AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods

AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/

Invasión de ecosistemas fluviales por cangrejo rojo americano, Procambarus clarkii

Trabajo presentado en las Jornadas españolas sobre conservación del cangrejo de río autóctono, celebradas el 21 y 22 de septiembre de 2015.Las invasiones biológicas son una de las mayores amenazas para la biodiversidad y conservación de las especies autóctonas, jugando un papel clave en el cambio global. Para intentar controlarlas, es importante entender dos tipos de fenómenos: los mecanismos que permiten a una especie establecerse con éxito en un nuevo ambiente, y las consecuencias ecológicas, evolutivas y económicas de una invasión. Nosotros abordaremos ambos tipos de fenómenos usando un enfoque multidisciplinar y un estudio multiescala, empleando como modelo de estudio una de las especies invasoras con mayor importancia global, la cual ya ha invadido la mayoría de aguas continentales: el cangrejo rojo americano, Procambarus clarkii. En su área nativa, esta especie vive principalmente en marismas; sin embargo, en las áreas invadidas ha sido capaz de invadir un nuevo ambiente, los arroyos, (en nuestro caso: el oeste de Andalucía en el suroeste de España). Desde su introducción hace unos 40 años, esta invasión está causando importantes daños a las especies autóctonas como el cangrejo de río, Austropotamobius pallipes. En este estudio, nos planteamos los siguientes cinco objetivos: (1) comparar la diversidad genética de las poblaciones invasoras con las de las áreas nativas, identificando patrones de introducción, propagación y flujo génico; (2) determinar qué mecanismos (a nivel de expresión de genes en diferentes tejidos) permiten que P. clarkii se adapte a nuevas condiciones o estrés ambiental: identificando genes y loci responsables para la adaptación local; (3) explorar los efectos ecológicos de P. clarkii en arroyos, en términos de estructura y funcionamiento del ecosistema, además de las interacciones con poblaciones nativas, tanto de cangrejo de río (A. pallipes) como de anfibios y peces autóctonos. Para hacer esto, compararemos los efectos ecológicos de las poblaciones de arroyo (las cuales potencialmente han evolucionado en respuesta a nuevos ambientes) con aquellas de poblaciones fundadoras desde las marismas; (4) comparar los efectos ecológicos de P. clarkii con aquellos de A. pallipes y determinar si la especie invasora está ocupando el mismo nicho ecológico que la especie nativa a la cual ha desplazado; y (5) examinar la prevalencia de Aphanomyces astaci en el cangrejo rojo americano, dado que esta especie invasora es portadora de la peste del cangrejo, afanomicosis, causando la muerte del cangrejo de río autóctono; y también la del hongo que causa la quitridiomicosis en anfibios. Con este proyecto, pretendemos dilucidar los mecanismos que permiten al cangrejo rojo americano establecerse exitosamente en un nuevo ambiente y las consecuencias que esto conlleva para las especies autóctonas.Peer reviewe

Invasion of fluvial ecosystems by red swamp crayfish, Procambarus clarkii

Trabajo presentado en el International Symposium on Conservation of Native European Freshwater Crayfish, celebrado en Olot (Girona) del 23 al 25 de septiembre de 2015.Biological invasions are one of the biggest threats to biodiversity and conservation of native species, playing a key role in global change. To try to control them, it is important to understand two types of phenomena: mechanisms that allow a species to successfully establish in a new environment, and the ecological, evolutionary and socio-economic consequences of an invasion. We will address both types of phenomena using a multidisciplinary approach and multi-scale research, employing as study model an invasive species of global importance, which has invaded many inland waters: the red swamp crayfish, Procambarus clarkii. In its native area, this species mainly lives in marshes; nevertheless, it has been able to invade a new environment, streams, in invaded areas (in our case: West Andalusia in South Western Spain). Since its introduction over 40 years ago, this invasion is causing serious damage to native species like the European freshwater crayfish, Austropotamobius pallipes. We have five main objectives in this study: (1) to compare the genetic diversity of invasive populations with the native area, identifying patterns of introduction, propagation and gene flow; (2) to determine what mechanisms (at the level of gene expression in different tissues) allow P. clarkii to adapt to new conditions or environmental stress: identify genes and loci responsible for local adaptation; (3) to explore the ecological effects of P. clarkii in streams, in terms of structure and ecosystem functioning, and interactions with populations of native crayfish (A. pallipes) and native amphibians and fishes. To do this, we will compare the ecological effects of stream populations (which have potentially evolved in response to the new environment) with those of founding populations from marshes; (4) to compare the ecological effects of P. clarkii with those of A. pallipes and determine whether the invasive species is occupying the same ecological niche as the native species which has displaced; and (5) to examine the prevalence of Aphanomyces astaci in the red swamp crayfish, given that this invasive species is a chronic carrier of the crayfish plague, aphanomycosis, causing the death of European freshwater crayfish; and that of the fungus that causes chytridiomycosis in amphibians. In this project, we expect to find mechanisms that allow the red swamp crayfish to successfully establish in a new environment and the consequences that this entails for native species.Peer reviewe

Common garden experiments in the genomic era : new perspectives and opportunities

PdV was supported by a doctoral studentship from the French Ministère de la Recherche et de l’Enseignement Supérieur. OEG was supported by the Marine Alliance for Science and Technology for Scotland (MASTS)The study of local adaptation is rendered difficult by many evolutionary confounding phenomena (e.g. genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specifically designed to deal with phenotypic plasticity has a clear role to play in the study of local adaptation, even (if not specifically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efficient, thorough and integrative study of local adaptation. Especially, evidence from genomic (e.g. genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits.PostprintPeer reviewe

Challenges in Survey Research

While being an important and often used research method, survey research has been less often discussed on a methodological level in empirical software engineering than other types of research. This chapter compiles a set of important and challenging issues in survey research based on experiences with several large-scale international surveys. The chapter covers theory building, sampling, invitation and follow-up, statistical as well as qualitative analysis of survey data and the usage of psychometrics in software engineering surveys.Comment: Accepted version of chapter in the upcoming book on Contemporary Empirical Methods in Software Engineering. Update includes revision of typos and additional figures. Last update includes fixing two small issues and typo