Biology subjects

Seth, A.

Publications and source records attributed to Seth, A..

45 records · Page 3Linked to original sources

bioRxiv2021

Leishmania major formins are cytosolic actin bundler play an important role in cell physiology

Formins are a highly conserved eukaryotic family of proteins that regulate actin dynamics. They play important physiological roles in cell adhesion, motility, vesicular trafficking and cytokinesis. Although sequence analysis of Trypanosomatida genomes predicted multiple formin-encoding genes, none of them are functionally characterized yet. We report here experimental identification and functional characterization of two constitutively expressed formins from the trypanosomatid protozoa Leishmania major viz. LmForminA and LmForminB. These formins exhibited irregular cytosolic distribution that co-localized with actin patches. Co-sedimentation assay and surface plasmon resonance confirmed that purified LmForminA and B FH2 domains can bind actin, albeit with differential affinity. Interestingly, both LmForminA and B FH2 domains were found to be actin bundlers as revealed by low-speed co-sedimentation assay and TIRF microscopy. LmForminA and B also had actin-nucleating activities, which was abolished by mutating their conserved Ile residue crucial for actin assembly. The Ile-mutant formins, however, retained their actin binding and bundling properties. Treatment of Leishmania cells with formin inhibitor SMIFH2 severely perturbed parasite growth and morphology indicating that Lmformins are physiologically important and may be considered as novel drug targets.

cell biology↗

bioRxiv2021

An automated workflow for label-free and multiplexed single cell proteomics sample preparation at unprecedented sensitivity.

The analysis of single-cell proteomes has recently become a viable complement to transcriptomics and genomics studies. Proteins are the primary driver of cellular functionality and mRNA levels are often an unreliable proxy of such. Therefore, the global analysis of the proteome is essential to study cellular identities. Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have lately attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lag. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation at surprising sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE(R), reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1,500 protein groups per analytical run at remarkable reporter ion signal to noise while reducing or eliminating the carrier proteome. We identified close to 2,600 proteins across 170 multiplexed single cells from two highly similar human cell types. This dedicated loss-less workflow allows distinguishing in vitro co-differentiated cell types of self-organizing cardiac organoids based on indicative markers across 150 single cells. In-depth characterization revealed enhanced cellular motility of cardiac endothelial cells and sarcomere organization in cardiomyocytes. Our versatile and automated sample preparation has not only proven to be easily adaptable but is also sufficiently sensitive to drive biological applications of single-cell proteomics.

biochemistry↗

bioRxiv2021

Simulating homeostatic, allostatic and goal-directed forms of interoceptive control using Active Inference

The adaptive regulation of bodily and interoceptive parameters, such as body temperature, thirst and hunger is a central problem for any biological organism. Here, we present a series of simulations using the framework of Active Inference to formally characterize interoceptive control and some of its dysfunctions. We start from the premise that the goal of interoceptive control is to minimize a discrepancy between expected and actual interoceptive sensations (i.e., a prediction error or free energy). Importantly, living organisms can achieve this goal by using various forms of interoceptive control: homeostatic, allostatic and goal-directed. We provide a computationally-guided analysis of these different forms of interoceptive control, by showing that they correspond to distinct generative models within Active Inference. Furthermore, we illustrate how these generative models may support empirical research, by predicting physiological and brain signals that may accompany both adaptive and maladaptive interoceptive control. HighlightsO_LIWe use Active Inference to provide formal models of interoceptive control C_LIO_LIWe model homeostatic, allostatic and goal-directed forms of interoceptive control C_LIO_LIOur simulations illustrate both adaptive interoceptive control and its dysfunctions C_LIO_LIWe discuss how the models can aid empirical research on interoception C_LI

neuroscience↗

bioRxiv2021

Muscle coordination retraining inspired by musculoskeletal simulations: a study on reducing knee loading

