Biology subjects

Taylor, J. A.

Publications and source records attributed to Taylor, J. A..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

In vivo photocontrol of microtubule dynamics and integrity, migration and mitosis, by the potent GFP-imaging-compatible photoswitchable reagents SBTubA4P and SBTub2M

Photoswitchable reagents to modulate microtubule stability and dynamics are an exciting tool approach towards micron- and millisecond-scale control over endogenous cytoskeleton-dependent processes. When these reagents are globally administered yet locally photoactivated in 2D cell culture, they can exert precise biological control that would have great potential for in vivo translation across a variety of research fields and for all eukaryotes. However, photopharmacologys reliance on the azobenzene photoswitch scaffold has been accompanied by a failure to translate this temporally- and cellularly-resolved control to 3D models or to in vivo applications in multi-organ animals, which we attribute substantially to the metabolic liabilities of azobenzenes. Here, we optimised the potency and solubility of metabolically stable, druglike colchicinoid microtubule inhibitors based instead on the styrylbenzothiazole (SBT) photoswitch scaffold, that are non-responsive to the major fluorescent protein imaging channels and so enable multiplexed imaging studies. We applied these reagents to 3D systems (organoids, tissue explants) and classic model organisms (zebrafish, clawed frog) with one- and two-protein imaging experiments. We successfully used systemic treatment plus spatiotemporally-localised illuminations in vivo to photocontrol microtubule dynamics, network architecture, and microtubule-dependent processes in these systems with cellular precision and second-level resolution. These nanomolar, in vivo-capable photoswitchable reagents can prove a game-changer for high-precision cytoskeleton research in cargo transport, cell motility, cell division and development. More broadly, their straightforward design can also inspire the development of similarly capable optical reagents for a range of protein targets, so bringing general in vivo photopharmacology one step closer to productive realisation.

cell biology↗

bioRxiv2021

Generalization of motor learning in psychological space

To generate adaptive movements we must generalize what we have previously learned to novel situations. The generalization of adapted movements has typically been framed as a consequence of neural tuning functions that overlap for similar movement kinematics - what might be considered bottom-up generalization. However, as is true in many domains of human behavior, generalization can also be framed as the result of deliberate decisions about how to act (top-down generalization). Here we attempt to broaden the scope of theories about motor generalization, hypothesizing that part of the typical motor generalization function can be characterized as a consequence of top-down decisions concerning the subjective similarity of different movement contexts. We tested this proposal by having participants make explicit similarity ratings over both traditional kinematic contextual dimensions (movement direction) and more abstract contextual dimensions (target shape), and perform a visuomotor adaptation generalization task where trials varied over those dimensions. Across five experiments, we measured the relationship between subjective similarity ratings and motor generalization. In some cases this link was rather strong, though it was determined by both task-relevance and explicit instruction. These results support a broadening of the descriptive framework used to understand the generalization of motor behaviors and support a more careful deployment of instructions in generalization studies. Significance StatementGeneralization describes the transfer of knowledge from one context to another, and is typically thought to result from a higher-order inference process. However, in the motor adaptation domain, generalization is thought to arise from neural representations tuned to low-level kinematics. To bridge these differing views, we measured peoples subjective similarity judgements of different task contexts during sensorimotor adaptation. We found that motor generalization was closely linked to participants subjective judgements, and that explicit instructions about the consequential dimension of different contexts further shaped generalization. These findings emphasize that in addition to low level kinematic considerations, top-down inferences about which action to take in a given context should be considered as another key component of motor generalization.

neuroscience↗

bioRxiv2021

CTP and parS control ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning

ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF--ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF--ParBF complex assembly. Together, parSF and CTP accelerate ParAF--ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF--ParBF and ParAF--ParBF interactions promoting efficient partitioning.

cell biology↗

bioRxiv2021

Endothelial NRP2 influences angiogenesis by regulating actin pattern development and α5-integrin-p-FAK complex recruitment to assembling adhesion sites

