCaspase-1 inhibition in dendritic cells decreases IL-1β production resulting in decreased pathogenic Th17Caspase-1 inhibition promotes regulatory T cells thereby inhibiting lung inflammation Caspase-1 inhibition protects lung damage from inflammation during β-glucan exposure Caspase-1 inhibition in dendritic cells decreases IL-1β production resulting in decreased pathogenic Th17 Caspase-1 inhibition promotes regulatory T cells thereby inhibiting lung inflammation

Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.

Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help us understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long read as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.

This paper aims to build up a model for an online remote gas and temperature checking device for worker’s safety in sewage pipelines. The device is WSN based microcontroller equipped with analog and digital sensor. The design included several units mainly: Arduino Microcontroller MQ-135, DHT11, Gas and Temperature Sensors, and the current regulator circuit. The sensors are connected with a microcontroller through an ADC for advanced flag change and information logging. An LCD show is likewise associated with the microcontroller to show the estimations. For examination and filing purposes, the information can be exchanged to a PC with a graphical UI program through a USB interface. The device displays toxic gas and workers real-time position, transmit information remotely via a graphical user interface to IBM bluemix provide adjacent help. By keeps observing, this model will prone to diminish mishaps and slowly spares an existence. The model has numerous points of interest when contrasted with other checking frameworks as far as its littler size, gigantic memory limits, on-gadget show, bring down cost and more noteworthy versatility.

The authors discuss their interaction with data using various data visualization techniques, which are a quick, easy way to convey concepts universally. Currently, data has become more and more important; it is also important how one can visualize that data in the mind. This chapter is based on extracting important information from one of the holy Swaminarayan scriptures. The authors explore the content of the Vachanamrut, a unique work of prose in the Gujarati language, which contains discourses of Lord Swaminarayan and his conversation with saints and devotees. They convert the data in graphical interface using some libraries of the R tool. So, one can get the main idea of that data quickly, without a need to explain more about that data. Summing it up, this chapter examines the techniques of describing data of any ancient scripture or ancient text in any language by visualizing that data.

Binding sites of the chromatin regulator protein CTCF function as important landmarks in the human genome. The recently characterized CTCF-binding sites at LINE-1 repeats depend on another repeat-regulatory protein CGGBP1. These CGGBP1-dependent CTCF-binding sites serve as potential barrier elements for epigenetic marks such as H3K9me3. Such CTCF-binding sites are associated with asymmetric H3K9me3 levels as well as RNA levels in their flanks. The functions of these CGGBP1-dependent CTCF-binding sites remain un-known. By performing targeted studies on candidate CGGBP1-dependent CTCF-binding sites cloned in an SV40 promoter-enhancer episomal system we show that these regions act as inhibitors of ectopic transcription from the SV40 promoter. CGGBP1-dependent CTCF-binding sites that recapitulate their genomic function of loss of CTCF binding upon CGGBP1 depletion and H3K9me3 asymmetry in immediate flanks are also the ones that show the strongest inhibition of ectopic transcription. By performing a series of strand-specific reverse transcription PCRs we demonstrate that this ectopic transcription results in the synthesis of RNA from the SV40 promoter in a direction opposite to the downstream reporter gene in a strand-specific manner. The unleashing of the bidirectionality of the SV40 promoter activity and a breach of the transcription barrier seems to depend on depletion of CGGBP1 and loss of CTCF binding proximal to the SV40 promoter. RNA-sequencing reveals that CGGBP1-regulated CTCF-binding sites act as barriers to transcription at multiple locations genomewide. These findings suggest a role of CGGBP1-dependent binding sites in restricting ectopic transcription.

