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.

Assessing heavy metal contamination in a Brazilian metropolis: a case study with a focus on (bio)indicators.

The continuous expansion of the global vehicle fleet poses a growing threat to environmental quality through heavy metal contamination. In this scenario, monitoring to safeguard public health in urban areas is necessary. Our study involved the collection of 36 street dust and 29 moss samples from roads of a Brazilian metropolis (Recife) with varying traffic intensities as follows: natural reserve (0 vehicles per day), low (< 15,000 vehicles per day), medium (15,000-30,000 vehicles per day), and high (> 30,000 vehicles per day). ICP-AES analysis was performed to determine the concentrations of nine potentially toxic metals (Ba, Cd, Cr, Cu, Mn, Ni, Pb, V, and Zn) to assess the influence of vehicular flow on urban contamination. In the street dust samples, the mean metal concentrations (mg kg-1) exhibited the following order: Ba (503.7) > Mn (303.0) > Zn (144.4) > Cu (95.3) > Cr (56.1) > Pb (34.2) > V (28.7) > Ni (11.3) > Cd (1.5). Conversely, in the moss samples, the metal concentration order was as follows (mg kg-1): Mn (63.8) > Zn (62.5) > Ba (61.0) > Cu (17.7) > Cr (8.0) > V (7.3) > Pb (7.0) > Ni (2.9) > Cd (0.3). Roads with higher traffic volumes exhibited the highest metal enrichments in moss samples for all metals and in dust samples for Cd, Cr, Mn, Ni, and V. However, dust from low-flow roads had higher enrichments for Ba, Cu, and Zn, indicating the influential role of other traffic-related factors in metal deposition. Our findings highlight traffic flow as the predominant source of pollution in urban centers, with both street dust and moss serving as sensitive indicators of metal input attributable to vehicular traffic. These indicators offer valuable insights for urban quality monitoring and pollution control efforts.

Rabies, the cause of fatal encephalitis.

To describe the clinical progression and medical protocols applied in a 41 year old man who was bited by a bat three months before. The patient did not ask for medical care until acute tremor and pain in the right thoracic limb and hydro-phobia started. For a history of a wild animal bite associated with a unique clinical condition, we suspected of rabies encephalitis, confirming the diagnostic by pathology after his death. This case ocurred in Guadalajara, Jalisco, México, in April, 2022. The last case of human rabies reported in Jalisco secondary to bat bite was almost 30 years ago. As an uncomon disease, medical personnel and facilities should be prepared to attend this sort of cases after clinical suspicion. For the present case, the medical history was the key for diagnosis. Rabies is a disease caused by the neurotropic virus belonging to the Rhabdoviridae family whose prognosis is bleak, with mortality close to 100% and therapeutic options limited. This case emphasizes the high mortality of rabies virus infection and the importance of increasing awareness and education to the public in general, with regard to applying the vaccine as post-exposure prophylaxis.

Impact of Treatment with Antioxidants as an Adjuvant to Standard Therapy in Patients with Septic Shock: Analysis of the Correlation between Cytokine Storm and Oxidative Stress and Therapeutic Effects.

Cellular homeostasis is lost or becomes dysfunctional during septic shock due to the activation of the inflammatory response and the deregulation of oxidative stress. Antioxidant therapy administered alongside standard treatment could restore this lost homeostasis. We included 131 patients with septic shock who were treated with standard treatment and vitamin C (Vit C), vitamin E (Vit E), N-acetylcysteine (NAC), or melatonin (MT), in a randomized trial. Organ damage quantified by Sequential Organ Failure Assessment (SOFA) score, and we determined levels of Interleukins (IL) IL1ß, Tumor necrosis factor alpha (TNFα), IL-6, monocyte chemoattractant protein-1 (MCP-1), Transforming growth factor B (TGFß), IL-4, IL-10, IL-12, and Interferon-γ (IFNγ). The SOFA score decreased in patients treated with Vit C, NAC, and MT. Patients treated with MT had statistically significantly reduced of IL-6, IL-8, MCP-1, and IL-10 levels. Lipid peroxidation, Nitrates and nitrites (NO3- and NO2-), glutathione reductase, and superoxide dismutase decreased after treatment with Vit C, Vit E, NAC, and MT. The levels of thiols recovered with the use of Vit E, and all patients treated with antioxidants maintained their selenium levels, in contrast with controls (p = 0.04). The findings regarding oxidative stress markers and cytokines after treatment with antioxidants allow us to consider to future the combined use of antioxidants in a randomized clinical trial with a larger sample to demonstrate the reproducibility of these beneficial effects.

