Biology subjects

Torralba, M.

Publications and source records attributed to Torralba, M..

9 recordsLinked to original sources

bioRxiv2026

Alpha oscillations support attentional orienting while beta supports perceptual decision-making.

Visuospatial attention enables the selective allocation of cognitive resources to relevant stimuli. A well-established neural signature of attentional shifts is the lateralised modulation of occipito-parietal alpha power, with decreases over the hemisphere contralateral to the attended location and increases over the ipsilateral hemisphere. However, growing evidence suggests that multiple oscillatory mechanisms contribute to attentional deployment, including beta-band activity. A key unresolved question that remains is whether the same neural rhythms support the deployment of attention and the perceptual decisions that follow. Here, we recorded EEG in 26 participants (22 females) during covert visuospatial orienting and investigated how alpha- and beta-band dynamics relate to behavioural measures, namely perceptual sensitivity (d') and decision criterion (c), and whether attended location could be preferentially decoded from alpha- or beta-band activity. We found that pre-target beta phase significantly predicted decision criterion at earlier pre-target intervals, whereas perceptual sensitivity was predicted closer to target onset, suggesting that beta is related to both sensory gain and the perceptual decision. In contrast, decoding analyses revealed that attended location was most strongly discriminable from alpha-band activity, as confirmed by time-frequency analysis of decoding accuracy. Together, these findings suggest a functional dissociation between oscillatory mechanisms supporting attentional orienting and perceptual decision-making. Whereas alpha-band activity primarily reflects the allocation of attention, beta-band dynamics predict trial-by-trial variability in perceptual decisions. Significance StatementAlthough alpha oscillations are commonly viewed as the principal neural mechanism underlying visuospatial attention, mounting evidence shows that such a complex function requires the involvement of other brain rhythms. Our findings show that different components of attention are associated with distinct brain rhythms. While alpha activity primarily reflects where attention is allocated, beta oscillations relate to how sensory information is transformed into perceptual decisions. These results suggest that attentional orienting and perceptual decision-making rely on dissociable neural processes, providing a comprehensive account of how brain oscillations support goal-directed behaviour.

neuroscience↗

bioRxiv2020

The phase of Theta oscillations modulates successful memory formation at encoding

Several past studies have shown that attention and perception can depend upon the phase of ongoing neural oscillations at stimulus onset. Here, we extend this idea to the memory domain. We tested the hypothesis that ongoing fluctuations in neural activity have an impact on memory encoding using a picture paired-associates task to gauge episodic memory performance. Experiment 1 capitalized on the principle of phase reset. We tested if subsequent memory performance fluctuates rhythmically, time-locked to a reset cue presented before the to-be-remembered pairs. We found indication that behavioral performance was periodically and selectively modulated at theta frequency ([~]4 Hz). In Experiment 2 we focused on prestimulus ongoing activity using scalp EEG recorded while participants performed the pair-associate task. We analyzed subsequent memory performance as a function of theta and alpha activity around the presentation of the to-be-remembered pairs. The results of the pre-registered analyses, using large electrode clusters and generic spectral ranges, returned null results of prestimulus phase-behavior correlation. However, we found that post-stimulus theta-power modulations in left frontal scalp predicted subsequent memory performance. This post-stimulus effect in theta power was used to guide a post-hoc prestimulus phase analysis, narrowed down to more precise scalp location and frequency. This analysis returned a correlation between prestimulus theta phase and subsequent memory. Altogether, these results suggest that the prestimulus theta activity at encoding has an impact on later memory performance.

neuroscience↗

bioRxiv2020

Can the occipital alpha-phase speed up visual detection through a real-time EEG-based brain-computer interface (BCI)?