Humans typically coordinate their muscles to meet movement objectives like minimizing energy expenditure. In the presence of pathology, new objectives gain importance, like reducing loading in an osteoarthritic joint, but people often do not change their muscle coordination patterns to meet these new objectives. Here we use musculoskeletal simulations to identify simple changes in coordination that can be taught by providing feedback of electromyographic activity to achieve a therapeutic goal--reducing joint loading. Our simulations predicted that changing the relative activation of the redundant ankle plantarflexors could reduce knee contact force during walking, but it was unclear whether humans could re-coordinate redundant muscles during a complex task like walking. With simple biofeedback of electromyographic activity, healthy individuals reduced the ratio of gastrocnemius to soleus muscle activation by 25{+/-}15% (p=0.004). The resulting "gastrocnemius avoidance" gait pattern reduced the late-stance peak of simulation-estimated knee contact force by 12{+/-}12% (p=0.029). Simulation-informed muscle coordination retraining could be a promising treatment for knee osteoarthritis and a powerful tool for optimizing coordination for a variety of rehabilitation and performance applications.

bioengineering↗

bioRxiv2020

CRISPR Turbo Accelerated Knock Out (CRISPy TAKO) for rapid in vivo screening of gene function

The development of CRISPR/Cas9 technology has vastly sped up the process of genome editing by introducing a bacterial system that can be exploited for reverse genetics-based research. However, generating homozygous knockout (KO) animals using traditional CRISPR/Cas9-mediated techniques requires three generations of animals. A founder animal with a desired mutation is crossed to produce heterozygous F1 offspring which are subsequently interbred to generate homozygous F2 KO animals. This study describes a novel adaptation of the CRISPR/Cas9-mediated method to develop a homozygous gene-targeted KO animal cohort in one generation. A well-characterized ethanol-responsive gene, MyD88, was chosen as a candidate gene for generation of MyD88-/- mice as proof of concept. Previous studies have reported changes in ethanol-related behavioral outcomes in MyD88 KO mice. Therefore, it was hypothesized that a successful one-generation KO of MyD88 should reproduce decreased responses to ethanols sedative effects, as well as increased ethanol consumption in males that were observed in previous studies. One-cell mouse embryos were simultaneously electroporated with four gRNAs targeting a critical Exon of MyD88 along with Cas9. DNA and RNA analysis of founder mice revealed a complex mix of genetic alterations, all of which were predicted to ablate MyD88 gene function. This study additionally compared responses of Mock treatment control mice generated through electroporation to controls purchased from a vendor. No substantial behavioral changes were noted between control cohorts. Overall, the CRISPR/Cas9 KO protocol reported here, which we call CRISPR Turbo Accelerated KnockOut (CRISPy TAKO), will be useful for reverse genetic in vivo screens of gene function in whole animals.

genetics↗

bioRxiv2020

A predictive processing model of episodic memory and time perception

Human perception and experience of time is strongly influenced by ongoing stimulation, memory of past experiences, and required task context. When paying attention to time, time experience seems to expand; when distracted, it seems to contract. When considering time based on memory, the experience may be different than in the moment, exemplified by sayings like "time flies when youre having fun". Experience of time also depends on the content of perceptual experience - rapidly changing or complex perceptual scenes seem longer in duration than less dynamic ones. The complexity of interactions between attention, memory, and perceptual stimulation is a likely reason that an overarching theory of time perception has been difficult to achieve. Here, we introduce a model of perceptual processing and episodic memory that makes use of hierarchical predictive coding, short-term plasticity, spatio-temporal attention, and episodic memory formation and recall, and apply this model to the problem of human time perception. In an experiment with ~ 13, 000 human participants we investigated the effects of memory, cognitive load, and stimulus content on duration reports of dynamic natural scenes up to ~ 1 minute long. Using our model to generate duration estimates, we compared human and model performance. Model-based estimates replicated key qualitative biases, including differences by cognitive load (attention), scene type (stimulation), and whether the judgement was made based on current or remembered experience (memory). Our work provides a comprehensive model of human time perception and a foundation for exploring the computational basis of episodic memory within a hierarchical predictive coding framework. Author summaryExperience of the duration of present or past events is a central aspect of human experience, the underlying mechanisms of which are not yet fully understood. In this work, we combine insights from machine learning and neuroscience to propose a combination of mathematical models that replicate human perceptual processing, long-term memory, attention, and duration perception. Our computational implementation of this framework can process information from video clips of ordinary life scenes, record and recall important events, and report the duration of these clips. To assess the validity of our proposal, we conducted an experiment with ~ 13, 000 human participants. Each was shown a video between 1-64 seconds long and reported how long they believed it was. Reports of duration by our computational model qualitatively matched these human reports, made about the exact same videos. This was true regardless of the video content, whether time was actively judged or based on memory of the video, or whether the participants focused on a single task or were distracted - all factors known to influence human time perception. Our work provides the first model of human duration perception to incorporate these diverse and complex factors and provides a basis to probe the deep links between memory and time in human experience.

