Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

Relaciones históricas entre olmos y vides

In Spanish, the expression «You cannot ask an elm for pears» denotes something that is impossible. Although its origin is unknown, it can be dated back to the 1st century BC, when appeared the Latin maxim Pirum, non ulmum accedas, si cupias pira (You should go to a pear-tree for pears, not to an elm), a sentence from which we believe the Spanish saying comes. The objective of this paper is to show how the historical relationship of elms and vines can be related to these expressions, because elms did not give pears but, figuratively, did give grapes. The cultivation of vines was soon included among the domestic plants at the beginning of the Neolithic Age. During the Assyrian Empire (7th century BC), vines are represented growing up around pine-like trees. The first documentary evidence of the marriage between elms and vines is found in the Ancient Greece: a wine called Pteleaikós oinos is mentioned, which refers to the region where it was produced, Ptelea (Elm). During the Roman Ages, the cultivation of vines married to elms became more important as it is reflected in the treatises in agriculture. This technique was so common that it appears recurrently as a topic in Poetry and Drama. The classical books were copied during the Middle Ages, and only the Arabian agronomists in the Iberian Peninsula gave new evidence of the relationship between vines and elms in the 12th century. Some four hundred years later the use of elms as props for vines was rare in Spain and, although not to elms, the marriage of vines to trees lasted in the South of Spain until the 19th century. In Italy, elms and vines were even planted together in the 20th century, before the Dutch Elm Disease began to kill the plantations of trees and farmers were forced to replace them with poles.En castellano, la expresión «No se le puede pedir peras al olmo» indica algo imposible. A pesar de que su origen es desconocido, puede situarse en el siglo I A.C., cuando aparece la máxima latina Pirum, non ulmum accedas, si cupias pira (Al peral acude, no al olmo, si quieres peras), de la cual creemos que procede la expresión española. En este trabajo se pretende mostrar que la relación histórica de los olmos y las vides puede estar relacionada con estas expresiones en la medida en que los olmos no daban peras mas, en sentido figurado, daban uvas. La vid fue una de las primeras plantas cultivadas ya desde el comienzo del Neolítico. En el Imperio Asirio (s. VII A.C.), las vides aparecen representadas creciendo alrededor de árboles que se asemejan a pinos. La primera evidencia documental del maridaje de olmos y vides la encontramos en la Grecia Clásica, donde se menciona un vino llamado Pteleaikós oinos que hace referencia a la región dónde se producía, Ptelea (Olmo). Durante la época Romana el cultivo de las vides maridadas a los olmos adquiere mayor importancia, como se refleja en los tratados de agricultura. La práctica fue tan común que aparece de modo recurrente como tópico en la literatura. Los textos clásicos son copiados durante la Edad Media, y sólo los agrónomos árabes de la península Ibérica proporcionan nuevas evidencias de la relación entre vides y olmos ya en el siglo XII. Cuatro siglos después la utilización de olmos como tutores de las vides era rara en España, pero el maridaje de las vides con árboles, aunque no olmos, duró en el Sur de España hasta el siglo XIX. Sin embargo en Italia olmos y vides se plantaban juntos incluso en el siglo XX, antes de que la grafiosis comenzara a matar las plantaciones de árboles y los agricultores se vieran obligados a sustituirlos por postes

Academic literacy and student diversity: evaluating a curriculum-integrated inclusive practice intervention in the United Kingdom