The ability to form a variety of cell-matrix connections is crucial for angiogenesis to take place. Without stable anchorage to the extracellular matrix (ECM), endothelial cells (ECs) are unable to sense, integrate and disseminate growth factor stimulated responses that drive growth of a vascular bed. Neuropilin-2 (NRP2) is a widely expressed membrane-bound multifunctional non-tyrosine kinase receptor, that has previously been implicated in influencing cell adhesion and migration by interacting with 5-integrin and regulating adhesion turnover. 5-integrin, and its ECM ligand fibronectin (FN) are both known to be upregulated during the formation of neo-vasculature. Despite being descriptively annotated as a candidate biomarker for aggressive cancer phenotypes, the EC-specific roles for NRP2 during developmental and pathological angiogenesis remain unexplored. The data reported here support a model whereby NRP2 actively promotes EC adhesion and migration by regulating dynamic cytoskeletal remodelling and by stimulating Rab11-dependent recycling of 5-integrin-p-FAK complexes to newly assembling adhesion sites. Furthermore, temporal depletion of EC-NRP2 in vivo impairs primary tumour growth by disrupting vessel formation. We also demonstrate that EC-NRP2 is required for normal postnatal retinal vascular development, specifically by regulating cell-matrix adhesion. Upon loss of endothelial NRP2, vascular outgrowth from the optic nerve during superficial plexus formation is disrupted, likely due to reduced FAK phosphorylation within sprouting tip cells.

cell biology↗

bioRxiv2021

Efficient prediction of microplastic counts from mass measurements

Microplastics must be characterized and quantified to assess their impact. Current quantification procedures are time-consuming and prone to human error. This study evaluates the use of machine learning to estimate the number of microplastic particles based on aggregate particle weight measurements. Synthetic datasets are used to test the performance of linear regression, kernel ridge regression and decision trees. Kernel ridge regression achieves the strongest performance, and it is also tested with experimental datasets. The numerical results show that the algorithm is better at predicting the counts of larger and more homogeneous samples, and that contamination by organics does not significantly increase error. In mixed samples, prediction error is lower for heavier particles, with an error rate comparable to or better than that of manual counting. Overall, the proposed method is faster and easier than current approaches.

ecology↗

bioRxiv2020

An associative learning account of sensorimotor adaptation

Traditional associative learning tasks focus on the formation of associations between salient events and arbitrary stimuli that predict those events. This is exemplified in cerebellar-dependent delay eyeblink conditioning, where arbitrary cues such as a light or tone act as conditioning stimuli that predict aversive sensations at the cornea. Here we ask if a similar framework could be applied to another type of cerebellar-dependent sensorimotor learning - sensorimotor adaptation. Models of sensorimotor adaptation posit that the introduction of an environmental perturbation results in an error signal that is used to update an internal model of a sensorimotor map for motor planning. Here we take a step towards an integrative account of these two forms of cerebellar-dependent learning, examining the relevance of core concepts from associative learning for sensorimotor adaptation. Using a visuomotor adaptation reaching task, we paired movement-related feedback with neutral auditory or visual contextual cues that served as conditioning stimuli (CSs). Trial-by trial changes in feedforward movement kinematics exhibited three key signatures of associative learning: Differential conditioning, sensitivity to the CS-US interval, and compound conditioning. Moreover, after compound conditioning, a robust negative correlation was observed between responses to the two elemental CSs of the compound (i.e., overshadowing), consistent with the additivity principle posited by theories of associative learning. The existence of associative learning effects in sensorimotor adaptation provides a proof-of-concept for linking cerebellar- dependent learning paradigms within a common theoretical framework.

neuroscience↗

bioRxiv2020

Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks

We demonstrate the use of a Generative Adversarial Network (GAN), trained from a set of over 400,000 light and heavy chain human antibody sequences, to learn the rules of human antibody formation. The resulting model surpasses common in silico techniques by capturing residue diversity throughout the variable region, and is capable of generating extremely large, diverse libraries of novel antibodies that mimic somatically hypermutated human repertoire response. This method permits us to rationally design de novo humanoid antibody libraries with explicit control over various properties of our discovery library. Through transfer learning, we are able to bias the GAN to generate molecules with key properties of interest such as improved stability and developability, lower predicted MHC Class II binding, and specific complementarity-determining region (CDR) characteristics. These approaches also provide a mechanism to better study the complex relationships between antibody sequence and molecular behavior, both in vitro and in vivo. We validate our method by successfully expressing a proof-of-concept library of nearly 100,000 GAN-generated antibodies via phage display. We present the sequences and homology-model structures of example generated antibodies expressed in stable CHO pools and evaluated across multiple biophysical properties. The creation of discovery libraries using our in silico approach allows for the control of pharmaceutical properties such that these therapeutic antibodies can provide a more rapid and cost-effective response to biological threats.

