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Over the past decades, Colombia has suffered complex social problems related to illicit crops, including forced displacement, violence, and environmental damage, among other consequences for vulnerable populations. Considerable effort has been made in the regulation of illicit crops, predominantly Cannabis sativa, leading to advances such as the legalization of medical cannabis and its derivatives, the improvement of crops, and leaving an open window to the development of scientific knowledge to explore alternative uses. It is estimated that C. sativa can produce approximately 750 specialized secondary metabolites. Some of the most relevant due to their anticancer properties, besides cannabinoids, are monoterpenes, sesquiterpenoids, triterpenoids, essential oils, flavonoids, and phenolic compounds. However, despite the increase in scientific research on the subject, it is necessary to study the primary and secondary metabolism of the plant and to identify key pathways that explore its great metabolic potential. For this purpose, a genome-scale metabolic reconstruction of C. sativa is described and contextualized using LC-QTOF-MS metabolic data obtained from the leaf extract from plants grown in the region of Pesca-Boyaca, Colombia under greenhouse conditions at the Clever Leaves facility. A compartmentalized model with 2101 reactions and 1314 metabolites highlights pathways associated with fatty acid biosynthesis, steroids, and amino acids, along with the metabolism of purine, pyrimidine, glucose, starch, and sucrose. Key metabolites were identified through metabolomic data, such as neurine, cannabisativine, cannflavin A, palmitoleic acid, cannabinoids, geranylhydroquinone, and steroids. They were analyzed and integrated into the reconstruction, and their potential applications are discussed. Cytotoxicity assays revealed high anticancer activity against gastric adenocarcinoma (AGS), melanoma cells (A375), and lung carcinoma cells (A549), combined with negligible impact against healthy human skin cells.

Late blight disease, caused by the plant pathogen Phytophthora infestans, is one of the major threats for tomato and potato crops. Monitoring the populations of P. infestans is important to determine if there are changes in the sensitivity to fungicides and host preference. In this study, microsatellite markers and mitochondrial haplotypes were used to assess the genotype of isolates of P. infestans collected from tomato and potato plants in Colombia. Furthermore, sensitivity to the three fungicides cymoxanil (penetrant fungicide), mefenoxam, and fluopicolide (systemic fungicides), and tomato–potato host preference, were evaluated. Mitochondrial haplotyping showed that isolates collected on tomato were from the genetic groups Ia and Ib, while isolates collected on potatoes belonged to group IIa. Microsatellite analyses showed that isolates from tomato form two groups, including the Ib mitochondrial haplotype (which is genetically close to the US-1 clonal lineage) and the Ia haplotype (related to the EC-3 lineage), whereas Colombian isolates from potato formed a separate group. Furthermore, differences in sensitivity to fungicides were observed. Eighty-one percent of the isolates tested were resistant to mefenoxam with an EC50 >10 μg ml−1. Forty-two percent of the isolates showed an intermediate resistance to cymoxanil. The EC50 values ranged between 1 and 10 μg ml−1. For fluopicolide, 90% of the isolates were sensitive, with EC50 −1. Host preference assays showed that potato isolates infected both host species. Thus, isolates that infect potatoes may pose a risk for tomato crops nearby.

Even though it is widely held that the theory of evolution is one of the pillars of the biological sciences, as we begin the third decade of the twenty-first century, it is alarming how little we know about science, technology, engineering, and mathematics (STEM) majors and non-STEM majors’ misconceptions about evolution in countries such as Brazil, Chile, Colombia, and Greece, to name a few. The situation is even more complicated if we acknowledge that contemporary educational approaches (e.g., student-centered learning) mean that students’ misconceptions are one of the multiple aspects that influence the construction of meaningful learning. Here, we present a picture of Colombian STEM/non-STEM majors’ misconceptions about evolution. Participants were 547 students from different STEM/non-STEM majors (278 females and 269 males, 16–24 years old). During 5 years (10 academic semesters), data were collected from students’ responses to an 11-item questionnaire administered in a Colombian university. We hypothesized that the academic semester within these 5 years in which each student completed the instrument as well as respondents’ age, gender, and/or major may influence their misconceptions about evolution. Results reveal that participants had a moderate understanding of evolution. Also, we found a limited understanding of microevolution among participants. Furthermore, cross-sectional analyses of differences in undergraduates’ responses across demographic variables showed that despite apparent differences, these were not reliable since the differences were not statistically significant. Implications for evolution education are discussed.

