A minimal CRISPR-Cas3 system for genome engineering [preprint]

CRISPR-Cas technologies have provided programmable gene editing tools that have revolutionized research. The leading CRISPR-Cas9 and Cas12a enzymes are ideal for programmed genetic manipulation, however, they are limited for genome-scale interventions. Here, we utilized a Cas3-based system featuring a processive nuclease, expressed endogenously or heterologously, for genome engineering purposes. Using an optimized and minimal CRISPR-Cas3 system (Type I-C) programmed with a single crRNA, large deletions ranging from 7 - 424 kb were generated in Pseudomonas aeruginosa with high efficiency and speed. By comparison, Cas9 yielded small deletions and point mutations. Cas3-generated deletion boundaries were variable in the absence of a homology-directed repair (HDR) template, and successfully and efficiently specified when present. The minimal Cas3 system is also portable; large deletions were induced with high efficiency in Pseudomonas syringae and Escherichia coli using an “all-in-one” vector. Notably, Cas3 generated bi-directional deletions originating from the programmed cut site, which was exploited to iteratively reduce a P. aeruginosa genome by 837 kb (13.5%) using 10 distinct crRNAs. We also demonstrate the utility of endogenous Cas3 systems (Type I-C and I-F) and develop an “anti-anti-CRISPR” strategy to circumvent endogenous CRISPR-Cas inhibitor proteins. CRISPR-Cas3 could facilitate rapid strain manipulation for synthetic biological and metabolic engineering purposes, genome minimization, and the analysis of large regions of unknown function

Heavy Metal Tolerance of Microorganisms Isolated from Coastal Marine Sediments and Their Lead Removal Potential

In this study, 338 microorganisms, comprising 271 bacteria and 67 fungi, were isolated from sediment samples collected from underexplored Pacific and Caribbean regions of Colombia. Screening trials were conducted on selected strains (n = 276) to assess their tolerance to cadmium (Cd2+), lead (Pb2+), and zinc (Zn2+), leading to the identification of six bacteria capable of withstanding 750 mg·L−1 of each heavy metal ion. Three promising microorganisms, identified as Enterobacter sp. INV PRT213, Pseudomonas sp. INV PRT215, and Stenotrophomonas sp. INV PRT216 were selected for lead removal experiments using LB broth medium supplemented with 400 mg·L−1 Pb2+. Among these, Pseudomonas sp. INV PRT215 exhibited significant potential, removing 49% of initial Pb2+ after 240 min of exposure (16.7 g wet biomass·L−1, pH 5, 30 °C). Infrared spectra of Pb-exposed biomass showed changes in functional groups, including carbonyl groups of amides, carboxylate, phosphate, hydroxyl, and amine groups, compared to the not-exposed control. These changes suggested interactions between the metal and functional groups in the biomass. The findings of this study highlight the potential of microorganisms derived from coastal marine environments as promising candidates for future applications in bioremediation of polluted environments contaminated with heavy metals

Nuevos registros del escarabajo indoafricano Digitonthophagus gazella (Fabricius 1787) (Coleoptera: Scarabaeinae) en Colombia