Impact on the Clinical Evolution of Patients with COVID-19 Pneumonia and the Participation of the NFE2L2/KEAP1 Polymorphisms in Regulating SARS-CoV-2 Infection.

In patients with severe pneumonia due to COVID-19, the deregulation of oxidative stress is present. Nuclear erythroid factor 2 (NRF2) is regulated by KEAP1, and NRF2 regulates the expression of genes such as NFE2L2-KEAP1, which are involved in cellular defense against oxidative stress. In this study, we analyzed the participation of the polymorphisms of NFE2L2 and KEAP1 genes in the mechanisms of damage in lung disease patients with SARS-CoV-2 infection. Patients with COVID-19 and a control group were included. Organ dysfunction was evaluated using SOFA. SARS-CoV-2 infection was confirmed and classified as moderate or severe by ventilatory status and by the Berlin criteria for acute respiratory distress syndrome. SNPs in the gene locus for NFE2L2, rs2364723C>G, and KEAP1, rs9676881A>G, and rs34197572C>T were determined by qPCR. We analyzed 110 individuals with SARS-CoV-2 infection: 51 with severe evolution and 59 with moderate evolution. We also analyzed 111 controls. Significant differences were found for rs2364723 allele G in severe cases vs. controls (p = 0.02); for the rs9676881 allele G in moderate cases vs. controls (p = 0.04); for the rs34197572 allele T in severe cases vs. controls (p = 0.001); and in severe vs. moderate cases (p = 0.004). Our results showed that NFE2L2 rs2364723C>G allele G had a protective effect against severe COVID-19, while KEAP1 rs9676881A>G allele G and rs34197572C>T minor allele T were associated with more aggressive stages of COVID-19.

Usefulness of Antioxidants as Adjuvant Therapy for Septic Shock: A Randomized Clinical Trial.

Background and objectives: Oxidative stress (OS) participates in the pathophysiology of septic shock, which leads to multiple organ failure (MOF), ischemia-reperfusion injury, and acute respiratory distress syndrome. Therefore, antioxidants have been proposed as therapy. Here, we evaluated the effect of antioxidant treatments in patients with septic shock with MOF and determined levels OS before and after treatment. This study was a randomized, controlled, triple-masked, and with parallel assignment clinical trial with a control group without treatment. Materials and Methods: It included 97 patients of either sex with septic shock. 5 treatments were used each in an independent group of 18 patients. Group 1 received vitamin C (Vit C), group 2 vitamin E (Vit E), group 3 n-acetylcysteine (NAC), group 4 melatonin (MT), and group 5 served as control. All antioxidants were administered orally or through a nasogastric tube for five days as an adjuvant to the standard therapy. Results: The results showed that all patients presented MOF due to sepsis upon admission and that the treatment decreased it (p = 0.007). The antioxidant treatment with NAC increased the total antioxidant capacity (p < 0.05). The patients that received Vit C had decreased levels of the nitrate and nitrite ratio (p < 0.01) and C-reactive protein levels (p = 0.04). Procalcitonin levels were reduced by Vit E (p = 0.04), NAC (p = 0.001), and MT (p = 0.04). Lipid-peroxidation was reduced in patients that received MT (p = 0.04). Conclusions: In conclusion, antioxidant therapy associated with standard therapy reduces MOF, OS, and inflammation in patients with septic shock.

