An Arabidopsis gene regulatory network for secondary cell wall synthesis.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.

The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.

Improvement on binding of chondroitin sulfate derivatives to midkine by increasing hydrophobicity.

The interactions between chondroitin sulfate (CS) and a wide number of proteins modulate important biological processes. Here, the binding properties to midkine and pleiotrophin of sulfated, fully protected intermediates, typically obtained in the chemical synthesis of CS oligosaccharides, were tested for the first time. Using a fluorescence polarization competition experiment, we discovered that these synthetic precursors strongly bound these two closely related cytokines involved in cancer and inflammation. The relative binding affinities of these intermediates were significantly higher than those displayed by the corresponding fully deprotected oligosaccharides, indicating that the presence of hydrophobic protecting groups strongly enhanced the binding of CS-like derivatives to midkine. These compounds offer novel opportunities for the development of potent inhibitors/activators of CS-protein interactions with potential therapeutic applications.

Analysis of Ecuador's SCOPUS scientific production during the 2001-2020 period by means of standardized citation indicators.

An analysis of the scientific production of Ecuador is performed by means of the composite indicator computed for Ecuador-based authors as compared to their counterparts of other South American countries. The dataset employed was obtained from the Databricks platform of the ELSEVIER's International Center for Science Research, ICSR. Therefore, this analysis is limited to the metadata of the documents published in journals indexed in SCOPUS. Comparison of the results obtained for two decades: 2001-2010 and 2011-2020 showed that the number of Ecuador-based researchers has significantly increased in different areas of knowledge. Moreover, comparison between the total number of authors that worked in Ecuador at any given year of the 2011-2020 period and the number of authors that are still working in this country up to the date of the data extraction (i.e., June 2021) showed an average of ∼68% of permanency. Analysis of the percentage distribution in terms of range quarters of the composite indicator (i.e., Q4: 0-1.5, Q3: 1.5-3.0, Q2: 3.0-4.5, and Q1: 4.5-6.0) showed that nearly the totality of the Ecuador-based researchers has composite indicators that lay in the Q4 and Q3 ranges for all the scientific fields considered. The latter was observed to be an effect of the scientific impact of South American countries, with larger investments in science and technology in comparison to Ecuador (i.e., Argentina, Brazil, and Chile). Exclusion of this group of countries in the calculation of the composite indicator of Ecuador-based authors resulted in a noticeable increment of scientists with composite indicators within Q2. Finally, our results suggest, in agreement with previous studies, a correlation between the sustained growth of scientific productivity in the decade 2011-2020 with the scientific programs and policies created by the state, where the initiative of scientific culture is shown as a strategy for growth and development.

Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors.

Cellular susceptibility to SARS-CoV-2 infection in the respiratory tract has been associated with the ability of the virus to interact with potential receptors on the host membrane. We have modeled viral dynamics by simulating various cellular systems and artificial conditions, including macromolecular crowding, based on experimental and transcriptomic data to infer parameters associated with viral growth and predict cell susceptibility. We have accomplished this based on the type, number and level of expression of the angiotensin-converting enzyme 2 (ACE2), transmembrane serine 2 (TMPRSS2), basigin2 (CD147), FURIN protease, neuropilin 1 (NRP1) or other less studied candidate receptors such as heat shock protein A5 (HSPA5) and angiotensin II receptor type 2 (AGTR2). In parallel, we studied the effect of simulated artificial environments on the accessibility to said proposed receptors. In addition, viral kinetic behavior dependent on the degree of cellular susceptibility was predicted. The latter was observed to be more influenced by the type of proteins and expression level, than by the number of potential proteins associated with the SARS CoV-2 infection. We predict a greater theoretical propensity to susceptibility in cell lines such as NTERA-2, SCLC-21H, HepG2 and Vero6, and a lower theoretical propensity in lines such as CaLu3, RT4, HEK293, A549 and U-251MG. An important relationship was observed between expression levels, protein diffusivity, and thermodynamically favorable interactions between host proteins and the viral spike, suggesting potential sites of early infection other than the lungs. This research is expected to stimulate future quantitative experiments and promote systematic investigation of the effect of crowding presented here.

Characterization of annexin A1 glycan binding reveals binding to highly sulfated glycans with preference for highly sulfated heparan sulfate and heparin.

