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Smith, R. J.

Publications and source records attributed to Smith, R. J..

18 recordsLinked to original sources

Functional remodeling of the parasubthalamic nucleus drives alcohol drinking escalation in dependence

The neurocircuitry changes mediating the development and maintenance of an alcohol use disorder are complex and dynamic. The parasubthalamic nucleus (PSTN), a small nucleus of the posterior lateral hypothalamus best known for suppressing appetite, is interconnected with brain regions disrupted in addiction; yet its potential role in the regulation of alcohol consumption had never been examined. Here we show that the PSTN exerts potent control over alcohol drinking in mice. Remarkably, the influence of endogenous PSTN activity on voluntary alcohol consumption switches from inhibitory to stimulatory upon induction of alcohol dependence. Among PSTN cells, Crh neurons represent a unique subpopulation that promotes alcohol drinking and fires more in dependent mice. Alcohol intake escalation driven by PSTN Crh neurons involves thalamic output and behavioral disinhibition. Based on our results, PSTN Crh neurons could represent a critical node in the brain circuitry overactive in alcohol addiction driven by reward seeking in humans.

neuroscience↗

EEG Functional Connectivity as a Marker of Evolution from Infantile Epileptic Spasms Syndrome to Lennox-Gastaut Syndrome

Background and ObjectivesTimely diagnosis and effective treatment of Lennox-Gastaut Syndrome (LGS) improve prognosis and lower healthcare costs, but the transition from infantile epileptic spasms syndrome (IESS) to LGS is highly variable and insidious. Objective biomarkers are needed to monitor this progression and guide clinical decision making. MethodsWe retrospectively collected longitudinal EEG data at the Childrens Hospital of Orange County from fifteen children who were diagnosed with IESS and later with LGS between 2012 and 2021. EEGs were from IESS and LGS diagnoses, between the two diagnoses, and following LGS diagnosis. Functional connectivity networks were calculated using a cross-correlation-based method and assessed relative to diagnostic timepoint, treatment response, presence of clinical markers of disease, age, and amplitude of interictal spikes. ResultsConnectivity strength was high at LGS diagnosis and decreased after favorable response to treatment, but it remained stable or increased when response was unfavorable. In all subjects, connectivity strength was higher at the time of LGS diagnosis than at the preceding timepoint. Presence of clinical markers of LGS were associated with high connectivity strength, but no single marker predicted connectivity strength. DiscussionComputational EEG analysis can be used to map the evolution from IESS to LGS. Changes in connectivity may enable prediction of impending LGS and treatment response monitoring, thus facilitating earlier LGS treatment and guiding medical management. Key pointsO_LIEEG functional connectivity analysis can track progression from infantile epileptic spasms syndrome (IESS) to Lennox-Gastaut Syndrome (LGS). C_LIO_LIHigh connectivity strength at LGS diagnosis decreases with favorable treatment response but remains high with poor response. C_LIO_LIClinical LGS markers correlate with high connectivity, but no single marker predicts connectivity strength. C_LIO_LIEEG functional connectivity analysis may help predict LGS onset, enabling early intervention and improving prognosis. C_LI

neuroscience↗

A Method for Electrical Stimulus Artifact Removal Exploiting Neural Refractoriness: Validation by Contrasting Cathodic and Anodic Stimulation