Phytophthora infestans, the causal agent of late blight disease of potatoes, is mainly controlled by the use of fungicides. Isolates that are resistant to commonly used fungicides have been reported. Also, several studies show that originally mefenoxam-sensitive isolates acquire resistance to this fungicide when exposed to sublethal concentrations. This phenomenon, termed “mefenoxam-acquired resistance,” has been observed in different Phytophthora species and seems to be unique to mefenoxam. In this study, we aimed to elucidate the molecular mechanism mediating this type of resistance as well as a possible regulatory process behind it. A combination of computational analyses and experimental approaches was used to identify differentially expressed genes with a potential association to the phenomenon. These genes were classified into seven functional groups. Most of them seem to be associated with a pleiotropic drug resistance (PDR) phenotype, typically involved in the expulsion of diverse metabolites, drugs, or other substances out of the cell. Despite the importance of RNA Polymerase I for the constitutive resistance of P. infestans to mefenoxam, our results indicate no clear interaction between this protein and the acquisition of mefenoxam resistance. Several small non-coding RNAs were found to be differentially expressed and specifically related to genes mediating the PDR phenotype, thus suggesting a possible regulatory process. We propose a model of the molecular mechanisms acting within the cell when P. infestans acquires resistance to mefenoxam after exposed to sublethal concentrations of the fungicide. This study provides important insights into P. infestans’ cellular and regulatory functionalities.

This manuscript builds on a novel, automatic, freely-available Bayesian approach to extract information in abstracts and titles to classify research topics by quartile. This approach is demonstrated for all N= 149,129 ISI-indexed publications in biological sciences journals during 2017. A Bayesian multinomial inverse regression approach is used to extract rankings of topics without the need of a pre-defined dictionary. Bigrams are used for extraction of research topics across manuscripts, and rankings of research topics are constructed by quartile. Worldwide and local results (e.g., comparison between two peer/aspirational research institutions in Colombia) are provided, and differences are explored both at the global and local levels. Some topics persist across quartiles, while the relevance of others is quartile-specific. Challenges in sustainable development appear as more prevalent in top quartile journals across institutions, while the two Colombian institutions favour plant and microorganism research. This approach can reduce information inequities, by allowing young/incipient researchers in biological sciences, especially within lower income countries or universities with limited resources, to freely assess the state of the literature and the relative likelihood of publication in higher impact journals by research topic. This can also serve institutions of higher education to identify missing research topics and areas of competitive advantage.

Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at local and national scales revealing a geographical genetic structure with temporal variations. A global epidemiology analysis of its causal agent Xanthomonas phaseoli pv. manihotis (Xpm) is needed to better understand the expansion of the disease for improving the monitoring of CBB. We targeted new tandem repeat (TR) loci with large repeat units, i.e. minisatellites, that we multiplexed in a scheme of Multi-Locus Variable number of TR Analysis (MLVA-8). This genotyping scheme separated 31 multilocus haplotypes in three clusters of single-locus variants and a singleton within a worldwide collection of 93 Xpm strains isolated over a period of fifty years. The major MLVA-8 cluster 1 grouped strains originating from all countries, except the unique Chinese strain. On the contrary, all the Xpm strains genotyped using the previously developed MLVA-14 microsatellite scheme were separated as unique haplotypes. We further propose an MLVA-12 scheme which takes advantage of combining TR loci with different mutation rates: the eight minisatellites and four faster evolving microsatellite markers, for global epidemiological surveillance. This MLVA-12 scheme identified 78 haplotypes and separated most of the strains in groups of double-locus variants (DLV) supporting some phylogenetic relationships. DLV groups were subdivided into closely related clusters of strains most often sharing the same geographical origin and isolated over a short period, supporting epidemiological relationships. The main MLVA-12 DLV group#1 was composed by strains from South America and all the African strains. The MLVA-12 scheme combining both minisatellite and microsatellite loci with different discriminatory power is expected to increase the accuracy of the phylogenetic signal and to minimize the homoplasy effects. Further investigation of the global epidemiology of Xpm will be helpful for a better control of CBB worldwide.

As we begin the third decade of the twenty-first century, argument and debate are not habitual practices of university science education. This can be explained by the hegemony of instructor-centered traditional approaches in many of these practices. The Covid-19 pandemic has not only pushed university education online but also seems to provide an unforeseen opportunity to develop deep educational transformations. Here, we report on the case of a university online science course that, because of the Covid-19 crisis, used online verbal argumentative interaction (OVAI) to provide students with explicit opportunities to co-construct reason-based and/or evidence-based arguments and counterarguments in an undergraduate-centered science learning environment. The written arguments and counterarguments co-constructed by forty students (20 females and 20 males, 19–24 years old) during OVAI sessions were analyzed to determine their quality. Also, students’ opinions about the use of OVAI in times of Covid-19 were documented. The results indicate that the students co-constructed high-quality arguments and counterarguments in the OVAI sessions. Most importantly, participants showed positive impressions about the use of OVAI in university online science education. The outcomes carry important educational implications considering the growing university online science courses in the pandemic and post-pandemic eras.

