Biology subjects

de la Cruz, F.

Publications and source records attributed to de la Cruz, F..

17 recordsLinked to original sources

bioRxiv2026

Increases in therapist-patient physiological synchrony after dog-patient contact in canine-assisted psychotherapy: an exploratory pilot study

Introduction: Canine-assisted psychotherapy (CAP) introduces a therapy dog into the therapist-patient relationship and may influence interpersonal processes underlying therapeutic change. This exploratory pilot study investigated whether direct patient-dog contact is associated with changes in autonomic arousal and therapist-patient physiological synchrony. Methods: Skin conductance was recorded from 18 patients with depressive disorders and one therapist during 53 routine CAP sessions. A total of 192 episodes of direct patient-dog contact were identified from video recordings. Three-minute periods before and after each contact onsets were compared. Skin conductance level (SCL), skin conductance fluctuations (SCF), and therapist-patient physiological synchrony were assessed using zero-lag correlation and maximum cross-correlation. Sliding-window analyses examined temporal changes in synchrony, while randomly selected pseudo-events served as controls. Results: SCL increased significantly following dog contact in both patients and the therapist, whereas SCF rate over 3 min did not change significantly. Therapist-patient physiological synchrony increased significantly after dog contact, as indicated by both zero-lag correlation and maximum cross-correlation. Sliding-window analyses confirmed these increases and showed a reduction in the temporal lag between the two physiological signals. Importantly, increases in synchrony were significantly greater following genuine dog-contact events than following pseudo-events. Discussion: Direct physical contact between patients and therapy dogs is followed by increased autonomic arousal and enhanced therapist-patient physiological synchrony. These findings suggest that dog-patient contact may function as an interactional event that promotes physiological coordination and interpersonal attunement within the therapeutic dyad.

physiology↗

bioRxiv2025

Jaccard Index Network Analysis for pangenome analysis

ii.Summary/AbstractJaccard Index Network Analysis (JINA) is a comprehensive workflow designed to explore bacterial genome relationships through an integrated network-based approach. This workflow combines existing tools such as Jaccard Index (1), Gephi (2) and Pangraph (3). By integrating these methodologies into a unified framework, JINA enables efficient visualization and stratification of genomic data, facilitating the identification of meaningful patterns, groups, and associations within bacterial populations. The use of JINA ensures precision in capturing genomic variation including single nucleotide polymorphisms, insertions and deletions. While JINA does not implement Gephi, BLAST, and PanGraph directly in a single software, it guides their coordinated use to analyze and interpret genomic data effectively.

bioinformatics↗

bioRxiv2025

Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial condition influenced by the gut microbiome (GM). While previous studies have reported inconsistent associations between MASLD and key microbial clades using low-resolution 16S rRNA profiling, we employed high-resolution metagenomic sequencing and multi-marker taxonomic classification across three independent cohorts to identify robust microbial and functional signatures of MASLD. We consistently detected a depletion of Agathobacter rectalis, a known butyrate producer, in MASLD patients. Functionally, MASLD was characterized by a depletion of genes involved in butyrate and methane biosynthesis-particularly within the crotonyl-butyryl-CoA axis-alongside an enrichment of genes driving the production of endogenous alcohols such as ethanol and 1-propanol. Genes encoding these fermentative pathways, often organized in operons like pdu and tor, were more abundant in MASLD samples, indicating a potential shift toward alcohol-producing metabolism. These geno-metabolic changes were accompanied by a broader displacement of beneficial taxa and an increase in accessory gene content across the GM, underscoring the limitations of taxonomy-based disease associations. Many of the differentially abundant genes were also found on plasmids, suggesting that horizontal gene transfer contributes to strain-level metabolic variability relevant to MASLD progression. Our findings support a model in which GM-driven metabolic shifts-rather than taxonomic changes alone-play a central role in MASLD pathogenesis, highlighting the importance of functional and mobile genetic element (MGEs) profiling for uncovering mechanistic links between the microbiome and liver disease.

microbiology↗

bioRxiv2025

The leading region of many conjugative plasmids is depleted in restriction-modification targets

