Biology subjects

Dabad, M.

Publications and source records attributed to Dabad, M..

5 recordsLinked to original sources

bioRxiv2022

A TetR-like transcriptional regulator in Stenotrophomonas maltophilia involved in fatty acid metabolism is controlled by quorum sensing signals

Stenotrophomonas maltophilia is an environmental bacterium and it is also an emerging opportunistic multidrug-resistant pathogen. It uses the endogenous DSF quorum sensing (QS) system to coordinate population behaviors and to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. Whole-transcriptome sequencing analyses were performed for S. maltophilia K279a in the exponential and stationary phases as well as in exponential cultures after treatment with exogenous DSF or AHLs. The results revealed that at the beginning of the stationary phase 1673 genes are differentially expressed. COG analysis showed that most of these genes were enriched for energetic metabolism processes and regulation of gene expression. After adding DSF or AHLs, 28 or 82 genes were found deregulated, respectively, 22 of which upregulated by both autoinducers. Interestingly, among these later genes, 14 were also upregulated in the stationary phase. Gene functions regulated by all conditions include lipid and amino acid metabolism, stress response and signal transduction, nitrogen and iron metabolism, and adaptation to microoxic conditions. Among the common top upregulated QS core genes, a putative TetR-like regulator (Smlt2053) was selected for functional characterization. This regulator has been shown to control a narrow regulon, including its own operon. It was found to sense long-chain fatty acids, including the QS signal DSF, and regulate a {beta}-oxidation catabolic pathway. Overall, our findings provide clues on the role that the QS could have in S. maltophilia in the transition from the exponential to the stationary phase and bacterial fitness under high-density growth. IMPORTANCEThe quorum sensing system in Stenotrophomonas maltophilia, in addition to coordinating the bacterial population, controls virulence-associated phenotypes, such as biofilm formation, motility, protease production, and antibiotic resistance mechanisms. Biofilm formation is frequently associated with the persistence and chronic nature of nosocomial infections. In addition, biofilms exhibit high resistance to antibiotics, making treatment of these infections extremely difficult. The importance of studying the metabolic and regulatory systems controlled by quorum sensing autoinducers will make it possible to discover new targets to control pathogenicity mechanisms in S. maltophilia.

microbiology↗

bioRxiv2022

Finding heterogeneously methylated genomicregions using ONT reads

SummaryNanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here we exploit this property to look for regions where one can define subpopulations of cells based on methylation patterns. As a benchmark we run our clustering algorithm on known imprinted genes and show that the clustering based on methylation is consistent with the phasing of the genome; we then scan chromosome 15 looking for windows corresponding to heterogeneous methylation. We can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads. Availabilityhttps://github.com/EmanueleRaineri/releases Contactemanuele.raineri@cnag.crg.eu, simon.heath@cnag.crg.eu Supplementary informationTables, figures, and some further explanations of the algorithms are available as online supplementary information.

bioinformatics↗

bioRxiv2022

Novel method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Long-read whole genome sequencing is prohibitively expensive for mtDNA heteroplasmy detection and often does not recapitulate the full mtDNA length. Here we describe a method to target, multiplex and sequence full-length, native single-molecule the human mitochondrial genome utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks as barcodes with long-read sequencing, we implemented a protocol in an optimal setting for both high or low integrity genomic DNA to target the circular mitochondrial genome with extremely high coverage. Our analytical pipeline efficiently detects single nucleotide heteroplasmy, physically determines phase and can accurately disentangle complex deletion patterns. This workflow is a unique tool for studying mtDNA variation in health and disease, and will accelerate mitochondrial research.

genomics↗

bioRxiv2021

Protamine lacking piscine spermatozoa are transcriptionally active

Transcriptional quiescence of post-meiotic spermatozoa associated with protamine-mediated chromatin condensation is widely recognized in animals. How sperm acquire the extratesticular maturational competence to move and fertilize the egg is therefore thought to occur via non-transcriptional mechanisms. Here, using transcriptional profiling during spermatozoon differentiation in a fish that does not condense chromatin with protamines, we uncover spatially distinct roles of the GnRH receptor and PDGF signaling pathways between the somatic epithelia of the extratesticular ducts and the maturing spermatozoa. In vitro induction and inhibition experiments demonstrate that the endocrine signaling pathways are conserved in different lineages of fish and activate de novo transcription of spermatozoon genes required for the acquisition of full motility. These experiments further confirmed that mitochondrial translation is important for sperm maturation in anamniotes as in amniotes, but that transcriptional quiescence of post-meiotic spermatozoa is not a pan vertebrate phenomenon. On the contrary, the data show that the identified signal transduction pathways between the soma and the sperm upregulate effector genes essential for maturational competence and male fertility.

cell biology↗

bioRxiv2021

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data

MotivationDNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods employ either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination. ResultsHere we present DeepMP, a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on E. coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets. AvailabilityDeepMP is implemented and freely available under MIT license at github.com/pepebonet/DeepMP Contactjose.bonet@irbbarcelona.org -- mandiche@kth.se

bioinformatics↗