Bioavailability and sequential extraction of mercury in soils and organisms of a mangrove contaminated by a chlor-alkali plant.

Botafogo river estuary poses the highest Hg concentration reported for mangrove soils in Brazil. Such high contamination took place owing to the improper waste disposal for 24 years from a chlor-alkali plant nearby the estuary. Here we determined Hg concentrations in soils, mangrove plants (Rhizophora mangle and Laguncularia racemosa), and an aquatic organism (the oyster species Crassostrea rhizophorae) to assess Hg bioavailability. Besides, a sequential extraction procedure was used to separate soil Hg into five fractions: water-soluble; 'human stomach acid' soluble; organically bound; elemental Hg; mercuric sulfide. Results showed that environmentally available concentration of Hg in the mangrove soils were up to 150-fold higher than a pristine mangrove under the same geological context used as a reference. Additionally, Hg concentration in soils was also above sediment quality guidelines and Hg adverse effects towards sensitive estuarine organisms are likely. Mercury concentrations in oysters were the highest reported in Brazil, but within safety standards according to the country food security agency. It seems that Hg stocks in the studied soils are governed by organic matter and redox conditions, but changing on environmental conditions and land use can alter this balance and convert these mangrove areas from sink to source of Hg to the environment.

Magnetic Behavior of Carbon Materials Made from Biomass by Fe-Assisted Hydrothermal Carbonization.

Biomass magnetic materials were synthesized by several hydrothermal carbonization methods, by which iron was provided in different ways: as FeCl3 prior to or during hydrothermal carbonization, as pure Fe particles, or as magnetic ferrofluid, followed or not by pyrolysis processes. The materials were thoughtfully characterized in terms of elemental composition, thermal degradation, porosity (N2 adsorption, SEM micrography), surface chemistry (FTIR spectroscopy, XRD diffraction), and magnetization curves on a self-made installation. The results indicated that the process design can significantly improve the structure and chemistry of the material, as well as the magnetization effect induced on the adsorbent. Fe as FeCl3 was more interesting in regards to the development of porosity, mainly creating micropores, although it did not provide magnetism to the material unless a further pyrolysis was applied. Thermal treatment at 600 °C did not only increase the BET-specific surface (SBET) (262 m2 g-1) of the hydrochar, but also involved the transformation of Fe into magnetite, providing magnetic behavior of the hydrochar. Increasing pyrolyisis temperature to 800 °C even enhanced a better development of porosity (SBET of 424 m2 g-1) and also increased the specific magnetic susceptibility of the hydrochar as a result of the further transition of Fe into wustite and hydroxi-ferrite.

Lead isotope ratios in lichen samples evaluated by ICP-ToF-MS to assess possible atmospheric pollution sources in Havana, Cuba.

Epiphytic lichens, collected from 119 sampling sites grown over "Roistonea Royal Palm" trees, were used to assess the spatial distribution pattern of lead (Pb) and identify possible pollution sources in Havana (Cuba). Lead concentrations in lichens and topsoils were determined by flame atomic absorption spectrophotometry and inductively coupled plasma (ICP) atomic emission spectrometry, respectively, while Pb in crude oils and gasoline samples were measured by ICP-time of flight mass spectrometry (ICP-ToF-MS). Lead isotopic ratios measurements for lichens, soils, and crude oils were obtained by ICP-ToF-MS. We found that enrichment factors (EF) reflected a moderate contamination for 71% of the samples (EF > 10). The 206Pb/207Pb ratio values for lichens ranged from 1.17 to 1.20 and were a mixture of natural radiogenic and industrial activities (e.g., crude oils and fire plants). The low concentration of Pb found in gasoline (<7.0 µg L-1) confirms the official statement that leaded gasoline is no longer used in Cuba.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.