ObjectiveTo present a novel method for removing stimulus transient that exploits the absolute refractory period of electrically excitable neural tissues. BackgroundElectrical stimulation often generates significant signal artifacts that can obscure important physiological signals. Removal of the artifact and understanding latent information from these signals could provide objective measures of circuit engagement, potentially driving advancements in neuromodulation research and therapies. MethodsWe conducted intracranial physiology studies on five consecutive patients with Parkinsons disease who underwent deep brain stimulation (DBS) surgery as part of their routine care. Monopolar stimuli (either cathodic or anodic) were delivered in pairs through the DBS electrode across a range of inter-stimulus intervals. Recordings from adjacent unused electrode contacts used broadband sampling and precise synchronization to generate a robust template for the stimulus transient during the absolute refractory period. These templates of stimulus transient were then subtracted from recordings at different intervals to extract and analyze the residual neural potentials. ResultsAfter artifact removal, the residual signals exhibited absolute and relative refractory periods with timing indicative of neural activity. Cathodic and anodic DBS pulses generated distinct patterns of local tissue activation, showing phase independence from the prior stimulus. The earliest detectable neural responses occurred at short peak latencies (ranging from 0.19 to 0.38 ms post-stimulus) and were completely or partially obscured by the stimulus artifact prior to removal. Cathodic stimuli produced stronger local tissue responses than anodic stimuli, aligning with clinical observations of lower activation thresholds for cathodic stimulation. However, cathodic and anodic pulses induced artifact patterns that were equivalent but opposite. InterpretationThe proposed artifact removal technique enhances prior approaches by allowing direct measurement of local tissue responses without requirements for stimulus polarity reversal, template scaling, or specialized filters. This approach could be integrated into future neuromodulation systems to visualize stimulus-evoked neural potentials that would otherwise be obscured by stimulus artifacts.

bioengineering↗

Punishment resistance for cocaine is associated with inflexible habits in rats

Addiction is characterized by continued drug use despite negative consequences. In an animal model, a subset of rats continues to self-administer cocaine despite footshock consequences, showing punishment resistance. We sought to test the hypothesis that punishment resistance arises from failure to exert goal-directed control over habitual cocaine seeking. While habits are not inherently permanent or maladaptive, continued use of habits under conditions that should encourage goal-directed control makes them maladaptive and inflexible. We trained male and female Sprague Dawley rats on a seeking-taking chained schedule of cocaine self-administration (2 h/day). We then exposed them to 4 days of punishment testing, in which footshock (0.4 mA, 0.3 s) was delivered randomly on one-third of trials, immediately following completion of seeking and prior to extension of the taking lever. Before and after punishment testing (4 days pre-punishment and [≥]4 days post-punishment), we assessed whether cocaine seeking was goal-directed or habitual using outcome devaluation via cocaine satiety. We found that punishment resistance was associated with continued use of habits, whereas punishment sensitivity was associated with increased goal-directed control. Although punishment resistance was not predicted by habitual responding pre-punishment, it was associated with habitual responding post-punishment. In parallel studies of food self-administration, we similarly observed that punishment resistance was associated with habitual responding post-punishment but not pre-punishment. These findings indicate that punishment resistance is related to habits that have become inflexible and persist under conditions that should encourage a transition to goal-directed behavior.

neuroscience↗

Drug Reinforcement Impairs Cognitive Flexibility by Inhibiting Striatal Cholinergic Neurons

The mechanisms underlying the reduction in cognitive flexibility associated with reinforcement of addictive substance use are unknown. This reinforcement is mediated by substance-induced synaptic plasticity in direct-pathway medium spiny neurons (dMSNs) that project to the substantia nigra (SNr). Cognitive flexibility is mediated by cholinergic interneurons (CINs), which receive extensive local inhibition from the striatum. Here, we report that cocaine or alcohol administration caused a long-lasting potentiation of local inhibitory dMSN[->]CIN transmission in the dorsomedial striatum (DMS), a brain region critical for goal-directed behavior and cognitive flexibility. This dMSN[->]CIN potentiation reduced CIN firing activity. Furthermore, chemogenetic and time-locked optogenetic inhibition of DMS CINs suppressed cognitive flexibility in an instrumental reversal learning task. Importantly, rabies-mediated tracing and physiological studies revealed that SNr-projecting dMSNs, which mediate reinforcement, sent axonal collaterals to inhibit DMS CINs, which mediate flexibility. Our findings demonstrate that the local inhibitory dMSN[->]CIN circuit mediates a reinforcement-induced reduction in cognitive flexibility. HIGHLIGHTSO_LICocaine reinforcement inhibits striatal cholinergic interneurons (CINs) and impairs cognitive flexibility. C_LIO_LIOptogenetic and chemogenetic CIN inhibition impairs cognitive flexibility. C_LIO_LIReinforcement behaviors potentiate inhibitory transmission from direct-pathway medium spiny neurons (dMSNs) to CINs. C_LIO_LISubstantia nigra-projecting dMSNs mediate reinforcement and also send collaterals that inhibit CINs. C_LI

neuroscience↗

A bifunctional kinase-phosphatase module integrates mitotic checkpoint and error-correction signalling to ensure mitotic fidelity