The sustainability of universities is based, among other aspects, on their ability to adapt to changes and the needs of students, an increasingly diverse population. In this sense, Academic literacy provision at universities tends to be centralized and to offer language support for general academic literacy purposes rather than language development that responds in a more nuanced way to the particular literacy needs of students’ disciplines. Yet, in recent years, several studies have supported the integration of academic literacy into subject teaching outlining the principles of an inclusive model of academic literacy instruction. This paper draws on a theoretical framework developed by Wingate to evaluate a curriculum-integrated inclusive practice intervention in the United Kingdom with students from a first-year credit-bearing module at Middlesex University Business School. The study used a mixed methods approach that includes a literature review, secondary data, feedback questionnaire and a focus group to evaluate our teaching method and reflect on the collaboration of the team members to develop this inclusive pedagogical approach. The findings suggest that, on the whole, this intervention was perceived by both the module teaching team and students as positive, welcoming and often crucial for supporting undergraduate students into the disciplinary discourse of their subject of study. Yet, recommendations were made with respect to developing better guidelines for subject lecturers on how to deliver the integrated academic literacy as well as the importance of the participation of students, student learning assistants and graduate teaching assistants in the design of the intervention. This study contributes to the literature on inclusive practice intervention and pedagogical approaches to integrating academic literacy into subject teaching for a diverse student population, contributing to the social sustainability of the universities

Identification of an inducible nitric oxide synthase in diaphragm mitochondria from septic miceIts relation with mitochondrial dysfunction and prevention by melatonin

Producción CientíficaSepsis provokes an induction of inducible nitric oxide synthase (iNOS) and melatonin down-regulates its expression and activity. Looking for an inducible mtNOS isoform, we induced sepsis by cecal ligation and puncture in both normal and iNOS knockout mice and studied the changes in mtNOS activity. We also studied the effects of mtNOS induction in mitochondrial function, and the role of melatonin against induced mtNOS and mitochondrial dysfunction. The activity of mtNOS and nitrite levels significantly increased after sepsis in iNOS+/+ mice. These animals showed a significant inhibition of the respiratory chain activity and an increase in mitochondrial oxidative stress, reflected in the disulfide/glutathione ratio, glutathione redox cycling enzymes activity and lipid peroxidation levels. Interestingly, mtNOS activity remained unchanged in iNOS-/- septic mice, and mitochondria of these animals were unaffected by sepsis. Melatonin administration to iNOS+/+ mice counteracted mtNOS induction and respiratory chain failure, restoring the redox status. The results support the existence of an inducible mtNOS that is likely coded by the same gene as iNOS. The results also suggest that sepsis-induced mtNOS is responsible for the increase of mitochondrial impairment due to oxidative stress in sepsis, perhaps due to the high production of NO. Melatonin treatment prevents mitochondrial failure at the same extend as the lack of iNOS gene

Community impacts of anthropogenic disturbance: natural enemies exploit multiple routes in pursuit of invading herbivore hosts.

This is the final version of the article. Available from the publisher via the DOI in this record.BACKGROUND: Biological invasions provide a window on the process of community assembly. In particular, tracking natural enemy recruitment to invading hosts can reveal the relative roles of co-evolution (including local adaptation) and ecological sorting. We use molecular data to examine colonisation of northern Europe by the parasitoid Megastigmus stigmatizans following invasions of its herbivorous oak gallwasp hosts from the Balkans. Local host adaptation predicts that invading gallwasp populations will have been tracked primarily by sympatric Balkan populations of M. stigmatizans (Host Pursuit Hypothesis). Alternatively, ecological sorting allows parasitoid recruitment from geographically distinct populations with no recent experience of the invading hosts (Host Shift Hypothesis). Finally, we test for long-term persistence of parasitoids introduced via human trade of their hosts' galls (Introduction Hypothesis). RESULTS: Polymorphism diagnostic of different southern refugial regions was present in both mitochondrial and nuclear microsatellite markers, allowing us to identify the origins of northern European invaded range M. stigmatizans populations. As with their hosts, some invaded range populations showed genetic variation diagnostic of Balkan sources, supporting the Host Pursuit Hypothesis. In contrast, other invading populations had an Iberian origin, unlike their hosts in northern Europe, supporting the Host Shift Hypothesis. Finally, both British and Italian M. stigmatizans populations show signatures compatible with the Introduction Hypothesis from eastern Mediterranean sources. CONCLUSIONS: These data reveal the continental scale of multi-trophic impacts of anthropogenic disturbance and highlight the fact that herbivores and their natural enemies may face very different constraints on range expansion. The ability of natural enemies to exploit ecologically-similar hosts with which they have had no historical association supports a major role for ecological sorting processes in the recent assembly of these communities. The multitude of origins of invading natural enemy populations in this study emphasises the diversity of mechanisms requiring consideration when predicting consequences of other biological invasions or biological control introductions.Funding was provided by NERC grant NE/B504406/1 to GNS and KS and NE/E014453/1 to GNS and JAN