To successfully transfer into a recipient, conjugative plasmids must overcome the new cells defense mechanisms. The leading region of many plasmids - the first part to enter the recipient - is highly enriched in anti-defense genes. Here, we investigate whether selective pressure from defense systems has also affected its sequence composition. We consider two possibilities: greater target depletion (to avoid triggering target-based defense systems) or greater codon adaptation (to more quickly express anti-defense genes). We analyse the leading region of 1,751 conjugative plasmids belonging to 13 plasmid taxonomic units (PTUs) present in the bacterial order Enterobacterales. First, we investigate GC content and possible depletion of short palindromic motifs (4-8bp) which could be a signature of selective pressure from Type II restriction-modification systems, and find evidence of depletion in certain PTUs. Then we use the codon adaptation index (CAI) to assess codon usage and find that different conjugative PTUs shown different patterns. We show that the leading region of plasmids with MOB-F and MOB-P relaxases is more adapted to optimal host codon usage, consistent with a selective pressure for translational efficiency in anti-defense genes that are transcribed while still single-stranded DNA. In particular, anti-restriction genes in the leading region have high CAI, and we use this fact to identify a single-stranded promoter in the F plasmid. Our findings uncover a new facet of plasmid evolution and emphasise the intensity of the selective pressure that plasmids face from defense systems.

microbiology↗

bioRxiv2025

Vertical transmission of core endophytes through the seeds

Plant-associated microorganisms, particularly endophytes, are essential for plant health and development. Endophytic microbiota is intimately associated with host plants colonizing various tissues, including seeds. Seed endophytes are particularly noteworthy because of their potential for vertical transmission. This pathway may play a role in the long-term establishment and evolution of stable bacteria-host interactions across plant generations. Hundreds of seed-bacteria associations have been recently uncovered; however, most seem to be transient or unspecific. While it is known that microorganisms can be transmitted from plant tissues to seeds and from seeds to seedlings, the experimental confirmation of bacterial transfer through successive plant generations remains unreported. In this study, we identified Pantoea as the unique core endophytic bacteria inhabiting the endosperms of 24 wheat seed samples originally harvested in different worldwide locations. Remarkably, Pantoea is the genus with the highest relative average abundance in wheat seeds (61%) and also in germinated seedlings grown under gnotobiotic conditions (30%). In the field, it was the only genus dwelling roots, shoots, spikes and seeds of 4 different wheat varieties tested and its abundance progressively increased across these tissues. This genuine pattern of vertical enrichment, which was not found in other common wheat-associated taxa, suggests a role in the transfer of these endophytic bacteria through the seeds. To confirm intergenerational transmission, parental plants were inoculated with labelled Pantoea isolates, which specifically colonized the next generations of Poaceae plants, experimentally demonstrating bacterial vertical inheritance to the offspring generations and suggesting transmission specificity.

microbiology↗

bioRxiv2024

Long-term evolution reveals the role of the circadian cycle in the environmental adaptation of cyanobacteria

Circadian clocks synchronize internal cellular states with diurnal rhythms. Widespread in bacteria and eukaryotes, they regulate a variety of physiological processes, from hormone secretion in animals to carbon fixation in photosynthetic organisms. The adaptive role of circadian clocks is assumed to stem from their ability to anticipate environmental change, yet their impact on ecological adaptation remains unclear. Here, we use experimental evolution to study the interplay between fitness and circadian regulation in the model cyanobacterium Synechococcus elongatus PCC 7942. After 1,200 generations under continuous, high-intensity illumination, we obtained a strain that grew six times faster than its ancestral counterpart. Genome sequencing revealed three mutations fixed in the population, two of which replicated the fast-growing phenotype in the wild-type. A deletion in SasA, a key circadian regulator, was essential for fast growth. Transcriptomic and metabolomic analyses revealed that this mutation perturbed the rhythmicity of the cycle, while simultaneously locking the cell in a transcriptomic response to high intensity illumination. A comparison with another fast- growing isolate, UTEX 2973, showed convergent transcriptomic states despite different driving mutations. Our results indicate that the clock acts not only as a timekeeping device, but also as an adaptive mechanism to optimize growth across diverse ecological conditions.