The identification and the evaluation of arguments are fundamental elements of critical thinking. However, the explicit promotion of these elements is virtually absent from university science courses. Much of the reason for this is that in most universities, across nearly all disciplines, instructors are required to see the conceptual content coverage of the syllabus as a priority. Moreover, lack of preparation and the fact that critical thinking activities are time-consuming rapidly reduce the interest of many instructors to include them in their courses. Here, we describe the use of a dialogue-based critical thinking classroom scenario (CTCS). The study used a mixed-methods approach with both quantitative and qualitative analyses of questionnaire responses. One hundred and seventeen undergraduates (73 females; 44 males; ages 16–24 years), enrolled in an introductory science course in Colombia, were asked to identify and evaluate arguments regarding a dialogue between two scientists who explore the controversial question of whether or not the concept of race is applicable to humans. It was found that the dialogue-based CTCS provided students with opportunities to identify and evaluate arguments both for and against the question and to make informed decisions about whether or not the concept of race in humans is biologically meaningful. Moreover, analyses of responses to closed-ended and open-ended questions revealed that more than half the participants were able to evaluate arguments in a fair-minded way. Practical implications for the cultivation of critical thinking skills in higher education and further research are discussed.

Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.

The aim of this research is to develop burger patties from fungal protein. For this purpose, to maximize fungal biomass production, an optimization of the growth medium was initially carried out by testing different carbon sources and its proportion with nitrogen. Subsequently, for the design of the fungal patties, the effect of different flours, binders, and colorants on the properties of texture, water retention capacity, and color were tested, with a traditional animal-based burger patty as a control. Based on the first results, two optimal formulations were chosen and analyzed using an electronic tongue with the same control as reference. The conditions that maximized biomass production were 6 days of incubation and maltodextrin as a carbon source at a concentration of 90 g/L. In terms of product design, the formulation containing quinoa flour, carboxymethylcellulose, and beet extract was the most similar to the control. Finally, through shelf-life analysis, it was determined that the physical characteristics of the fungal meat substitute did not change significantly in an interval of 14 days. However, the product should be observed for a longer period. In addition, by the proximate analysis, it was concluded that fungal patties could have nutritional claims such as rich content in protein and fiber.

Traditionally, cognitive skills in mathematics and language have been described as key indicators for success. However, the social, technological, and economic changes that have occurred in the 21st century have made critical thinking, creativity, communication, and collaboration, key competences to face the challenges of a rapidly changing world. In this study, we developed a Computational Thinking (CT) curriculum based on student-centred pedagogical strategies to enhance these four competences. This curriculum was designed under the socio-cultural vision of learning, in which individuals interact in communities to build significant knowledge. An embedded mixed-method approach was implemented to evaluate improvements in competence development both in quantitative and qualitative ways in a sample of 42 students. The results indicate an encouraging increase in skills related to the competences of interest thanks to the implementation of a student-centred pedagogical curriculum based on CT. Additionally, by designing the curriculum under socio-cultural ideas of education the results show that the students and the teacher were able to form a community to facilitate teaching and learning.

Recent studies show that English as the medium of instruction seems impractical and ineffective in countries where English is the second or foreign language. The situation becomes even more complic...

The aim of this research is to develop burger patties from fungal protein. For this purpose, to maximize fungal biomass production, an optimization of the growth medium was initially carried out by testing different carbon sources and its proportion with nitrogen. Subsequently, for the design of the fungal patties, the effect of different flours, binders, and colorants on the properties of texture, water retention capacity, and color were tested, with a traditional animal-based burger patty as a control. Based on the first results, two optimal formulations were chosen and analyzed using an electronic tongue with the same control as reference. The conditions that maximized biomass production were 6 days of incubation and maltodextrin as a carbon source at a concentration of 90 g/L. In terms of product design, the formulation containing quinoa flour, carboxymethylcellulose, and beet extract was the most similar to the control. Finally, through shelf-life analysis, it was determined that the physical characteristics of the fungal meat substitute did not change significantly in an interval of 14 days. However, the product should be observed for a longer period. In addition, by the proximate analysis, it was concluded that fungal patties could have nutritional claims such as rich content in protein and fiber.

Background The use of respiratory devices can mitigate the spread of diseases such as COVID-19 in community settings. We aimed to determine the effectiveness of closed face shields with surgical face masks to prevent SARS-CoV-2 transmission in working adults during the COVID-19 pandemic in Bogotá, Colombia. Methods An open-label non-inferiority randomized controlled trial that randomly assigned participants to one of two groups: the intervention group was instructed to wear closed face shields with surgical face masks, and the active control group was instructed to wear only surgical face masks. The primary outcome was a positive reverse transcription polymerase chain reaction test, IgG/IgM antibody test for SARS-CoV-2 detection, or both during and at the end of the follow-up period of 21 days. The non-inferiority limit was established at − 5%. Results A total of 316 participants were randomized, 160 participants were assigned to the intervention group and 156 to the active control group. In total, 141 (88.1%) participants in the intervention group and 142 (91.0%) in the active control group completed the follow-up. Primary outcome: a positive SARS-CoV-2 test result was identified in one (0.71%) participant in the intervention group and three (2.1%) in the active control group. In the intention-to-treat analysis, the absolute risk difference was − 1.40% (95% CI [− 4.14%, 1.33%]), and in the per-protocol analysis, the risk difference was − 1.40% (95% CI [− 4.20, 1.40]), indicating non-inferiority of the closed face shield plus face mask (did not cross the non-inferiority limit). Conclusions The use of closed face shields and surgical face masks was non-inferior to the surgical face mask alone in the prevention of SARS-CoV-2 infection in highly exposed groups. Settings with highly active viral transmission and conditions such as poor ventilation, crowding, and high mobility due to occupation may benefit from the combined use of masks and closed face shields to mitigate SARS-CoV-2 transmission. Trial registration ClinicalTrials.gov NCT04647305. Registered on November 30, 2020