Effect of OAS genes on SARS-CoV-2 infection and the induction of innate immune responses

Resumen del trabajo presentado en el 8th European Congress of Virology, celebrado en Gdańsk (Polonia), del 4 al 7 de mayo de 2023Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) infections cause different clinical symptoms ranging from asymptomatic patients to patients suffering severe respiratory disease leading to death in some of them. Genetic and functional studies have shown inborn-errors of interferon (IFN)-related genes in severe COVID-19 patients explaining why some young patients devoid of co-morbidities succumbed to infection. In addition, very large genomic studies identified common genetic variants affecting the expression and splicing of IFN-stimulated genes (ISGs) of the 2",5"- oligoadenylate (2-5A) synthetase (OAS) family associated with COVID-19 severity. We have sequenced the whole genome of 274 patients who required hospitalization after SARS-CoV-2 infection, finding ultrarare mutations in OAS1 and OAS3 genes. Upon double-stranded (ds)RNA binding, the OAS1, OAS2, and OAS3 proteins synthetize 2¿- 5¿olygoadenylates which activate the endonuclease RNAseL. This endonuclease degrades viral and cellular RNAs, inhibiting viral replication. We have analyzed the effect of OAS1 and OAS3 genetic variants identified in our patients, and found that some of them impair the RNAseL activation. In addition, by using OAS3 knock-out cells generated in our laboratory and performing overexpression experiments, we have shown that OAS3 negatively modulates proinflammatory responses induced by immune challenges, and that the activation of the RNAseL activity seems necessary for this function. In addition, by using OAS3 knock-out mice infected with SARS-CoV-2 or treated with the double-stranded RNA analog poly(I:C), we have shown that OAS3 deficiency leads to a higher mouse susceptibility to SARS-CoV-2 infection and that OAS3 counteracts the induction of innate immune responses in the mouse infectedlungs, leading to a higher inflammatory response in OAS3 knock-out mice, compared to the parental mice. Given the contribution of exacerbated inflammatory responses to COVID-19 disease severity, our results suggest that OAS1/OAS3 could play a role limiting the severity of the clinical symptoms after SARS-CoV-2 infection

The microbiome and mosquito vectorial capacity: rich potential for discovery and translation

Microbiome research has gained considerable interest due to the emerging evidence of its impact on human and animal health. As in other animals, the gut-associated microbiota of mosquitoes affect host fitness and other phenotypes. It is now well established that microbes can alter pathogen transmission in mosquitoes, either positively or negatively, and avenues are being explored to exploit microbes for vector control. However, less attention has been paid to how microbiota affect phenotypes that impact vectorial capacity. Several mosquito and pathogen components, such as vector density, biting rate, survival, vector competence, and the pathogen extrinsic incubation period all influence pathogen transmission. Recent studies also indicate that mosquito gut-associated microbes can impact each of these components, and therefore ultimately modulate vectorial capacity. Promisingly, this expands the options available to exploit microbes for vector control by also targeting parameters that affect vectorial capacity. However, there are still many knowledge gaps regarding mosquito–microbe interactions that need to be addressed in order to exploit them efficiently. Here, we review current evidence of impacts of the microbiome on aspects of vectorial capacity, and we highlight likely opportunities for novel vector control strategies and areas where further studies are required

Evaluación de indicadores físicos de degradación en mallines del Sur de Santa Cruz

