Biology subjects

Beck, J. M.

Publications and source records attributed to Beck, J. M..

7 recordsLinked to original sources

bioRxiv2022

The PTEX pore component EXP2 is important for intrahepatic development during the Plasmodium liver stage

During vertebrate infection, obligate intracellular malaria parasites develop within a parasitophorous vacuole which constitutes the interface between the parasite and its hepatocyte or erythrocyte host cells. To transcend this barrier, Plasmodium spp. utilize a dual-function pore formed by EXP2 for nutrient transport and, in the context of the PTEX translocon, effector protein export across the vacuole membrane. While critical to blood stage survival, less is known about EXP2/PTEX function in the liver stage, although major differences in the export mechanism are indicated by absence of the PTEX unfoldase HSP101 in the intrahepatic vacuole. Here, we employed the glucosamine-activated glmS ribozyme to study the role of EXP2 during Plasmodium berghei liver stage development in hepatoma cells. Insertion of the glmS sequence into the exp2 3UTR enabled glucosamine-dependent depletion of EXP2 after hepatocyte invasion, allowing separation of EXP2 function during intrahepatic development from a recently reported role in hepatocyte invasion. Post-invasion EXP2 knockdown reduced parasite size and largely abolished expression of the mid to late liver stage marker LISP2. As an orthogonal approach to monitor development, EXP2-glmS parasites and controls were engineered to express nanoluciferase. Activation of glmS after invasion substantially decreased luminescence in hepatoma monolayers and in culture supernatants at later time points corresponding with merosome detachment that marks the culmination of liver stage development. Collectively, our findings extend the utility of the glmS ribozyme to study protein function in the liver stage and reveal EXP2 is important for intrahepatic parasite development, indicating PTEX components also function at the hepatocyte-parasite interface.

microbiology↗

bioRxiv2022

Promising Antimalarials targeting Apicoplast DNA Polymerase from Plasmodium falciparum

Malaria is caused by the parasite Plasmodium falciparum, which contains an essential non-photosynthetic plastid called the apicoplast. A single DNA polymerase, apPOL, is targeted to the apicoplast, where it replicates and repairs the genome. apPOL has no direct orthologs in mammals and is considered a promising drug target for the treatment and/or prevention of malaria. We previously reported screening the Malaria Box to identify MMV666123 as an inhibitor of apPOL. Herein we extend our studies and report structure-activity relationships for MMV666123 and identify key structural motifs necessary for inhibition. Although attempts to crystallize apPOL with the inhibitor were not fruitful, kinetic analysis and crystal structure determinations of WT and mutant apo-enzymes, facilitated model building and provided insights into the putative inhibitor binding site. Our results validate apPOL as an antimalarial target and provide an avenue for the design of high potency, specific inhibitors of apPOL and other A-family DNA polymerases.

biochemistry↗

bioRxiv2020

Why sensory neurons are tuned to multiple stimulus features

Many sensory neurons encode information about more than one stimulus feature. Multidimensional tuning increases ambiguity in stimulus-response relationships, but we find that it also offers an unexpected computational advantage, allowing the brain to better reconstruct sensory stimuli. From the responses of sensory neurons, populations, and sensory-driven movement behavior, more information can be recovered about a stimulus vector than about its individual components. We term this coding advantage "stimulus synergy" and show that it is distinct from other coding synergies, arising from inseparability of the response-conditioned stimulus distribution along individual stimulus dimensions. From extracellular recordings in motion sensitive cortex and measurements of pursuit eye movements, we demonstrate that stimulus synergy in cortical populations is preserved downstream in the precision of pursuit, and that a common decoding model predicts the level of synergy in pursuit behavior. This suggests that the brain exploits the information advantage afforded by multidimensional sensory tuning.

neuroscience↗

bioRxiv2019

EXP1 is required for organization of the intraerythrocytic malaria parasite vacuole

