RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

Applying the Global Monitoring Plan and analysis of POPs results in atmospheric air in Mexico (2017-2018).

Air is one of the target matrices of the Global Monitoring Plan (GMP) of the Stockholm Convention to determine concentrations and transport of Persistent Organic Pollutants (POPs). Mexico participates in the GMP for POPs in ambient air through the AIR-Global Environment Facility (GEF) program. The objective of this study was to analyze the results of POPs monitoring of air samples collected in Los Mochis, Sinaloa, Mexico, between 2017 and 2018. Passive samplers were used for the determination of chlorinated basic POPs, indicator polychlorinated biphenyls (Ind. PCBs), polybrominated biphenyl ethers (PBDEs), polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs). A principal component analysis was applied to determine relationships between pollutants and groups present in the ambient air of the rural study area. Of the total POPs analyzed, 85.56% were detected in ambient air samples from Mexico. Organochlorine compounds, as DDT derivatives, were identified mainly, as well as PBDEs, PCDDs, and PCDFs. The prevalence of compounds differed according to the seasonality of sampling, with no change in average concentration between monitoring years.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.

Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.

Eficiência de um sistema piloto de dessalinização de água salobra / Efficiency of a brackish water desalination pilot system

RESUMO Com a escassez da disponibilidade de água doce e o aumento da demanda de água no mundo e no Brasil, uma das alternativas são os sistemas de dessalinização de água, que removem os sais das águas salobra ou salgada. Este estudo teve como objetivo avaliar a eficiência de um sistema piloto de dessalinização de água salobra a qual foi obtida a partir da mistura de águas do mar e de rio até atingir concentração de sólidos dissolvidos totais (SDT) de 1.500 mg.L-1. O sistema piloto de dessalinização, com capacidade de 1,0 m3.h-1, é composto de ultrafiltração (UF) e abrandamento como pré-tratamento à osmose reversa (OR). Foram realizadas análises de qualidade da água na entrada e saída das unidades de tratamento relativas a SDT, condutividade elétrica, turbidez, pH, cor aparente, alcalinidade, dureza total, cálcio, magnésio, cloreto, sulfato e temperatura. Foram avaliadas a pressão osmótica, o fluxo de filtração e a taxa de recuperação de água no sistema de OR. Com os resultados obtidos, conclui-se que a eficiência de remoção de SDT e condutividade foi de 99%. A UF foi eficiente na remoção de turbidez, enquanto a OR apresentou maiores eficiências de remoção de sais. O sistema piloto de tratamento foi capaz de remover todos os parâmetros estudados. A taxa de recuperação na OR foi de 74,64%.

ABSTRACT Considering the shortage of fresh water availability and an increased demand for water in the world, including Brazil, one of the alternatives for water supply are water desalination systems, which remove salts from brackish or seawater. The objective of this study was to evaluate the efficiency of pilot water desalination system treating brackish water which was obtained mixing fresh water and seawater up to reach 1,500 mg L-1 of total dissolved solids (TDS) concentration. The pilot desalination plant with production capacity of 1.0 m3 h-1 is composed of ultrafiltration (UF) and softener working as a pre-treatment to reverse osmosis (RO). Experiments were performed to analyze some water quality parameters as TDS, electrical conductivity, turbidity, pH, apparent color, alkalinity, total hardness, calcium, magnesium, chlorides, sulfates, and temperature. Osmotic pressure, filtration flow and water recovery rate were also measured for the RO. Analyzing the result obtained, it can be concluded that the efficiency of TDS removal and conductivity were 99%. UF was efficient in removing turbidity, whereas RO reached higher salt removal efficiencies. The pilot plant system could remove all water quality parameters studied. Recovery rate in RO was 74.64%.