Electrical brain oscillations reflect fluctuations in neural excitability. Fluctuations in the alpha band (, 8-12 Hz) in the occipito-parietal cortex are thought to regulate sensory responses, leading to cyclic variations in visual perception. Inspired by this theory, some past and recent studies have addressed the relationship between -phase from extra-cranial EEG and behavioural responses to visual stimuli in humans. The latest studies have used offline approaches to confirm -gated cyclic patterns. However, a particularly relevant implication is the possibility to use this principle online for real-time neurotechnology, whereby stimuli are time-locked to specific -phases leading to predictable outcomes in performance. Here we aimed at providing a proof-of-concept for such real-time neurotechnology. Participants performed a speeded response task to visual targets that were presented upon a real-time estimation of the -phase via an EEG closed-loop brain-computer interface (BCI). We predicted, according to the theory, a modulation of reaction times (RTs) along the -cycle. Our BCI system achieved reliable trial-to-trial phase-locking of stimuli to the phase of individual occipito-parietal -oscillations. Yet, the behavioural results did not support a consistent relation between RTs and the phase of the -cycle neither at group nor single participant levels. We must conclude that although the -phase might play a role in perceptual decisions from a theoretical perspective, its impact on EEG-based BCI application appears negligible.

neuroscience↗

bioRxiv2019

Neural evidence of cognitive conflict during binocular rivalry

To make sense of ambiguous and, at times, incomplete sensory input, the brain relies on a process of active interpretation. At any given moment, only one of several possible perceptual outcomes prevails in our conscious experience. Our hypothesis is that the competition between alternative representations induces cognitive conflict, eventually leading to fluctuations between different perceptual interpretations. We used binocular rivalry, a popular protocol to probe changes in perceptual awareness [1-3] and drew on the conflict monitoring theory, which holds that cognitive control is invoked by the detection of conflict during information processing. We looked for an increase in power of fronto-medial theta oscillations (5-7 Hz), an established EEG marker of conflict detection [4-7]. Our results show that fm-theta power increases right before perceptual alternations and decreases thereafter, suggesting that conflict monitoring is related to perceptual competition. Furthermore, to investigate conflict resolution via attentional engagement, as held by the conflict monitoring theory [8], we also looked for changes in parieto-occipital alpha oscillations (8-12 Hz) associated to perceptual switches. These oscillations have been associated to attention allocation via functional inhibition in sensory cortices [9-12]. The power of parieto-occipital alpha was inversely related to that of fm-theta, reflecting periods of high inter-ocular inhibition during stable perception, and low inhibition around moments of perceptual change. Our findings validate a prediction made 20 years ago in the seminal paper formulating the conflict monitoring theory, and establish a previously unknown link between conflict mechanisms and the processes leading to perceptual awareness. HighlightsO_LIBinocular rivalry induces conflict between competing perceptual representations C_LIO_LIMid-frontal theta power increases around the resolution of perceptual conflict C_LIO_LIPosterior alpha decreases reflect neural excitability around perceptual switches C_LIO_LIThe results link cognitive conflict theory with perceptual inference C_LI

neuroscience↗

bioRxiv2019

The concentration of heterotrophic growth substrates in culture medium is a crucial determinant of the culturability of subsurface soil microbes

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted extracted cells into one of two custom-designed defined growth media that differed only by a 100-fold difference in the concentration of amino acids and organic carbon. Across both media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria. The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria. We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically-divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic-acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and the concentration of substrates in culture medium influences the culturability of specific microbial lineages. ImportanceIsolating environmental microbes and studying their physiology under controlled conditions is an essential aspect of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities--the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.

microbiology↗

bioRxiv2019

Nutritional Immunity and Antibiotic Drug Treatments Influence Microbial Composition but Fail to Eliminate Urethral Catheter Biofilms in Recurrently Catheterized Patients