Two major mechanisms have evolved to safeguard genome stability during mitosis: the mitotic checkpoint delays mitosis until all chromosomes have attached to microtubules, and the kinetochore-microtubule error-correction pathway keeps this attachment process free from errors. We demonstrate here that the optimal strength and dynamics of both processes is set by a kinase-phosphatase pair (PLK1-PP2A) that engage in negative feedback on the BUB complex. Uncoupling this homeostatic feedback to skew the balance towards PLK1 produces a strong checkpoint, weak microtubule attachments, and mitotic delays. Conversely, skewing the balance towards PP2A causes a weak checkpoint, strong microtubule attachments, and chromosome segregation errors. The number of MELT motifs on the KNL1 signalling scaffold sets the optimal levels of each enzyme, because engineering KNL1 to recruit too many BUB complexes increases KNL1-PLK1/PP2A levels, and enhances checkpoint/microtubule attachment strength. In contrast, recruiting too few BUB complexes lowers KNL1-PLK1/PP2A, and decreases checkpoint/microtubule attachment strength. Both of these situations are associated with chromosome segregation errors. Together, these data demonstrate how a single bifunctional kinase-phosphatase module integrates two major mitotic processes to help preserve genome stability.

cell biology↗

Heavy metals in moss guide environmental justice investigation: a case study using community science in Seattle, WA, USA

Heavy metals concentrations often vary at small spatial scales not captured by air monitoring networks, with implications for environmental justice in industrial-adjacent communities. Pollutants measured in moss tissues are commonly used as a screening tool to guide use of more expensive resources, like air monitors. Such studies, however, rarely address environmental justice issues or involve the residents and other decision-makers expected to utilize results. Here, we piloted a community science approach, engaging over 55 people from nine institutions, to map heavy metals using moss in two industrial-adjacent neighborhoods. This area, long known for disproportionately poor air quality, health outcomes, and racial inequities, has only one monitor for heavy metals. Thus, an initial understanding of spatial patterns is critical for gauging whether, where, and how to invest further resources towards investigating heavy metals. Local youth led sampling of the moss Orthotrichum lyellii from trees across a 250x250-m sampling grid (n = 79) and generated data comparable to expert-collected samples (n = 19). We mapped 21 chemical elements measured in moss, including 6 toxic priority metals: arsenic, cadmium, chromium, cobalt, lead, and nickel. Compared to other urban O. lyellii studies, local moss had substantially higher priority metals, especially arsenic and chromium, encouraging community members to investigate further. Potential hotspots of priority metals varied somewhat but tended to peak near the central industrial core where many possible emissions sources, including legacy contamination, converge. Informed by these findings, community members successfully advocated regulators for a second study phase - a community-directed air monitoring campaign to evaluate residents exposure to heavy metals - as is needed to connect moss results back to the partnerships core goal of understanding drivers of health disparities. This follow-up campaign will measure metals in the PM10 fraction owing to clues in the current study that airborne soil and dust may be locally important carriers of priority metals. Future work will address how our approach combining bioindicators and community science ultimately affects success addressing longstanding environmental justice concerns. For now, we illustrate the potential to co-create new knowledge, to help catalyze and strategize next steps, in a complex air quality investigation.

