Biology subjects

Dash, S.

Publications and source records attributed to Dash, S..

40 records · Page 3Linked to original sources

bioRxiv2019

Impairment but not abolishment of express saccades after unilateral- or bilateral cryogenic FEF inactivation

Express saccades (ESs) are a manifestation of a visual grasp reflex triggered when visual information arrives in the intermediate layers of the superior colliculus (SCi), which in turn orchestrates the lower level brainstem saccade generator to evoke a saccade with a very short latency ([~]100ms). A prominent theory regarding express saccades generation is that they are facilitated by preparatory signals, presumably from cortical areas, which prime the SCi prior to the arrival of visual information. Here, we test this theory by reversibly inactivating a key cortical input to the SCi, the frontal eye fields (FEF), while monkeys perform an oculomotor task that promotes ES generation. Across three tasks with a different combination of potential target locations and uni- or bilateral FEF inactivation, we found a spared ability for monkeys to generate ESs, despite decreases in ES frequency during FEF inactivation. This result is consistent with the FEF having a facilitatory but not critical role in ES generation, likely because other cortical areas compensate for the loss of preparatory input to the SCi. However, we did find decreases in the accuracy and peak velocity of ESs generated during FEF inactivation, which argues for an influence of the FEF on the saccadic burst generator even during ESs. Overall, our results shed further light on the role of the FEF in the shortest-latency visually-guided eye movements.\n\nNew & NoteworthyExpress saccades (ESs) are the shortest-latency visually-guided saccade. The frontal eye fields (FEF) is thought to promote ES by establishing the necessary preconditions in the superior colliculus. Here, by reversibly inactivate the FEF either unilaterally or bilaterally, we support this view by showing that the FEF plays an assistive but not critical role in ES generation. We also found that FEF inactivation lowered ES peak velocity, emphasizing a contribution of the FEF to ES kinematics.

neuroscience↗

bioRxiv2018

Incremental BLAST: incremental addition of new sequence databases through e-value correction

MotivationSearch results from local alignment search tools use statistical parameters sensitive to the size of the database. NCBI BLAST, for example, reports important matches using similarity scores and expect or e-values calculated against database size. Over the course of an investigation, the database grows and the best matches may change. To update the results of a sequence similarity search to find the most optimal hits, bioinformaticians must rerun the BLAST search against the entire database; this translates into irredeemable spent time, money, and computational resources.\n\nResultsWe develop an efficient way to redeem spent BLAST search effort by introducing the Incremental BLAST. This tool makes use of the previous BLAST search results as it conducts new searches on only the incremental part of the database, recomputes statistical metrics such as e-values and combines these two sets of results to produce updated results. We develop statistics for correcting e-values of any BLAST result against any arbitrary sequence database. The experimental results and accuracy analysis demonstrate that Incremental BLAST can provide search results identical to NCBI BLAST at a significantly reduced computational cost. We apply three case studies to showcase different use cases where Incremental BLAST can make biological discovery more efficiently at a reduced cost. This tool can be used to update sequence blasts during the course of genomic and transcriptomic projects, such as in re-annotation projects, and to conduct incremental addition of taxon-specific sequences to a BLAST database. Incremental BLAST performs (1 +{delta} )/{delta} times faster than NCBI BLAST for{delta} fraction of database growth.\n\nAvailabilityIncremental BLAST is available at https://bitbucket.org/sajal000/incremental-blast.\n\nContactsajal@vt.edu\n\nSupplementary informationSupplementary data are available at https://bitbucket.org/sajal000/incremental-blast

bioinformatics↗

bioRxiv2017

Frontal eye field inactivation reduces saccade preparation in the superior colliculus, but does not alter how preparatory activity relates to saccade latency

A neural correlate for saccadic reaction times (SRTs) in the gap saccade task is the level of preparatory activity in the intermediate layers of the superior colliculus (iSC) just before visual target onset: greater levels of iSC preparatory activity precede shorter SRTs. The frontal eye fields (FEF) are one likely source of such iSC preparatory activity, since FEF preparatory activity is also inversely related to SRT. To better understand the FEFs role in saccade preparation, and the way in which such preparation relates to SRT, in two male rhesus monkeys we examined iSC preparatory activity during unilateral reversible cryogenic inactivation of the FEF. FEF inactivation increased contralesional SRTs, and lowered ipsilesional iSC preparatory activity. FEF inactivation also reduced fixation-related activity in the rostral iSC. Importantly, the distributions of SRTs generated with or without FEF inactivation overlapped, enabling us to conduct a novel population-level analyses examining iSC preparatory activity just before generation of SRT-matched saccades. These analyses revealed no change during FEF inactivation in the relationship between iSC preparatory activity and SRT-matched saccades across a range of SRTs, even for the occasional express saccade. Thus, while our results emphasize that the FEF has an overall excitatory influence on preparatory activity in the iSC, the communication between the iSC and downstream oculomotor brainstem is unaltered for SRT-matched saccades, suggesting that the integration of preparatory and visual signals in the SC just before saccade initiation is largely independent of the FEF for saccades generated in this task.\n\nSignificance statementHow does the brain decide when to move? Here, we investigate the role of two oculomotor structures, the superior colliculus (SC) and frontal eye fields (FEF), in dictating visually-guided saccadic reaction times (SRTs). In both structures, higher levels of preparatory activity precede shorter SRTs. Here, we show that FEF inactivation increases SRTs and decreases SC preparatory activity. Surprisingly, a population-level analysis of SC preparatory activity showed a negligible impact of FEF inactivation, providing one examines SRT-matched saccades. Thus, while the FEF is one source of preparatory input to the SC, it is not a critical source, and it is not involved in the integration of preparatory activity and visual signals that precedes saccade initiation in simple visually-guided saccade tasks.

neuroscience↗

bioRxiv2017

Frontal Eye Field inactivation diminishes Superior Colliculus activity, but delayed saccadic accumulation governs reaction time increases

Stochastic accumulator models provide a comprehensive framework for how neural activity could produce behavior. Neural activity within the frontal eye fields (FEF) and intermediate layers of the superior colliculus (iSC) support such models for saccade initiation, by relating variations in saccade reaction time (SRT) to variations in parameters such as baseline, rate of accumulation of activity, or threshold. Here, by recording iSC activity during reversible cryogenic inactivation of the FEF in non-human primates, we causally test which parameter(s) best explains concomitant increases in SRT. While FEF inactivation decreased all aspects of ipsilesional iSC activity, decreases in accumulation rate and threshold poorly predicted accompanying increases in SRT. Instead, SRT increases best correlated with delays in the onset of saccade-related accumulation. We conclude that FEF signals govern the onset of saccade-related accumulation within the iSC, and that the onset of accumulation is a relevant parameter for stochastic accumulation models of saccade initiation.\n\nSignificance StatementThe superior colliculus (SC) and frontal eye fields (FEF) are two of the best-studied areas in the primate brain. Surprisingly, little is known about what happens in the SC when the FEF is temporarily inactivated. Here, we show that temporary FEF inactivation decreases all aspects of functionally-related activity in the SC. This combination of techniques also allowed us to relate changes in SC activity to concomitant increases in saccadic reaction time (SRT). Although stochastic accumulator models relate SRT increases to reduced rates of accumulation or increases in threshold, such changes were not observed in the SC. Instead, FEF inactivation delayed the onset of saccade-related accumulation, emphasizing the importance of this parameter in biologically-plausible models of saccade initiation.

neuroscience↗