Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Trajectories of socio-ecological systems: A case study in the tropical Andes

Scenario and policy assessments in socioeconomic and environmental studies face significant challenges in socio-ecological systems (SES). There are a limited number of studies that have looked at the impact of different scenarios within integrated approaches, and many have used a static approach with a single driver of change. The present work analyzes the SES dynamics for a strategic basin in the Colombian Andes when implementing and analyzing scenarios and policies related to land cover and land use change using a system dynamics simulation model. The model includes natural, ecosystem services, sociocultural, and economic components. Scenarios and policy options are analyzed both individually and jointly to identify synergies or trade-off effects between the different SES components. The results showed the different trajectories of the socio-ecological system according to the cases studied, and its impact on different variables in the analyzed components. Some counterintuitive effects were also identified, such as the importance of intrinsic motivations in decision-making processes, and determinants in land management and policy design.

Clinical-functional correlation with brain volumetry in severe perinatal asphyxia: a case report

BACKGROUND

Hypoxic-ischemic encephalopathy (HIE) appears in neurological conditions where some brain areas are likely to be injured, such as deep grey matter, basal ganglia area, and white matter subcortical periventricular áreas. Moreover, modeling these brain areas in a newborn is challenging due to significant variability in the intensities associated with HIE conditions. This paper aims to evaluate functional measurements and 3D machine learning models of a given HIE case by correlating the affected brain areas with the pathophysiology and clinical neurodevelopmental.

CASE PRESENTATION

A comprehensive analysis of a term infant with perinatal asphyxia using longitudinal 3D brain information from Machine Learning Models is presented. The clinical analysis revealed the perinatal asphyxia diagnosis with APGAR <5 at 5 and 10 minutes, umbilical arterial pH of 7.0 BE of -21.2 mmol / L), neonatal seizures, and invasive ventilation mechanics. Therapeutic interventions: physical, occupational, and language neurodevelopmental therapies. Epilepsy treatment: vagus nerve stimulation, levetiracetam, and phenobarbital. Furthermore, the 3D analysis showed how the volume decreases due to age, exhibiting an increasing asymmetry between hemispheres. The results of the basal ganglia area showed that thalamus asymmetry, caudate, and putamen increase over time while globus pallidus decreases.

CLINICAL OUTCOMES

spastic cerebral palsy, microcephaly, treatment-refractory epilepsy.

CONCLUSIONS

Slight changes in the basal ganglia and cerebellum require 3D volumetry for detection, as standard MRI examinations cannot fully reveal their complex shape variations. Quantifying these subtle neurodevelopmental changes helps in understanding their clinical implications. Besides, neurophysiological evaluations can boost neuroplasticity in children with neurological sequelae by stimulating new neuronal connections.

Protective effect of sucrose esters from cape gooseberry (Physalis peruviana L.) in TNBS-induced colitis

Phytotherapy is an attractive strategy to treat inflammatory bowel disease (IBD) that could be especially useful in developing countries. We previously demonstrated the intestinal anti-inflammatory effect of the total ethereal extract from the Physalis peruviana (Cape gooseberry) calyces in TNBS-induced colitis. This work investigates the therapeutic potential of Peruviose A and B, two sucrose esters that constitute the major metabolites of its calyces. The effect of the Peruvioses A and B mixture on TNBS-induced colitis was studied after 3 (preventive) and 15-days (therapy set-up) of colitis induction in rats. Colonic inflammation was assessed by measuring macroscopic/histologic damage, MPO activity, and biochemical changes. Additionally, LPS-stimulated RAW 264.7 macrophages were treated with test compounds to determine the effect on cytokine imbalance in these cells. Peruvioses mixture ameliorated TNBS-induced colitis in acute (preventive) or established (therapeutic) settings. Although 3-day treatment with compounds did not produce a potent effect, it was sufficient to significantly reduce the extent/severity of tissue damage and the microscopic disturbances. Beneficial effects in the therapy set-up were substantially higher and involved the inhibition of pro-inflammatory enzymes (iNOS, COX-2), cytokines (TNF-α, IL-1β, and IL-6), as well as epithelial regeneration with restoration of goblet cells numbers and expression of MUC-2 and TFF-3. Consistently, LPS-induced RAW 264.7 cells produced less NO, PGE2, TNF-α, IL-6, and MCP-1. These effects might be related to the inhibition of the NF-κB signaling pathway. Our results suggest that sucrose esters from P. peruviana calyces, non-edible waste from fruit production, might be useful as an alternative IBD treatment.

Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information

One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.

A location discrete choice model of crime: Police elasticity and optimal deployment

Despite the common belief that police presence reduces crime, there is mixed evidence of such causal effects in major Latin America cities. In this work we identify the casual relationship between police presence and criminal events by using a large dataset of a randomized controlled police intervention in Bogotá D.C., Colombia. We use an Instrumental Variables approach to identify the causal effect of interest. Then we consistently estimate a Conditional Logit discrete choice model with aggregate data that allow us to identify agents' utilities for crime location using Two Stage Least Squares. The estimated parameters allow us to compute the police own and cross-elasticities of crime for each of the spatial locations and to evaluate different police patrolling strategies. The elasticity of crime to police presence is, on average across spatial locations, -0.26 for violent crime, -0.38 for property crime and -0.38 for total crime, all statistically significant. Estimates of cross-elasticities are close to zero; however, spillover effects are non-negligible. Counterfactual analysis of different police deployment strategies show, for an optimal allocating algorithm, an average reduction in violent crime of 7.09%, a reduction in property crimes of 8.48% and a reduction in total crimes of 5.15% at no additional cost. These results show the potential efficiency gains of using the model to deploy police resources in the city without increasing the total police time required.

Effect of Protein Corona on the Specificity and Efficacy of Nanobioconjugates to Treat Intracellular Infections

Encapsulating drugs into functionalized nanoparticles (NPs) is an alternative to reach the specific therapeutic target with lower doses. However, when the NPs are in contact with physiological media, proteins adsorb on their surfaces, forming a protein corona (PC) biomolecular layer, acquiring a distinct biological identity that alters their interactions with cells. Itraconazole (ITZ), an antifungal agent, is encapsulated into PEGylated and/or functionalized NPs with high specificity for macrophages. It is evaluated how the PC impacts their cell uptake and antifungal effect. The minimum inhibitory concentration and colony-forming unit assays demonstrate that encapsulated ITZ into poly(ethylene glycol) (PEG) NPs improves the antifungal effect compared with NPs lacking PEGylation. The improvement can be related to the synergistic effect of the encapsulated ITZ and NPs composition and the reduction of PC formation in PEG NPs. Functionalized NPs with anti-F4/80 and anti-MARCO antibodies, or mannose without PEG and treated with PC, show an improved uptake but, in the presence of PEG, significantly reduce the endocytosis, dominating the stealth effect from PEG. Therefore, the PC plays a crucial role in the nanosystem uptake and antifungal effects, which suggests the need for in vivo model studies to evaluate the effect of PC in the specificity and biodistribution.

Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance

Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.

Systematic analysis of the scientific-technological production on the use of the UV, H2O2, and/or Cl2 systems in the elimination of bacteria and associated antibiotic resistance genes

This study presents a systematic review of the scientific and technological production related to the use of systems based on UV, H2O2, and Cl2 for the elimination of antibiotic-resistant bacteria (ARB) and genes associated with antibiotic resistance (ARGs). Using the Pro Know-C (Knowledge Development Process-Constructivist) methodology, a portfolio was created and analyzed that includes 19 articles and 18 patents published between 2011 and 2022. The results show a greater scientific-technological production in UV irradiation systems (8 articles and 5 patents) and the binary combination UV/H2O2 (9 articles and 4 patents). It was emphasized that UV irradiation alone focuses mainly on the removal of ARB, while the addition of H2O2 or Cl2, either individually or in binary combinations with UV, enhances the removal of ARB and ARG. The need for further research on the UV/H2O2/Cl2 system is emphasized, as gaps in the scientific-technological production of this system (0 articles and 2 patents), especially in its electrochemically assisted implementation, have been identified. Despite the gaps identified, there are promising prospects for the use of combined electrochemically assisted UV/H2O2/Cl2 disinfection systems. This is demonstrated by the effective removal of a wide range of contaminants, including ARB, fungi, and viruses, as well as microorganisms resistant to conventional disinfectants, while reducing the formation of toxic by-products.