Repeated exposure to the fungal pathogen Aspergillus fumigates triggers spleen tyrosine kinase (SYK) signalling through dectin-1 activation, which is associated with deleterious airway inflammation. β-Glucan-induced dectin-1 signalling activates the NLRP3 inflammasome, which in turn rapidly produces IL-1β, a master regulator of inflammation. IL-1β expression results in Th17/Treg imbalance, pulmonary inflammation, and bystander tissue injury. This study reports that 3,4 methylenedioxy-β-nitrostyrene (MNS), a potent SYK inhibitor, markedly decreased the expression of pro-inflammatory cytokines and increased the expression of anti-inflammatory cytokines in vitro. Furthermore, SYK inhibition markedly decreased β-glucan-induced IL-1β expression, suggesting that SYK is indispensable for NLRP3 inflammasome activation. Decreased IL-1β expression correlated with reduced Th17 response and enhanced immunosuppressive Treg response. Notably, SYK inhibition ameliorated inflammation caused by repeated intranasal β-glucan challenge in BALB/C mice. SYK inhibition also restored the Th17/Treg balance via decreased Th17 and increased Treg responses, as evidenced by decreased IL-17 and ror-γ levels. Additionally, inhibition of SYK increased IL-10 secreting CD4+FOXP3+ T cells that accompanied reduced T cell proliferation. Decreased IgA in the Bronchoalveolar lavage (BAL) fluid and serum also indicated the immunosuppressive potential of SYK inhibition. Histopathology data revealed that repeated β-glucan challenge caused substantial pulmonary damage, as indicated by septal thickening and interstitial lymphocytic, neutrophil and granulocyte recruitment. These processes were effectively prevented by SYK inhibition, resulting in lung protection. Collectively, our findings suggest that SYK inhibition ameliorates dectin-1- mediated detrimental pulmonary inflammation and subsequent tissue damage. Therefore, SYK can be a new target gene in the therapeutic approach against fungal induced airway inflammation.

This work reports a one pot facile route for complete valorization of domestic organic waste into biogenic carbon dots (BCDs) and biochar for application as nanosensor and adsorbent respectively. Among the various precursors used, dried rose petals derived (BCDRP) and ripe banana peel derived (BCDBP) carbon dots demonstrated quantum yields comparable to other previously reported biomass derived green fluorescing carbon dots. The BCDs exhibited sizes 90% removal efficiencies. This protocol ensures a complete repurposing of organic waste into modified materials via a zero waste process as demonstrated by its schematic life cycle inventory chart.

The antineoplastic agent Givinostat inhibits histone deacetylases. We present here our finding that the DNA-binding of human CGGBP1 is also inhibited by Givinostat. CGGBP1, a DNA-binding protein, is required for cancer cell proliferation. In our quest to exploit the potential anti-proliferative effects of CGGBP1 inhibition, we have developed a simple screening assay to identify chemical inhibitors of DNA-protein interactions. We have applied this screen for human CGGBP1 on a library of 1685 compounds and found that Givinostat is a direct inhibitor of CGGBP1-DNA interaction. The mechanism of action of Givinostat should thus extend beyond HDACs to include the inhibition of the myriad functions of CGGBP1 that depend on its binding to the DNA.

Additional file 12. Raw data for Fig. 3k. As indicated, the chemiluminescence scans of H3K4me3 and total histone H3 blots are shown either alone or as an overlay with the white light image that shows the molecular weight markers.

Additional file 6. A white light image of DBID blots shown in Fig. 3b. The well marked with a red X symbol contains a sample irrelevant to the experiments described. The names of the inhibitors are indicated at the top of each well.

Additional file 3. A white light image of DBID blots shown in Fig. 3a.The well marked with a red X symbol contains a sample irrelevant to the experiments described. The names of the inhibitors are indicated at the top of each well.

Additional file 2. CGGBP1 depletion in HEK293T cells: HEK293T cells were transduced with non-targeting shRNA or CGGBP1-targeting shRNA lentiviruses. Lentivirus-transduced cells were selected with 10 μg/ml Puromycin for 1 week and subjected to immunoblotting. The level of CGGBP1 and GAPDH are shown in the upper and lower panel respectively. A CGGBP1 knockdown of approximately 77% is observed when normalized to GAPDH levels.

Additional file 3. Tabulation of the sequencing and alignment statistics for CT and KD MeDIP in HEK293T and GM02639.

