Biology subjects

Nouri, A.

Publications and source records attributed to Nouri, A..

5 recordsLinked to original sources

bioRxiv2026

An intestinal cell atlas and organoid model for the threespine stickleback

The intestine plays a crucial role in physiology, nutrition, and immune function, but intestinal anatomy and cell types have yet to be fully characterized in many fish species, the most diverse group of vertebrates. To address this gap, we characterized the structure and composition of the intestine of threespine stickleback (Gasterosteus aculeatus), an emerging model teleost in biological research. Using histology, myeloperoxidase staining, single-cell RNA sequencing, and RNA in situ hybridization, we defined major intestinal epithelial, immune, stromal, and stem/progenitor populations. Goblet cells were abundant in proximal and hindgut, while myeloperoxidase-positive granulocytes were evenly distributed throughout the intestine. To facilitate future experimental studies of stickleback intestinal function, we also developed the first intestinal organoid culture from stickleback and show that these cultures recapitulate epithelial architecture and retain expression of canonical intestinal epithelial markers. This organoid platform enables future functional studies of mucosal immunity, host-microbe interactions, and intestinal physiology in stickleback and related teleosts. Together, our integrated approach provides a comprehensive cell atlas and a novel experimental model for studying digestive and immune functions in threespine stickleback.

Cell Biology↗

bioRxiv2022

Competition between endogenous and exogenous attention delays the selection of task-relevant working memory content.

External selective attention is mediated by competition between endogenous (goal-driven) and exogenous (stimulus-driven) factors, with the balance of competition determining which stimuli are selected. Occasionally, exogenous factors "win" this competition and drive the selection of task-irrelevant stimuli. Endogenous and exogenous selection mechanisms may also compete to control the selection of internal representations (e.g., those stored in working memory), but how this competition manifests and whether it is resolved in the same way as external attention is unknown. Here, we leveraged the high temporal resolution of human EEG to determine how competition between endogenous and exogenous factors influences the selection of internal representations. Unlike external attention, competition between endogenous and exogenous factors did not prompt the selection of task-irrelevant working memory content. Instead, it simply delayed the endogenous selection of task-relevant working memory content by several hundred milliseconds. Thus, competition between endogenous and exogenous factors influences internal selective attention, but in a different way than external selective attention.

neuroscience↗

bioRxiv2021

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence

Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods. ImportanceEnvironmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made towards containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) [1], a large-scale environmental monitoring effort in elementary school and child care settings, has processed > 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.

microbiology↗

bioRxiv2019

Information recovery following a retrospective cue decreases with time.

Working memory (WM) performance can be enhanced by an informative cue presented during storage. This effect, termed a retrocue benefit, can be used to explore how observers prioritize information stored in WM to guide behavior. Recent studies have demonstrated that neural representations of task-relevant memoranda are strengthened following the appearance of a retrocue, suggesting that participants can consult alternative information stores to supplement active memory traces. Here, we sought to better understand the nature of these memory store(s) by asking whether they are subject to the same temporal degradation seen in active memory representations. We reconstructed and quantified representations of remembered positions from alpha-band EEG activity recorded while participants performed a retrospectively cued spatial WM task, and varied the temporal interval separating the encoding display and retrocue. Although we observed a partial recovery of location information in all cue conditions, the magnitude of recovery was linearly and inversely related to the timing of the retrocue. This suggests that participants ability to supplement active memory representations with information from additional memory stores is not static: the information maintained in these stores may be subject to temporal degredation, or the stores themselves may become more difficult to access with time.

neuroscience↗

bioRxiv2018

Retrospective cues mitigate information loss in human cortex during working memory storage.

Working memory (WM) enables the flexible representation of information over short intervals. It is well-established that WM performance can be enhanced by a retrospective cue presented during storage, yet the neural mechanisms responsible for this benefit are unclear. Here, we tested several explanations for retro-cue benefits by quantifying changes in spatial WM representations reconstructed from alpha-band (8-12 Hz) EEG activity recorded from human participants (both sexes) before and after presentation of a retrospective cue. This allowed us to track cue-related changes in WM representations with high temporal resolution (tens of milliseconds). Participants encoded the locations of two colored discs for subsequent report. During neutral trials an uninformative cue instructed participants to remember the locations of both discs across a blank delay, and we observed a monotonic decrease in the fidelity of reconstructed spatial WM representations with time. During valid trials a 100% reliable cue indicated the color of the disc participants would be probed to report. Critically, valid cues were presented immediately after termination of the encoding display (\"valid early\", or VE trials) or midway through the delay period (\"valid late\" or VL trials). During VE trials the gradual loss of location-specific information observed during neutral trials was eliminated, while during VL trials it was partially reversed. Our findings suggest that retro-cues engage several different mechanisms that together serve to mitigate information loss during WM storage.\n\nSignificance StatementWorking memory (WM) performance can be improved by a cue presented during storage. This effect, termed a retrospective cue benefit, has been used to explore the limitations of attentional prioritization in WM. However, the mechanisms responsible for retrospective cue benefits are unclear. Here we tested several explanations for retrospective cue benefits by examining how they influence WM representations reconstructed from human EEG activity. This approach allowed us to visualize, quantify, and track the effects of retrospective cues with high temporal resolution (on the order of tens of milliseconds). We show that under different circumstances retrospective cues can both eliminate and even partially reverse information loss during WM storage, suggesting that retrospective cue benefits have manifold origins.

neuroscience↗