Intra-urban variability of long-term exposure to PM2.5 and NO2 in five cities in Colombia

Rapidly urbanizing cities in Latin America experience high levels of air pollution which are known risk factors for population health. However, the estimates of long-term exposure to air pollution are scarce in the region. We developed intraurban land use regression (LUR) models to map long-term exposure to fine particulate matter (PM2.5) and nitrogen dioxide (NO2) in the five largest cities in Colombia. We conducted air pollution measurement campaigns using gravimetric PM2.5 and passive NO2 sensors for 2 weeks during both the dry and rainy seasons in 2021 in the cities of Barranquilla, Bucaramanga, Bogotá, Cali, and Medellín, and combined these data with geospatial and meteorological variables. Annual models were developed using multivariable spatial regression models. The city annual PM2.5 mean concentrations measured ranged between 12.32 and 15.99 µg/m3 while NO2 concentrations ranged between 24.92 and 49.15 µg/m3. The PM2.5 annual models explained 82% of the variance (R2) in Medellín, 77% in Bucaramanga, 73% in Barranquilla, 70% in Cali, and 44% in Bogotá. The NO2 models explained 65% of the variance in Bucaramanga, 57% in Medellín, 44% in Cali, 40% in Bogotá, and 30% in Barranquilla. Most of the predictor variables included in the models were a combination of specific land use characteristics and roadway variables. Cross-validation suggests that PM2.5 outperformed NO2 models. The developed models can be used as exposure estimate in epidemiological studies, as input in hybrid models to improve personal exposure assessment, and for policy evaluation.

Analysis of scientific and technological trends in the incorporation of activated carbon in advanced oxidation processes-a bibliometric study

There is high interest in the development of water pollution remediation technologies. Advanced oxidation processes (AOPs) are a promising alternative for the degradation of organic compounds; however, these technologies have been limited mainly by high operating costs and, in some cases, by forming byproducts, which can be more hazardous than the original pollutants. Activated carbon (AC) is a porous material that can be combined with AOP systems in various ways, given its adsorbent and catalytic characteristics. In addition, AC is a flexible, adaptable, and low-cost material. This article presents a bibliometric analysis of AOPs incorporating CA in scientific research and patents; the Scopus database was used to obtain patents and Orbit Express for patents. The most investigated AOPs incorporating AC are photocatalysis processes, Fenton processes, persulfate-based AOP, electrochemical processes, and ozonation. However, it is the persulfate-based AOP that has seen the greatest growth in scientific publications in recent years; this great interest can be related to the synergy that the process has with AC, allowing the degradation of contaminants via radical and non-radical. According to the maturity analysis of scientific publications, photocatalysis, Fenton, electrochemistry, ozonation, and persulfate technologies are in a growth stage and will reach maturity in 2034, 2042, 2040, 2034, and 2035, respectively; these technologies coupled with AC are expected to generate a greater number of patents when they reach maturity.

New Y-SNPs in QM3 indigenous populations of Colombia

In evolutionary studies of human populations based on the Y chromosome, the majority of Native Americans belong to the QM3 lineage. Therefore, to study the history of groups inhabiting northern South America, it is necessary to have a higher resolution of the tree. The objective of this work was to identify new SNPs of the QM3 lineage that would allow the evaluation of the phylogenetic relationships between Andean and Amazonian populations of Colombia. Sequences previously obtained from two Y chromosomes of Amazonian populations were used, from which 13 potential SNPs were selected and typed in 171 Amazonian samples from the Vaupés region and in 60 samples from the Pasto, Nasa, Embera, Arhuaco and Kogüi ethnic groups of the Andean region. In addition, the main SNPs/markers (L56, L54, M346, M848, Z780, CTS11780) defining autochthonous Q lineages were typed, along with others defined by different SNPs/markers as reported in the literature (CTS11357, SA05, Z19319, Z5915, and Z19384). It was found that all the new SNPs are present in the Amazonian samples and only 2 of them are shared with the Embera, Nasa and Pasto, but none with the Kogüi and Arhuaco from the northern Andes, in the Colombian Caribbean. Combining the 13 variants of the present study with 14 previously reported and using TMRCA, a new QM3 tree proposal is generated. This method makes it possible to increase the number of sublineages of QM3 with a higher resolution and to detect differences between the different populations of Vaupés in the Amazon, as in the case of the Kubeos and Pisamiras, the latter of which is in grave danger of extinction. These new sublineages are useful for microevolutionary studies of the Amerindian populations of South America.

Phenotypic and Genetic Factors Associated with Absence of Cardiomyopathy Symptoms in PLN:c.40_42delAGA Carriers

The c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, there are carriers who remain asymptomatic at older ages. To understand the mechanisms behind this incomplete penetrance, we evaluated potential phenotypic and genetic modifiers in 74 PLN:c.40_42delAGA carriers identified in 36,339 participants of the Lifelines population cohort. Asymptomatic carriers (N = 48) showed shorter QRS duration (- 5.73 ms, q value = 0.001) compared to asymptomatic non-carriers, an effect we could replicate in two different independent cohorts. Furthermore, symptomatic carriers showed a higher correlation (rPearson = 0.17) between polygenic predisposition to higher QRS (PGSQRS) and QRS (p value = 1.98 × 10-8), suggesting that the effect of the genetic variation on cardiac rhythm might be increased in symptomatic carriers. Our results allow for improved clinical interpretation for asymptomatic carriers, while our approach could guide future studies on genetic diseases with incomplete penetrance.

Development of a highly tolerant bacterial consortium for asphaltene biodegradation in soils

Asphaltenes are the most polar and heavy fraction of petroleum, and their complex structure and toxicity make them resistant to biodegradation. The ability to tolerate high asphaltene concentrations is crucial to reducing the toxicity-related inhibition of microbial growth and improving their capacity for adaptation, survival, and biodegradation in soils highly contaminated with asphaltenes. This study developed a highly tolerant consortium for efficient asphaltene biodegradation in soils from 22 bacterial isolates obtained from heavy-crude oil-contaminated soils. Isolates corresponded to the Rhodococcus, Bacillus, Stutzerimonas, Cellulosimicrobium, Pseudomonas, and Paenibacillus genera, among others, and used pure asphaltenes and heavy crude oil as the only carbon sources. Surface plate assays were used to evaluate the tolerance of individual isolates to asphaltenes, and the results showed variations in the extension and inhibition rates with maximum tolerance levels at 60,000 mg asphaltenes l-1. Inhibition assays were used to select non-antagonistic bacterial isolates among those showing the highest tolerance levels to asphaltenes. A consortium made up of the five most tolerant and non-antagonistic bacterial isolates was able to degrade up to 83 wt.% out of 10,000 mg asphaltenes kg-1 in the soil after 52 days. Due to its biological compatibility, high asphaltene tolerance, and ability to utilise it as a source of energy, the degrading consortium developed in this work has shown a high potential for soil bioremediation and is a promising candidate for the treatment of aged soil areas contaminated with heavy and extra-heavy crude oil. This would be the first research to assess and consider extreme bacterial tolerance and microbial antagonism between individual degrading microbes, leading to the development of an improved consortium capable of efficiently degrading high amounts of asphaltenes in soil.

Phylogenetic analysis of the partial sequences of the env and tax BLV genes reveals the presence of genotypes 1 and 3 in dairy herds of Antioquia, Colombia

Bovine leukemia virus (BLV) is a retrovirus that primarily infects dairy cows. Although few studies have also used the tax gene, phylogenetic studies of BLV use mostly the env gene. The aim of this work was to establish the circulating genotypes of BLV in specialized dairy cattle from Antioquia, Colombia. Twenty blood samples from Holstein Friesian cows were collected, and their DNA was isolated. A PCR was performed for a partial region of the env and tax genes. A phylogenetic analysis was carried out using the maximum likelihood and Bayesian methods for both genes. Nineteen sequences were identified as genotype 1 by env and tax genes. Only one sequence was clustered with genotype 3 and had the highest proportion of different nucleotide sites compared to other strains. Four amino acid substitutions in the 134 amino acid residue fragment of the Env protein were identified in the Colombian sequences, and three new amino acid substitutions were reported in the 296 amino acid residue fragment of the Tax protein. R43K (Z finger), A185T (Activation domain), and L105F changes were identified in the genotype 3 sample. This genotype has been reported in the United States, Japan, Korea, and Mexico, but so far, not in Colombia. The country has a high rate of imported live animals, semen, and embryos, especially from the United States. Although it is necessary to evaluate samples from other regions of the country, the current results indicate the presence of two BLV genotypes in specialized dairy herds.