The Indo-african beetle Digitonthophagus gazella was introduced into the Americas as a bio-controller of parasites and flies in livestock systems. This dung scarab is characterized for its high dispersal ability, reproduction and efficient use of cattle manure. In Colombia, the most recent survey situated this beetle only in lowland areas. In the present study D. gazella was found in two new Colombian departments (Meta and Valle del Cauca) and its presence was confirmed in Antioquia. In this study, few individuals were collected and they were associated with vegetation systems with poor cover, such as livestock pastures and sugar cane monoculture, suggesting early stages of colonization and corroborating the preference of the species for open areas. Besides with the range extension with new records, this work also provides insights on D. gazella apparent colonization above 500 m of altitude. The distribution of this species across the Magdalena River valley appears to be associated with inter-department bovine transport. The importance of a continuous monitoring of the dispersion of D. gazella in Colombia, to establish its dispersal rate, habitat preference and pest status is also highlighted.Digitonthophagus gazella es un escarabajo indoafricano introducido en el continente americano como biocontrolador de parásitos y moscas en sistemas ganaderos. Se caracteriza por su alta capacidad de dispersión, reproducción y uso eficiente del estiércol bovino. En Colombia, los registros más recientes de esta especie lo sitúan sólo en áreas de tierras bajas. En el presente artículo se registra la presencia de D. gazella en dos nuevos departamentos de Colombia (Meta y Valle del Cauca) y se confirma para el departamento de Antioquia. En los muestreos se colectaron pocos individuos de esta especie, los cuales se encontraban asociados a sistemas simplificados como pastizales y monocultivos de caña de azúcar, con baja cobertura de dosel, lo cual demuestra la preferencia de la especie por sitios abiertos. El presente artículo actualiza la información de distribución con nuevos registros y provee, además, datos sobre el avance de esta especie por encima de los 500 m s.n.m. Se sugiere la dispersión natural de la especie a través de los valles interandinos del río Magdalena y el alcance de nuevos territorios a través del transporte interdepartamental de bovinos en el país. Se resalta la importancia de continuar monitoreando el avance de D. gazella en Colombia, para establecer su tasa de dispersión, preferencia de hábitats y determinar su relación con las especies nativas

New records of the Indo-african beetle <em>Digitonthophagus gazella<em> (Fabricius 1987) (Coleoptera: Scarabaeinae) in Colombia

The Indo-african beetle Digitonthophagus gazella was introduced into the Americas as a bio-controller of parasites and flies in livestock systems. This dung scarab is characterized for its high dispersal ability, reproduction and efficient use of cattle manure. In Colombia, the most recent survey situated this beetle only in lowland areas. In the present study D. gazella was found in two new Colombian departments (Meta and Valle del Cauca) and its presence was confirmed in Antioquia. In this study, few individuals were collected and they were associated with vegetation systems with poor cover, such as livestock pastures and sugar cane monoculture, suggesting early stages of colonization and corroborating the preference of the species for open areas. Besides with the range extension with new records, this work also provides insights on D. gazella apparent colonization above 500 m of altitude. The distribution of this species across the Magdalena River valley appears to be associated with inter-department bovine transport. The importance of a continuous monitoring of the dispersion of D. gazella in Colombia, to establish its dispersal rate, habitat preference and pest status is also highlighted

Maternal Dietary Inflammatory Index during Pregnancy Is Associated with Perinatal Outcomes: Results from the IMPACT BCN Trial

The information available on the effects of maternal dietary habits on systemic inflammation and adverse maternal outcomes is limited. We aimed to evaluate whether Dietary Inflammatory Index (DII) score during pregnancy is associated with maternal body mass index (BMI), Mediterranean diet (MD) adherence, and perinatal outcomes. At 19-23 weeks' gestation, 1028 pregnant women were recruited. Dietary information was assessed using a 17-item dietary score to evaluate MD adherence and a validated 151-item food frequency questionnaire. DII score was established according to 33 food and nutritional proinflammatory and anti-inflammatory items. Participants were distributed into tertiles according to the DII score, where a lower DII score (first tertile) represented an anti-inflammatory diet and the third tertile represented the more proinflammatory diet. Maternal characteristics and perinatal outcomes were collected, and newborns' birthweight percentiles were calculated. Adjusted logistic regression models were used to assess the association of the DII score with maternal and perinatal characteristics, setting the third tertile as the reference group. Women in the third tertile showed lower adherence to MD score compared to the first tertile: median (25th to 75th percentile) 9 (7 to 11) vs. 6 (4.25 to 8), p < 0.001. The proinflammatory diet was significantly associated with a higher maternal pre-pregnancy BMI (adjusted β = 0.88; 95% CI: 0.31 to 1.45) and lower newborn's birthweight percentile (adjusted β = −9.84th; 95% CI: −19.6 to −0.12). These data show that a proinflammatory diet profile may be associated with maternal overweight and fetal undergrowth