Polymicrobial biofilms that form on indwelling urethral catheters used by neurogenic bladder patients are known to recur following catheter replacements. Uropathogens dominate in catheter biofilms (CBs), grow and disperse as multi-cellular aggregates. Their microbial complexity, the characteristics of host immune responses and the molecular crosstalk in this ecosystem are incompletely understood. By surveying eight patients over up to six months with meta-omics analysis methods, we shed new light on the longitudinal microbial dynamics in CBs and the microbial-host crosstalk. There was evidence of chronic innate immune responses in all patients. Pathogens dominated the microbial contents. Proteus mirabilis often out-competed other species in cases of salt encrustation of catheters. The examination of proteomes in CBs and associated urinary pellets revealed many abundant bacterial systems for transition metal ion (TMI) acquisition. TMIs are sequestered by effector proteins released by activated neutrophils and urothelial cells, such as lactotransferrin and calgranulins, which were abundant in the host proteomes. We identified positive quantitative correlations among systems responsible for siderophore biosynthesis, TMI/siderophore uptake and TMI cellular import in bacterial species, suggesting competition for TMIs to support their metabolism and growth in CBs. Enterococcus faecalis was prevalent as a cohabitant of CBs and expressed three lipoproteins with apparent TMI acquisition functions. Fastidious anaerobic bacteria such as Veillonella, Actinobaculum, and Bifidobacterium grew in CB communities that appeared to be oxygen starved. Finally, antibiotic drug treatments were shown to influence microbial composition of CBs but failed to prevent re-colonization of urethral catheters with persisting and/or drug-resistant newly emerging pathogens.

microbiology↗

bioRxiv2018

Longitudinal Surveys Show that Urethral Catheters Harbor Recurrent Polymicrobial Biofilms with Cooperative and Competitive Behaviors Among Cohabitating Pathogens

The analysis of catheter biofilms (CBs) from patients with neurogenic bladder disorders revealed persistent colonization by polymicrobial communities. The recurrence of bacterial species in the CBs of sequentially replaced catheters suggests urothelial reservoirs responsible for recolonization of the catheter surface. Proteomic data for CB samples were indicative of chronic inflammation in the patients urinary tracts via neutrophil and eosinophil infiltration and epithelial cell exfoliation. These host defense pathways, effective in killing pathogens during uncomplicated urinary tract infection, failed to eliminate CBs. Intermittent antibiotic drug treatment had different outcomes: either replacement of drug-susceptible by drug-tolerant bacteria or transient microbial biomass reduction followed by resurgence of the previously colonizing bacteria. Proteins that sequester iron and zinc such as lactotransferrin, lipocalin-2 and calprotectin were abundant in the patients CBs and urine sediments. Indicative of a host-pathogen battle for bivalent metal ions, acquisition and transport systems for such ions were highly expressed by many organisms residing in CBs. Species part of the Enterococcaceae and Aerococcaceae families, generally not well-characterized in their ability to synthesize siderophores, frequently cohabitated biofilms dominated by siderophore-producing Enterobacteriaceae. In support of metal acquisition cooperativity, we noticed positive abundance correlations for a Proteus mirabilis yersiniabactin-type siderophore system and two Enterococcus faecalis ABC transporters. Distinct bacterial strains highly expressed known or putative cytotoxins that appeared to compromise the survival of co-resident bacteria, e.g. a P. mirabilis hemolysin and Pseudomonas aeruginosa type 6 secretion and pyoverdin biosynthesis systems. In conclusion, there is support for cooperative and competitive behaviors among bacteria cohabitating CBs.

microbiology↗

bioRxiv2018

Supragingival plaque microbiome ecology and functional potential in the context of health and disease

To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely-related previously-uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology and our results provide the information needed for next generation diagnostic tools and therapeutics for caries.

microbiology↗

bioRxiv2017

Microbial Metagenome Of Urinary Tract Infection

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora in infection and health, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while whole genome shotgun sequencing data was successfully generated for samples from 49 participants. Analysis of these datasets supports the definition of the patterns of infection and colonization/contamination. Although 16S rDNA sequencing was more sensitive, whole genome shotgun sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by whole genome shotgun sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses revealed cases of infection with potential pathogens (e.g., Alloscardovia sp, Actinotignum sp, Ureaplasma sp) that are often missed during routine urine culture due to species specific growth requirements. We also observed gender differences in the microbial metagenome. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to comprehensively and quantitatively describe the urinary microbiome.

microbiology↗