Biomarkers for the diagnosis, treatment follow-up, and prediction of cardiac complications in Chagas disease in chronic phase: Recent advances

Chagas disease is caused by the Trypanosoma cruzi parasite and is transmitted by infected triatomine bugs. This infection affects approximately 8 million people in the Americas, and due to globalisation and displacement, it is becoming increasingly common to find infected patients worldwide. Diagnosis of the disease in its acute form is relatively simple, as the parasite can be detected in peripheral blood smears, and symptoms are visible. However, in its chronic condition, the parasite is almost undetectable, and indirect tests are necessary to determine the presence of antibodies in infected patients. It is important to note that a single test is not enough to confirm the disease in this phase, as a second serological test should confirm the diagnosis. If the results are contradictory, a third test should be performed to confirm or discard the disease. Unfortunately, laboratories may not have access to all necessary tests in many rural areas where the disease is more frequent. Rapid tests to diagnose this disease present problems, such as significant variations in sensitivity and specificity in different countries. Therefore, searching for new biomarkers that allow for optimal correlation is essential. In this work, we have searched scientific literature from the last 10 years for mentions of novel biomarkers for diagnosis, treatment follow-up, and prediction of cardiac complications in Chagas disease in its chronic phase.

Impact of health-related behavioral factors on participation in a cervical cancer screening program: the lifelines population-based cohort

BACKGROUND

Regular participation in cervical cancer screening is critical to reducing mortality. Although certain sociodemographic factors are known to be associated with one-time participation in screening, little is known about other factors that could be related to regular participation. Therefore, this study evaluated the association between health-related behavioral factors and regular participation in cervical cancer screening.

METHODS

The Lifelines population-based cohort was linked to data for cervical cancer screening from the Dutch Nationwide Pathology Databank. We included women eligible for all four screening rounds between 2000 and 2019, classifying them as regular (4 attendances), irregular (1-3 attendances), and never participants. Multinomial logistic regression was performed to evaluate the association between behavioral factors and participation regularity, with adjustment made for sociodemographic factors.

RESULTS

Of the 48,325 included women, 55.9%, 35.1%, and 9% were regular, irregular, and never screening participants. After adjustment for sociodemographic factors, the likelihood of irregular or never screening participation was increased by smoking, obesity, marginal or inadequate sleep duration, alcohol consumption and low physical activity, while it was decreased by hormonal contraception use.

CONCLUSION

An association exists between unhealthy behavioral factors and never or irregular participation in cervical cancer screening.

Bioengineered skin constructs based on mesenchymal stromal cells and acellular dermal matrix exposed to inflammatory microenvironment releasing growth factors involved in skin repair

BACKGROUND

Skin tissue engineering is a rapidly evolving field of research that effectively combines stem cells and biological scaffolds to replace damaged tissues. Human Wharton's jelly mesenchymal stromal cells (hWJ-MSCs) are essential to generate tissue constructs, due to their potent immunomodulatory effects and release of paracrine factors for tissue repair. Here, we investigated whether hWJ-MSC grown on human acellular dermal matrix (hADM) scaffolds and exposed to a proinflammatory environment maintain their ability to produce in vitro growth factors involved in skin injury repair and promote in vivo wound healing.

METHODS

We developed a novel method involving physicochemical and enzymatic treatment of cadaveric human skin to obtain hADM scaffold. Subsequently, skin bioengineered constructs were generated by seeding hWJ-MSCs on the hADM scaffold (construct 1) and coating it with human platelet lysate clot (hPL) (construct 2). Either construct 1 or 2 were then incubated with proinflammatory cytokines (IL-1α, IL-1β, IL-6, TNF-α) for 12, 24, 48, 72 and 96 h. Supernatants from treated and untreated constructs and hWJ-MSCs on tissue culture plate (TCP) were collected, and concentration of the following growth factors, bFGF, EGF, HGF, PDGF, VEGF and Angiopoietin-I, was determined by immunoassay. We also asked whether hWJ-MSCs in the construct 1 have potential toward epithelial differentiation after being cultured in an epithelial induction stimulus using an air-liquid system. Immunostaining was used to analyze the synthesis of epithelial markers such as filaggrin, involucrin, plakoglobin and the mesenchymal marker vimentin. Finally, we evaluated the in vivo potential of hADM and construct 1 in a porcine full-thickness excisional wound model.

RESULTS

We obtained and characterized the hADM and confirmed the viability of hWJ-MSCs on the scaffold. In both constructs without proinflammatory treatment, we reported high bFGF production. In contrast, the levels of other growth factors were similar to the control (hWJ-MSC/TCP) with or without proinflammatory treatment. Except for PDGF in the stimulated group. These results indicated that the hADM scaffold maintained or enhanced the production of these bioactive molecules by hWJ-MSCs. On the other hand, increased expression of filaggrin, involucrin, and plakoglobin and decreased expression of vimentin were observed in constructs cultured in an air-liquid system. In vivo experiments demonstrated the potential of both hADM and hADM/hWJ-MSCs constructs to repair skin wounds with the formation of stratified epithelium, basement membrane and dermal papillae, improving the appearance of the repaired tissue.

CONCLUSIONS

hADM is viable to fabricate a tissue construct with hWJ-MSCs able to promote the in vitro synthesis of growth factors and differentiation of these cells toward epithelial lineage, as well as, promote in a full-thickness skin injury the new tissue formation. These results indicate that hADM 3D architecture and its natural composition improved or maintained the cell function supporting the potential therapeutic use of this matrix or the construct for wound repair and providing an effective tissue engineering strategy for skin repair.

Effect of environmental variables on mercury accumulation in sediments of an anthropogenically impacted tropical estuary (Buenaventura Bay, Colombian Pacific)

Estuaries are the main entry areas of mercury to the marine environment and are important to understand the effect of this contaminant on marine organisms, since it accumulates in the sediments becoming available to enter the food trophic chain. This study aims to determine the environmental variables that mainly influence the spatiotemporal dynamics of total mercury accumulation in sediments of tropical estuaries. Sediment samples were collected from interior and exterior areas of the estuary during the dry and rainy seasons, representing the spatiotemporal gradients of the estuary. The grain size, organic matter content (OM), and total mercury concentration (THg) of the sediment samples were determined. In addition, salinity, temperature, dissolved oxygen, and pH of the water column associated with each sediment sample were assessed. The variations in environmental conditions, OM and THg in sediment were in accordance with a gradient which goes from conditions influenced by fresh water in the inner estuary to conditions influenced by sea water in the outer part of the estuary. The OM and THg in sediments presented similar variation patterns; they were higher in the rainy season than in the dry season and in the interior area of the estuary than in the exterior area. Despite the complex dynamic observed in the distribution and accumulation processes of mercury in sediments, these processes could be modeled from OM and salinity parameters. Due to the correlations found, in the process of accumulation of mercury in sediments the OM could represents the pathway of transport and accumulation of THg, and salinity could represent the influence of the hydroclimatic variations and environmental gradients of the estuary.