Covid-19 literacy, induced by the coronavirus disease (2019), is characterized as the understanding of Covid-19 as well as informed decisions based upon this understanding. This type of literacy is closely related to health literacy, scientific literacy, and scientific media literacy. It may be obvious to say that Covid-19 literacy is a key factor for governments to effectively manage the Covid-19 transition. However, lack of literature exists about Covid-19 literacy among university students. Therefore, the current study aimed to determine the Covid-19 literacy level among 4168 students from a Colombian university. The data were derived from students’ responses to a 25–item anonymous online self-reporting questionnaire. We found that 21–25-year age group, graduate students, students enrolled prior to 2015, and medical students had a significantly higher mean score. Moreover, the Internet (86.8%) was the most popular source of information from which participants gained most information regarding Covid-19. Furthermore, 58.5% of the participants considered health workers as a source that can provide accurate information. Most importantly, the findings reveal the students’ knowledge about (1) the role of an eventual process of vaccination, (2) the test currently used as diagnostic for Covid-19, and (3) the fatality rate, three aspects of Covid-19 literacy that deserve more attention. The findings provide a useful basis for the formulation of policies and concrete actions in improving Covid-19 literacy.

Vascular wilt caused by Fusarium oxysporum is one of the most devastating diseases that affect cape gooseberry plants. In order to contribute to its management, the objective of this work was to evaluate the plant activator acibenzolar-S-methyl (ASM) as a reducer of vascular wilt symptoms in cape gooseberry. Sixty-day-old plants were sprayed twice with eleven concentrations of ASM ranging from 10 to 200 mg L−1, respectively. The phytotoxic effect was assessed for a period of eight weeks. The appearance of symptoms such as stunting, a decrease in the shoot and roots dry weight, leaf malformation and defoliation was associated with the ASM concentration. The two lowest concentrations of ASM assessed (10 and 20 mg L−1) were selected to evaluate their effectiveness against F. oxysporum in greenhouse conditions. Both concentrations reduced vascular colonization and necrosis generated by seven isolates of F. oxysporum, and in consequence, the area under the disease progress curve (AUDPC) decreased significantly during the eight weeks of evaluation. These results suggest that ASM induces resistance to F. oxysporum in cape gooseberry under greenhouse conditions.

