Impact of SARS-CoV-2 Mu variant on vaccine effectiveness: A comparative genomics study at the peak of the third wave in Bogota, Colombia.

We assessed the circulation of severe acute respiratory syndrome coronavirus-2 variants amongst vaccinated military personnel in Bogotá, Colombia to evaluate the mutations of certain variants and their potential for breakthrough infection in vaccinated subjects. We observed that in vaccinated individuals the most frequent infecting lineage was Mu (B.1.621 and B.1.621.1). The above is possibly associated with specific mutations that confer it with vaccine-induced immune escape ability. Our findings highlight the importance of how genomic tracking coupled with epidemiological surveillance can assist in the study of novel emerging variants (e.g., Omicron) and their impact on vaccination efforts worldwide.

Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes.

RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and inositol 1,4,5-trisphosphate receptor type 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF-FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.

CRMP2 and CRMP4 are required for the formation of commissural tracts in the developing zebrafish forebrain.

Axonal connections between the two sides of the brain are essential for processing sensorimotor functions, especially in animals with bilateral symmetry. The anterior commissure and postoptic commissure are two crucial axonal projections that develop early in the zebrafish central nervous system. In this study, we characterized the function of collapsin response mediator protein 2 (CRMP2) and CRMP4 in patterning the development of the anterior and postoptic commissures by analyzing morpholino-knockdown zebrafish morphants and CRISPR/Cas9-edited gene-knockout mutants. We observed a loss of commissural structures or a significant reduction in axon bundles connecting the two hemispheres, but the defects could be largely recovered by co-injecting CRMP2 or CRMP4 mRNA. Loss of both CRMP2 and CRMP4 function resulted in a synergistic increase in the number of commissural defects. To elucidate the mechanism by which CRMP2 and CRMP4 provide guidance cues for the development of the anterior and postoptic commissures, we included neuropilin 1a (Nrp1a) morphants and double morphants (CRMP2/Nrp1a and CRMP4/Nrp1a) for analysis. Our experimental results indicated that CRMP2 and CRMP4 might mediate their activities through the common semaphorin 3/Nrp1a signaling pathway.

Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia.

Background: The third wave of the global health crisis attributed to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus reached Colombia in March 2021. Over the following 6 months, it was interpolated by manifestations of popular disapproval to the actual political regime-with multiple protests sprouting throughout the country. Large social gatherings seeded novel coronavirus disease 2019 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths. Methods: In this article, we evaluate the effective reproduction number (Rt) dynamics of SARS-CoV-2 in Cali, Colombia, between 4 April 2021 and 31 July 2021 based on the analysis of 228 genomes. Results: Our results showed clear contrast in Rt values between the period of frequent protests (Rt > 1), and the preceding and following months (Rt < 1). Genomic analyses revealed 16 circulating SARS-CoV-2 lineages during the initial period-including variants of concern (VOCs) (Alpha, Gamma, and Delta) and variants of interest (VOIs) (Lambda and Mu). Furthermore, we noticed the Mu variant dominating the COVID-19 distribution schema as the months progressed. We identified four principal clusters through phylogenomic analyses-each one of potentially independent introduction to the city. Two of these were associated with the Mu variant, one associated with the Gamma variant, and one with the Lambda variant. Conclusion: Our results chronicle the impact of large group assemblies on the epidemiology of COVID-19 during this intersection of political turmoil and sanitary crisis in Cali, Colombia. We emphasize upon the effects of limited biosecurity strategies (which had characterized this time period), on the spread of highly virulent strains throughout Cali and greater Colombia.

Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia.

The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1-2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.

Epidemiological Indicators of SARS-CoV-2 (COVID-19) and Vaccination Effectiveness on the Report of Positive Cases in the Colombian Army.

The description of the epidemiological indicators of SARS-CoV-2 (COVID-19), such as the mortality rate (MR), the case fatality rate (CFR), and the attack rate (AR), as well as the geographical distribution and daily case reports, are used to evaluate the impact that this virus has had within the Colombian Army and its health system. As military forces around the world represent the force that defends sovereignty, independence, the integrity of the national territory, and the constitutional order, while maintaining migration controls in blocked border areas during this critical pandemic times, they must carry out strict epidemiological surveillance to control the situation among the servicemen. Up to date, the Colombian Army has faced a very high attack rate (AR = 8.55%) due, among others, to living conditions where active military personnel share bedrooms, bathrooms, and dining facilities, which facilitate the spread of the virus. However, being a mainly young and healthy population, the MR was 1.82 deaths/1,000 ha, while the CFR = 2.13% indexes consistently low if compared with those values reported for the national population. In addition, the effectiveness of vaccination is shown in daily cases of COVID-19, where, for the third peak, the active military population presented a decrease of positive patients compared to the dynamics of national transmission and the total population of the military forces (active, retired, and beneficiaries).

Dpysl2 (CRMP2) is required for the migration of facial branchiomotor neurons in the developing zebrafish embryo.

