Josep Francesc Abril

University of Barcelona | UB · Department of Genetics

For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-caten...

The loss-of-function conditions for an l(3)malignant brain tumour (l(3)mbt) in larvae reared at 29 °C results in malignant brain tumours and hyperplastic imaginal discs. Unlike the former that have been extensively characterised, little is known about the latter. Here we report the results of a study of the hyperplastic l(3)mbt mutant wing imaginal...

Atypical femoral fractures (AFF) are rare fragility fractures in the subtrocantheric or diaphysis femoral region associated with long-term bisphosphonate (BP) treatment. The etiology of AFF is still unclear even though a genetic basis is suggested. We performed whole exome sequencing (WES) analysis of 12 patients receiving BPs for at least 5 years...

Introduction: A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables deep study of the viral quasispecies in samples from infected individuals. Methods: In this study, the viral quasispecies complexity and single nucleotide polymorp...

In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV...

A woman at the first stage of labour infected with SARS-CoV-2 was admitted to our hospital with symptomatology compatible with mild respiratory disease. Respiratory and non-respiratory samples from the mother were all positive for the virus, but not from the baby. Laboratory tests rejected vertical transmission. Whole-genome sequencing was performe...

Embryonic specification of the first body axis requires the formation of an Organizer, a group of cells with the ability to instruct fates in the surrounding tissue. The existence of organizing regions in adults, i.e. during regeneration, which also requires patterning of new tissues, remains unstudied. To that aim, we study regeneration in planari...

Expansion of a CAG repeat in ATXN3 causes the dominant polyglutamine disease spinocerebellar ataxia type 3 (SCA3), yet the physiological role of ATXN3 remains unclear. Here, we focus on unveiling the function of Ataxin-3 (ATXN3) in the retina, a neurological organ amenable to morphological and physiological studies. Depletion of Atxn3 in zebrafish...

NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before N...

Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used a...

There is an increasing amount of transcriptomic and genomic data available for planarians with the advent of both traditional and single–cell RNA sequencing technologies. Therefore, exploring, visualizing, and making sense of all these data in order to understand planarian regeneration and development can be challenging. In this work we present Pl...

How cells communicate to initiate a regenerative response after damage has captivated scientists during the last few decades. It is known that one of the main signals emanating from injured cells is the Reactive Oxygen Species (ROS), which propagate to the surrounding tissue to trigger the replacement of the missing cells. However, the link between...

RPGeNet offers researchers a user-friendly queriable tool to visualize the interactome network of visual disorder genes, thus enabling the identification of new potential causative genes and the assignment of novel candidates to specific retinal or cellular pathways. This can be highly relevant for clinical applications as retinal dystrophies affec...

Objectives: Atypical femoral fractures (AFF) are rare, often related to long-term bisphosphonate (BPs) treatment. Their pathogenic mechanisms are not precisely known and there is no evidence to identify patients with a high risk of AFF. The aim of this work is to study the genetic bases of AFFs. Materials and methods: Whole-exome sequencing was ca...

Motivation: Protein-protein interactions (PPIs) are very important to build models for understanding many biological processes. Although several databases hold many of these interactions, exploring them, selecting those relevant for a given subject, and contextualizing them can be a difficult task for researchers. Extracting PPIs directly from the...

Atypical femoral fractures (AFFs) are a rare but potentially devastating event, often but not always linked to bisphosphonate (BP) therapy. The pathogenic mechanisms underlying AFFs remain obscure, and there are no tests available that might assist in identifying those at high risk of AFF. We previously used exome sequencing to explore the genetic...

Genome annotation is the process of identifying functional elements along the sequence of a genome, thus giving meaning to it. It is necessary because the sequencing of DNA produces sequences of unknown function. In the last three decades, genome annotation has evolved from the computational annotation of long protein-coding genes on single genomes...

Motivation: Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein-protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities. Results: We have developed a protocol to predict protein-protein interactions using sequence ho...

Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients wit...

Individual phylogenetic trees computed from contigs over reference genome locations in HEV. (DOCX)

Individual phylogenetic trees computed from contigs over reference genome locations in Anelloviridae family. (DOCX)

Motivation: The selection of a Single Nucleotide Polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that...

