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- Diversity patterns of P450 genes in 17 honey bee subspeciesPublication . Li, Fernanda; Yadró Garcia, Carlos A.; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; Graaf, Dirk C.; Smet, Lina de; Pinto, M. Alice; Henriques, DoraHoney bees (Apis mellifera) inhabit a vast geographical range, spanning diverse natural and agricultural ecosystems. They are exposed to different levels and types of natural (such as plant allelochemicals) and synthetic (such as pesticides) xenobiotics within this range. Several genes have been implicated in the resistance of insects to pesticides, including the P450 monooxygenases superfamily that contains 46 genes. Here, the sequences of P450 monooxygenases from >1500 individuals representing 17 subspecies of the four honey bee main lineages will be analyzed. The functional annotation and effects of each variant will then be predicted using SnpEff and the allele frequency and FST (fixation index) of each SNP per population and evolutionary lineages will be calculated. It is expected to have highly differentiated SNPs among the different subspecies/lineages.
- Bioinformatics pipeline to evaluate patterns of diversity in detoxification genes in Western Honey BeePublication . Barbosa, Daniela; Li, Fernanda; Bashir, Sana; Lopes, Ana; Yadró García, Carlos A.; Quaresma, Andreia; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; Graaf, Dirk C.; Smet, Lina de; Pinto, M. Alice; Henriques, DoraThe Western honey bee, Apis mellifera, displays significant genetic diversity in detoxification genes, which is pivotal for environmental adaptation and resilience. Herein, we developed a bioinformatics pipeline to investigate patterns of diversity in these genes, focusing on single nucleotide polymorphisms (SNPs) across A. mellifera populations, with variant annotation performed using both snpEff and the Variant Effect Predictor (VEP). Our pipeline integrates GATK, VCFtools, PLINK, bcftools, snpEff, and VEP to process genomic data systematically. Regions of interest were defined in a BED file for variant filtering. Using GATK, SNPs were extracted from a VCF file and conversion to PLINK format for population genetics analyses. Variants were filtered by minor allele frequency (MAF) and population differentiation (FST index) to identify SNPs with considerable. Variants were annotated with snpEff and VEP to predict functional impacts, enabling a comparative analysis of their annotation consistency and depth. Custom scripts were developed to map SNPs to detoxification genes, quantify SNP density, and integrated gene descriptions and lineage data. The resulting data were visualized using a combination of and generate different graphs using ggplot2 and chromoMap for chromossomal maps. Quality control steps were applied through the pipeline ensuring data reliability. Our findings reveal distinct SNP patterns in detoxification genes, highlighting candidate SNPs associated with A. mellifera subspecies-specific adaptations. The comparison of snpEff and VEP annotations provides insights into their strengths and limitations, which can help optimize software selection for genomic studies. This pipeline offers a reproducible framework for studying genetic diversity in A. mellifera that is adaptable to other species, advancing conservation and evolutionary genomics.
- Reconstruction of meteorological records by methods based on dimension reduction of the predictor datasetPublication . Balsa, Carlos; Breve, Murilo Montanini; Rodrigues, Carlos Veiga; Rufino, JoséThe reconstruction or prediction of meteorological records through the Analog Ensemble (AnEn) method is very efficient when the number of predictor time series is small. Thus, in order to take advantage of the richness and diversity of information contained in a large number of predictors, it is necessary to reduce their dimensions. This study presents methods to accomplish such reduction, allowing the use of a high number of predictor variables. In particular, the techniques of Principal Component Analysis (PCA) and Partial Least Squares (PLS) are used to reduce the dimension of the predictor dataset without loss of essential information. The combination of the AnEn and PLS techniques results in a very efficient hybrid method (PLSAnEn) for reconstructing or forecasting unstable meteorological variables, such as wind speed. This hybrid method is computationally demanding but its performance can be improved via parallelization or the introduction of variants in which all possible analogs are previously clustered. The multivariate linear regression methods used on the new variables resulting from the PCA or PLS techniques also proved to be efficient, especially for the prediction of meteorological variables without local oscillations, such as the pressure.