immunology↗

bioRxiv2020

Cerebellar degeneration selectively disrupts continuous mental operations in visual cognition

Here we test the hypothesis that the cerebellum aids in the dynamic transformation of mental representations. We report a series of neuropsychological experiments comparing the performance of individuals with cerebellar degeneration (CD) on cognitive tasks that either entail continuous, movement-like mental operations or more discrete mental operations. In visual cognition, individuals with CD exhibited an impaired rate of mental rotation, an operation hypothesized to require the continuous manipulation of a visual representation. In contrast, individuals with CD showed a normal processing rate when scanning items in visual working memory, an operation hypothesized to require the maintenance and retrieval of representations. In mathematical cognition, individuals with CD were impaired at single-digit addition, an operation hypothesized to require iterative manipulations along a mental number-line; this group was not impaired on arithmetic tasks requiring memory retrieval (e.g., single-digit multiplication). These results, obtained in tasks from two disparate domains, suggest one potential constraint on the contribution of the cerebellum to cognitive tasks. This constraint may parallel the cerebellums role in motor control, involving coordinated dynamic transformations in a mental workspace.

neuroscience↗

bioRxiv2020

Single cell plasticity and population coding stability in auditory thalamus upon associative learning

Cortical and limbic brain areas are regarded as centres for learning. However, how thalamic sensory relays participate in plasticity upon associative learning, yet support stable long-term sensory coding remains unknown. Using a miniature microscope imaging approach, we monitor the activity of populations of auditory thalamus (MGB) neurons in freely moving mice upon fear conditioning. We find that single cells exhibit mixed selectivity and heterogeneous plasticity patterns to auditory and aversive stimuli upon learning, which is conserved in amygdala-projecting MGB neurons. In contrast to individual cells, population level encoding of auditory stimuli remained stable across days. Our data identifies MGB as a site for complex neuronal plasticity in fear learning upstream of the amygdala that is in an ideal position to drive plasticity in cortical and limbic brain areas. These findings suggest that MGBs role goes beyond a sole relay function by balancing experience-dependent, diverse single cell plasticity with consistent ensemble level representations of the sensory environment to support stable auditory perception with minimal affective bias.

neuroscience↗

bioRxiv2020

Multi-dimensional predictions of psychotic symptoms via machine learning

The diagnostic criteria for schizophrenia comprise a diverse range of heterogeneous symptoms. As a result, individuals each present a distinct set of symptoms despite having the same overall diagnosis. Whilst previous machine learning studies have primarily focused on dichotomous patient-control classification, we predict the severity of each individual symptom on a continuum. We applied machine learning regression within a multi-modal fusion framework to fMRI and behavioural data acquired during an auditory oddball task in 80 schizophrenia patients. Brain activity was highly predictive of some, but not all symptoms, namely hallucinations, avolition, anhedonia and attention. Critically, each of these symptoms was associated with specific functional alterations across different brain regions. We also found that modelling symptoms as an ensemble of subscales was more accurate, specific and informative than models which predict compound scores directly. In principle, this approach is transferrable to any psychiatric condition or multi-dimensional diagnosis.

neuroscience↗

bioRxiv2019

Distinct Processing of Selection and Execution Errors in Neural Signatures of Outcome Monitoring

Losing a point in tennis could result from poor shot selection or faulty stroke execution. To explore how the brain responds to these different types of errors, we examined feedback-locked EEG activity while participants completed a modified version of a standard three-armed bandit probabilistic reward task. Our task framed unrewarded outcomes as either the result of errors of selection or errors of execution. We examined whether amplitude of a medial frontal negativity (the Feedback-Related Negativity; FRN) was sensitive to the different forms of error attribution. Consistent with previous reports, selection errors elicited a large FRN relative to rewards and amplitude of this signal correlated behavioral adjustment following these errors. A different pattern was observed in response to execution errors. These outcomes produced a larger FRN, a frontocentral attenuation in activity preceding this component, and a subsequent enhanced error positivity in parietal sites. Notably, the only correlations with behavioral adjustment were with the early frontocentral attenuation and amplitude of the parietal signal; FRN differences between execution errors and rewarded trials did not correlate with subsequent changes in behavior. Our findings highlight distinct neural correlates of selection and execution error processing, providing insight into how the brain responds to the different classes of error that determine future action.