Genome-wide association study reveals candidate genes for traits related to meat quality in Colombian Creole hair sheep

Genome-wide association studies (GWAS) allow identifying genomic regions related to traits of economic importance in animals of zootechnical interest. The objective of this research was to conduct a genome-wide association study on meat quality traits using the Illumina OvineSNPs50 BeadChip array. The animals were sampled in the departments of Córdoba, Cesar, and Valle del Cauca. The genotypes obtained with the Illumina OvineSNP50 BeadChip microarray were analyzed SNP (single-nucleotide polymorphism) data to conduct a GWAS for pH and water-holding capacity (WHC) traits measured after 7 days of maturation, in the Longissimus dorsi (LD) muscle, in 167 Creole hair sheep of 12 months old belonging to Pelibuey (CHSP, n = 60), Ethiopian (CHSE, n = 44), and Sudan (CHSS, n = 63) breeds. The GWAS was done using a mixed linear model (MLMA) and based on the Ovis aries v3.1 genome. The CHSE showed the lowest meat juice release and, consequently, the highest water-holding capacity (WHC = 30.6 ± 0.1), suggesting that this breed has better performance in the meat industry compared with CHSS (WHC = 41.7 ± 0.1) and CHSP (WHC = 36.8 ± 0.1), since there is a relationship between WHC and juiciness. For the character pH, it was not possible to annotate genes related to meat quality, while, for the WHC, they have obtained 11 candidate genes associated (ELOVL2, ARAP2, LOC101102527, SHOC2, AIPL1, CSRNP3, IFRD, KDM8, NANS, DAPK1, IBN2, TPM2). Particularly, ELOVL2, ARAP2, IBN2, and TPM2 genes are involved in muscle contraction and fatty acid composition in sheep. In this study, we generated a baseline for GWAS related to meat quality traits in Colombian Creole hair sheep that can be used for future genomic selection plans.

Evolution of major flowering pathway integrators in Orchidaceae

The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.

Convertase-dependent regulation of membrane-tethered and secreted ligands tunes dendrite adhesion

During neural development, cellular adhesion is crucial for interactions among and between neurons and surrounding tissues. This function is mediated by conserved cell adhesion molecules, which are tightly regulated to allow for coordinated neuronal outgrowth. Here, we show that the proprotein convertase KPC-1 (homolog of mammalian furin) regulates the Menorin adhesion complex during development of PVD dendritic arbors in Caenorhabditis elegans. We found a finely regulated antagonistic balance between PVD-expressed KPC-1 and the epidermally expressed putative cell adhesion molecule MNR-1 (Menorin). Genetically, partial loss of mnr-1 suppressed partial loss of kpc-1, and both loss of kpc-1 and transgenic overexpression of mnr-1 resulted in indistinguishable phenotypes in PVD dendrites. This balance regulated cell-surface localization of the DMA-1 leucine-rich transmembrane receptor in PVD neurons. Lastly, kpc-1 mutants showed increased amounts of MNR-1 and decreased amounts of muscle-derived LECT-2 (Chondromodulin II), which is also part of the Menorin adhesion complex. These observations suggest that KPC-1 in PVD neurons directly or indirectly controls the abundance of proteins of the Menorin adhesion complex from adjacent tissues, thereby providing negative feedback from the dendrite to the instructive cues of surrounding tissues.

BACE1 and SCD1 are associated with neurodegeneration

Introduction

Proteolytic processing of amyloid protein precursor by β-site secretase enzyme (BACE1) is dependent on the cellular lipid composition and is affected by endomembrane trafficking in dementia and Alzheimer's disease (AD). Stearoyl-CoA desaturase 1 (SCD1) is responsible for the synthesis of fatty acid monounsaturation (MUFAs), whose accumulation is strongly associated with cognitive dysfunction.

Methods

In this study, we analyzed the relationship between BACE1 and SCD1 in vivo and in vitro neurodegenerative models and their association in familial AD (FAD), sporadic AD (SAD), and cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) using microscopy, biochemical, and mass SPECT approach.

Results

Our findings showed that BACE1 and SCD1 immunoreactivities were increased and colocalized in astrocytes of the hippocampus in a rat model of global cerebral ischemia (2-VO). A synergistic effect of double BACE1/SCD1 silencing on the recovery of motor and cognitive functions was obtained. This neuroprotective regulation involved the segregation of phospholipids (PLs) associated with polyunsaturated fatty acids in the hippocampus, cerebrospinal fluid, and serum. The double silencing in the sham and ischemic groups was stronger in the serum, inducing an inverse ratio between total phosphatydilcholine (PC) and lysophosphatidylcholine (LPC), represented mainly by the reduction of PC 38:4 and PC 36:4 and an increase in LPC 16:0 and LPC 18:0. Furthermore, PC 38:4 and PC:36:4 levels augmented in pathological conditions in in vitro AD models. BACE1 and SCD1 increases were confirmed in the hippocampus of FAD, SAD, and CADASIL.

Conclusion

Therefore, the findings suggest a novel convergence of BACE-1 and SCD1 in neurodegeneration, related to pro-inflammatory phospholipids.

Plasma cell-free DNA concentration increases during luteolysis in beef cows

During cell death, DNA is fragmented and reaches the bloodstream in the form of cell-free DNA (cfDNA). Luteal cells must undergo an apoptotic process during structural luteolysis to begin a new oestrous cycle. We hypothesized that cfDNA concentrations would increase when inducing luteolysis by applying prostaglandin F2α (PGF2α) analog to the cycling cow. Multiparous non-pregnant and non-lactating Angus cows (Bos taurus; n = 15) were synchronized using the 7-day CoSynch + CIDR protocol. Ten days after oestrus was detected, two treatments were applied (PGF2α, n = 10; or Con, n = 5). Twice a day, grey mode and colour Doppler ultrasonography were used to calculate area (CL-A) and luteal blood perfusion (LBP%). Additionally, we collected one blood sample for plasma progesterone (P4) and cfDNA concentrations for four consecutive days. Data analysis was performed using the GLM procedure of SAS. The luteolysis induction was demonstrated by a decrease in P4 concentrations (p ≤ .01) and CL-A (p ≤ .01) in the PGF2α group after 12 h of the PGF2α injection. Reduction of LBP% (p ≤ .01) in the PGF2α group after 36 h of the injection. The concentration of cfDNA showed a significant increase (p = .05) after 48 h of the PGF2α application in the PGF2α group. In conclusion, cfDNA showed a significantly increased concentration after luteolysis induction, which can imply that cfDNA could be used as a luteolysis biomarker in plasma.

Empirical model to assess leaching of pesticides in soil under a steady-state flow and tropical conditions

Abstract

An empirical model of leaching of pesticides was developed to simulate the concentration of fungicides throughout unsaturated soil. The model was based on chemical reactions and the travel time of a conservative tracer to represent the travel time required for water to flow between soil layers. The model's performance was then tested using experimental data from dimethomorph and pyrimethanil applied to the soil under field and laboratory conditions. The empirical model simulated fungicide concentration on soil solids and in soil solution at different depths over time (mean square error between 2.9 mg2 kg-2 and 61mg2 kg-2) using sorption percentages and degradation rates under laboratory conditions. The sorption process was affected by the organic carbon, clay, and the effective cation exchange capacity of the soil. The degradation rate values of dimethomorph (0.039 d-1-0.009 d-1) and pyrimethanil (0.053 d-1-0.004 d-1) decreased from 0 to 40 cm and then remained constant in deeper soil layers (60-80 cm). Fungicide degradation was a critical input in the model at subsurface layers. The model was determined to be a reliable mathematical tool to estimate the leachability of pesticides in tropical soil under a steady-state flow. It may be extended to other substances and soils for environmental risk assessment projects.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13762-023-05038-w.