La mayoría de las encuestas serológicas específicas de la comunidad para anticuerpos contra el SARS-CoV-2 se han realizado en trabajadores e instituciones de atención médica. En este estudio, se evaluaron anticuerpos IgG específicos del virus en personas que trabajan en un campus universitario en Bogotá, Colombia. Nuestro objetivo era determinar la exposición previa al SARS-CoV-2 en los asistentes al campus durante el cierre de la ciudad. Un total de 237 personas, incluidas 93 mujeres y 144 hombres, fueron evaluadas mediante detección quimioluminiscente de proteína IgG anti-N-viral entre noviembre y diciembre de 2020. Hubo 32 personas positivas, es decir, una seroprevalencia del 13,5% (10 mujeres y 22 hombres) en su mayoría asintomáticos (68,75%); identificamos tres grupos de individuos seropositivos. Solo 13 de los individuos seropositivos tenían una detección positiva previa de ARN del SARS-CoV-2 por RT-qPCR realizada en promedio 91 días antes de la prueba serológica. Los seropositivos no procedían de los municipios con mayor porcentaje de casos de SARS-CoV-2 en la ciudad. La encuesta se realizó después del primer pico de transmisión del SARS-CoV-2 en la ciudad y antes de la preparación para reabrir el campus para estudiantes en 2021, lo que demuestra una baja seroprevalencia en un alto porcentaje de individuos asintomáticos. Estos resultados ayudarán a evaluar algunas de las estrategias establecidas para controlar la propagación del virus en el campus u otras comunidades similares. Palabras clave: Coronavirus; SARS-CoV-2; COVID-19; serología. La encuesta se realizó después del primer pico de transmisión del SARS-CoV-2 en la ciudad y antes de la preparación para reabrir el campus para estudiantes en 2021, lo que demuestra una baja seroprevalencia en un alto porcentaje de individuos asintomáticos. Estos resultados ayudarán a evaluar algunas de las estrategias establecidas para controlar la propagación del virus en el campus u otras comunidades similares. Palabras clave: Coronavirus; SARS-CoV-2; COVID-19; serología. La encuesta se realizó después del primer pico de transmisión del SARS-CoV-2 en la ciudad y antes de la preparación para reabrir el campus para estudiantes en 2021, lo que demuestra una baja seroprevalencia en un alto porcentaje de individuos asintomáticos. Estos resultados ayudarán a evaluar algunas de las estrategias establecidas para controlar la propagación del virus en el campus u otras comunidades similares. Palabras clave: Coronavirus; SARS-CoV-2; COVID-19; serología. Most community-specific serological surveys for SARS-CoV-2 antibodies have been performed in healthcare workers and institutions. In this study, IgG antibodies specific to the virus were evaluated in individuals working at a university campus in Bogotá, Colombia. Our aim was to determine previous exposure to SARS-CoV-2 in those attending the campus during city lockdown. A total of 237 individuals including 93 women and 144 men were evaluated using chemiluminescent detection of IgG anti-N-viral protein between November and December 2020. There were 32 positive individuals, i.e., a seroprevalence of 13.5% (10 women and 22 men) mostly asymptomatic (68.75%); we identified three clusters of seropositive individuals. Only 13 of the seropositive individuals had previous positive detection of SARS-CoV-2 RNA by RT-qPCR performed on average 91 days before the serological test. Seropositive individuals did not come from the boroughs with higher percentages of SARS-CoV-2 cases in the city. The survey was carried out after the first peak of SARS-CoV-2 transmission in the city and before the preparedness to reopen the campus for students in 2021, which demonstrates a low seroprevalence in a high percentage of asymptomatic individuals. These results will help to evaluate some of the strategies stablished to control virus spread on the campus or other similar communities. Key words: Coronavirus; SARS-CoV-2; Covid-19; serology.

A well-informed populace is vitally important for the proper functioning of democracy. Media news articles constitute an essential means by which the public comes into contact with scientific issues. However, not all of the scientific information presented in news articles is trustworthy or accurate. Naturally, the situation becomes more complicated because most university science departments spend little empirical effort considering how to foster undergraduates’ scientific media literacy (SML). This article discusses the effect of a teaching-learning sequence (TLS) in (1) providing undergraduates with opportunities to explicitly reflect on the ways in which news articles promote the public (mis)understanding of science and (2) engaging them in argumentative classroom interactions (such as debates). It examines the written and oral arguments produced by 115 undergraduates (62 females and 53 males, 17–23 years old) in Colombia during a complete TLS supervised by the same instructor. The data used in this analysis were collected from students’ written responses and audio recordings. The findings suggest that the TLS can be a good start to show undergraduates some of the different ways in which news articles promote the public (mis)understanding of science and, thus, enrich their SML. The study contributes to the development of a research-based university science education that can inform the design of the SML curriculum for higher education.

Two morphologically similar halophilic strains, named USBA 874 and USBA 960T, were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. Both isolates had non-spore-forming, Gram-stain-negative and motile cells that grew aerobically. The strains grew optimally at 30 °C, pH 7.0 and with 25 % NaCl (w/v). The isolates showed almost identical 16S rRNA gene sequences (99.0 % similarity). The predominant quinones of USBA-960T were Q-8, Q-7 and Q-9. The major cellular fatty acids were C19 : 0 cyclo ω8c, C18 : 0 and C16 : 0. According to 16S rRNA gene sequencing, the closest phylogenetic relatives are Salinisphaera species (similarity between 93.6 and 92.3 %), Abyssibacter profundi OUC007T (88.6 %) and Oceanococcus atlanticus 22II-S10r2T (88.7 %). In addition, the result of genome blast distance phylogeny analysis between strains USBA 874 and USBA 960T, Salinisphaera halophila (YIM 95161T), Salinisphaera shabanensis (E1L3AT), Salinisphaera orenii (MK-B5T) and Salinisphaera japonica (YTM-1T) was 18.5 %. Other in silico species delineation analyses also showed low identity such as ANIb and ANIm values (T revealed a genome size of 2.47 Mbp and a G+C content of 59.71 mol%. Phylogenetic analysis of strains USBA 874 and USBA 960T indicated that they formed a different lineage within the family Salinisphaeraceae . Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness values, along with identity at whole genome level, it can be concluded that strains USBA 960T and USBA 874 represent a novel genus of the family Salinisphaeraceae and the name Salifodinibacter halophilus gen. nov., sp. nov. is proposed. The type strain is USBA 960T (CMPUJ U095T=CECT 30006T).