scientific communication and education↗

Genetic assimilation of ancestral plasticity during parallel adaptation

Phenotypic plasticity in ancestral populations is hypothesised to facilitate adaptation, but evidence supporting its contribution is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel genetic and phenotypic adaptive changes has not been explored. The most general finding is that nearly all ancestral gene expression plasticity is reversed following adaptation, but this is usually examined transcriptome-wide rather than focused on the genes directly involved in adaptation. We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared to ancestral, zinc-sensitive plants. Our experiments show that reinforcement of ancestral plasticity plays an influential role in the evolution of plasticity in derived populations and, surprisingly, one third of constitutive differences between ecotypes are the result of genetic assimilation of ancestral plasticity. Ancestral plasticity also increases the chance that genes are recruited repeatedly during adaptation. However, despite a high degree of convergence in gene expression levels between independently adapted lineages, genes with ancestral plasticity are as likely to have similar expression levels in adapted populations as genes without. Overall, these results demonstrate that ancestral plasticity does play an important role in adaptive parallel evolution, particularly via genetic assimilation across evolutionary replicates.

evolutionary biology↗

Source-sink connectivity: a novel resting-state EEG marker of the epileptogenic zone

Over 15 million epilepsy patients worldwide have drug-resistant epilepsy (DRE). Successful surgery is a standard of care treatment for DRE but can only be achieved through complete resection or disconnection of the epileptogenic zone (EZ), the brain region(s) where seizures originate. Surgical success rates vary between 20-80% because no clinically validated biological markers of the EZ exist. Localizing the EZ is a costly and time-consuming process beginning with non-invasive neuroimaging and often followed by days to weeks of intracranial EEG (iEEG) monitoring. Clinicians visually inspect iEEG data to identify abnormal activity (e.g., low-voltage high frequency activity) on individual channels occurring immediately before seizures or spikes that occur on interictal iEEG (i.e., between seizures). In the end, the clinical standard mainly relies on a small proportion of the iEEG data captured to assist in EZ localization (minutes of seizure data versus days of recordings), missing opportunities to leverage these largely ignored interictal data to better diagnose and treat patients. Intracranial EEG offers a unique opportunity to observe epileptic cortical network dynamics but waiting for seizures increases patient risks associated with invasive monitoring. In this study, we aim to leverage interictal iEEG data by developing a new network-based interictal iEEG marker of the EZ. We hypothesize that when a patient is not clinically seizing, it is because the EZ is inhibited by other regions. We developed an algorithm that identifies two groups of nodes from the interictal iEEG network: those that are continuously inhibiting a set of neighboring nodes ("sources") and the inhibited nodes themselves ("sinks"). Specifically, patient-specific dynamical network models (DNMs) were estimated from minutes of iEEG and their connectivity properties revealed top sources and sinks in the network, with each node being quantified by source-sink metrics (SSMs). We validated the SSMs in a retrospective analysis of 65 patients by using the SSMs of the annotated EZ to predict surgical outcomes. The SSMs predicted outcomes with an accuracy of 79% compared to an accuracy of 43% for clinicians predictions (surgical success rate of this dataset). In failed outcomes, we identified regions of the brain with high SSMs that were untreated. When compared to high frequency oscillations, the most commonly proposed interictal iEEG feature for EZ localization, SSMs outperformed in predictive power (by a factor of 1.2) suggesting SSMs may be an interictal iEEG fingerprint of the EZ.

bioengineering↗

Synergy of turbulence and fishing reduce aquatic biomass

A universal scaling relationship exists between organism abundance and body size1,2. Within ocean habitats this relationship deviates from that generally observed in terrestrial systems2-4, where marine macro-fauna display steeper size-abundance scaling than expected. This is indicative of a fundamental shift in food-web organization, yet a conclusive mechanism for this pattern has remained elusive. We demonstrate that while fishing has partially contributed to the reduced abundance of larger organisms, a larger effect comes from ocean turbulence: the energetic cost of movement within a turbulent environment induces additional biomass losses among the nekton. These results identify turbulence as a novel mechanism governing the marine size-abundance distribution, highlighting the complex interplay of biophysical forces that must be considered alongside anthropogenic impacts in processes governing marine ecosystems.