neuroscience↗

bioRxiv2019

Implicit adaptation processes appear unable to account for learning in sensorimotor adaptation tasks

Learning in sensorimotor adaptation tasks has been viewed as an implicit learning phenomenon. The implicit process affords recalibration of existing motor skills so that the system can adjust to changes in the body or environment without relearning from scratch. However, recent findings suggest that the implicit process is heavily constrained, calling into question its utility in motor learning and the theoretical framework of sensorimotor adaptation paradigms. These inferences have been based mainly on results from single bouts of training, where explicit compensation strategies, such as explicitly re-aiming the intended movement direction, contribute a significant proportion of adaptive learning. It is possible, however, that the implicit process supersedes explicit compensation strategies over repeated practice sessions. We tested this by dissociating the contributions of explicit re-aiming strategies and the implicit process over five consecutive days of training. Despite a substantially longer duration of training, the implicit process still plateaued at a value far short of complete learning and, as has been observed in previous studies, was inappropriate for a mirror reversal task. Notably, we find significant between subject differences that call into question traditional interpretation of these group-level results. Significance StatementIn this set of studies, we find that the implicit process cannot fully account for learning in adaptation tasks, such as the visuomotor rotation and mirror reversal tasks, even following several days of training. In fact, the implicit process can be counterproductive to learning. Most notably, we find significant between subject differences that call into question traditional interpretation of these group-level results.

neuroscience↗

bioRxiv2019

Explicit strategies in force field adaptation

In recent years, it has become increasingly clear that a number of learning processes are at play in visuomotor adaptation tasks. In addition to the presumed formation of an internal model of the perturbation, learners can also develop explicit knowledge allowing them to select better actions in responding to a given perturbation. Advances in visuomotor rotation experiments have underscored the important role that such \"explicit learning\" plays in shaping adaptation to kinematic perturbations. Yet, in adaptation to dynamic perturbations, its contribution has been largely overlooked, potentially because compensation of a viscous force field, for instance, is difficult to assess by commonly-used verbalization-based approaches. We therefore sought to assess the contribution of explicit learning in learners adapting to a dynamic perturbation by two novel modifications of a force field experiment. First, via an elimination approach, we asked learners to abandon any cognitive strategy before selected force channel trials to expose consciously accessible parts of overall learning. Learners indeed reduced compensatory force compared to standard Catch channels. Second, via a manual reporting approach, we instructed a group of learners to mimic their right hands adaptation by moving with their naive left hand. While a control group displayed negligible left-hand force compensation, the Mimic group reported forces that approximated right-hand adaptation but appeared to under-report the velocity component of the force field in favor of a more position-based component. We take these results to clearly demonstrate the contribution of explicit learning to force adaptation, underscoring its relevance to motor learning in general.\n\nNew & NoteworthyWhile the role of explicit learning has recently been appreciated in visuomotor adaptation tasks, their contribution to force field adaptation has not been as widely acknowledged. To address this issue, we employed two novel methods to assay explicit learning in force field adaptation tasks and found that learners can voluntarily control aspects of force production and manually report them with their untrained limb. This suggests that an explicit component contributes to force field adaptation and may provide alternative explanations to behavioral phenomena commonly thought to reveal a complex organization of internal models in the brain.

neuroscience↗

bioRxiv2019

Epigenome-wide analysis uncovers a blood-based DNA methylation biomarker of lifetime cannabis use.

Cannabis use is highly prevalent and is associated with adverse and beneficial effects. To better understand the full spectrum of health consequences, biomarkers that accurately classify cannabis use are needed. DNA methylation (DNAm) is an excellent candidate, yet no blood-based epigenome-wide association studies (EWAS) in humans exist. We conducted an EWAS of lifetime cannabis use (ever vs. never) using blood-based DNAm data from a case-cohort study within Sister Study, a prospective cohort of women at risk of developing breast cancer (Discovery N=1,730 [855 ever users]; Replication N=853 [392 ever users]). We identified and replicated an association with lifetime cannabis use at cg15973234 (CEMIP): combined P=3.3x10-8. We found no overlap between published blood-based cis-meQTLs of cg15973234 and reported lifetime cannabis use-associated SNPs (P<0.05), suggesting that the observed DNAm difference was driven by cannabis exposure. We also developed a multi-CpG classifier of lifetime cannabis use using penalized regression of top EWAS CpGs. The resulting 49-CpG classifier produced an area under the curve (AUC)=0.74 (95% confidence interval [0.72, 0.76], P=2.00x10-5) in the discovery sample and AUC=0.54 ([0.51, 0.57], P=4.64x10-2) in the replication sample. Our EWAS findings provide evidence that blood-based DNAm is associated with lifetime cannabis use.