Aportes a la educación ambiental para la conservación de tortugas marinas

Sea turtles are in danger of extinction due to anthropic actions. Today's society demands to think about environmental education as a tool that strengthens critical thinking and environmental awareness. Consequently, this documentary investigation was carried out, which consisted of two moments. First, the review of various sources on environmental education aimed at the conservation of sea turtles, at the national and international level (1987-2018) and the choice of four thematic nuclei (target audience, educational strategy, purpose of the proposal, level of deepening) to carry out the analysis. Second, the design of an educational proposal that takes up the main contributions identified in the literature review. 70 materials of various types were found: books, web pages, articles, reports, wich were published in 17 countries. The largest number of material correspond to Colombia and the United States. For the most part, the materials are aimed at the Local Community, being the conservation of sea turtles their main purpose. Additionally, different Didactic Strategies are implemented. The most used is Experiences Experiences. In the documents found, the biological component prevails over the educational-environmental one, therefore, it is expected that the didactic proposal will contribute to future experiences and contribute to the conservation of turtles from a more integrative perspectiveLas tortugas marinas se encuentran en vía de extinción debido las acciones antrópicas. La sociedad actual exige pensar en la educación ambiental como herramienta que fortalece el pensamiento crítico y la conciencia ambiental. Por consiguiente, se realizó esta investigación documental que consistió en dos momentos. Primero, la revisión de diversas fuentes sobre educación ambiental dirigidas a la conservación de tortugas marinas, en el ámbito nacional e internacional (1987-2018) y la elección de cuatro núcleos temáticos (público objetivo, estrategia educativa, objetivo de la propuesta, nivel de profundización) para llevar a cabo el análisis. Segundo, el diseño de una propuesta educativa que retoma los principales aportes identificados en la revisión de literatura. Se encontraron 70 materiales de diversos tipos: libros, páginas web, artículos e informes, que fueron publicados en 17 países. El mayor número de hallazgos de material corresponden a Colombia y Estados Unidos. En su mayoría, los materiales tienen como objetivo la Comunidad Local, siendo la conservación de las tortugas marinas su propósito principal. Adicionalmente, se implementan distintas estrategias didácticas, siendo la más usada, experiencias vivenciales. En los documentos encontrados prevalece el componente biológico sobre el educativo-ambiental; por ello, se espera que la propuesta didáctica contribuya a futuras experiencias y aporte a la conservación de las tortugas desde una mirada más integradora

Validation of a pregnancy-adapted Mediterranean Diet Adherence Screener (preg-MEDAS): a validation study nested in the Improving Mothers for a better PrenAtal Care Trial BarCeloNa (IMPACT BCN) trial

Background: Non-time-consuming and easy-to-administer dietary assessment tools specific for pregnancy are needed. Objectives: The aim of this validation study nested in the IMPACT BCN (Improving Mothers for a better PrenAtal Care Trial BarCeloNa) trial is to determine the concurrent validity of the 17-item pregnancy-adapted Mediterranean diet score (preg-MEDAS) and to analyze whether changes in the preg-MEDAS score were associated with maternal favorable dietary and cardiometabolic changes after 3 mo of intervention in pregnant women. Methods: Dietary data was collected in 812 participants using the preg-MEDAS and a 151-item validated food frequency questionnaire (FFQ) at baseline (19-23 wk gestation) and final visit (31-34 wk gestation). Concurrent preg-MEDAS validity was evaluated by Pearson and intraclass correlation coefficients, κ statistic, and Bland-Altman methods. Results: The preg-MEDAS had a good correlation with the FFQ (r = 0.76 and intraclass correlation coefficient 0.75). The agreement of each of the preg-MEDAS items ranged from 40.9% to 93.8% with a substantial agreement mean concordance (κ = 0.61). A 2-point increase in preg-MEDAS was associated with a decrease in maternal mean and systolic blood pressure (β: -0.51 mmHg; 95% confidence interval [CI]: -0.97, -0.04 mmHg and -0.87 mmHg; 95% CI: -1.48, -0.26 mmHg, respectively). Conclusions: The preg-MEDAS displays good validity for assessing adherence to the Mediterranean diet, allowing detection of dietary changes over time. In addition, changes observed in preg-MEDAS are significantly associated with a decrease in maternal blood pressure. Therefore, we propose preg-MEDAS as a rapid and simple dietary assessment tool during pregnancy. This trial was registered at clinicaltrials.gov as NCT03166332