Cholinergic-like neurons and cerebral spheroids bearing the PSEN1 p.Ile416Thr variant mirror Alzheimer's disease neuropathology

Familial Alzheimer's disease (FAD) is a complex neurodegenerative disorder for which there are no therapeutics to date. Several mutations in presenilin 1 (PSEN 1), which is the catalytic component of γ-secretase complex, are causal of FAD. Recently, the p.Ile416Thr (I416T) PSEN 1 mutation has been reported in large kindred in Colombia. However, cell and molecular information from I416T mutation is scarce. Here, we demonstrate that menstrual stromal cells (MenSCs)-derived planar (2D) PSEN 1 I416T cholinergic-like cells (ChLNS) and (3D) cerebral spheroids (CSs) reproduce the typical neuropathological markers of FAD in 4 post-transdifferentiating or 11 days of transdifferentiating, respectively. The models produce intracellular aggregation of APPβ fragments (at day 4 and 11) and phosphorylated protein TAU at residue Ser202/Thr205 (at day 11) suggesting that iAPPβ fragments precede p-TAU. Mutant ChLNs and CSs displayed DJ-1 Cys106-SO3 (sulfonic acid), failure of mitochondria membrane potential (ΔΨm), and activation of transcription factor c-JUN and p53, expression of pro-apoptotic protein PUMA, and activation of executer protein caspase 3 (CASP3), all markers of cell death by apoptosis. Moreover, we found that both mutant ChLNs and CSs produced high amounts of extracellular eAβ42. The I416T ChLNs and CSs were irresponsive to acetylcholine induced Ca2+ influx compared to WT. The I416T PSEN 1 mutation might work as dominant-negative PSEN1 mutation. These findings might help to understanding the recurring failures of clinical trials of anti-eAβ42, and support the view that FAD is triggered by the accumulation of other intracellular AβPP metabolites, rather than eAβ42.

5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus

The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-genome sequencing technologies to resolve the sequences of the genome ends. We modified a protocol for rapid amplification of cDNA ends (RACE) to determine the complete sequences of the 5' and 3' UTRs of a previously reported ZIKV isolate (GenBank no. MH544701.1). This strategy is useful for determining 5' and 3' UTR sequences of ZIKV isolates and will be useful for comparative genomics applications.

Anti-GM-CSF Neutralizing Autoantibodies in Colombian Patients with Disseminated Cryptococcosis

BACKGROUND

Cryptococcosis is a potentially life-threatening fungal disease caused by encapsulated yeasts of the genus Cryptococcus, mostly C. neoformans or C. gattii. Cryptococcal meningitis is the most frequent clinical manifestation in humans. Neutralizing autoantibodies (auto-Abs) against granulocyte-macrophage colony-stimulating factor (GM-CSF) have recently been discovered in otherwise healthy adult patients with cryptococcal meningitis, mostly caused by C. gattii. We hypothesized that three Colombian patients with cryptococcal meningitis caused by C. neoformans in two of them would carry high plasma levels of neutralizing auto-Abs against GM-CSF.

METHODS

We reviewed medical and laboratory records, performed immunological evaluations, and tested for anti-cytokine auto-Abs three previously healthy HIV-negative adults with disseminated cryptococcosis.

RESULTS

Peripheral blood leukocyte subset levels and serum immunoglobulin concentrations were within the normal ranges. We detected high levels of neutralizing auto-Abs against GM-CSF in the plasma of all three patients.

CONCLUSIONS

We report three Colombian patients with disseminated cryptococcosis associated with neutralizing auto-Abs against GM-CSF. Further studies should evaluate the genetic contribution to anti-GM-CSF autoantibody production and the role of the GM-CSF signaling pathway in the immune response to Cryptococcus spp.

Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae)

Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.

Hybrid prediction of infections and deaths due to COVID-19 in two Colombian data series

The prediction of the number of infected and dead due to COVID-19 has challenged scientists and government bodies, prompting them to formulate public policies to control the virus' spread and public health emergency worldwide. In this sense, we propose a hybrid method that combines the SIRD mathematical model, whose parameters are estimated via Bayesian inference with a seasonal ARIMA model. Our approach considers that notifications of both, infections and deaths are realizations of a time series process, so that components such as non-stationarity, trend, autocorrelation and/or stochastic seasonal patterns, among others, must be taken into account in the fitting of any mathematical model. The method is applied to data from two Colombian cities, and as hypothesized, the prediction outperforms the obtained with the fit of only the SIRD model. In addition, a simulation study is presented to assess the quality of the estimators of SIRD model in the inverse problem solution.

Non-natural amino acids into LfcinB-derived peptides: effect in their (i) proteolytic degradation and (ii) cytotoxic activity against cancer cells

The dimeric peptide ²⁶[F]: (RRWQWRFKKLG)₂-K-Ahx has exhibited a potent cytotoxic effect against breast cancer cell lines, with position 26 (F) being the most relevant for anti-cancer activity. In this investigation, six analogues of the ²⁶[F] peptide were synthesized in which the 26th position was replaced by non-natural hydrophobic amino acids, finding that some modifications increased the resistance to proteolytic degradation exerted by trypsin or pepsin. Additionally, these modifications increased the cytotoxic effect against breast cancer cells and generated cell death mediated by apoptosis pathways, activating caspases 8 and 9, and did not compromise the integrity of the cytoplasmic membrane. Finally, it was found that the modified peptides have a broad spectrum of action, since they also have a cytotoxic effect against the HeLa human cervical cancer cell line. Peptide ²⁶[F] was inoculated in mice by ip administration and the lethal dose 50 (LD₅₀) was between 70 and 140 mg kg^-1. While for the ²⁶[1-Nal]: (RRWQWR-1-Nal-KKLG)₂-K-Ahx peptide, a dose-response test was performed, and the survival rate was 100%. These results suggested that these peptides are safe in this animal model and could be considered as promissory to develop a treatment against breast cancer.

Sex-specific alterations in adaptive responses of Chironomus columbiensis triggered by imidacloprid chronic and acute sublethal exposures

The use of imidacloprid is a common pest control practice in the Neotropical region. However, the imidacloprid unintended sublethal effects on Neotropical aquatic non-target arthropods and undesirable consequences for aquatic environments remain unclear. Here, we assessed the susceptibility of Chironomus columbiensis (Diptera: Chironomidae) larvae to the neonicotinoid imidacloprid and evaluated whether sublethal exposure types would trigger sex-dependent adaptive responses (e.g., emergence, body mass, reproduction, wing morphology). We conducted a concentration-mortality curve (96 h of exposure) and established chronic and acute sublethal exposure bioassays. While chronic sublethal exposures consisted of exposing individuals during their entire larval and pupal stages, the acute sublethal exposures represented a single short duration (24 h) exposure episode during either the first or fourth larval instar. Our results revealed that chronic sublethal exposure reduced the body mass of males, while acute sublethal exposures during the first instar resulted in heavier males than those that were not exposed to imidacloprid. Chronic exposure also reduced the reproduction of males and females, while the acute sublethal exposure only affected the reproduction of individuals that were imidacloprid-exposed on their later larval instar. Chronic and acute sublethal exposures did differentially affect the wing properties of C. columbiensis males (e.g., increased size when chronically exposed and highly asymmetric wings when acutely exposed in early larval phase) and females (e.g., highly asymmetric wings when chronically and acutely exposed). Collectively, our findings demonstrated that imidacloprid can cause unintended sublethal effects on C. columbiensis, and those effects are dependent on sex, exposure type, and developmental stage.

NeuN distribution in brain structures of normal and Zika-infected suckling mice

Microcephaly is the more severe brain malformation because of Zika virus infection. Increased vulnerability of neural stem and progenitor cells to Zika infection during prenatal neurodevelopment impairs the complete formation of cortical layers. Normal development of cerebellum is also affected. However, the follow-up of apparently healthy children born to Zika exposed mothers during pregnancy has revealed other neurological sequelae. This suggests Zika infection susceptibility remains in nervous tissue after neurogenesis end, when differentiated neuronal populations predominate. The neuronal nuclear protein (NeuN) is an exclusive marker of postmitotic neurons. Changes in NeuN expression are associated with neuronal degeneration. We have evaluated immunohistochemical expression of NeuN protein in cerebral cortex, hippocampus, and cerebellum of normal and Zika-infected neonatal Balb/c mice. The highest NeuN immunoreactivity was found mainly in neurons of all cortical layers, pyramidal layer of hippocampus, granular layer of dentate gyrus and in internal granular layer of cerebellum. Viral infection caused marked loss of NeuN immunostaining in all these brain areas. This suggests neurodegenerative effects of Zika virus infection during postmitotic neuron maturation and contribute to interpretation of neuropathogenic mechanisms of Zika.

Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing

Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.

