Biology subjects

Lee, A. S.

Publications and source records attributed to Lee, A. S..

26 records · Page 2Linked to original sources

bioRxiv2023

Convergent mutations in phage virion assembly proteins enable evasion of Type I CBASS immunity

CBASS is an anti-phage defense system that protects bacteria from phage infection and is evolutionarily related to human cGAS-STING immunity. cGAS-STING signaling is initiated by viral DNA but the stage of phage replication which activates bacterial CBASS remains unclear. Here we define the specificity of Type I CBASS immunity using a comprehensive analysis of 975 operon-phage pairings and show that Type I CBASS operons composed of distinct CD-NTases, and Cap effectors exhibit striking patterns of defense against dsDNA phages across five diverse viral families. We demonstrate that escaper phages evade CBASS immunity by acquiring mutations in structural genes encoding the prohead protease, capsid, and tail fiber proteins. Acquired CBASS resistance is highly operon-specific and typically does not affect overall fitness. However, we observe that some resistance mutations drastically alter phage infection kinetics. Our results define late-stage virus assembly as a critical determinant of CBASS immune activation and evasion by phages.

microbiology↗

bioRxiv2023

Evidence of thermal adaptation in a widely distributed mosquito species

How mosquitoes may respond to rapid climate warming remains unknown for most species, but will have major consequences for their future distributions, with cascading impacts on human well-being, biodiversity, and ecosystem function. We investigated the adaptive potential of a wide-ranging mosquito species, Aedes sierrensis, across a large climatic gradient by conducting a common garden experiment measuring the thermal limits of mosquito life history traits. Although field-collected populations originated from vastly different thermal environments that spanned over 1,200 km, we found remarkably limited variation in upper thermal tolerance between populations, with the upper thermal limits of fitness varying by <1{degrees}C across the species range. For one life history trait--pupal development rate--we did detect significant variation in upper thermal limits between populations, and this variation was strongly correlated with source temperatures, providing evidence of local thermal adaptation for pupal development. However, we found environmental temperatures already regularly exceed our highest estimated upper thermal limits throughout most of the species range, suggesting limited potential for mosquito thermal tolerance to evolve on pace with warming. Strategies for avoiding high temperatures such as diapause, phenological shifts, and behavioral thermoregulation are likely important for mosquito persistence.

ecology↗

bioRxiv2022

RAPTOR: A Five-Safes approach to a secure, cloud native and serverless genomics data repository

Genomic researchers are increasingly utilizing commercial cloud platforms (CCPs) to manage their data and analytics needs. Commercial clouds allow researchers to grow their storage and analytics capacity on demand, keeping pace with expanding project data footprints and enabling researchers to avoid large capital expenditures while paying only for IT capacity consumed by their project. Cloud computing also allows researchers to overcome common network and storage bottlenecks encountered when combining or re-analysing large datasets. However, cloud computing presents a new set of challenges. Without adequate security controls, the risk of unauthorised access may be higher for data stored on the cloud. In addition, regulators are increasingly mandating data access patterns and specific security protocols on the storage and use of genomic data to safeguard rights of the study participants. While CCPs provide tools for security and regulatory compliance, utilising these tools to build the necessary controls required for cloud solutions is not trivial as such skill sets are not commonly found in a genomics lab. The Research Assets Provisioning and Tracking Online Repository (RAPTOR) by the Genome Institute of Singapore is a cloud native genomics data repository and analytics platform focusing on security and regulatory compliance. Using a "five-safes" framework (Safe Purpose, Safe People, Safe Settings, Safe Data and Safe Output), RAPTOR provides security and governance controls to data contributors and users leveraging cloud computing for sharing and analysis of large genomic datasets without the risk of security breaches or running afoul of regulations. RAPTOR can also enable data federation with other genomic data repositories using GA4GH community-defined standards, allowing researchers to boost the statistical power of their work and overcome geographic and ancestry limitations of data sets

genomics↗

bioRxiv2021

Moving outside the lab: The viability of conducting sensorimotor learning studies online