Study of knowledge, attitudes, and practices related to leishmaniasis : evidence of government neglect in the Colombian Darién

ABSTRACT: American cutaneous leishmaniasis (ACL) is considered a public health problem worldwide, and incidence in Colombia is 12,000 cases per year. Colombia has implemented control programs for years which have often overlooked the social, economic, and demographic characteristics of the regions where the disease occurs. As part of an epidemiological study, this article presents the results of a survey on knowledge, attitudes, and practices (KAP) related to leishmaniasis in rural populations in Acandí in the Colombian Darién. Qualitative and quantitative tools were used (ethnography and surveys, respectively). The results show scarce knowledge among the population on basic aspects such as recognition of the sand fly vector. There were also differences in KAP according to gender and type of population, rather than by geographic area. The study points to government neglect as a critical factor in the persistence of the disease.RESUMEN: La leishmaniasis cutánea americana (LCA) es considerada un problema de salud pública a nivel mundial, y su incidencia en Colombia es de 12 mil casos por año. Durante años se han implementado programas de control, que frecuentemente ignoran características sociales, económicas y demográficas de las regiones afectadas. Como parte de un estudio de tipo epidemiológico, en este artículo se presentarán los resultados de un estudio sobre los conocimientos, actitudes y prácticas (CAP) frente a la leishmaniasis, que tienen las poblaciones de las zonas rurales del municipio de Acandí, en el Darién Colombiano. Para el estudio se utilizaron herramientas cualitativas como la etnografía y cuantitativas, como las encuestas dirigidas. Los resultados ponen en manifiesto el desconocimiento de la población en aspectos fundamentales como el reconocimiento del vector. Además, existen diferencias en las CAP por género y por tipo de población, pero no por su distribución geográfica. Se evidenció el abandono estatal como factor determinante en la perpetuación de la enfermedad.

Novel genes and sex differences in COVID-19 severity

[EN] Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10−8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10−22 and P = 8.1 × 10−12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10−8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10−8) and ARHGAP33 (P = 1.3 × 10−8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10−8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.S

Línea de investigación en Helicobacter pylori para la formación de recurso humano en ciencia, tecnología e innovación en el programa de microbiología

Este libro nace de la unión de un maestro altamente calificado y alumnos dedicados con unas creatividades activas y dispuestas a trabajar por resolver los problemas que trae una bacteria a la humanidad. Las investigaciones aquí consignadas son producto de los trabajos de grado de los estudiantes del programa de Microbiología, quienes además fueron miembros del semillero de investigación, MICROORGANISMOS DE IMPORTANCIA EN SALUD HUMANA Y ANIMAL “OBVIO-MICROBIO”. Apoyados y dirigidos por la doctora Adalucy Alvarez-Aldana, quien gracias a su amplio conocimiento en el microorganismo supo sembrar curiosidad sobre el mismo durante las sesiones del semillero, incentivando a muchos de sus alumnos a dedicar su trabajo de grado a resolver alguna pregunta que les surgiera en torno a este microorganismo. Aunque diferentes son las investigaciones, todas fueron trazadas con un fin común, entregarle a la humanidad un poco más de conocimiento sobre Helicobacter pylori, por esto la unión de estas investigaciones en una sola consigna, son importantes para entender más sobre todo lo que rodea esta bacteria y pretenden resolver muchos misterios que aún aquejan la epidemiología detrás de la misma. Estos trabajos son fruto de muchos esfuerzos, materiales y académicos, de personas grandiosas, de la unión de universidades, doctores y docentes de diferentes disciplinas, razón que demuestra una vez más que la unión hace la fuerza, porque solo llegarás más rápido, pero en compañía llegarás más lejos. Además, contamos con la fortuna de tener un capitulo invitado, cuyo tema no es sobre Helicobacter pylori, pero si un sobre un tópico de gran interes en la actualidad como es la resistencia bacteriana. Capitulo titulado: “Caracterización epidemiológica y microbiológica de las bacteriemias y su perfil de resistencia durante el periodo junio 2011 a junio 2015”