Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA).

NAD+-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. NAD+-dependent DNA ligases comprise several discrete structural domains, including a BRCT domain at the C-terminus that is highly-conserved in this group of proteins. The over-expression and purification of various fragments of E. coli LigA allowed the investigation of the different domains in DNA-binding and ligation by this enzyme. Compared to the full-length protein, the deletion of the BRCT domain from LigA reduced in vitro ligation activity by 3-fold and also reduced DNA binding. Using an E. coli strain harbouring a temperature-sensitive mutation of ligA, the over-expression of protein with its BRCT domain deleted enabled growth at the non-permissive temperature. In gel-mobility shift experiments, the isolated BRCT domain bound DNA in a stable manner and to a wider range of DNA molecules compared to full LigA. Thus, the BRCT domain of E. coli LigA can bind DNA, but it is not essential for DNA nick-joining activity in vitro or in vivo

Optical Wireless Communication for the Internet of Things

Wal-e-Cities - Région wallonn

Complex effects of flavopiridol on the expression of primary response genes

<p>Abstract</p> <p>Background</p> <p>The Positive Transcription Elongation Factor b (P-TEFb) is a complex of Cyclin Dependent Kinase 9 (CDK9) with either cyclins T1, T2 or K. The complex phosphorylates the C-Terminal Domain of RNA polymerase II (RNAPII) and negative elongation factors, stimulating productive elongation by RNAPII, which is paused after initiation. P-TEFb is recruited downstream of the promoters of many genes, including primary response genes, upon certain stimuli. Flavopiridol (FVP) is a potent pharmacological inhibitor of CDK9 and has been used extensively in cells as a means to inhibit CDK9 activity. Inhibition of P-TEFb complexes has potential therapeutic applications.</p> <p>Results</p> <p>It has been shown that Lipopolysaccharide (LPS) stimulates the recruitment of P-TEFb to Primary Response Genes (PRGs) and proposed that P-TEFb activity is required for their expression, as the CDK9 inhibitor DRB prevents localization of RNAPII in the body of these genes. We have previously determined the effects of FVP in global gene expression in a variety of cells and surprisingly observed that FVP results in potent upregulation of a number of PRGs in treatments lasting 4-24 h. Because inhibition of CDK9 activity is being evaluated in pre-clinical and clinical studies for the treatment of several pathologies, it is important to fully understand the short and long term effects of its inhibition. To this end, we determined the immediate and long-term effect of FVP in the expression of several PRGs. In exponentially growing normal human fibroblasts, the expression of several PRGs including FOS, JUNB, EGR1 and GADD45B, was rapidly and potently downregulated before they were upregulated following FVP treatment. In serum starved cells re-stimulated with serum, FVP also inhibited the expression of these genes, but subsequently, JUNB, GADD45B and EGR1 were upregulated in the presence of FVP. Chromatin Immunoprecipitation of RNAPII revealed that EGR1 and GADD45B are transcribed at the FVP-treatment time points where their corresponding mRNAs accumulate. These results suggest a possible stress response triggered by CDK9 inhibition than ensues transcription of certain PRGs.</p> <p>Conclusions</p> <p>We have shown that certain PRGs are transcribed in the presence of FVP in a manner that might be independent of CDK9, suggesting a possible alternative mechanism for their transcription when P-TEFb kinase activity is pharmacologically inhibited. These results also show that the sensitivity to FVP is quite variable, even among PRGs.</p

Poster: Technical Feasibility of Visible Light Communication Systems for Low Bitrate Smart Cities and the Industry 4.0 Applications

peer reviewedVisible Light Communication (VLC) is a growing technology in the context of new telecommunication systems. It uses the visible and infrared spectrum to communicate data to light sensitive equipment. Thus it enables Light Emitting Diodes (LEDs) lamps to have the dual role of illuminating and communicating. This means of communication is very much studied and commercialized for indoor applications. However, with the popularization of smart city applications in urban areas as well as in industries, it appears that the VLC technology could be relevant in those environments too. In order to measure its feasibility of deployment, this work proposes tools, including an innovative smoke model and the use of advanced modulation schemes, to simulate the coverage of a VLC communication in order to estimate its theoretical feasibility as well as a set of prototypes that demonstrate the technical feasibility of this technology.3253 - Wal-e-Cities - Wal-e-Cities - Région wallonn

Li-Fi and Visible Light Communication for Smart Cities and Industry 4.0: Challenges, research & market status in 2023

peer reviewedThe development of technologies that use cellular Radio Frequency (RF) networks to transmit information wirelessly has increased dramatically over the last decade. These technologies include mobile phones, tablets, connected gadgets and the Internet of Things (IoT). The simultaneous use of all these devices quickly saturates the available network. As the RF spectrum resource is limited and regulated, it is important to find alternative connectivity. To reply to this shortage of wireless connectivity, Li-Fi (Light Fidelity) and Visible Light Communication (VLC) are good candidates. Li-Fi is the high data rate bidirectional application of VLC. VLC uses visible and infrared light to transmit data wirelessly. Over the last decade, interest in VLC grew in the scientific community and on the market. However, most scientific works and products are focused on the indoor environment. The external environment for VLC applications, which would be very relevant for smart cities as well as some industrial applications, is very little covered in the literature. This sixty minutes tutorial aims to present the advances of these technologies, their challenges and their relevance in these two environments.3253 - Wal-e-Cities - Wal-e-Cities - Région wallonn

Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex

DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54. We show that LIN-54 DNA-binding activity recruits DRM to promoters enriched for adjacent putative E2F/DP and LIN-54 binding sites, suggesting that these two DNA–binding moieties together direct DRM to its target genes. Chromatin immunoprecipitation and gene expression profiling reveals conserved roles for DRM in regulating genes involved in cell division, development, and reproduction. We find that LIN-54 promotes expression of reproduction genes in the germline, but prevents ectopic activation of germline-specific genes in embryonic soma. Strikingly, C. elegans DRM does not act uniformly throughout the genome: the DRM recruitment motif, DRM binding, and DRM-regulated embryonic genes are all under-represented on the X chromosome. However, germline genes down-regulated in lin-54 mutants are over-represented on the X chromosome. We discuss models for how loss of autosome-bound DRM may enhance germline X chromosome silencing. We propose that autosome-enriched binding of DRM arose in C. elegans as a consequence of germline X chromosome silencing and the evolutionary redistribution of germline-expressed and essential target genes to autosomes. Sex chromosome gene regulation may thus have profound evolutionary effects on genome organization and transcriptional regulatory networks.National Institutes of Health (U.S.) (grant GM24663)National Institutes of Health (U.S.) (grant DK068429)National Institutes of Health (U.S.) (grant GM082971)National Institutes of Health (U.S.) (grant GM076378

Evaluation of Annual Companion Crops for the Establishment of Perennial Forage Crops in Eastern Canada

The use of companion crops when establishing perennial forages is desirable as it often reduces weed growth and increases forage biomass in the seeding year. In eastern Canada, oat (Avena sativa L.) is the main species used as companion crop; although other species are used, they have not been systematically evaluated. A field study was established in 2019 at three sites in Québec, Canada, to contrast the use of six annual species as companion crops for the establishment of lucerne (Medicago sativa L.)-timothy (Phleum pratense L.) mixtures. Species evaluated include berseem clover (Trifolium alexandrinum L.), annual ryegrass (Lolium multiflorum Lamarck), forage pea (Pisum sativum L.), forage oat, Japanese millet [Echinochloa esculenta (A. Braun) H. Scholz], and sudangrass [Sorghum × drummondii (Nees ex. Steud.) Millsp. & Chase]. The control treatment consisted of the perennial species seeded without companion crop. Treatments were seeded at three dates (mid-May to early-June, mid-June to early-July, and early August) and evaluated during the seeding year based on biomass production and botanical composition. Overall, across sites, for the first two seeding dates, highest annual forage yields were observed with sudangrass, Japanese millet, and oat as companion crops. The use of these species increased yields by 1.8 to 2.5 Mg ha-1 on a dry matter basis (DM) compared to the control which yielded an average of 3.7 Mg DM ha-1. For the early August seeding, response varied significantly across sites. Annual yields were the highest with the use of oat at two sites (avg. of 2.4 Mg DM ha-1), whereas no differences between treatments were observed at the other site. Companion crop species which maximized total forage yields in the seeding year often reduced weed biomass, but also that of perennial species. The impact of treatments on the survival of perennial forages and their production during the first post-seeding year will be presented in a later publication

[Invited] Visible light communication challenges in the frame of smart cities

Visible Light Communication (VLC) is the family of telecommunication technologies that uses the visible range of the electromagnetic spectrum to send data. The main asset of this emerging technology is that a light can simultaneously illuminate and communicate. This technology is for now, only possible by using Light Emitting Diodes (LEDs) and can reach up to hundreds of Mbit/s bidirectional. Furthermore, thanks to the adoption of LED lighting by cities and for car lights, VLC is about to bring a lot of interconnectivity possibilities among devices in the city, making this latter smarter. Even though outdoor VLC is still in the research phase, the main promising applications foreseen by this technology are urban Li-Fi (Light Fidelity) to complement the Wi-Fi offer, VLC-IoT (Internet of Things) and V2X (Vehicle to Vehicle or Vehicle to Infrastructure). VLC-IoT is envisioned as a streetlight communicating with the surrounding urban furniture or a streetlight sending location-based content to a visitor located under its light beam. V2X is intended to communicate with each other and/or with the street infrastructure. In this way, VLC could reply to the lack of connectivity in some places and relieve the RF spectrum when it gets crowded. This work outlines and surveys the current state of Visible Light Communication in outdoor environments, its main challenges (mainly due to weather variability), the most promising outdoor applications and the still ongoing standardisation efforts in the context of Smart Cities.Wal-e-Cities - Région wallonn