Comparison of Chemical and Enzymatic Interesterification of Fully Hydrogenated Soybean Oil and Walnut Oil to Produce a Fat Base with Adequate Nutritional and Physical Characteristics.

The optimal physical, chemical and nutritional properties of natural lipids depend on the structure and composition of triacylglycerols. However, they are not always mutually compatible. Lipid modification is a good way to give them specific functionalities, increase their oxidative stability, or improve their nutritional value. As such, chemical and enzymatic interesterification may be used to modify them and produce structured lipids. In accordance, the aim of this study is to compare chemical and enzymatic interesterification of binary blends of fully hydrogenated soybean oil and walnut oil, using sodium methoxide or Lipozyme TL IM, respectively, to produce a fat base with adequate nutritional and physical characteristics. Three different mass ratios of fully hydrogenated soybean oil and walnut oil blends (20:80, 40:60 and 60:40) were interesterified and evaluated. Total interesterification was determined by the stabilization of the solid fat content. Chemical reaction of the 20:80 blend was completed in 10 min and of the 40:60 and 60:40 blends in 15 min. Enzymatically interesterified blends were stabilized in 120 min at all of the mass ratios. Complete interesterification significantly reduced the solid fat content of the blends at any composition. Chemical and enzymatically interesterified fully hydrogenated blend of soybean and walnut oil at mass ratio of 40:60 showed the plastic curve of an all-purpose- -type shortening rich in polyunsaturated fatty acids, with a high linolenic acid (C18:3n3) content and with zero trans-fatty acids.

Mobility networks in Greater Mexico City.

Based on more than 11 billion geolocated cell phone records from 33 million different devices, daily mobility networks were constructed over a 15-month period for Greater Mexico City, one of the largest and most diverse metropolitan areas globally. The time frame considered spans the entire year of 2020 and the first three months of 2021, enabling the analysis of population movement dynamics before, during, and after the COVID-19 health contingency. The nodes within the 456 networks represent the basic statistical geographic areas (AGEBs) established by the National Institute of Statistics, Geography, and Informatics (INEGI) in Mexico. This framework facilitates the integration of mobility data with numerous indicators provided by INEGI. Edges connecting these nodes represent movement between AGEBs, with edge weights indicating the volume of trips from one AGEB to another. This extensive dataset allows researchers to uncover travel patterns, cross-reference data with socio-economic indicators, and conduct segregation studies, among other potential analyses.

Intermunicipal travel networks of Mexico during the COVID-19 pandemic.

Human mobility networks are widely used for diverse studies in geography, sociology, and economics. In these networks, nodes usually represent places or regions and links refer to movement between them. They become essential when studying the spread of a virus, the planning of transit, or society's local and global structures. Therefore, the construction and analysis of human mobility networks are crucial for a vast number of real-life applications. This work presents a collection of networks that describe the human travel patterns between municipalities in Mexico in the 2020-2021 period. Using anonymized mobile location data, we constructed directed, weighted networks representing the volume of travels between municipalities. We analysed changes in global, local, and mesoscale network features. We observe that changes in these features are associated with factors such as COVID-19 restrictions and population size. In general, the implementation of restrictions at the start of the COVID-19 pandemic in early 2020, induced more intense changes in network features than later events, which had a less notable impact in network features. These networks will result very useful for researchers and decision-makers in the areas of transportation, infrastructure planning, epidemic control and network science at large.

Randomized Clinical Trial of Antioxidant Therapy Patients with Septic Shock and Organ Dysfunction in the ICU: SOFA Score Reduction by Improvement of the Enzymatic and Non-Enzymatic Antioxidant System.

