Detailed study of the ELAIS N1 field with the uGMRT - I. Characterizing the 325 MHz foreground for redshifted 21 cm observations

In this first paper of the series, we present initial results of newly upgraded Giant Meterwave Radio Telescope (uGMRT) observation of European Large-Area ISO Survey-North 1 (ELAIS-N1) at 325 MHz with 32 MHz bandwidth. Precise measurement of fluctuations in Galactic and extragalactic foreground emission as a function of frequency as well as angular scale is necessary for detecting redshifted 21-cm signal of neutral hydrogen from Cosmic Dawn, Epoch of Reionization (EoR) and post-reionization epoch. Here, for the first time we have statistically quantified the Galactic and extragalactic foreground sources in the ELAIS-N1 field in the form of angular power spectrum using the newly developed Tapered Gridded Estimator (TGE). We have calibrated the data with and without direction-dependent calibration techniques. We have demonstrated the effectiveness of TGE against the direction dependent effects by using higher tapering of field of view (FoV). We have found that diffuse Galactic synchrotron emission (DGSE) dominates the sky, after point source subtraction, across the angular multipole range $1115 \leqslant \mathcal{\ell} \leqslant 5083$ and $1565 \leqslant \mathcal{\ell} \leqslant 4754$ for direction-dependent and -independent calibrated visibilities respectively. The statistical fluctuations in DGSE has been quantified as a power law of the form $\mathcal{C}_{\mathcal{\ell}}= A \mathcal{\ell}^{-\beta}$. The best fitted values of (A, $\beta$) are ($62 \pm 6$ $mK^{2}$, $2.55 \pm 0.3$) and ($48 \pm 4$ $mK^{2}$, $2.28 \pm 0.4$ ) for the two different calibration approaches. For both the cases, the power law index is consistent with the previous measurements of DGSE in other parts of sky.Comment: 13 pages, 5figures, 4 tables; accepted for publication in MNRA

Organization and Biology of the Porcine Serum Amyloid A (SAA) Gene Cluster: Isoform Specific Responses to Bacterial Infection.

Serum amyloid A (SAA) is a prominent acute phase protein. Although its biological functions are debated, the wide species distribution of highly homologous SAA proteins and their uniform behavior in response to injury or inflammation in itself suggests a significant role for this protein. The pig is increasingly being used as a model for the study of inflammatory reactions, yet only little is known about how specific SAA genes are regulated in the pig during acute phase responses and other responses induced by pro-inflammatory host mediators. We designed SAA gene specific primers and quantified the gene expression of porcine SAA1, SAA2, SAA3, and SAA4 by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in liver, spleen, and lung tissue from pigs experimentally infected with the Gram-negative swine specific bacterium Actinobacillus pleuropneumoniae, as well as from pigs experimentally infected with the Gram-positive bacterium Staphylococcus aureus. Our results show that: 1) SAA1 may be a pseudogene in pigs; 2) we were able to detect two previously uncharacterized SAA transcripts, namely SAA2 and SAA4, of which the SAA2 transcript is primarily induced in the liver during acute infection and presumably contributes to circulating SAA in pigs; 3) Porcine SAA3 transcription is induced both hepatically and extrahepatically during acute infection, and may be correlated to local organ affection; 4) Hepatic transcription of SAA4 is markedly induced in pigs infected with A. pleuropneumoniae, but only weakly in pigs infected with S. aureus. These results for the first time establish the infection response patterns of the four porcine SAA genes which will be of importance for the use of the pig as a model for human inflammatory responses, e.g. within sepsis, cancer, and obesity research

Interplay of Rad51 with NF-κB pathway stimulates expression of HIV-1.

Transcription from the HIV-1 promoter is controlled by a series of ubiquitous and inducible cellular proteins with the ability to enter the nucleus and interact with the promoter. A DNA sequence spanning nucleotides -120 to -80, which supports the association of the inducible NF-κB transcription factor, has received much attention. Here we demonstrate that the interplay between Rad51, a key regulator of the homologous recombination pathway of DNA repair and whose level is induced upon HIV-1 infection, with the NF-κB pathway, augments transcription of the viral promoter. Evidently, stimulation of the NF-κB pathway by PMA and/or TSA promotes association of Rad51 with the LTR DNA sequence and that the p65 subunit of NF-κB is important for this event. Our results also demonstrate that, similar to p65, Rad51 utilizes the NF-κB pathway to position itself in the nucleus as ectopic expression of an IκB mutant impedes its nuclear appearance and transcriptional activity upon the HIV-1 LTR. Treatment of peripheral blood mononuclear cells with small molecules that inhibit Rad51 activity results in greater than 50% decrease in the HIV-1 infection of cells. These observations provide evidence for the involvement of DNA repair factors in control of HIV-1 gene activation and offer a new avenue for the development of anti-viral therapeutics that affect viral gene transcription in latently infected cells