Isolation of urease-producing bacteria from cocoa farms soils in Santander, Colombia, for cadmium remediation

Cadmium (Cd) is a toxic heavy metal that causes serious health problems and is present in agriculturally important soils in Colombia, such as the ones used for cocoa farming. Recently, the use of ureolytic bacteria by the Microbiologically Induced Carbonate Precipitation (MICP) activity has been proposed as an alternative to mitigate the availability of Cd in contaminated soils. In this study, 12 urease-positive bacteria able to grow in the presence of Cd(II) were isolated and identified. Three were selected based on urease activity, precipitates formation and growth, with two belonging to the genus Serratia (codes 4.1a and 5b) and one to Acinetobacter (code 6a). These isolates exhibited low urease activity levels (3.09, 1.34 and 0.31 μmol mL-1 h-1, respectively), but could raise the pH to values close to 9.0 and to produce carbonate precipitates. It was shown that the presence of Cd affects the growth of the selected isolates. However, urease activity was not negatively influenced. In addition, the three isolates were observed to efficiently remove Cd from solution. The two Serratia isolates presented maximum removals of 99.70% and 99.62%, with initial 0.05 mM Cd(II) in the culture medium (supplemented with urea and Ca(II)) at 30 °C and 144 h of incubation. For the Acinetobacter isolate, the maximum removal was 91.23% at the same conditions. Thus, this study evidences the potential use of these bacteria for bioremediation treatments in samples contaminated with Cd, and it is one of the few reports that shows the high cadmium removal capacity of bacteria from the genus Serratia.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03495-1.

Xylose Metabolization by a Saccharomyces cerevisiae Strain Isolated in Colombia

Saccharomyces cerevisiae (S. cerevisiae) is the most widely used yeast in biotechnology in the world because its well-known metabolism and physiology as well as its recognized ability to ferment sugars such as hexoses. However, it does not metabolize pentoses such as arabinose and xylose, which are present in lignocellulosic biomass. Lignocellulose is a widely available raw material, with xylose content of approximately 35% of total sugars. This xylose fraction could be used to obtain high added-value chemical products such as xylitol. One of these yeasts isolated from a Colombian locality, designated as 202-3, showed interesting properties. 202-3 was identified through different approaches as a strain of S. cerevisiae, with an interesting consumption of xylose metabolizing into xylitol, in addition with excellent ability as a hexose fermenter with high ethanol yields and shows resistance to inhibitors present in lignocellulosic hydrolysates. The xylose metabolization by the 202-3 strain and their kinetics parameters had not been previously reported for any other natural strain of S. cerevisiae. These results suggest the great potential of natural strains for obtaining high value-added chemical products using sugars available in lignocellulosic biomass.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01054-z.

Randomized trial evaluating an mHealth intervention for the early community-based detection and follow-up of cutaneous leishmaniasis in rural Colombia

BACKGROUND

In Latin America, cutaneous leishmaniasis primarily affects dispersed rural communities, that have limited access to the public health system and medical attention. Mobile health (mHealth) strategies have shown potential to improve clinical management and epidemiological surveillance of neglected tropical diseases, particularly those of the skin.

METHODS

The Guaral +ST app for Android was designed to monitor cutaneous leishmaniasis treatment and assess therapeutic response. We carried out a randomized trial in the coastal municipality of Tumaco in southwestern Colombia, with parallel arms comparing a) follow-up aided by the app to b) standard institution-based follow-up. Treatment was prescribed according to national guidelines. Follow-up of therapeutic response was scheduled at the end of treatment and at 7, 13 and 26 weeks after the start of treatment. The primary endpoint was the proportion of participants who were monitored at or around week 26, allowing outcome and effectiveness of treatment to be determined.

RESULTS

Follow-up of treatment and outcome assessment was achieved in significantly more patients in the intervention arm than the controls, Of the 75 participants in the two randomized arms, 74 had information on whether or not treatment was followed and outcome determined at or around week 26. Among these, 26/49 (53.1%) were evaluated in the intervention arm, and none (0/25, 0%) in the control arm (difference = 53.1%, 95% confidence interval 39.1-67.0%, p<0.001). Of the 26 participants evaluated at or around week 26 in the intervention arm, 22 (84.6%) had cured. There were no serious adverse events, nor events of severe intensity among patients monitored by CHW using the app.

CONCLUSION

This study provides proof of concept for mHealth to monitor treatment of CL in remote and complex settings, deliver improved care and to provide information to the health system on the effectiveness of treatment as it is delivered to affected populations.

CLINICAL TRIAL REGISTRATION

ISRCTN54865992.

Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming

Climate change is radically altering coral reef ecosystems, mainly through increasingly frequent and severe bleaching events. Yet, some reefs have exhibited higher thermal tolerance after bleaching severely the first time. To understand changes in thermal tolerance in the eastern tropical Pacific (ETP), we compiled four decades of temperature, coral cover, coral bleaching, and mortality data, including three mass bleaching events during the 1982 to 1983, 1997 to 1998 and 2015 to 2016 El Niño heatwaves. Higher heat resistance in later bleaching events was detected in the dominant framework-building genus, Pocillopora, while other coral taxa exhibited similar susceptibility across events. Genetic analyses of Pocillopora spp. colonies and their algal symbionts (2014 to 2016) revealed that one of two Pocillopora lineages present in the region (Pocillopora "type 1") increased its association with thermotolerant algal symbionts (Durusdinium glynnii) during the 2015 to 2016 heat stress event. This lineage experienced lower bleaching and mortality compared with Pocillopora "type 3", which did not acquire D. glynnii. Under projected thermal stress, ETP reefs may be able to preserve high coral cover through the 2060s or later, mainly composed of Pocillopora colonies that associate with D. glynnii. However, although the low-diversity, high-cover reefs of the ETP could illustrate a potential functional state for some future reefs, this state may only be temporary unless global greenhouse gas emissions and resultant global warming are curtailed.

Neoadjuvant chemotherapy modulates exhaustion of T cells in breast cancer patients

Breast cancer is the leading cause of cancer deaths in women worldwide. It has been observed that the incidence of breast cancer increases linearly with age after 45, which suggest a link between cancer, aging, and senescence. A growing body of evidence indicates that the immunosuppressive tumor network in breast cancer patients can lead to T-cell exhaustion and senescence. Cytotoxic chemotherapy is a common treatment for many cancers, and it is hypothesized that its efficacy may be related to immune activation. However, the effects of neoadjuvant chemotherapy on T-cell dysfunction in breast cancer patients are not fully understood. This study aimed to evaluate the impact of neoadjuvant chemotherapy on the expression of exhaustion and senescence markers in T cells in women with breast cancer. Our results showed that T cells from breast cancer patients have a reduced ability to respond to stimulation in-vitro and an increased expression of senescence and exhaustion-associated markers, such as TIM-3, LAG3, and CD57. Furthermore, we found that neoadjuvant chemotherapy has an immunomodulatory effect and reduces the expression of exhaustion markers. Our observations of the immune phenotype of T cells during neoadjuvant chemotherapy treatment highlight its ability to stimulate the immune system against cancer. Therefore, monitoring the response of T cells during chemotherapy may enable early prediction of clinical response.

Toxicity of tributyltin to the European flat oyster Ostrea edulis: Metabolomic responses indicate impacts to energy metabolism, biochemical composition and reproductive maturation

Tri-Butyl Tin (TBT) remains as a legacy pollutant in the benthic environments. Although the toxic impacts and endocrine disruption caused by TBT to gastropod molluscs have been established, the changes in energy reserves allocated to maintenance, growth, reproduction and survival of European oysters Ostrea edulis, a target species of concerted benthic habitat restoration projects, have not been explored. This study was designed to evaluate the effect of TBT chloride (TBTCl) on potential ions and relevant metabolomic pathways and its association with changes in physiological, biochemical and reproductive parameters in O. edulis exposed to environmental relevant concentrations of TBTCl. Oysters were exposed to TBTCl 20 ng/L (n = 30), 200 ng/L (n = 30) and 2000 ng/L (n = 30) for nine weeks. At the end of the exposure, gametogenic stage, sex, energy reserve content and metabolomic profiling analysis were conducted to elucidate the metabolic alterations that occur in individuals exposed to those compounds. Metabolite analysis showed significant changes in the digestive gland biochemistry in oysters exposed to TBTCl, decreasing tissue ATP concentrations through a combination of the disruption of the TCA cycle and other important molecular pathways involved in homeostasis, mitochondrial metabolism and antioxidant response. TBTCl exposure increased mortality and caused changes in the gametogenesis with cycle arrest in stages G0 and G1. Sex determination was affected by TBTCl exposure, increasing the proportion of oysters identified as males in O. edulis treated at 20ng/l TBTCl, and with an increased proportion of inactive stages in oysters treated with 2000 ng/l TBTCl. The presence and persistence of environmental pollutants, such as TBT, could represent an additional threat to the declining O. edulis populations and related taxa around the world, by increasing mortality, changing reproductive maturation, and disrupting metabolism. Our findings identify the need to consider additional factors (e.g. legacy pollution) when identifying coastal locations for shellfish restoration.