BACKGROUND AND AIM: Here, we assess the effect of adjuvant antioxidant therapies in septic shock patients with organ dysfunction and their effect on the enzymatic and non-enzymatic antioxidant systems. METHODS: Randomized clinical trial run between 2018 and 2022. One hundred and thirty-one patients with septic shock were included in five groups with 25, 27, 24, 26 and 29 patients each. Group 1 received vitamin C (Vit C), Group 2 vitamin E (Vit E), Group 3 n-acetylcysteine (NAC), Group 4 melatonin (MT) and group 5 no treatment. All antioxidants were administered orally or through a nasogastric tube for 5 days as an adjuvant to standard therapy. RESULTS: All patients had multiple organ failure (MOF) and low Vit C levels. Vit C therapy decreased CRP, PCT and NO3-/NO2- but increased Vit C levels. The SOFA score decreased with MT in 75%, Vit C 63% and NAC 50% vs. controls 33% (p = 0.0001, p = 0.03 and p = 0.001 respectively). MT diminished lipid peroxidation (LPO) (p = 0.01) and improved total antioxidant capacity (TAC) (p = 0.04). Vit E increased thiol levels (p = 0.02) and tended to decrease LPO (p = 0.06). Selenium levels were decreased in the control group (p = 0.04). CONCLUSIONS: Antioxidants used as an adjuvant therapy in the standard treatment of septic shock decrease MOF and oxidative stress markers. They increase the TAC and thiols, and maintain selenium levels.

Comparative Analysis of the Thermal Conductivity of Handmade and Mechanical Bricks Used in the Cultural Heritage.

During interventions to improve the energy efficiency of cultural heritage, it is common to use methodologies that are used for current buildings with different thermal behaviour. For this reason, research has been carried out on the thermal behaviour of old brick walls by carrying out thermal flow tests in the laboratory on brickwork specimens, in order to compare the behaviour of handmade bricks and mechanical bricks from more than a century ago, and to analyse the relationship between the values of thermal conductivity, humidity, density and porosity, as well as to compare these results with those obtained by applying the procedure of the EN-1745 standard. It was concluded that bricks behave thermally differently, depending on the manufacturing process: handmade or mechanical, in both types of brick it was found that the higher the moisture content and density were, the higher the brick's thermal conductivity value. It has also been concluded that old bricks have thermal conductivity values different from those indicated in EN-1745 as a function of density, and that the ratio detected in these specimens in the dry state and in the wet state does not conform to the processes indicated in the standard. With regard to porosity, it is important to note that the greater the closed porosity, the lower the conductivity. It has been concluded that in order to intervene in cultural heritage buildings, it is necessary to carry out a specific study of the behaviour of the systems with which they were constructed.

Hyperglycemia and Loss of Redox Homeostasis in COVID-19 Patients.

The infection with SARS-CoV-2 impairs the glucose−insulin axis and this contributes to oxidative (OS) and nitrosative (NSS) stress. Here, we evaluated changes in glucose metabolism that could promote the loss of redox homeostasis in COVID-19 patients. This was comparative cohort and analytical study that compared COVID-19 patients and healthy subjects. The study population consisted of 61 COVID-19 patients with and without comorbidities and 25 healthy subjects (HS). In all subjects the plasma glucose, insulin, 8-isoprostane, Vitamin D, H2S and 3-nitrotyrosine were determined by ELISA. The nitrites (NO2−), lipid-peroxidation (LPO), total-antioxidant-capacity (TAC), thiols, glutathione (GSH) and selenium (Se) were determined by spectrophotometry. The glucose, insulin and HOMA-IR (p < 0.001), 8-isoprostanes, 3-nitrotyrosine (p < 0.001) and LPO were increased (p = 0.02) while Vitamin D (p = 0.01), H2S, thiols, TAC, GSH and Se (p < 0.001) decreased in COVID-19 patients in comparison to HS. The SARS-CoV-2 infection resulted in alterations in the glucose−insulin axis that led to hyperglycemia, hyperinsulinemia and IR in patients with and without comorbidities. These alterations increase OS and NSS reflected in increases or decreases in some oxidative markers in plasma with major impact or fatal consequences in patients that course with metabolic syndrome. Moreover, subjects without comorbidities could have long-term alterations in the redox homeostasis after infection.