Intraerythrocytic malaria parasites reside within a parasitophorous vacuole membrane (PVM) that closely overlays the parasite plasma membrane (PPM) and constitutes the barrier between parasite and host compartments. The PVM is the site of several essential transport activities but the basis for organization of this membrane system is unknown. We utilized the second-generation promiscuous biotin ligase BioID2 fused to EXP2 or HSP101 to probe the content of the PVM, identifying known and novel candidate PVM proteins. Among the best represented hits were members of a group of single-pass integral membrane proteins that constitute a major component of the PVM proteome but whose function remains unclear. We investigated the function of EXP1, the longest known member of this group, by adapting a CRISPR/Cpf1 genome editing system to install the TetR-DOZI-aptamers system for conditional translational control. EXP1 knockdown was essential for intraerythrocytic development and accompanied by profound changes in vacuole ultrastructure, including increased separation of the PVM and PPM and formation of abnormal membrane structures in the enlarged vacuole lumen. While previous in vitro studies indicated EXP1 possesses glutathione S-transferase activity, a mutant version of EXP1 lacking a residue important for this activity in vitro still provides substantial rescue of endogenous exp1 knockdown in vivo. Intriguingly, while activity of the Plasmodium translocon of exported proteins was not impacted by depletion of EXP1, the distribution of the translocon pore-forming protein EXP2 was substantially altered. Collectively, our results reveal a novel PVM defect that indicates a critical role for EXP1 in maintaining proper PVM organization.\n\nImportanceLike other obligate intracellular apicomplexans, blood-stage malaria parasites reside within a membrane-bound compartment inside the erythrocyte known as the parasitophorous vacuole. Although the vacuole is the site of several transport activities essential to parasite survival, little is known about its organization. To explore vacuole biology, we adopted recently developed proteomic (BioID2) and genetic (CRISPR/Cpf1) tools for use in Plasmodium falciparum, which allowed us to query the function of the prototypical vacuole membrane protein EXP1.\n\nKnockdown of EXP1 showed that a previously reported glutathione S-transferase activity cannot fully account for the essential function(s) of EXP1 and revealed a novel role for this protein in maintaining normal vacuole morphology and PVM protein arrangement. Our results provide new insight into vacuole organization and illustrate the power of BioID2 and Cpf1 (which utilizes a T-rich PAM uniquely suited to the P. falciparum genome) for proximity protein identification and genome editing in P. falciparum.

microbiology↗

bioRxiv2019

Properties of decision-making tasks govern the tradeoff between model-based and model-free learning

When decisions must be made between uncertain options, optimal behavior depends on accurate estimations of the likelihoods of different outcomes. The contextual factors that govern whether these estimations depend on model-free learning (tracking outcomes) vs. model-based learning (learning generative stimulus distributions) are poorly understood. We studied model-free and model-based learning using serial decision-making tasks in which subjects selected a rule and then used it to flexibly act on visual stimuli. A factorial approach defined a family of behavioral models that could integrate model-free and model-based strategies to predict rule selection trial-by-trial. Bayesian model selection demonstrated that the subjects strategies varied depending on lower-level task characteristics such as the identities of the rule options. In certain conditions, subjects integrated learned stimulus distributions and tracked reward rates to guide their behavior. The results thus identify tradeoffs between model-based and model-free decision strategies, and in some cases parallel utilization, depending on task context.

neuroscience↗

bioRxiv2019

Separable codes for read-out of mouse primary visual cortex across attentional states

Attentional modulation of neuronal activity in sensory cortex could alter perception by enhancing the local representation of attended stimuli or its behavioral read-out downstream. We tested these hypotheses using a task in which mice are cued on interleaved trials to attend visual or auditory targets. Neurons in primary visual cortex (V1) that encode task stimuli have larger visually-evoked responses when attention is directed toward vision. To determine whether the attention-dependent changes in V1 reflect changes in representation or read-out, we decoded task stimuli and choices from population activity. Surprisingly, both visual and auditory choices can be decoded from V1, but decoding takes advantage of unique activity patterns across modalities. Furthermore, decoding of choices, but not stimuli, is impaired when attention is directed toward the opposite modality. The specific effect on choice suggests behavioral improvements with attention are largely due to targeted read-out of the most informative V1 neurons.

neuroscience↗

bioRxiv2018

Neuronal adaptation reveals a suboptimal decoding of orientation tuned populations in the mouse visual cortex

Sensory information is encoded by populations of cortical neurons. Yet, it is unknown how this information is used for even simple perceptual choices such as discriminating orientation. To determine the computation underlying this perceptual choice, we took advantage of the robust adaptation in the mouse visual system. We find that adaptation increases animals thresholds for orientation discrimination. This was unexpected since optimal computations that take advantage of all available sensory information predict that the shift in tuning and increase in signal-to-noise ratio in the adapted condition should improve discrimination. Instead, we find that the effects of adaptation on behavior can be explained by the appropriate reliance of the perceptual choice circuits on target preferring neurons, but the failure to discount neurons that prefer the distractor. This suggests that to solve this task the circuit has adopted a suboptimal strategy that discards important task-related information to implement a feed-forward visual computation.

neuroscience↗