Some species of fusaria are well-known pathogens of humans, animals and plants. Fusarium oxysporum and Neocosmospora solani (formerly Fusarium solani) cause human infections that range from onychomycosis or keratitis to severe disseminated infections. In general, these infections are difficult to treat due to poor therapeutic responses in immunocompromised patients. Despite that, little is known about the molecular mechanisms and transcriptional changes responsible for the antifungal resistance in fusaria. To shed light on the transcriptional response to antifungals, we carried out the first reported high-throughput RNA-seq analysis for F. oxysporum and N. solani that had been exposed to amphotericin B (AMB) and posaconazole (PSC). We detected significant differences between the transcriptional profiles of the two species and we found that some oxidation-reduction, metabolic, cellular and transport processes were regulated differentially by both fungi. The same was found with several genes from the ergosterol synthesis, efflux pumps, oxidative stress response and membrane biosynthesis pathways. A significant up-regulation of the C-22 sterol desaturase (ERG5), the sterol 24-C-methyltransferase (ERG6) gene, the glutathione S-transferase (GST) gene and of several members of the major facilitator superfamily (MSF) was demonstrated in this study after treating F. oxysporum with AMB. These results offer a good overview of transcriptional changes after exposure to commonly used antifungals, highlights the genes that are related to resistance mechanisms of these fungi, which will be a valuable tool for identifying causes of failure of treatments.

Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control.

Phenotypic diversity among individuals defines the potential for evolutionary selection in a species. Phytophthora infestans epidemics are generally thought to be favored by moderate to low temperatures, but temperatures in many locations worldwide are expected to rise as a result of global climate change. Thus, we investigated variation among individuals of P. infestans for relative growth at different temperatures. Isolates of P. infestans came from three collections: (i) individual genotypes recently dominant in the United States, (ii) recently collected individuals from Central Mexico, and (iii) progeny of a recent sexual recombination event in the northeastern United States. In general, these isolates had optimal mycelial growth rates at 15 or 20°C. However, two individuals from Central Mexico grew better at higher temperatures than did most others and two individuals grew relatively less at higher temperatures than did most others. The isolates were also assessed for mefenoxam sensitivity and mating type. Each collection contained individuals of diverse sensitivities to mefenoxam and individuals of the A1 and A2 mating type. We then searched for genomic regions associated with phenotypic diversity using genotyping-by-sequencing. We found one single nucleotide polymorphism (SNP) associated with variability in mycelial growth at 20°C, two associated with variability in mycelial growth at 25°C, two associated with sensitivity to mefenoxam, and one associated with mating type. Interestingly, the SNPs associated with mefenoxam sensitivity were found in a gene-sparse region, whereas the SNPs associated with growth at the two temperatures and mating type were found both at more gene-dense regions.

Host–pathogen interactions of a new species of Phytophthora, causal agent of late blight of tree tomato (Solanum betaceum Cav.), identified as Phytophthora betacei, were investigated with four different cultivars. Thirty-six P. betacei isolates, collected from southern Colombia between 2008 and 2009, were used to inoculate common tree tomato cultivars, Común, Híbrido, Injerto, and Holandés. Data on incubation and latent periods as well as infection efficiency, lesion development, and total sporulation were collected via detached leaf assays. Significant differences in susceptibility, based on the parameters measured, were observed. Común was the most susceptible cultivar, followed by Injerto, Híbrido, and Holandés. The mean incubation period was lowest for Común at 125.6 h post-inoculation (hpi) and highest for Híbrido at 139.4 hpi. No significant differences in latent period were observed. All 36 isolates produced necrotic lesions on Común, and 33, 24, and 21 caused infection on Injerto, Híbrido, and Holandés, respectively. Two isolates were able to cause infection only on Común, and 13 isolates were able to infect all four cultivars. Infection efficiency was significantly higher for the cultivar Común, followed by Injerto, Híbrido, and Holandés. Average lesion size was larger on Común than on any other cultivar. An inverse relationship of lesion size and total sporulation was observed. Común had significantly lower total sporulation than Híbrido and Holandés, which had the smallest average lesion sizes. These data show variation in pathogenicity of P. betacei isolates, under controlled conditions, and differential susceptibility of four distinct S. betaceum cultivars.