microbiology↗

bioRxiv2023

Hemispheric divergence of interoceptive processing across psychiatric disorders

Interactions between top-down attention and bottom-up visceral inputs are assumed to produce conscious perceptions of interoceptive states, and while each process has been independently associated with aberrant interoceptive symptomatology in psychiatric disorders, the neural substrates of this interface are unknown. We conducted a preregistered functional neuroimaging study of 46 individuals with anxiety, depression, and/or eating disorders (ADE) and 46 propensity-matched healthy comparisons (HC), comparing their neural activity across two interoceptive tasks differentially recruiting top-down or bottom-up processing within the same scan session. During an interoceptive attention task, top-down attention was voluntarily directed towards cardiorespiratory or visual signals, whereas during an interoceptive perturbation task, intravenous infusions of isoproterenol (a peripherally-acting beta-adrenergic receptor agonist) were administered in a double-blinded and placebo-controlled fashion to drive bottom-up cardiorespiratory sensations. Across both tasks, neural activation converged upon the insular cortex, localizing within the granular and ventral dysgranular subregions bilaterally. However, contrasting hemispheric differences emerged, with the ADE group exhibiting (relative to HCs) an asymmetric pattern of overlap in the left insula, with increased or decreased proportions of co-activated voxels within the left or right dysgranular insula, respectively. The ADE group also showed less agranular anterior insula activation during periods of bodily uncertainty (i.e., when anticipating possible isoproterenol-induced changes that never arrived). Finally, post-task changes in insula functional connectivity were associated with anxiety and depression severity. These findings confirm the dysgranular mid-insula as a key cortical interface where attention and prediction meet real-time bodily inputs, especially during heightened awareness of interoceptive states. Further, the dysgranular mid-insula may indeed be a "locus of disruption" for psychiatric disorders.

neuroscience↗

bioRxiv2023

Harnessing the pangenome for genomic surveillance: Salmonella enterica serotype Typhi as a paradigm

Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone - an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome - homology-by-admixture - could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution. Significance StatementBacterial relatedness is often measured and visualized using chromosomal comparison and phylogenetic trees. While valuable, this approach captures only the vertical evolutionary dimension and excludes genetic material acquired or lost through horizontal gene transfer. We present an approach for measuring and visualizing bacterial relatedness using all core and accessory genetic material and discuss the interpretation of resulting reticulate networks of bacterial genomes. In application to Salmonella Typhi, Jaccard Index Network Analysis revealed structure in populations of this pathogen that may be harnessed for public health applications. This approach captures both vertical and horizontal evolutionary dimensions, offering an intricate genetic framework for exploring pathogen evolution.

genomics↗

bioRxiv2023

Fundamental parameters governing the transmission of conjugative plasmids

Because their ability to spread infectiously, conjugative plasmids represent a major route for the propagation of antibiotic resistances. In the wild, there are hundreds of different plasmids, but their distribution, prevalence and host range are extremely variable. To understand the reasons behind these ecological differences, we need to obtain precise models for plasmid transmission dynamics. Here, we show that the dynamics of plasmid transmission follow a simple ecological model known as Hollings Type II Functional Response. Plasmid transmission dynamics can be faithfully captured using two parameters: the searching rate (the pace at which a donor bacterium encounters a suitable recipient) and the handling time (the time required for a donor to transfer the plasmid). By analyzing the dynamics of different plasmid prototypes, we show that these parameters are characteristic of the plasmid transfer machinery. Quantifying the dynamics of plasmid spread may shed light on the epidemiology of antibiotic resistance genes.

microbiology↗

bioRxiv2022

Characterization of the DNA binding domain of StbA, a key protein of a new type of DNA segregation system

Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 [A] resolution. It folds into an HTH DNA-binding motif, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.

microbiology↗

bioRxiv2021

Evolution of plasmid mobility: origin and fate of non-conjugative plasmids

Conjugation drives horizontal gene transfer of many adaptive traits across prokaryotes. Yet, only a fourth of the plasmids encode the functions necessary to conjugate autonomously, others being non-mobile or mobilizable by other elements. How these different plasmids evolve is poorly understood. Here, we studied plasmid evolution in terms of their gene repertoires and relaxases. We observed that gene content in plasmid varies rapidly in relation to the rate of evolution of relaxases, such that plasmids with 95% identical relaxases have on average fewer than 50% of homologs. The identification of 249 recent transitions in terms of mobility types revealed that they are associated with even greater changes in gene repertoires, possibly mediated by transposable elements that are more abundant in such plasmids. These changes include pseudogenization of the conjugation locus, exchange of replication initiators, and extensive gene loss. In some instances, the transition between mobility types also leads to the genesis of novel plasmid taxonomic units. Most of these transitions are short-lived, suggesting a source-sink dynamic, where conjugative plasmids constantly generate mobilizable and putatively non-mobilizable plasmids by gene deletion. Yet, in few cases such transitions resulted in the emergence of large clades of relaxases present only in mobilizable plasmids, suggesting successful specialization of these families in the hijacking of diverse conjugative systems. Our results shed further light on the huge plasticity of plasmids, suggest that many non-conjugative plasmids emerged recently from conjugative elements and allowed to quantify how changes in plasmid mobility shape the variation of their gene repertoires.