The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this go...

Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contam...

This letter describes the detection of GGPS1 and other mutations in three sisters who had atypical femoral fractures associated with long-term bisphosphonate use, which suggests that genes in the isoprenoid biosynthetic pathway may confer susceptibility to atypical fractures.

Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentrati...

Distribution of reads on kingdom level of the 16 method combinations and their associated negative controls. Samples were processed in triplicate, and the data shown is the average. _S = sample, _C = Negative extraction control. Databases used are listed in S1 Table. (PDF)

HAdV concentration measured by qPCR. (A) HAdV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box, whiskers and circles represents median, inter-quartile range, inter-quartile range times 1.5, and outliers, respectively. Asterisks represent significance level of a pairwise t-test...

Overview of reference sequence databases and associated download information. Reference sequence information can be obtained from the URL’s shown in ‘Download information’. (PDF)

Sequence information. Number of raw reads, reads after quality assessment, and reads not mapping to PhiX, and thus usable for subsequent analysis. _S = sample, _C = Negative control. (PDF)

qPCR inhibition of MNV and HAdV. Inhibition of the 16 combinations of concentration and extraction methods. Inhibition was measured using qPCR of undiluted (1:1) and tenfold diluted (1:10) DNA/RNA extracts. The values in the tables represents Δct between the undiluted and 10 fold diluted samples. A Δct = -3.3 represent a perfect 10 fold dilution. S...

MNV concentrations measured by qPCR. (A) MNV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box and whiskers represents the median, the inter-quartile range, and the inter-quartile range times 1.5, respectively. Asterisks represent significance level of a pairwise t-test with “H...

Abundance of all detected viral families. Heatmap showing the abundance of all detected viral families, measured in reads per million, in each biological replica for the different method combinations as well as the controls. _S = sample, _C = Negative control. (PDF)

Specifications of the four concentration methods applied in this study. (PDF)

Properties of the four nucleic acid extraction kits applied in this study. (PDF)

Retinitis pigmentosa (RP) is a highly heterogeneous genetic visual disorder with more than 70 known causative genes, some of them shared with other non-syndromic retinal dystrophies (e.g. Leber congenital amaurosis, LCA). The identification of RP genes has increased steadily during the last decade, and the 30% of the cases that still remain unassig...

Coscinasterias is a cosmopolitan genus of large asteroid sea stars with the ability of somatic fission as a clonal reproductive strategy. During fission, the animals tear themselves apart across their central disc, where the lost body parts are regenerated afterwards. Here, we have sequenced and subsequently analysed the transcriptome of the coelom...

Conventional wastewater treatment does not completely remove and/or inactive viruses; consequently, viruses excreted by the population can be detected in the environment. This study was undertaken to investigate the distribution and seasonality of human viruses and faecal indicator bacteria (FIB) in a river catchment located in a typical Mediterran...

The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable refere...

Xenacoelomorpha is, most probably, a monophyletic group that includes three clades: Acoela, Nemertodermatida and Xenoturbellida. The group still has contentious phylogenetic affinities; though most authors place it as the sister group of the remaining bilaterians, some would include it as a fourth phylum within the Deuterostomia. Over the past few...

Xenacoelomorpha is, most probably, a monophyletic group that includes three clades: Acoela, Nemertodermatida and Xenoturbellida. The group still has contentious phylogenetic affinities; though most authors place it as the sister group of the remaining bilaterians, some would include it as a fourth phylum within the Deuterostomia. Over the past few...

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a...

Matrix metalloproteinases (MMPs) are major executors of extracellular matrix remodeling and, consequently, play key roles in the response of cells to their microenvironment. The experimentally accessible stem cell population and the robust regenerative capabilities of planarians offer an ideal model to study how modulation of the proteolytic system...

Smed-mt-mmpB(RNAi) does not produce any phenotype. (A) Bright-field images of head and tail fragments at 5 days of regeneration in S. mediterranea. Control: β-gal(RNAi), mt-mmpA/mt-mmpB(RNAi): simultaneous Smed-mt-mmpA(RNAi) and Smed-mt-mmpB(RNAi). No morphological difference between the β-gal(RNAi) controls and Smed-mt-mmpB(RNAi) animals is detect...