Dihydropyrimidinase-like family proteins (Dpysls) are relevant in several processes during nervous system development; among others, they are involved in axonal growth and cell migration. Dpysl2 (CRMP2) is the most studied member of this family; however, its role in vivo is still being investigated. Our previous studies in zebrafish showed the requirement of Dpysl2 for the proper positioning of caudal primary motor neurons and Rohon-Beard neurons in the spinal cord.In the present study, we show that Dpysl2 is necessary for the proper migration of facial branchiomotor neurons during early development in zebrafish. We generated a dpysl2 knock-out (KO) zebrafish mutant line and used different types of antisense morpholino oligonucleotides (AMO) to analyze the role of Dpysl2 in this process. Both dpysl2 KO mutants and morphants exhibited abnormalities in the migration of these neurons from rhombomers (r) 4 and 5 to 6 and 7. The facial branchiomotor neurons that were expected to be at r6 were still located at r4 and r5 hours after the migration process should have been completed. In addition, mutant phenotypes were rescued by injecting dpysl2 mRNA into the KO embryos. These results indicate that Dpysl2 is involved in the proper migration of facial branchiomotor neurons in developing zebrafish embryos.

Condiciones para el análisis de proteínas del micelio de Lentinuia edodes obtenido por fermentación en estado líquido / Conditions for protein analysis of Lentinuia edodes mycelium obtained from liquid state fermentation / Condições para a análise de proteínas do micélio de Lentinuia edodes obtidas por fermentação em estado líquido

Resumen Pocos son los trabajos enfocados en la producción biotecnológica y el desarrollo de herramientas analíticas en torno a la Lentinuia edodes, seta comestible con potencial para el desarrollo de nutracéuticos. Por esto, en esta investigación, se estudió la producción de biomasa del hongo en el tiempo, mediante fermentación en estado líquido, y se seleccionaron las condiciones que permitieron la obtención de extractos para la aplicación de herramientas para análisis proteómico. Los métodos de extracción de proteínas, ácido tricloroacético (TCA) - acetona y TCA - acetona - fenol, fueron comparados en términos del rendimiento de extracción y los perfiles de separación usando electroforesis en 1D (SDS-PAGE) y 2D (IEF-SDS PAGE). Se determinó que a los 10 días de crecimiento se obtiene la mayor producción de biomasa y proteína total. La extracción con TCA - acetona - fenol presentó un mayor rendimiento, resolución y número de bandas en la electroforesis 1D. En 2DE, los dos métodos permitieron la extracción de proteínas con puntos isoeléctricos en el rango de pH 3-10, pero el método TCA - acetona - fenol conllevó a una extracción diferencial, favoreciendo el rango de masa de 33 a 113 kDa. Estos resultados se constituyen en una primera aplicación de técnicas de separación electroforética para futuros estudios proteómicos.

Abstract Few are the investigations focused on the biotechnological production and the development of analytical tools about Lentinuia edodes, an edible mushroom which has a potential for being used in the development of nutraceutical products. For this reason, in this research, the production of biomass of the mushroom over time by liquid state fermentation (LSF) was studied. Then, the conditions that allow obtaining protein extracts for the application of tools for proteomic analysis were selected. Trichloroacetic acid (TCA) - acetone and TCA - acetone - phenol were the two protein extraction methods which were compared in terms of extraction yield and separation profiles in 1D (SDS-PAGE) and 2D (IEF-SDS PAGE) electrophoresis. The highest production of biomass and total protein content was obtained after 10 days of LSF. Protein extraction with TCA - acetone -phenol presented the highest yield, resolution and number of bands in 1D electrophoresis. In 2DE the two methods allowed the extraction of proteins with isoelectric points in pH 3-10 range but, the TCA - acetone - phenol method favored a differential extraction of proteins in the range of 33 to 113 kDa. These results constitute a first application of electrophoretic separation techniques for future proteomic studies.

Resumo Lentinuia edodes é um cogumelo comestível com potencial para o desenvolvimento de nutracêuticos. Entretanto, os trabalhos voltados para a produção biotecnológica e o desenvolvimento de ferramentas analíticas que permitem aprofundar sua composição são incipientes. Nesta pesquisa, a produção de biomassa do fungo ao longo do tempo por meio de fermentação no estado líquido foi estudada e as condições que permitem obter extratos para a aplicação de ferramentas para análise proteômica foram selecionadas. Os métodos de extração de proteínas usados foram ácido tricloroacético (TCA) - acetona e TCA - acetona - fenol e comparada em termos de rendimento de extracção e perfis de separação utilizando electroforese 1D (SDS-PAGE) e 2D (IEF-SDS PAGE). Foi determinado que após 10 dias de crescimento, a maior produção de biomassa e proteína total foi obtida. A extração com TCA - acetona - fenol apresentou maior rendimento, maior resolução e número de bandas em eletroforese 1D. No 2DE os dois métodos permitiram a extração de proteínas com pontos isoelétricos na faixa de pH 3-10, mas o método TCA - acetona - fenol levou a uma extração diferencial, favorecendo a faixa de 33 a 113 kDa. Estes resultados constituem uma primeira aplicação de técnicas de separação eletroforética para futuros estudos proteômicos.