evolutionary biology↗

bioRxiv2020

COPLA, a taxonomic classifier of plasmids

The Plasmid Taxonomic Unit (PTU) concept is an initial step for a natural classification of plasmids. Here we present COPLA, a software for plasmid assignation to existing PTUs. To assess its performance, we used a sample of 1,000 plasmids missing from its current database. Overall, 41% of samples could be assigned an existing PTU (63% within the most abundant order, Enterobacterales), while 4% of samples could help to define new PTUs once COPLA database was updated.

bioinformatics↗

bioRxiv2019

ArdC protein overpasses the recipient hsdRMS restriction system broadening conjugation host range

Plasmids, when transferred by conjugation, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida, but not from E. coli to E. coli. Surprisingly, expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. Thus, ArdC has antirestriction activity against HsdRMS system, and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and in the presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity is not needed for antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggers an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies.

microbiology↗

bioRxiv2019

Comparative analysis of MOBQ4 plasmids demonstrates that MOBQ is a cis-acting-enriched relaxase protein family

A group of small mobilizable plasmids is increasingly being reported in epidemiology surveys of enterobacteria. Some of them encode colicins, while others are cryptic. All of them encode a relaxase belonging to a previously non-described group of the MOBQ class, MOBQ4. While highly similar in their mobilization module, two families with unrelated replicons can be distinguished, MOBQ41 and MOBQ42. Members of both groups were compatible between them and stably maintained in E. coli. MOBQ4 plasmids were mobilized by conjugation. They contain two transfer genes, mobA coding for the MOBQ4 relaxase and mobC, which was non-essential but enhanced the plasmid mobilization frequency. The origin of transfer was located between these two divergently transcribed mob genes. MPFI conjugative plasmids were the most efficient helpers for MOBQ4 conjugative transmission. No interference in mobilization was observed when both MOBQ41 and MOBQ42 were present in the same donor cell. Remarkably, MOBQ4 relaxases exhibited a cis-acting preference for their oriTs, a feature already observed in other MOBQ plasmids. These findings indicate that MOBQ4 plasmids can efficiently spread among enterobacteria aided by coresident IncI1, IncK and IncL/M plasmids, while ensuring their self-dissemination over highly-related elements.\n\nIMPORTANCEPlasmids are key vehicles of horizontal gene transfer and contribute greatly to bacterial genome plasticity. A group of plasmids, called mobilizable, is able to disseminate aided by helper conjugative plasmids. Here, we studied a group of phylogenetically-related mobilizable plasmids, MOBQ4, commonly found in clinically-relevant enterobacteria, uncovering the helper plasmids responsible for their dissemination. We found that the two plasmid species encompassed in the MOBQ4 group can coexist and transfer orthogonally, despite origin-of-transfer cross-recognition by their relaxases. Specific discrimination among their highly similar oriT sequences is guaranteed by the preferential cis activity of the MOBQ4 relaxases. Such strategy would be biologically relevant in a scenario of co-residence of non-divergent elements to favor self-dissemination.

microbiology↗

bioRxiv2018

Dynamical Task Switching in Cellular Computers

We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embeddingof multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.

synthetic biology↗

bioRxiv2018

Host range expansion and genetic plasticity drive the trade-off between integrative and extrachromosomal mobile genetic elements

Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where differential plasticity and transmissibility range explain the co-occurrence of integrative and extra-chromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element s host range.

evolutionary biology↗

bioRxiv2017

In-Depth Resistome Analysis by Targeted Metagenomics

We developed ResCap, a targeted sequence capture platform based on SeqCapEZ technology, to analyse resistomes and other genes related to antimicrobial resistance (heavy metals, biocides and plasmids). ResCap includes probes for 8,667 canonical resistance genes (7,963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), plus 2,517 relaxase genes (plasmid markers). Besides, it includes 78.600 genes homologous to the previous ones (47,806 for antibiotics and 30,794 for biocide or metals). ResCap enriched 279-fold the targeted sequences detected by metagenomic shotgun sequencing and improves their identification. Novel bioinformatic approaches allow quantifying \"gene abundance\" and \"gene diversity\". ResCap, the first targeted sequence capture specifically developed to analyse resistomes, enhances the sensitivity and specificity of available metagenomic methods to analyse antibiotic resistance in complex populations, enables the analysis of other genes related to antimicrobial resistance and opens the possibility to accurately study other complex microbial systems.

microbiology↗