Characterization of mt-mmpA(RNAi) phenotype in D. japonica, at 5 days of regeneration. (A) Bright–field images of head and tail fragments, after two rounds of dsRNA injections and amputation. Control: β-gal(RNAi) fragments. Following Dj-mt-mmpA(RNAi) the fragments show a significantly reduced blastema. Relative blastema size between Dj-mt-mmpA(RNAi...

Analysis of efficiency and specificity of each RNAi silencing in S. mediterranea. (A) Smed-mmp1 expression level as detected by WISH and Real Time RT-PCR in controls and Smed-mmp1(RNAi) demonstrates the efficiency of the treatment. Moreover, Smed-mmp1(RNAi) does not affect the expression level of Smed-mmp2, Smed-mt-mmpA and Smed-mt-mmpB. (B) Smed-m...

Immunostaining with anti-H3P antibody in Smed-mt-mmpA(RNAi) fragments, at 6 days of head regeneration. (A) β-gal(RNAi) control. (B) Smed-mt-mmpA(RNAi). After Smed-mt-mmpA(RNAi) silencing the regenerative blastema results reduced in size and a smaller number of anti-H3P-positive cells migrated into the blastema with respect to the control. Scale bar...

Amino acid sequence alignment of MMP1, MMP2, MT-MMPA and MT-MMPB from S. mediterranea and D. japonica. (A) S. mediterranea SMED-MMP1 and D. japonica DJ-MMP1. SMED-MMP1 is 495 amino acids in length. The pro-domain consists of 80 amino acids (1 to 80) and contains the pro-peptide cleavage site in position 18 and an atypical cysteine switch (GRCGGKD,...

Expression pattern of mmp1 and mmp2 in S. mediterranea. WISH depicting the distribution of Smed-mmp1 and Smed-mmp2 expression on intact planarians. (A) Smed-mmp1 antisense probe. (B) Smed-mmp2 antisense probe. Anterior to the left. To characterize further the cell types expressing Smed-mmp1 and Smed-mmp2, ISH experiments were carried out on wax lon...

Expression of mt-mmpA in S. mediterranea. (A) WISH with antisense Smed-mt-mmpA probe in intact planarians detects widespread expression, while lack of signal with sense Smed-mt-mmpA probe confirms the specificity of the expression. Anterior is up. Scale bar: 1 mm. (B) Real Time RT-PCR analysis of Smed-mt-mmpA expression level in lethally-irradiated...

Smed-mmp1(RNAi) does not inhibit regeneration. Bright-field images of head and tail fragments of water-injected controls and following Smed-mmp1(RNAi), as visualized at 3 days after amputation in S. mediterranea. Neither blastema formation nor blastema size are altered in Smed-mmp1(RNAi) regenerating head and tail fragments. Anterior is up. Scale b...

TUNEL assay after Dj-mmp1(RNAi) in D. japonica. Apoptotic cells are detected as red spots in longitudinal cryosections, visualized at the pre-pharyngeal level in an intact D. japonica. (A) A water-injected control. (B) A Dj-mmp1(RNAi) planarian. e: eye. Anterior is to the left. Consistent with the data obtained in S. mediterranea, a decrease in the...

Intron-exon organization and phylogeny of the planarian mmp genes. Exons shown in orange boxes are joined by introns denoted by grey lines. Green boxes represent 3′ UTRs. The number of the exon is indicated in the boxes. The diagram is to scale. Kbp: kilo base pairs. (A) Smed-mmp1 is organized in 10 exons and 9 introns. (B) Smed-mmp2 is organized i...

Characterization of Smed-mt-mmpA(RNAi) phenotypes in intact S. mediterranea. (A) Bright-field image of a β-gal(RNAi) control and a Dj-mt-mmpA(RNAi) planarian, at 8 days after the first injection. Dorsal view, anterior is up. Scale bar: 1 mm. (B) Real Time RT-PCR analysis reveals that the expression level of both Smedwi-1 and Smed-prog-1 is not affe...

UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M transition of the cell cycle....