Do different robot appearances change emotion recognition in children with ASD?

Introduction

Socially Assistive Robotics has emerged as a potential tool for rehabilitating cognitive and developmental disorders in children with autism. Social robots found in the literature are often able to teach critical social skills, such as emotion recognition and physical interaction. Even though there are promising results in clinical studies, there is a lack of guidelines on selecting the appropriate robot and how to design and implement the child-robot interaction.

Methods

This work aims to evaluate the impacts of a social robot designed with three different appearances according to the results of a participatory design (PD) process with the community. A validation study in the emotion recognition task was carried out with 21 children with autism.

Results

Spectrum disorder results showed that robot-like appearances reached a higher percentage of children's attention and that participants performed better when recognizing simple emotions, such as happiness and sadness.

Discussion

This study offers empirical support for continuing research on using SAR to promote social interaction with children with ASD. Further long-term research will help to identify the differences between high and low-functioning children.

Entomological parameters and population structure at a microgeographic scale of the main Colombian malaria vectors Anopheles albimanus and Anopheles nuneztovari

Population subdivision among several neotropical malaria vectors has been widely evaluated; however, few studies have analyzed population variation at a microgeographic scale, wherein local environmental variables may lead to population differentiation. The aim of the present study was to evaluate the genetic and geometric morphometric structure of Anopheles nuneztovari and Anopheles albimanus in endemic localities of northwestern Colombia. Genetic and phenetic structures were evaluated using microsatellites markers and wing geometric morphometrics, respectively. In addition, entomological indices of importance in transmission were calculated. Results showed that the main biting peaks of Anopheles nuneztovari were between 20:00 and 22:00, whereas Anopheles albimanus exhibited more variation in biting times among localities. Infection in An. nuneztovari by Plasmodium spp. (IR: 4.35%) and the annual entomological inoculation rate (30.31), indicated high vector exposure and local transmission risk. We did not detect Plasmodium-infected An. albimanus in this study. In general, low genetic and phenetic subdivision among the populations of both vectors was detected using a combination of phenotypic, genetic and environmental data. The results indicated high regional gene flow, although local environmental characteristics may be influencing the wing conformation differentiation and behavioral variation observed in An. albimanus. Furthermore, the population subdivision detected by microsatellite markers for both species by Bayesian genetic analysis provides a more accurate picture of the current genetic structure in comparison to previous studies. Finally, the biting behavior variation observed for both vectors among localities suggests the need for continuous malaria vector surveys covering the endemic region to implement the most effective integrated local control interventions.

Multiregional Sequencing Analysis Reveals Extensive Genetic Heterogeneity in Gastric Tumors from Latinos

Gastric cancer is a leading cause of cancer mortality and health disparities in Latinos. We evaluated gastric intratumoral heterogeneity using multiregional sequencing of >700 cancer genes in 115 tumor biopsies from 32 patients, 29 who were Latinos. Analyses focused on comparisons with The Cancer Genome Atlas (TCGA) and on mutation clonality, druggability, and signatures. We found that only approximately 30% of all mutations were clonal and that only 61% of the known TCGA gastric cancer drivers harbored clonal mutations. Multiple clonal mutations were found in new candidate gastric cancer drivers such as EYS, FAT4, PCDHA1, RAD50, EXO1, RECQL4, and FSIP2. The genomically stable (GS) molecular subtype, which has the worse prognosis, was identified in 48% of our Latino patients, a fraction that was >2.3-fold higher than in TCGA Asian and White patients. Only a third of all tumors harbored clonal pathogenic mutations in druggable genes, with most (93%) GS tumors lacking actionable clonal mutations. Mutation signature analyses revealed that, in microsatellite-stable (MSS) tumors, DNA repair mutations were common for both tumor initiation and progression, while tobacco, POLE, and inflammation signatures likely initiate carcinogenesis. MSS tumor progression was likely driven by aging- and aflatoxin-associated mutations, as these latter changes were usually nonclonal. In microsatellite-unstable tumors, nonclonal tobacco-associated mutations were common. Our study, therefore, contributed to advancing gastric cancer molecular diagnostics and suggests clonal status is important to understanding gastric tumorigenesis. Our findings of a higher frequency of a poor prognosis associated molecular subtype in Latinos and a possible new aflatoxin gastric cancer etiology also advance cancer disparities research.

SIGNIFICANCE

Our study contributes to advancing our knowledge of gastric carcinogenesis, diagnostics, and cancer health disparities.

Les misérables: a Parallel Between Antimicrobial Resistance and COVID-19 in Underdeveloped and Developing Countries

Purpose of Review

The COVID-19 pandemic has been responsible for more than 6.3 million deaths worldwide. During the pandemic, the indiscriminate use of antibiotics has increased, contributing to the spread of multidrug-resistant bacteria. In this review, we aim to determine the spread and impact of antibiotic treatments in patients with COVID-19, focusing on underdeveloped and developing countries.

Recent Findings

Meta-analysis revealed that bacterial co-infections and secondary infections are relatively rare in COVID-19 patients, corresponding to less than 20% of hospitalized patients. Even so, most of these patients have received antibiotic treatments.

Summary

This review discusses how the COVID-19 pandemic could increase the emergence of multidrug-resistant strains to currently available antibiotics. Initially, we discussed the spread and impact of multidrug resistance of ESKAPE pathogens associated with nosocomial infections and analyzed their risk of secondary infections in patients with COVID-19. Then we highlight three factors related to the spread of resistant bacteria during the current pandemic: overprescription of antibiotics followed by self-medication. Finally, we discussed the lack of availability of diagnostic tests to discriminate the etiologic agent of a disease. All these factors lead to inappropriate use of antibiotics and, therefore, to an increase in the prevalence of resistance, which can have devastating consequences shortly. The data compiled in this study underscore the importance of epidemiological surveillance of hospital isolates to provide new strategies for preventing and controlling infections caused by multidrug-resistant bacteria. In addition, the bibliographic research also highlights the need for an improvement in antibiotic prescribing in the health system.

Production of xylose through enzymatic hydrolysis of glucuronoarabinoxylan from brewers' spent grain

Xylose is an abundant bioresource for obtaining diverse chemicals and added-value products. The production of xylose from green alternatives like enzymatic hydrolysis is an important step in a biorefinery context. This research evaluated the synergism among four classes of hydrolytic purified enzymes-endo-1,4-β-xylanase, α-L-arabinofuranosidase, β-xylosidase, and α-D-glucuronidase-over hydrolysis of glucuronoarabinoxylan (GAX) obtained from brewers' spent grain (BSG) after alkaline extraction and ethanol precipitation. First, monosaccharides, uronic acids and glycosidic-linkages of alkaline extracted GAX fraction from BSG were characterized, after that different strategies based on the addition of one or two families of enzymes-endo-1,4-β-xylanase (GH10 and GH11) and α-L-arabinofuranosidase (GH43 and GH51)-cooperating with one β-xylosidase (GH43) and one α-D-glucuronidase (GH67) into enzymatic hydrolysis were assessed to obtain the best yield of xylose. The xylose release was monitored over time in the first 90 min and after a prolonged reaction up to 48 h of reaction. The highest yield of xylose was 63.6% (48 h, 40 ℃, pH 5.5), using a mixture of all enzymes devoid of α-L-arabinofuranosidase (GH43) family. These results highlight the importance of GH51 arabinofuranosidase debranching enzyme to allow a higher cleavage of the xylan backbone of GAX from BSG and their synergy with 2 endo-1,4-β-xylanase (GH10 and GH11), one β-xylosidase (GH43) and the inclusion of one α-D-glucuronidase (GH67) in the reaction system. Therefore, this study provides an environmentally friendly process to produce xylose from BSG through utilization of enzymes as catalysts.