Additional file 9. Methylation differences between CT and KD are discernible at small genomic length ranges: Genome-wide methylation signal distribution was compared between CT and KD by using “deeptools multiBigwigSummary”. Methylation signals were compared at bin sizes of 10 kb, 5 kb, 1 kb and 0.2 kb. Correlation between CT and KD was computed by the Spearman method by using “deeptools plotCorrelation” for GM02639 cells. These correlation coefficients can be compared with those for HEK293T (Additional file 7).

Additional file 4. Table represents GC content and percentage enrichment of CpG and non-CpG context cytosines in MeDIP read sequences for CT and KD in HEK293T and GM02639. The percentage of CpG, CHG and CHH represents the relative abundance for each cytosine context as a percentage of the total methylated cytosines enriched in MeDIP for CT and KD in HEK293T and GM02639.

Young male, height-175 cm, no comorbidity presents with rapidly worsening respiratory failure. No other organ involvement. On controlled mechanical ventilation. V t 420 mL, FiO 2 –1.0, PEEP 18 cm H 2 O, Pplat 34 cm H 2 O (under paralysis). ABG analysis shows: PO 2 –45 mm Hg, PCO 2 89 mm Hg, pH 7.14, HCO 3 –28. How do we proceed?

Additional file 5. Methylation differences between CT and KD are discernible at small genomic length ranges. Genome-wide methylation signal distribution was compared between CT and KD by using “deeptools multiBigwigSummary”. Methylation signals were compared at bin sizes of 10 kb, 5 kb, 1 kb and 0.2 kb. Correlation between CT and KD was computed by the Spearman method by using “deeptools plotCorrelation” for HEK293T cells.

Additional file 2. Chemiluminescence scan at a weaker intensity of DBID blots shown in Fig. 3a. The well marked with a red X symbol contains a sample irrelevant to the experiments described. The names of the inhibitors are indicated at the top of each well.

Additional file 11. Repeat content analysis in HEK293T CT and KD MeDIP DNA shows subfamily-specific methylation changes: Methylation bin frequency plots for HEK293T CT and KD. CT and KD reads for each methylation bin (From 5 to 30) were merged and sequences for merged regions (> 150 bp long) were extracted and subjected to repeat identification. The figures depict the occurrence of the three most populous repeats (Satellites, L1-LINEs and Alu-SINEs). (A) No overall differences in repeat content were observed between CT and KD. (B) A classification of the Alu SINEs into J, S and Y subfamilies revealed subfamility-specific differences in methylation between CT and KD. AluJb and AluSx showed consistently higher methylation in KD across all the methylation bins (top two panels), while AluY showed lower methylation in KD (bottom panel). (C) A subfamily classification of L1 repeats revealed that the L1HS and P family LINE1 such as L1P1, L1P2 and L1PA4 are reduced in KD although these repeat subtypes are more prevalent in highly methylated regions. (D) In contrast, the early originated LINE1 such as L1M1, L1M3, L1M4 and L1M5 showed increased methylation in KD and these repeat subtypes are prevalent in regions with low levels of methylation.

Additional file 7. Chemiluminescence scan of DBID blots used for quantification and plotting in Fig. 3d. The Givinostat concentrations are indicated at the top of each well.

Additional file 4. Chemiluminescence scan of DBID blots shown in Fig. 3b. The well marked with a red X symbol contains a sample irrelevant to the experiments described. The names of the inhibitors are indicated at the top of each well.

Additional file 7. The MeDIP reads distribution for HEK293T CT and KD at low methylation signal bins (1 to 4): Lower methylation signal bins account for a major fraction of MeDIP reads. The frequency of the MeDIP reads for these bins with less than 5 methylation read signals were calculated separately from those in the range 5–30.

Additional file 6. The MeDIP signal correlation between CT and KD at different genomic bin sizes decline with a reduction in bin size specifically as randomization of coordinates (and thus corresponding sequences) changes the correlation stochastically away from the observed correlation coefficients with actual MeDIP sequences (refer to Additional file 5 for a comparison with correlation coefficients without any randomization).