ecology↗

Identification of Target Objects from Gaze Behavior during a Virtual Navigation Task

Eye tracking has been an essential tool within the vision science community for many years. However, the majority of studies involving eye-tracking technology employ a relatively passive approach through the use of static imagery, prescribed motion, or video stimuli. This is in contrast to our everyday interaction with the natural world where we navigate our environment while actively seeking and using task-relevant visual information. For this reason, vision researchers are beginning to use virtual environment platforms, which offer interactive, realistic visual environments while maintaining a substantial level of experimental control. Here, we recorded eye movement behavior while participants freely navigated through a complex virtual environment. Within this environment, participants completed a visual search task where they were asked to find and count occurrence of specific targets among numerous distractor items. We assigned each participant into one of four target groups: Humvees, motorcycles, aircraft, or furniture. Our results show a significant relationship between gaze behavior and target objects across subject groups. Specifically, we see an increased number of fixations and increase dwell time on target relative to distractor objects. In addition, we included a divided attention task to investigate how search patterns changed with the addition of a secondary task. With increased cognitive load, subjects slowed their speed, decreased gaze on objects, and increased the number of objects scanned in the environment. Overall, our results confirm previous findings from more controlled laboratory settings and demonstrate that complex virtual environments can be used for active visual search experimentation, maintaining a high level of precision in the quantification of gaze information and visual attention. This study contributes to our understanding of how individuals search for information in a naturalistic virtual environment. Likewise, our paradigm provides an intriguing look into the heterogeneity of individual behaviors when completing an un-timed visual search task while actively navigating.

neuroscience↗

Computational characteristics of interictal EEG as objective markers of epileptic spasms

ObjectiveFavorable neurodevelopmental outcomes in epileptic spasms (ES) are tied to early diagnosis and prompt treatment, but uncertainty in the identification of the disease can delay this process. Therefore, we investigated five computational electroencephalographic (EEG) measures as markers of ES. MethodsWe measured 1) amplitude, 2) power spectra, 3) entropy, 4) long-range temporal correlations, via detrended fluctuation analysis (DFA) and 5) functional connectivity of EEG data from ES patients (n=40 patients) and healthy controls (n=20 subjects), with multiple blinded measurements during wakefulness and sleep for each patient. ResultsIn ES patients, EEG amplitude was significantly higher in all electrodes. Shannon and permutation entropy were lower in ES patients than control subjects, while DFA intercept values in ES patients were significantly higher than control subjects. DFA exponent values were not significantly different between the groups. EEG functional connectivity networks in ES patients were significantly stronger than controls. Using logistic regression, a multi-attribute classifier was derived that accurately distinguished cases from controls (area under curve of 0.96). ConclusionsComputational EEG features successfully distinguish ES patients from controls in a large, blinded study. SignificanceThese objective EEG markers, in combination with other clinical factors, may speed the diagnosis and treatment of the disease, thereby improving long-term outcomes. HighlightsO_LIObjective computational EEG features may aid diagnosis of epileptic spasms (ES) C_LIO_LIES EEG has increased delta and theta power and decreased entropy relative to controls C_LIO_LIStronger functional connectivity networks differentiate ES patients from controls C_LI

neuroscience↗

Temporal dynamics of functional networks in long-term infant scalp EEG

Human functional connectivity networks are modulated on time scales ranging from milliseconds to days. Rapid changes in connectivity over short time scales are a feature of healthy cognitive function, and variability over long time scales can impact the likelihood of seizure occurrence. However, relatively little is known about modulation of healthy functional networks over long time scales. To address this, we analyzed functional connectivity networks calculated from long-term EEG recordings from 19 healthy infants. Networks were subject-specific, as inter-subject correlations between weighted adjacency matrices were low. However, within individual subjects, both sleep and wake networks were stable over time, with stronger functional connectivity during sleep than wakefulness. This enabled automatic separation of wakefulness and sleep states via principle components analysis of the functional network time series, with median classification accuracy of 91%. Lastly, we found that network strength, degree, clustering coefficient, and path length significantly varied with time of day, when measured in both wakefulness and sleep. Together, these results suggest that modulation of healthy functional networks occurs over long timescales and is robust and repeatable. Accounting for such temporal periodicities may improve the physiological interpretation and use of functional connectivity analysis to investigate brain function in health and disease.