Holistic approach to assess the association between the synergistic effect of physical activity, exposure to greenspace, and fruits and vegetable intake on health and wellbeing: Cross-sectional analysis of UK Biobank

Background

Urban agriculture has been shown to contribute to healthy lifestyle behaviors, such as increased fruit and vegetable intake and greater exposure to greenspaces and there is plenty of evidence linking these lifestyle behaviors to better health and wellbeing. However, most evidence relates to assessing one behavior at a time despite available epidemiological research showing how the combined effects of multiple behaviors are associated with health and wellbeing. This research aims to examine the association of the interactions between various lifestyle behaviors and exposures related to urban agriculture and health and wellbeing.

Methods

We used data from the UK Biobank baseline questionnaire (N~500, 000) to assess the association of two lifestyle behaviors (fruit and vegetable intake and physical activity) and greenspace exposure, with four health and wellbeing markers (blood pressure, BMI, self-health assessment, and self-reported loneliness) independently, and in combination. Associations between lifestyle behaviors, greenspace exposure, and the possible interactions with health and wellbeing were explored using general linear models (GLMs), adjusted for socio-demographic confounders including age, sex, educational qualifications, index of multiple deprivation, and ethnicity, and a lifestyle confounder: smoking status.

Results

After removing missing data, as well as participants who did not meet the inclusion criteria, the final study sample was n = 204,478. The results indicate that meeting recommended levels of the World Health Organization (WHO) for fruits and vegetable intake, and the advice from the UK Chief Medical Officer for physical activity, is linked to better health and wellbeing markers. We found that UK Biobank participants who lived in greener areas and were physically active were more likely to feel alone and think their health was poor. Participants who were physically active and met the recommended intake of fruits and vegetables were more likely to have healthy blood pressure, feel less lonely, and rate their health as good. Evidence of three-way interactions was weak, and mostly was not associated with the health and wellbeing markers assessed here.

Conclusion

Taken in combination, healthy diets, physical activity and exposure to greenspaces are associated with health and wellbeing. In some cases, these effects are synergistic, indicating associations above and beyond the mere additive effect of the behaviors considered independently. Promoting such behaviors together, for example, through urban agriculture, is therefore more likely to generate greater public health changes than if they are promoted through independent policies and programs. Inter-relationships between these pathways and different health and wellbeing markers, however, are complex, and require further investigation to understand optimal environments and conditions for urban health promotion.

New microsatellite markers for the shallow coral Madracis auretenra from the Caribbean

Coral reefs species represent one-third of all marine species described in the ocean. They are also responsible for providing habitat and support to different species. Recently, Caribbean coral reefs ecosystems have suffered an alarming decrease in their populations as a result of overexploitation. Madracis auretenra in particular, is a widespread shallow coral in marine protected areas (MPAs) of the Caribbean. Due to the important role of MPAs as a biodiversity conservation tool, this species can be used as a model to estimate its dispersion/migration among Caribbean reefs through the use of informative genetic markers (microsatellites) specifically designed for it. Seventeen new polymorphic microsatellites markers for M. auretenra were developed and tested in 330 samples from Colombia, Guatemala, Curacao and Barbados. The gene diversity (1-D) ranged from 0.482 to 0.903, while the evenness ranged from 0.456 to 0.884 after clone removal. The expected heterozygosity (He) ranged from 0.347 to 0.742, while the observed heterozygosity (Ho) ranged from 0.078 to 0.578. The specificity of our microsatellites shows the potential use of these markers in a-posteriori analysis to detect population structure at different spatial scales, where M. auretenra is reported.

Gene expression profiling identifies candidate biomarkers for new latent tuberculosis infections. A cohort study

Objective

To determine the gene expression profile in individuals with new latent tuberculosis infection (LTBI), and to compare them with people with active tuberculosis (TB) and those exposed to TB but not infected.

Design

A prospective cohort study. Recruitment and follow-up were conducted between September 2016 to December 2018. Gene expression and data processing and analysis from April 2019 to April 2021.

Setting

Two male Colombian prisons.

Participants

15 new tuberculin skin test (TST) converters (negative TST at baseline that became positive during follow-up), 11 people that continued with a negative TST after two years of follow-up, and 10 people with pulmonary ATB.

Main outcome measures

Gene expression profile using RNA sequencing from PBMC samples. The differential expression was assessed using the DESeq2 package in Bioconductor. Genes with |logFC| >1.0 and an adjusted p-value < 0.1 were differentially expressed. We analyzed the differences in the enrichment of KEGG pathways in each group using InterMiner.

Results

The gene expression was affected by the time of incarceration. We identified group-specific differentially expressed genes between the groups: 289 genes in people with a new LTBI and short incarceration (less than three months of incarceration), 117 in those with LTBI and long incarceration (one or more years of incarceration), 26 in ATB, and 276 in the exposed but non-infected individuals. Four pathways encompassed the largest number of down and up-regulated genes among individuals with LTBI and short incarceration: cytokine signaling, signal transduction, neutrophil degranulation, and innate immune system. In individuals with LTBI and long incarceration, the only enriched pathway within up-regulated genes was Emi1 phosphorylation.

Conclusions

Recent infection with MTB is associated with an identifiable RNA pattern related to innate immune system pathways that can be used to prioritize LTBI treatment for those at greatest risk for developing active TB.

Uncovering anthocyanin diversity in potato landraces (Solanum tuberosum L. Phureja) using RNA-seq

Potato (Solanum tuberosum L.) is the third largest source of antioxidants in the human diet, after maize and tomato. Potato landraces have particularly diverse contents of antioxidant compounds such as anthocyanins. We used this diversity to study the evolutionary and genetic basis of anthocyanin pigmentation. Specifically, we analyzed the transcriptomes and anthocyanin content of tubers from 37 landraces with different colorations. We conducted analyses of differential expression between potatoes with different colorations and used weighted correlation network analysis to identify genes whose expression is correlated to anthocyanin content across landraces. A very significant fraction of the genes identified in these two analyses had annotations related to the flavonoid-anthocyanin biosynthetic pathway, including 18 enzymes and 5 transcription factors. Importantly, the causal genes at the D, P and R loci governing anthocyanin accumulation in potato cultivars also showed correlations to anthocyanin production in the landraces studied here. Furthermore, we found that 60% of the genes identified in our study were located within anthocyanin QTLs. Finally, we identified new candidate enzymes and transcription factors that could have driven the diversification of anthocyanins. Our results indicate that many anthocyanins biosynthetic genes were manipulated in ancestral potato breeding and can be used in future breeding programs.

Type 1 and type 2 diabetes mellitus: Clinical outcomes due to COVID-19. Protocol of a systematic literature review

Introduction

Diabetes has been associated with an increased risk of complications in patients with COVID-19. Most studies do not differentiate between patients with type 1 and type 2 diabetes, which correspond to two pathophysiological distinct diseases that could represent different degrees of clinical compromise.

Objective

To identify if there are differences in the clinical outcomes of patients with COVID-19 and diabetes (type 1 and type 2) compared to patients with COVID-19 without diabetes.

Methods

Observational studies of patients with COVID-19 and diabetes (both type 1 and type 2) will be included without restriction of geographic region, gender or age, whose outcome is hospitalization, admission to intensive care unit or mortality compared to patients without diabetes. Two authors will independently perform selection, data extraction, and quality assessment, and a third reviewer will resolve discrepancies. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes.

Expected results

Update the evidence regarding the risk of complications in diabetic patients with COVID-19 and in turn synthesize the information available regarding type 1 and type 2 diabetes mellitus, to provide keys to a better understanding of the pathophysiology of diabetics.

Systematic review registry

This study was registered at the International Prospective Registry for Systematic Reviews (PROSPERO)—CRD42021231942.