Phytophthora infestans is the causal agent of late blight disease of potatoes and tomatoes. This disease causes devastating economic losses each year, and control is mainly achieved by the use of fungicides. Unfortunately, populations of P. infestans resistant to fungicides have been documented. Furthermore, studies have reported that sensitive isolates to the phenylamide fungicide, mefenoxam, become less sensitive in vitro after a single passage through sublethal concentrations of fungicide-amended medium. The first objective of this study was to investigate if isolates of P. infestans are capable of acquiring resistance to two additional systemic fungicides, fluopicolide (benzamide) and cymoxanil (cyanoacetamide-oxime). In contrast to the situation with mefenoxam, exposure of isolates to sublethal concentrations of fluopicolide and cymoxanil did not induce reduced sensitivity to these two fungicides. The second objective was to assess if reduced sensitivity to mefenoxam could occur in naturally sensitive isolates of other Phytophthora species and of Phytopythium sp., another oomycete plant pathogen. All Phytophthora spp. assessed (P. infestans, P. betacei, and P. pseudocryptogea) as well as Phytopythium sp. acquired resistance to mefenoxam after previous exposure through medium containing 1 µg ml−1 of mefenoxam. Interestingly, isolate 66 of Phytopythium sp. and the isolate of P. pseudocryptogea tested do not seem to be acquiring resistance to mefenoxam after exposure to medium containing 5 µg ml−1 of this fungicide. The tested isolates of P. palmivora and P. cinnamomi were extremely sensitive to mefenoxam, and thus it was not possible to perform a second transfer to access acquisition of resistance to this fungicide.

Continued waves, new variants, and limited vaccine deployment mean that SARS-CoV-2 tests remain vital to constrain the COVID-19 pandemic. Affordable, point-of-care (PoC) tests allow rapid screening in non-medical settings. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is an appealing approach. A crucial step is to optimize testing in low/medium resource settings. Here, we optimized RT-LAMP for SARS-CoV-2 and human β-actin, and tested clinical samples in multiple countries. “TTTT” linker primers did not improve performance, and while guanidine hydrochloride, betaine and/or Igepal-CA-630 enhanced detection of synthetic RNA, only the latter two improved direct assays on nasopharygeal samples. With extracted clinical RNA, a 20 min RT-LAMP assay was essentially as sensitive as RT-PCR. With raw Canadian nasopharygeal samples, sensitivity was 100% (95% CI: 67.6% - 100%) for those with RT-qPCR Ct values ≤ 25, and 80% (95% CI: 58.4% - 91.9%) for those with 25 < Ct ≤ 27.2. Highly infectious, high titer cases were also detected in Colombian and Ecuadorian labs. We further demonstrate the utility of replacing thermocyclers with a portable PoC device (FluoroPLUM). These combined PoC molecular and hardware tools may help to limit community transmission of SARS-CoV-2.

Late blight disease, caused by the plant pathogen

La mayoría de las evaluaciones serológicas comunitarias específicas para los anticuerpos de SARSCoV-2 se han realizado en instituciones y en trabajadores de la salud. En este estudio, se evaluaron anticuerpos IgG específicos para el virus en personas que trabajaban en una universidad de Bogotá, Colombia. El objetivo fue determinar la exposición previa a SARS-CoV-2 en los asistentes al campus durante el cierre de la ciudad. Se evaluaron 237 personas, incluidas 93 mujeres y 144 hombres, mediante la detección quimioluminiscente de anticuerpos IgG anti-proteína N viral entre noviembre y diciembre de 2020. Se encontraron 32 individuos positivos, es decir, una seroprevalencia del 13,5 % (10 mujeres y 22 hombres), en su mayoría asintomáticos (68,75 %) y se determinaron tres grupos de individuos seropositivos. Solo 13 de los individuos serorreactivos tenían una detección positiva previa del ARN del SARS-CoV-2 mediante RT-qPCR realizada, en promedio, 91 días antes de la prueba serológica. Los individuos seropositivos no provenían de las localidades con los porcentajes más altos de casos de SARS-CoV-2 en la ciudad. La encuesta se realizó después del primer pico de transmisión del SARS-CoV-2 en la ciudad y antes de la preparación para la reapertura del campus a estudiantes en el 2021, y demostró una baja seroprevalencia con un alto procentaje de asintomáticos. Estos resultados ayudarán a evaluar algunas de las estrategias establecidas para controlar la propagación del virus en instituciones educativas u otras comunidades similares.

The 2016 Peace Agreement has increased access to Colombia’s unique ecosystems, which remain understudied and increasingly under threat. The Colombian government has recently announced its National Bioeconomic Strategy (NBS), founded on the sustainable characterization, management, and conservation of the nation's biodiversity as a means to achieve sustainability and peace. Molecular tools will accelerate such endeavors, but capacity remains limited in Colombia. The Earth Biogenome Project's (EBP) objective is to characterize the genomes of all eukaryotic life on Earth through networks of partner institutions focused on sequencing either specific taxa or eukaryotic communities at regional or national scales. Colombia’s immense biodiversity and emerging network of stakeholders have inspired the creation of the national partnership “EBP-Colombia.” Here, we discuss how this Colombian-driven collaboration between government, academia, and the private sector is integrating research with sustainable, environmentally focused strategies to develop Colombia’s postconflict bioeconomy and conserve biological and cultural diversity. EBP-Colombia will accelerate the uptake of technology and promote partnership and exchange of knowledge among Colombian stakeholders and the EBP’s global network of experts; assist with conservation strategies to preserve Colombia’s vast biological wealth; and promote innovative approaches among public and private institutions in sectors such as agriculture, tourism, recycling, and medicine. EBP-Colombia can thus support Colombia’s NBS with the objective of sustainable and inclusive development to address the many social, environmental, and economic challenges, including conflict, inequality, poverty, and low agricultural productivity, and so, offer an alternative model for economic development that similarly placed countries can adopt.