- Honey bee collected pollen for botanical identification via its2 metabarcoding: a comparison of preservation methods for citizen sciencePublication . Quaresma, Andreia; Brodschneider, Robert; Gratzer, Kristina; Gray, Alison; Keller, Alexander; Kilpinen, Ole; Rufino, José; Steen, Jozef van der; Vejsnaes, Flemming; Pinto, M. AliceWhile classical palynology has been the method of choice to assess botanical diversity of bee-collected pollen for multiple purposes, DNA metabarcoding is emerging as a powerful alternative being able to achieve high taxonomic identification accuracy. Moreover,DNA metabarcoding allows analysis of hundreds of samples in a single high-throughput sequencing run, therefore offering unprecedented scale in citizen science projects. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. Hence, it is important to test how sample preservation influences quality and quantitative performance of pollen metabarcoding. While inmetabarcoding studies pollen has typically been preserved at −20°C (FRZ), this is not the best method to be applied by citizen scientists.
- Distributed heterogeneous computing with clOpenCLPublication . Ribeiro, Tiago Filipe Rodrigues; Afonso, Mário João da Costa; Rufino, José; Alves, AlbanoClusters of heterogeneous computing nodes provide an opportunity to significantly increase the performance of parallel and High-Performance Computing (HPC) applications, by combining traditional multi-core CPUs coupled with accelerator devices, interconnected by high throughput and low latency networking technologies. However, developing efficient applications to run in clusters that integrate GPUs and other accelerators often requires a great effort, demanding programmers to follow complex development methodologies in order to suit algorithms and applications to the new heterogeneous parallel environment. OpenCL is an open programming standard for heterogeneous computing. It suffers, however, from a major limitation: applications can only make use of the local compute devices, present on a single machine. clOpenCL (cluster OpenCL) supports the simple deployment and efficient running of unmodified OpenCL-based parallel applications that may span several cluster nodes, expanding the original single-node OpenCL model.
- Autent+ Desenvolvimento de abordagem inovadoras com vista à valorização e exploração do potencial de mercado do mel PortuguêsPublication . Amaral, Joana S.; Quaresma, Andreia; Rodrigues, Pedro João; Rufino, José; Henriques, Dora; Calaim, Luís; Gaspar, Albino; Pinto, M. AliceA FENAPICOLA candidatou-se, como proponente, a uma medida de investigação aplicada, tendo convidado o Instituto Politécnico de Bragança (IPB) como entidade parceira, envolvendo este último uma equipa multidisciplinar de 6 investigadores provenientes dos centros de investigação CIMO (Centro de Investigação de Montanha) e CEDRI (Centro de Investigação em Digitalização e Robótica Inteligente). Assim foi criado o projeto AUTENT+, um projeto financiado pelo Instituto de Financiamento da Agricultura e Pescas (IFAP), em resultado da candidatura submetida ao Plano Apícola Nacional (PAN) 2020/2022, medida 5.1 "Apoio a projetas de investigação aplicada”. O AUTENT + tem como principal objetivo a valorização do mel nacional como um produto autêntico e sustentável, através de abordagens que visam diferenciar, acrescentar valor e o potencial de mercado a este produto. Para tal, o projeto centra-se no desenvolvimento de metodologias inovadoras com vista à deteção de adulterações do mel, em particular no que respeita à origem botânica e entomológica/geográfica, e no desenvolvimento de ferramentas que permitam , de uma forma simples, informar o consumidor sobre as caraterísticas do produto que adquirem.