neuroscience↗

bioRxiv2019

Gsα stimulation of mammalian adenylate cyclases regulated by their hexahelical membrane anchors

Mammalian adenylate cyclases (ACs) are pseudoheterodimers with dissimilar hexahelical membrane-anchors, isoform-specifically conserved for more than half a billion years. We exchanged both membrane anchors of the AC isoform 2 by the isosteric quorum-sensing receptor from Vibrio, CqsS, which has a ligand, Cholera-Autoinducer-1 (CAI-1). In the chimera, AC activity was stimulated by Gs, CAI-1 had no effect. Surprisingly, CAI-1 inhibited Gs stimulation. We report that Gs stimulation of human AC isoforms 2, 3, 5, and 9 expressed in Sf9 cells is inhibited by serum as is AC activity in membranes from rat brain cortex. AC2 activation by forskolin or forskolin/Gs was similarly inhibited. Obviously, serum contains as yet unidentified factors affecting AC activity. The data establish a linkage in ACs, in which the membrane anchors, as receptors, transduce extracellular signals to the cytosolic catalytic dimer. A mechanistic three state model of AC regulation is presented compatible with all known regulatory inputs into mammalian ACs. The data allow designating the membrane anchors of mammalian ACs as orphan receptors and establish a new level of AC regulation.

biochemistry↗

bioRxiv2018

Domain-general enhancements of metacognitive ability through adaptive training

The metacognitive ability to introspect about self-performance varies substantially across individuals. Given that effective monitoring of performance is deemed important for effective behavioural control, intervening to improve metacognition may have widespread benefits, for example in educational and clinical settings. However, it is unknown whether and how metacognition can be systematically improved through training independently of task performance, or whether metacognitive improvements generalize across different task domains. Across 8 sessions, here we provided feedback to two groups of participants in a perceptual discrimination task: an experimental group (N = 29) received feedback on their metacognitive judgments, while an active control group (N = 32) received feedback on their decision performance only. Relative to the control group, adaptive training led to increases in metacognitive calibration (as assessed by Brier scores) which generalized both to untrained stimuli and an untrained task (recognition memory). Leveraging signal detection modeling we found that metacognitive improvements were driven both by changes in metacognitive efficiency (meta-d/d) and confidence level, and that later increases in metacognitive efficiency were positively mediated by earlier shifts in confidence. Our results reveal a striking malleability of introspection and indicate the potential for a domain-general enhancement of metacognitive abilities.

animal behavior and cognition↗

bioRxiv2018

The illusion of uniformity does not depend on low-level vision: evidence from sensory adaptation

Visual experience appears richly detailed despite the poor resolution of the majority of the visual field, thanks to foveal-peripheral integration. The recently described Uniformity Illusion (UI), in which peripheral elements of a pattern seem to take on the properties of foveal elements, may shed light on this integration. We examined the basis of UI by generating adaptation to a pattern of Gabors suitable for producing UI on orientation. After removing the pattern, participants reported the tilt of a single peripheral Gabor. The tilt after-effect (TAE) followed the physical adapting orientation rather than the global orientation perceived under UI, even when the illusion had been reported for a long time. Conversely, a control experiment replacing illusory for physical uniformity for the same durations did produce an after-effect to the global orientation. Our results indicate that the UI is not associated with changes in sensory encoding, but likely depends on high-level processes.

neuroscience↗