Additional file 7: Table. Description of the variables associated with the state of health of the participants during the follow-up period.

Additional file 8: Table. Post hoc analysis of the primary outcome considering the adherence.

Additional file 7: Table. Description of the variables associated with the state of health of the participants during the follow-up period.

Additional file 4. Questionnaire to evaluate the state of health and proper use of the intervention during the follow-up period.

Additional file 6. Definition of the categories of the adherence variable.

Additional file 1. CONSORT checklist.

Recent studies show that the exploration of ways to involve students in effective bi/multilingual science education is gaining attention at all educational levels. Introducing students to the construction of bilingual scientific argument maps – visual representations of scientific argument structure using two languages – contributes to the quality of bilingual science education as they are a key aspect of bilingual scientific literacy; however, very little is known about how to promote the construction of these maps in bilingual science courses. Here we provide evidence for the claim that peer feedback and instructor feedback can be integrated to support the construction of bilingual scientific argument maps. A pedagogical strategy that integrates both peer feedback and instructor feedback was implemented in a university bilingual science course with 29 students (23 females and 6 males, 18–24 years-old) in Colombia. Results show that the strategy effectively supported the construction of scientific argument maps in Spanish and English. Implications for research and practice are discussed.

Additional file 2. Description of the face shield implemented during the intervention.

The Covid-19 pandemic has accelerated the development and implementation of online education in higher education institutions around the globe. Online lecturing to large groups has been part of this acceleration. The problem is that synchronous face-to-face lectures and synchronous online lectures are widely criticized for reinforcing the hegemony of instructor-centered traditional approaches and rarely involving instructor-student and student-student argumentative interaction. This study aimed to provide evidence that online informal formative assessment (OIFA) can be used to provide undergraduates with explicit opportunities to participate in instructor-student argumentative interaction. An OIFA-based pedagogical strategy was implemented amidst the Covid-19 pandemic in the online lecturing sessions of a science course with 76 undergraduates (40 females and 36 males, 16–23 years old) in Colombia. It was found that OIFA can contribute to instructor-student argumentative interaction as well as to being able to better address undergraduate learning needs. Practical implications for university science education in the pandemic and post-pandemic eras are discussed. Keywords: Covid-19, formative assessment, instructor-student argumentative interaction, online learning, university science education.

Additional file 8: Table. Post hoc analysis of the primary outcome considering the adherence.

Additional file 5. Case definitions for COVID-19 according to the Ministry of Health and Social Protection of Colombia.

Additional file 3. Recorded educational intervention during the follow-up period.

Background: Across the world, the COVID-19 pandemic has disproportionately affected economically disadvantaged groups. This differential impact has numerous possible explanations, each with significantly different policy implications. We examine, for the first time in a low- or middle-income country, which mechanisms best explain the disproportionate impact of the virus on the poor. Methods: We use primary data from the CoVIDA project, including the results of 59,770 RT-PCR tests in Bogota´, targeted on a mostly asymptomatic adult population June 2020 to March 3rd, 2021. This is combined with administrative data that covers all reported cases in Bogota´. We estimate a number of parameters that are likely to drive inequality in COVID-19 infection rates across socioeconomic groups, then use these estimates in an individual-level branching process model of the epidemic. We use counterfactual scenarios to estimate the relative importance of different channels for explaining inequality in infection rates. Findings: Total infections and inequalities in infections are largely driven by inequalities in the ability to work remotely and in within-home secondary attack rates. Inequalities in isolation behavior are less important but non-negligible, while access to testing and contract-tracing plays practically no role. Interventions that mitigate transmission are found to be more effective when targeted on socioeconomically disadvantaged groups. Interpretation: Socioeconomically disadvantaged groups are particularly vulnerable to COVID-19 infections, and this appears to be driven by the need to work out of home, and higher transmission within home. Policies that can successfully reduce these channels of transmission among the poor are likely to have large benefits. Funding: The authors acknowledge generous support from the Interamerican Development Bank, the Development Bank of Latin America (CAF), the University of Los Andes and the Universidad Nacional de Colombia. Duncan Webb gratefully acknowledges support from the ED 465 at University Paris 1, and the EUR project ANR-17-EURE-0001. Declaration of Interest: The authors have no competing interests to declare. Ethical Approval: Ethics approval was obtained from the ethics committee of Universidad de los Andes (Act number 1278 of 2020). The ethics committee approved that the participants would receive the information via telephone and give their verbal consent, in order to comply with physical distancing and limit the restriction for a study is part of a public health surveillance strategy implemented jointly with the Health Secretary of Bogota.