- An architecture for reliable transportation of delicate goodsPublication . Matos, Paulo; Rufino, José; Lopes, Rui PedroAdequate conditions are critical to avoiding damage or degradation of products during transportation, especially in the case of delicate goods like food products, live animals, precision machinery or art items, among others. The damages are not always readily identified: sometimes they are only detected several days or weeks after the merchandise has been delivered. Moreover, it may be hard to assess if the problems resulted from the transport conditions, and it may be even harder to prove it, making it difficult to determine and assign responsibilities. Also, transport is a global business, typically involving different companies and means (truck, train, plane, ship, …). Usually, customers hire the service to a single commercial entity, but the service is performed by several companies, like transporters, stockists and dispatchers. To know whether the transport requirements are fulfilled or not is thus essential to assessing responsibilities and encouraging compliance by all the players in the process. In this paper, the authors propose an architecture that allows certifying, in an exempt manner, the conditions under which the transport of sensitive goods are carried out. In case of compliance, it protects the entities of the transport chain and ensures the customer that the merchandise has not been subject to conditions that may have affected its integrity or quality. If problems are detected, it allows to identify the non‐compliant players and to assign responsibilities. The solution is based on ultra‐low‐power, low‐cost devices (equipped with several sensors, a real‐time clock, and Bluetooth Low Energy services), a mobile application and several cloud services (including a Coordinated Universal Time service)
- MCSFilter performance: a comparison studyPublication . Monteiro, Luís; Rufino, José; Romanenko, Andrey; Fernandes, Florbela P.
- Applications of the analog ensembles method to meteorological data reconstruction in the Northeast of PortugalPublication . Breve, Murilo Montanini; Rufino, José; Balsa, Carlos; Costa, LuísThe observation of weather states has always been a human need. Our most distant ancestors already tried to understand and predict the weather, but did not have reliable methods. In the 19th century, modern meteorology took its first steps: the French government, motivated by the sinking of ships near the coast of Crimea, because of a heavy rainstorm, created a network of 24 stations spread across Europe, which began to observe the weather. In recent years, due to computational advances, different methods of predicting weather states have begun to emerge, increasing the forecast extent and its accuracy. The Analog Ensembles method (AnEn), introduced by Luca Delle Monache in 2011 [1], is a post-processing tool that has shown good results to improve whether predictions or perform hindcasting (reconstruction of missing meteorological data). The goal of this study is to use the AnEn method to perform hindcasting, in order to reconstruct past weather conditions in a specific area of the northeeast of Portugal and verify its similarity with the actual forecast.
- Identification of botanical origin of bee-collected mixed pollen samples: a comparison between palynological and DNA metabarcoding methodsPublication . Quaresma, Andreia; Steen, Jozef van der; Amaral, Joana S.; Biron, David G.; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Formato, Giovanni; Gratzer, Kristina; Hatjina, Fani; Kilpinem, Ole; Pietropaoli, Marco; Rufino, José; Vejsnaes, Flemming; Pinto, M. AliceIdentification of botanical origin of mixed pollen samples has several applications, including unraveling plant-pollinator interactions, determining botanical origin of honey, monitoring allergy-related airborne pollen sources, or even monitoring pesticide use in crops. These applications have typically been addressed using light microscopy, a costly approach that often provides low taxonomic resolution. However, with high-throughput sequencing (HTS) becoming increasingly affordable, DNA metabarcoding is emerging as a promising alternative to classical palynology. In addition to be time- and cost-effective for large sample sizes, metabarcoding has the potential to allow identification of pollen mixtures at the species level. However, before it can be widely employed in pollen analysis, the reliability of this molecular tool must be appraised. Herein, we compared the two approaches on 61 bee-collected pollen samples from eight European countries. The samples were homogenized and split into two sub-samples. One set of 61 sub-samples was analyzed by palynology experts from the “Institut für Bienenkunde”, Germany, and the other one was subjected to HTS, using ITS2 as the barcode, in the labs of CIMO and CIBIO. Comparisons of the relative abundances at the family level show no significant differences (P ≥ 0.1057, Wilcoxon signed-rank test) and high correlation values (0.2736 ≤ r ≤ 1.000, Pearson’s correlation) between the two approaches. The highest correlation values were observed for Italian samples (0.7245 ≤ r ≤ 0.9842; global r = 0.8958) and the lowest for Greek samples (0.0266 ≤ r ≤ 0.9703; global r = 0.5149). These results suggest that ITS2 metabarcoding offers a reliable alternative to classical palynology and this approach is now being employed in the European project INSIGNIA (https://www.insignia-bee.eu/), which is developing a standard protocol for using the honey bee as a tool for environmental monitoring.