Distribution Patterns of Invasive Buffelgrass (Cenchrus ciliaris) in Mexico Estimated with Climate Niche Models under the Current and Future Climate.

In Mexico, buffelgrass (Cenchrus ciliaris) was introduced in the middle of the 20th century. Currently, buffelgrass has become an invasive species and has colonized various ecosystems in the country. In addition to its invasive capacity, climate change is a factor that has to be taken into account when considering how to effectively manage and control this species. The climatic niche models (CNM) and their projections for climate change scenarios allow for estimating the extent of biological invasions. Our study aimed to calibrate a CNM for buffelgrass in Mexico under the current climatic conditions and to project the extent of its biological invasion under climate change scenarios. For that, we used MaxEnt to generate the current CNM and to detect if climate change could cause future changes, we then evaluated the distribution patterns over the periods of 2041-2060, 2061-2080, and 2081-2100 for all the shared socioeconomic pathways (SSPs). Linear regressions were used to compare the outputs between current and future scenarios. Under the current climate, the CNM estimated that 42.2% of the continental surface of Mexico is highly suitable for buffelgrass. The regression analyses indicated no effects from climate change on the distribution of buffelgrass. Moreover, when the projected period is further in the future, and when the SSPs intensify, the surface of suitable areas for the species increases. These analyses clearly suggest Mexico is facing a biological invasion from buffelgrass, which may represent a threat to native biodiversity.

Environmental Niche Dynamics of Blue Grama (Bouteloua gracilis) Ecotypes in Northern Mexico: Genetic Structure and Implications for Restoration Management.

Understanding the genetic structure adopted by natural populations and its relation to environmental adaptation is critical for the success of restoration programs. We evaluated the genetic structure and temporal environmental niche dynamics of blue grama (Bouteloua gracilis) in 48 populations. The genetic evaluation was performed through amplified fragment length polymorphism (AFLP) molecular markers. The maximum entropy method was used to model the past, present, and future environmental niches of the three clusters derived from the genetic analysis. The environmental niches of the three genetic clusters showed dynamic overlaps and isolations during the last interglacial and glacial maximum. The paleoclimatic events, which occurred during those periods, may have reinforced genetic exchange among populations and affected their genetic structure. Genetic clusters also presented different environmental niches in the present. Thus, they can be considered as three distinct ecotypes and restoration programs must be carried out using local germplasm from each environmental niche to increase their chance of success. Based on the environmental niches of the genetic clusters, changes are expected in the near and mid-century future. Therefore, climate change must be considered for species conservation management and future restoration programs.

Greenhouse Rearing Methods for Brown Marmorated Stink Bug (Hemiptera: Pentatomidae) on Live Cowpea Plants.

Brown marmorated stink bug (BMSB), Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is a pest of concern that must be controlled for market access of host material and regulated articles to certain countries. This work outlines a rearing system for BMSB on live cowpea plants, Vigna unguiculata (L.) Walp. (Fabales: Fabaceae), including methods to induce adults to both enter and exit diapause. This scalable system affords continuous access to >600 specimens per week of each life stage and/or age group, which is particularly advantageous when developing treatment efficacy data.

Metal contaminants in rice from Cuba analyzed by ICP-MS, ICP-AES and CVAAS.

Mercury, lead, cadmium and arsenic are considered hazardous pollutants in the environment, which can result in a risk for human health. This study aimed to determine the contents of As, Cd, Cr, Cu, Hg, Ni, Pb and Zn by ICP-MS, CVAAS and ICP-AES in paddy and brown rice, grown in different soils of Cuba. The interest to include Cr, Ni, Cu and Zn was because these elements are found in very high levels in agricultural soils. To assess the safety of the dietary intake of these metals, the estimated weekly intake was calculated. The contents of Cd and As were below the maximum limits. A higher value was obtained for Pb when compared to Codex Alimentarius limits. The weekly intake of Cr and Ni was higher than the maximum weekly intake recommended by FAO/WHO.