En Patagonia, los mallines son ambientes muy productivos pero afectados por el pastoreo intensivo y continuo del ganado, provocando compactación del suelo por pisoteo en condiciones húmedas. Esto genera alteraciones en la vegetación, propiedades físico-químicas edáficas y procesos de erosión hídrica. A partir de ello, el uso de indicadores de degradación que permitan definir la condición de deterioro de los mallines facilitaría el manejo de estos ambientes para amortiguar su deterioro. El objetivo del presente estudio fue evaluar indicadores físicos del suelo en mallines húmedos con distinta condición de deterioro, durante dos ciclos de crecimiento. El trabajo se realizó en tres mallines de valle bajo condición buena (51º03’37,6’’ LS; 71º45’33,5’’ LO), moderada (51º23’37,4’’ LS; 70º12’14,1’’LO), y muy deteriorada (51º22’49,8’’LS; 70º13’38,6’’ LO) por el pastoreo ovino. Así, en tres sitios seleccionados de cada mallín se midió la resistencia mecánica del suelo (como indicador del grado de compactación) en los primeros 5 cm de profundidad con un penetrómetro de cono (PENETRÓMETRO ANALÓGICO MERIDIENS), y se recolectó con un cilindro metálico de 100 cm3 una muestra de un perfil similar para la determinación de la densidad aparente. El muestreo se realizó en dos fechas correspondientes al inicio (diciembre) y final (abril) del período de uso del mallín y durante dos ciclos de crecimiento (Diciembre-Abril de 2010/11 y 2011/12). Los valores de las variables descriptas se sometieron a un análisis de regresión lineal para determinar su relación con la humedad edáfica. El diseño experimental fue completamente aleatorizado con tres repeticiones en un arreglo factorial de tres factores (condición, fecha y ciclo). Los datos para cada factor se analizaron mediante ANVA y las diferencias entre medias de las condiciones se evaluaron con la prueba de Duncan con un nivel del significación del 5%. El análisis detectó efectos significativos (p0,05%) entre los factores evaluados. Los valores medios de resistencia mecánica y densidad aparente variaron (p<0,05) respecto a la condición del mallín, siendo mayores en el mallín muy deteriorado en relación a los mallines restantes (Tabla 1), lo cual indicaría una mayor compactación. Se concluye que la evaluación de la resistencia mecánica y la densidad aparente del suelo en los mallines húmedos permitiría describir su condición de deterioro y no estaría influenciada por la fecha y año de medición.EEA Santa CruzFil: Utrilla, Víctor Ricardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz. Santa Cruz; Argentina.Fil: Utrilla, Víctor Ricardo. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina.Fil: Andrade, Miguel Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; ArgentinaFil: Andrade, Miguel Alberto. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Billoni, Sabrina L. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina.Fil: Rogel, Bibiana. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos. Santa Cruz; Argentina

Monitoreo de indicadores de degradación en mallines del sur de Santa Cruz

Los principales disturbios que afectan los mallines en Patagonia se relacionan con variaciones en su dinámica hídrica y el pastoreo intensivo y continuo durante períodos prolongados (Raffaele, 1999) que producen alteraciones en la vegetación, en las propiedades físico-químicas del suelo, la calidad del agua y en los procesos de desertificación. Existen antecedentes de indicadores cuantitativos de deterioro para los mallines de Santa Cruz, a partir de claves objetivas como herramienta para planificar su uso (Suárez et al., 2010; Ormaechea et al., 2010). Sin embargo, es importante determinar las causas que resultan en distintas condiciones de degradación considerando variables de la vegetación, suelo y agua. Estos estudios deberían colaborar en generar acciones de mitigación que resulten en un uso ganadero mas sustentable del pastizal, suelo y agua de éstos ambientes (Bran, 2009).EEA Santa CruzFil: Utrilla, Víctor Ricardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Utrilla, Víctor Ricardo. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina.Fil: Andrade, Miguel Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Billoni, Sabrina L. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Rogel, Bibiana. Universidad Nacional de la Patagonia Austral. Unidad Académica Río Gallegos; Argentina