neuroscience↗

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. Here, we found that rapid parallel adaptation to anthropogenic pollution has taken place without geneflow spreading adaptive alleles between populations of the mine ecotype. Across replicate ecotype pairs, we identified shared targets of selection with functions linked to physiological differences between the ecotypes, although the genetic response is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

evolutionary biology↗

Kinetochore phosphatases suppress autonomous kinase activity to control the spindle assembly checkpoint

AO_SCPLOWBSTRACTC_SCPLOWLocal phosphatase regulation is critical for determining when phosphorylation signals are activated or deactivated. A typical example is the spindle assembly checkpoint (SAC) during mitosis, which regulates kinetochore PP1 and PP2A-B56 activities to switch-off signalling events at the correct time. In this case, kinetochore phosphatase activation dephosphorylates MELT motifs on KNL1 to remove SAC proteins, including the BUB complex. We show here that, surprisingly, neither PP1 or PP2A are required to dephosphorylate the MELT motifs. Instead, they remove polo-like kinase 1 (PLK1) from the BUB complex, which can otherwise maintain MELT phosphorylation in an autocatalytic manner. This is their principle role in the SAC, because both phosphatases become redundant if PLK1 is inhibited or BUB-PLK1 interaction is prevented. Therefore, phosphatase regulation is critical for the SAC, but primarily to restrain and extinguish autonomous kinase activity. We propose that these circuits have evolved to generate a semi-autonomous SAC signal that can be synchronously silenced following kinetochore-microtubule tension.

cell biology↗

PP1 and PP2A use opposite phospho-dependencies to control distinct processes at the kinetochore

PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalising with substrates. At the kinetochore, however, both phosphatases localise to an almost identical molecular space and yet they still manage to regulate unique pathways and processes. By switching or modulating the positions of PP1/PP2A-B56 at kinetochores, we show that their unique downstream effects are not due to either the identity of the phosphatase or its precise location. Instead, these phosphatases signal differently because their kinetochore recruitment can be either inhibited (PP1) or enhanced (PP2A) by phosphorylation inputs. Mathematical modelling explains how these inverse phospho-dependencies elicit unique forms of cross-regulation and feedback, which allows otherwise indistinguishable phosphatases to produce distinct network behaviours and control different mitotic processes. Therefore, the kinetochore uses PP1 and PP2A-B56 because their binding motifs respond to kinase inputs in opposite ways. Genome-wide motif analysis suggests that many other pathways also select for these same key features, implying that these similar catalytic enzymes may have diverged during evolution to allow opposite modes of phospho-regulation.

cell biology↗

Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking

Hearing loss is associated with ~8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants. The majority of these variants are classified as variants of uncertain significance to reflect our inability to ascribe a phenotypic effect to the observed amino acid change. A promising source of pathogenicity information are atomic resolution simulations, although input protein structures often contain defects due to limitations in experimental data and/or only distant homology to a template. Here we combine the polarizable AMOEBA force field, many-body optimization theory and GPU acceleration to repack all deafness-associated proteins and thereby improve average structure resolution from 2.2 [A] to 1.0 [A] based on assessment with MolProbity. We incorporate these data into the Deafness Variation Database to inform deafness pathogenicity prediction, and show that advanced polarizable force fields could now be used to repack the entire human proteome using the Force Field X software.

biophysics↗

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex

Grapevines, like other perennial crops, are affected by so-called trunk diseases, which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e., metatranscriptomics) approach that can monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for mapping and quantifying DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally-infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.

genomics↗