Detailed study of ELAIS N1 field with the uGMRT - II. Source properties and spectral variation of foreground power spectrum from 300-500 MHz observations

Understanding the low-frequency radio sky in depth is necessary to subtract foregrounds in order to detect the redshifted 21 cm signal of neutral hydrogen from the cosmic dawn, the epoch of reionization and the post-reionization era. In this second paper of the series, we present the upgraded Giant Metrewave Radio Telescope (uGMRT) observation of the ELAIS N1 field made at 300-500 MHz. The image covers an area of similar to 1.8 deg(2) and has a central background rms noise of similar to 15 mu Jy beam(-1). We present a radio source catalogue containing 2528 sources (with flux densities > 100 mu Jy) and normalized source counts derived from that. A detailed comparison of detected sources with previous radio observations is shown. We discuss flux-scale accuracy, positional offsets, spectral index distribution and correction factors in source counts. The normalized source counts are in agreement with previous observations of the same field, as well as model source counts from the Square Kilometre Array Design Study simulation. It shows a flattening below similar to 1 mJy that corresponds to a rise in populations of star-forming galaxies and radio-quiet active galactic nuclei. For the first time, we estimate the spectral characteristics of the angular power spectrum or multi-frequency angular power spectrum of diffuse Galactic synchrotron emission over a wide frequency bandwidth of 300-500 MHz from radio interferometric observations. This work demonstrates the improved capabilities of the uGMRT

Recruitment of Rad51 to an integrated copy of the HIV-1 LTR and activation of its transcription.

<p><b>(A)</b> TZM-bl cells were treated with TSA or PMA and the level of promoter activity was determined after 36 hours by luciferase assay. <b>(B)</b> ChIP analysis of extracts from TZM-bl cells treated with TSA and PMA illustrating the presence of LTR DNA corresponding to the κB motif in immunocomplexes pulled down by anti-Rad51 and anti-p65 antibodies. The bar graphs illustrate quantitative analyses of the intensity of bands corresponding to LTR DNA detected in the complex pulled down by anti-Rad51 and anti-p65 antibodies. The intensity of the input band was used for normalizing the data of each. <b>(C)</b> ChIP analysis for detection of Rad51 association with endogenous LTR DNA in TZM-bl cells, untreated or treated with PMA, after transfection with plasmids expressing non-target (NT) siRNA or NF-κB p65-specific siRNA. The bar graph illustrates quantitative analysis of the intensity of bands corresponding to LTR DNA detected in the complex pulled down by anti-Rad51 antibody. The intensity of the input band was used for normalizing the data. <b>(D)</b> ChIP analysis demonstrating the interaction of NF-κB p65 with integrated copies of the LTR under various conditions as indicated. ADU (Absorption density units) were set at the arbitrary unit of one. Ten represents the intensity of the bands obtained from ChIP assay.</p

Activation of the HIV-1 LTR by Rad51 and NF-κB p65 requires the κB motif.

<p><b>(A)</b> Primary cultures of human astrocytes were transfected with luciferase reporter plasmids pGL3-LTR encompassing various segments of the LTR (as indicated), either alone or together with plasmids expressing NF-κB p65 and/or Rad51. The total amount of DNA was equalized with relevant plasmid vector DNA. <b>(B)</b> Western blot of protein extracts from the cells shown in Panel A showing NF-κB p65 and Rad51 levels in each sample. α-Tubulin served as a protein loading control. <b>(C)</b> Primary cultures of human astrocytes were transfected with NF-κB p65 siRNA and Rad51 siRNA alone or together. The total amount of siRNA was equalized with non-target siRNA. After 48 hours, cells were lysed and luciferase assays performed. <b>(D)</b> Western blot analysis illustrating the levels of NF-κB p65 and Rad51 in cells treated with various siRNAs as indicated. Transcriptional activity represents fold effect in which controls (NF-κB p65 and Rad51) were set at 1.0.</p

Inhibition of Rad51 function represses HIV-1 infection.

<p><b>(A)</b> Top: PBMCs isolated from 3 different donors were infected with HIV-1 SF₁₆₂ and incubated in the presence of 10 or 50 µM of Rad51 inhibitor (RI-1) for 3 days. Infection was quantified by examining the level of virus in the supernatants from the infected cells using p24 Gag ELISA. <b>(B)</b> Western blot analysis of protein extracts from the infected cells using anti-Rad51 and anti-α-tubulin antibody. The ratio of the intensity of the Rad51 and α-tubulin in each sample is shown. <b>(C)</b> MTT assay showing cell viability upon treatment under the same conditions used in Panel A.</p