Annexin A1 is a multifunctional, calcium-dependent phospholipid binding protein involved in a host of processes including inflammation, regulation of neuroendocrine signaling, apoptosis, and membrane trafficking. Binding of annexin A1 to glycans has been implicated in cell attachment and modulation of annexin A1 function. A detailed characterization of the glycan binding preferences of annexin A1 using carbohydrate microarrays and surface plasmon resonance served as a starting point to understand the role of glycan binding in annexin A1 function. Glycan array analysis identified annexin A1 binding to a series of sulfated oligosaccharides and revealed for the first time that annexin A1 binds to sulfated non-glycosaminoglycan carbohydrates. Using heparin/heparan sulfate microarrays, highly sulfated heparan sulfate/heparin were identified as preferred ligands of annexin A1. Binding of annexin A1 to heparin/heparan sulfate is calcium- but not magnesium-dependent. An in-depth structure-activity relationship of annexin A1-heparan sulfate interactions was established using chemically defined sugars. For the first time, a calcium-dependent heparin binding protein was characterized with such an approach. N-Sulfation and 2-O-sulfation were identified as particularly important for binding.

Fundamentals and applications of photoelectrocatalysis as an efficient process to remove pollutants from water: A review.

Water pollution is an environmental problem in constant raising because of population growing, industrial development, agricultural frontier expansion, and principally because of the lack of wastewater treatment technology to remove organic recalcitrant and toxic pollutants from industrial and domestic wastewater. Recalcitrant compounds are a serious environmental and health problem mainly due to their toxicity and potential hazardous effects on living organisms, including human beings. Conventional wastewater treatments have not been able to remove efficiently pollutants from water; however, electrochemical advanced oxidation processes (EAOPs) are able to solve this environmental concern. One of the most recent EAOPs technology is photoelectrocatalysis (PEC), it consists in applying an external bias potential to a semiconductor film placed over a conductive substrate to avoid the recombination of photogenerated electron-hole (e-/h+) pairs, increasing h+ availability and hydroxyl radicals' formation, responsible for promoting the degradation/mineralization of organic pollutants in aqueous medium. This review summarizes the recent advances in PEC as a promising technology for wastewater treatment. It addresses the fundamentals and kinetic aspects of PEC. An analysis of photoanode materials and of the configuration of photoelectrochemical reactors is also presented, including an analysis of the influence of the main operational parameters on the treatment of contaminated water. Finally, the most recent applications of PEC are reviewed, and the challenges and perspectives of PEC in wastewater treatment are discussed.

Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach.

The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.

Determination of diquat by flow injection-chemiluminescence.

A simple, economic, sensitive and rapid method for the determination of the pesticide diquat was described. This new method was based on the coupling of flow injection analysis methodology and direct chemiluminescent detection; to the authors' knowledge, this approach had not been used up to now with this pesticide. It was based on its oxidation with ferricyanide in alkaline medium; significant improvements in the analytical signal were achieved by using high temperatures and quinine as sensitiser. Its high throughput (144 h(-1)), together with its low limit of detection (2 ng mL(-1)), achieved without need of preconcentration steps, permitted the reliable quantification of diquat over the linear range of (0.01-0.6) microg mL(-1) in samples from different origins (river, tap, mineral and ground waters), even in the presence of a 40-fold concentration of paraquat, a pesticide commonly present in the commercial formulations of diquat.

On the inoperativeness of the ESIPT process in the emission of 1-hydroxy-2-acetonaphthone: a reappraisal.

For a molecule which contains an intramolecular hydrogen bond (IMHB) in its chemical structure to undergo an excited singlet intramolecular proton transfer (ESIPT) process, on photoexcitation, there must occur a simultaneous increase, in a substantial manner, in the acidity of the proton donor and the basicity of the proton acceptor forming the IMHB [J. Am. Chem. Soc. 2001, 123, 11940]. For the reason that those changes occur on photoexcitation of the 2-hydroxyacetophenone but not for 1-hydroxy-acetonaphthone, one draws the conclusion that, while ESIPT is operative in the 1(pi,pi*)(1) electronic state of the monocyclic compound 2-hydroxyacetophenone, it is not operative in its bicyclic homolog 1-hydroxy-2-acetonaphthone. We have shown the photophysics of 1-hydroxy-2-acetonaphthone in its first excited electronic state to be governed by two stable, easily reconverted enol structures, the presence of which causes the peaks in the free-jet fluorescence excitation spectrum for the compound to split into two of similar strength. In this paper, we rationalize photophysical evidence for 1-hydroxy-2-acetonaphthone obtained by femtosecond spectroscopy over the past 13 years in the light of existing photophysical patterns based on steady-state spectra for the compound [J. Am. Chem. Soc. 1993, 115, 4321].