genomics↗

bioRxiv2019

Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates

Bacterial colonization of the urogenital tract is limited by innate defenses, including the production of antimicrobial peptides (AMPs). Uropathogenic Escherichia coli (UPEC) resist AMP-killing to cause a range of urinary tract infections (UTIs) including asymptomatic bacteriuria, cystitis, pyelonephritis, and sepsis. UPEC strains have high genomic diversity and encode numerous virulence factors that differentiate them from non-UTI causing strains, including ompT. As OmpT homologues cleave and inactivate AMPs, we hypothesized that high OmpT protease activity-levels contribute to UPEC colonization during symptomatic UTIs. Therefore, we measured OmpT activity in 58 UPEC clinical isolates. While heterogeneous OmpT activities were observed, OmpT activity was significantly greater in UPEC strains isolated from patients with symptomatic infections. Unexpectedly, UPEC strains exhibiting the greatest protease activities harboured an additional ompT-like gene called arlC (ompTp). The presence of two OmpT-like proteases in some UPEC isolates led us to compare the substrate specificities of OmpT-like proteases found in E. coli. While all three cleaved AMPs, cleavage efficiency varied on the basis of AMP size and secondary structure. Our findings suggest the presence ArlC and OmpT in the same UPEC isolate may confer a fitness advantage by expanding the range of target substrates.

microbiology↗

bioRxiv2019

Of hands, tools, and exploding dots: How different action states and effects separate visuomotor memories

Humans can operate a variety of modern tools, which are often associated with different visuomotor transformations. Studies investigating this ability have repeatedly found that the simultaneous acquisition of different transformations appears inextricably tied to distinct states associated with movement, such as different postures or action plans, whereas abstract contextual associations can be leveraged by explicit aiming strategies. It still remains unclear how different transformations are remembered implicitly when target postures are similar. We investigated if features of planning to manipulate a visual tool, such as its visual identity or the intended effect enable implicit learning of opposing visuomotor rotations. Both cues only affected implicit aftereffects indirectly through generalization around explicit strategies. In contrast, practicing transformations with different hands resulted in separate aftereffects. It appears that different (intended) body states are necessary to separate aftereffects, supporting the idea that underlying implicit adaptation is limited to the recalibration of a body model.

neuroscience↗

bioRxiv2019

Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori

Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.

microbiology↗

bioRxiv2019

Sensorimotor adaptation compensates for distortions of 3D shape information

Visual perception often fails to recover the veridical 3D shape of objects in the environment due to ambiguity and variability in the available depth cues. However, we rely heavily on 3D shape estimates when planning movements, for example reaching to pick up an object from a slanted surface. Given the wide variety of distortions that can affect 3D perception, how do our actions remain accurate across different environments? One hypothesis is that the visuomotor system performs selective filtering of 3D information to minimize distortions. Indeed, some studies have found that actions appear to preferentially target stereo information when it is put in conflict with texture information. However, since these studies analyze averages over multiple trials, this apparent preference could be produced by sensorimotor adaptation. In Experiment 1, we create a set of cue-conflict stimuli where one available depth cue is affected by a constant bias. Sensory feedback rapidly aligns the motor output with physical reality in just a few trials, which can make it seem as if action planning selectively relies on the reinforced cue--yet no change in the relative influences of the cues is necessary to eliminate the constant errors. In contrast, when one depth cue becomes less correlated with physical reality, variable movement errors will occur, causing canonical adaptation to fail as the opposite error corrections cancel out. As a result, canonical adaptation cannot explain the preference for stereo found in studies with variable errors. However, Experiment 2 shows that persistent errors can produce a novel form of adaptation that gradually reduces the relative influence of an unreliable depth cue. These findings show that grasp control processes are continuously modified based on sensory feedback to compensate for both biases and noise in 3D visual processing, rather than having a hardwired preference for one type of depth information.

neuroscience↗