Collecting data online via crowdsourcing platforms has proven to be a very efficient way to recruit a large and diverse sample. Studies of motor learning, however, have been largely confined to the lab due to the need for special equipment to record movement kinematics and, as such, are typically only accessible to specific participants (e.g., college students). As a first foray to make motor learning studies accessible to a larger and more diverse audience, we developed an online, web-based platform (OnPoint) to collect kinematic data, serving as a template for researchers to create their own online sensorimotor control and learning experiments. As a proof-of-concept, we asked if fundamental motor learning phenomena discovered in the lab could be replicated online. In a series of three experiments, we observed a close correspondence between the results obtained online with those previously reported from research conducted in the laboratory. This web-based platform paired with online crowdsourcing can serve as a powerful new method for the study of motor control and learning.

neuroscience↗

bioRxiv2020

Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens

BackgroundSeveral point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for diagnosis of SARS-CoV-2. The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. ObjectivesThe aim of this study was to assess test performance of the Accula SARS-CoV-2 test. Study designThe performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT) targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohens kappa coefficient. ResultsOverall percent agreement between the assays was 84.0% (95% confidence interval [CI] 75.3 to 90.6%), PPA was 68.0% (95% CI 53.3 to 80.5%) and the kappa coefficient was 0.68 (95% CI 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test, and showed low viral load burden with a median cycle threshold value of 37.7. NPA was 100% (95% CI 94.2 to 100%). ConclusionCompared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings, and for confirmatory testing in individuals with moderate to high pre-test probability of SARS-CoV-2 who test negative on Accula.

microbiology↗

bioRxiv2020

A molecular filter for the cnidarian stinging response

All animals detect and integrate diverse environmental signals to mediate behavior. Cnidarians, including jellyfish and sea anemones, both detect and capture prey using stinging cells called nematocytes which fire a venom-covered barb via an unknown triggering mechanism. Here, we show that nematocytes from Nematostella vectensis use a specialized voltage-gated calcium channel (nCav) to distinguish salient sensory cues and control the explosive discharge response. Adaptations in nCav confer unusually-sensitive, voltage-dependent inactivation to inhibit responses to non-prey signals, such as mechanical water turbulence. Prey-derived chemosensory signals are synaptically transmitted to acutely relieve nCav inactivation, enabling mechanosensitive-triggered predatory attack. These findings reveal a molecular basis for the cnidarian stinging response and highlight general principles by which single proteins integrate diverse signals to elicit discrete animal behaviors.

physiology↗

bioRxiv2019

Postural representations of the hand in primate sensorimotor cortex

Dexterous hand control requires not only a sophisticated motor system but also a sensory system to provide tactile and proprioceptive feedback. To date, the study of the neural basis of proprioception in cortex has focused primarily on reaching movements, at the expense of hand-specific behaviors such as grasp. To fill this gap, we record both the time-varying hand kinematics and the neural activity evoked in somatosensory and motor cortices as monkeys grasp a variety of different objects. We find that neurons in somatosensory cortex, as well as in motor cortex, preferentially track postures of multi-joint combinations spanning the entire hand. This contrasts with neural responses during reaching movements, which preferentially track movement kinematics of the arm rather than its postural configuration. These results suggest different representations of arm and hand movements likely adapted to suit the different functional roles of these two effectors.

neuroscience↗

bioRxiv2018

Spontaneous but not voluntary eye blinks during spatial working memory are associated with successful performance

Spontaneous eye blink rate (SBR) has been associated with central dopamine (DA) levels, raising the intriguing possibility that SBR is related to cognitive functions dependent on DA, such as spatial working memory (WM). We tested this hypothesis in two behavioral experiments, examining the relationship between SBR, WM load and individual differences in spatial WM performance in 126 young adults. In Experiment 1, we examined the temporal profile of SBR during a spatial delayed recognition task requiring maintenance of 1, 2, 4, 6 or 7 dot locations. We observed a suppression in SBR during dot- and recognition probe-presentation, and a significant increase in SBR afterwards. High performers showed significantly lower SBR than low performers during the first 500 ms of the delay period. In Experiment 2, we used a similar spatial WM task as Experiment 1 to test whether an instructed voluntary blink during the early delay would directly dampen WM performance. While the temporal dynamics of SBR across task events were comparable to Experiment 1, WM performance was not significantly different between the voluntary blink and no blink conditions. Together, these results suggest that spontaneous but not voluntary eye blinking is closely linked to spatial WM, and that lower SBR during WM encoding and early phase of maintenance is associated with better WM task performance.

neuroscience↗