Biology subjects

Cao, R.

Publications and source records attributed to Cao, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Maintenance of Bound or Independent Features in Visual Working Memory is Taskdependent

Conflicting findings exist regarding whether features of an object are stored separately or bound together in visual working memory. This controversy is based on an implicit assumption about a default, or fixed, mode of working memory storage. In contrast, here we asked whether the anticipated task might determine the format in which information is maintained in working memory, consistent with its task-oriented function. To test this flexible maintenance hypothesis, we recorded EEG while subjects performed a delayed (Yes/No) recognition task with different requirements and loads. Across three experiments, we compared event-related potentials (ERPs) in conditions with and without the necessity of maintaining conjunctions between features, while controlling for differences in visual stimulation. In Experiment 1 (N=24), involving color-location conjunctions, we identified a delay-period effect characterized by a positive potential shift in central-parietal channels when conjunction was not required by the task. This pattern, distinct from the effect caused by an increased working memory load, was confirmed in Experiment 2 (N=23) with an independent group of subjects using a similar paradigm, while also controlling for the physical appearance of probes. Finally, the observation of color and location conjunction in Experiments 1 and 2 was extended to Color and Orientation conjunction in Experiment 3 (N=22). Collectively, these three experiments provided reliable evidence demonstrating that the maintenance of feature conjunctions in working memory, whether spatial (location) or non-spatial (non-location), depends on the task goal. HighlightsO_LITask demands determine whether objects are represented as separate features or as conjoined items (maintenance format) in visual working memory. C_LIO_LIEEG recordings show differential activity despite similar stimulation, reflecting task demands. C_LIO_LIThe effect of the task is evident in the early stages of working memory processing. C_LIO_LIFlexibility in maintenance format was observed for both color-location and color-orientation conjunctions. C_LIO_LIThe findings challenge the notion of fixed maintenance format during visual working memory. C_LI

neuroscience↗

bioRxiv2024

Interactive design and validation of antibody panels using single-cell RNA-seq atlases

Single-cell RNA-sequencing holds promise for identifying novel markers of cellular variation for antibody-based technologies. However, antibody panel design is often difficult due to multiple experimental and biological constraints. We introduce Cytomarker, an interactive platform enabling human-in-the-loop design of antibody panels from single-cell transcriptomic data. We use Cytomarker to spatially profile human mammary tissue subpopulations and develop a novel antibody screening approach to validate granular subpopulation predictions across >3.5M cells.

bioinformatics↗

bioRxiv2024

A hippocampal astrocytic sequence emerges during learning and memory

Abstract.The dorsal hippocampus is a heterogeneous structure with numerous cell types involved in generating and maintaining detailed representations of space and time. Prior work has established that pyramidal cells contribute to these crucial aspects of associative memory. For example, hippocampal "time cells" encode temporal information through sequential activity. However, the roles of non-neuronal cell types are less often explored. In this study, we investigated dorsal hippocampal CA1 astrocytes using one-photon calcium imaging in freely moving animals during a contextual fear conditioning paradigm, enabling tracking of a population of glial cells across days. In response to foot shock, astrocytes generated robust calcium-event sequences with a time-compressed structure akin to canonical hippocampal time cells. Upon re-exposure to the conditioned context, we again detected astrocytic sequences -- in the absence of shock -- displaying similar time-compressed structure. Importantly, this phenomenon was not observed in a context different from the initial fear conditioning chamber. Lastly, spontaneous astrocytic activity in the initial conditioning context was associated with behavioral state transitions (e.g. freezing), but this was not observed in a novel context. Taken together, these results suggest a direct role for astrocytes in generating hippocampal representations of associative memory, and future work may continue to study how diverse cell types process temporal features of associative memory.

neuroscience↗

bioRxiv2024

Unsilenced inhibitory cortical ensemble gates remote memory retrieval

Acquired information can be consolidated to remote memory for storage but persists in a dormant state until its retrieval. However, it remains unknown how dormant memory is reactivated. Using a combination of simultaneous two-photon calcium imaging and holographic optogenetics in the anterior cingulate cortex (ACC) in vivo, we discover a subset of GABAergic neurons that are specifically associated with dormant memory retrieval. These interneurons display persistent activity and inter-neuronal synchronization at the remote memory stage. In the absence of natural contextual cues, directly activating these interneurons reliably recalls cortical ensembles relevant to remote memory retrieval with context specificity. Conversely, targeted volumetric inactivation of these interneurons suppresses context-induced memory retrieval. Our results reveal an unexpected role of unsilenced inhibitory cortical ensembles in causally gating the retrievability of dormant remote memory.

neuroscience↗

bioRxiv2024

Distinct attentional profile and functional connectivity of neurons with visual feature coding in the primate brain

Visual attention and object recognition are two critical cognitive functions that significantly influence our perception of the world. While these neural processes converge on the temporal cortex, the exact nature of their interactions remains largely unclear. Here, we systematically investigated the interplay between visual attention and object feature coding by training macaques to perform a free-gaze visual search task using natural face and object stimuli. With a large number of units recorded from multiple brain areas, we discovered that units exhibiting visual feature coding displayed a distinct attentional response profile and functional connectivity compared to units not exhibiting feature coding. Attention directed towards search targets enhanced the pattern separation of stimuli across brain areas, and this enhancement was more pronounced for units encoding visual features. Our findings suggest two stages of neural processing, with the early stage primarily focused on processing visual features and the late stage dedicated to processing attention. Importantly, feature coding in the early stage could predict the attentional effect in the late stage. Together, our results suggest an intricate interplay between visual feature and attention coding in the primate brain, which can be attributed to the differential functional connectivity and neural networks engaged in these processes.

neuroscience↗

bioRxiv2024

Spatiotemporal regulation of Pseudorabies Virus Thymidine kinase UL23 by post-translational modification

Post-translational modification plays a significant role in the interaction between viruses and their hosts. The pseudorabies virus (PRV) is a highly contagious herpesvirus that affects the central nervous system and respiratory tract of swine. However, the role of post-translational modifications, including Ubiquitination and SUMOylation, in host and PRV interplays is poorly understood. Here we examined the SUMO modification of PRV proteins and revealed that the PRV thymidine kinase UL23 can undergo SUMO modification. Bioinformatic analysis suggested four potential modification sites for UL23. Site-directed mutagenesis indicates that SUMO modification occurs at sites K242 and K267 as the wild type localizes in the nucleus while the mutants localize in the cytoplasm. Subsequently, polyclonal antibodies against mouse derived UL23 were employed to reveal that wild type UL23 was mainly located in the nucleus during PRV infection. Co-expression of UL23 with SUMO deconjugating enzymes showed that SENP1/2 inhibited the nuclear import of UL23. Whereas SUMO modification significantly impacted the localization of UL23, it did not detectably affect its stability.

cell biology↗

bioRxiv2024

Structural Requirements for Activity of Mind bomb1 in Notch Signaling

Mind bomb 1 (MIB1) is a RING E3 ligase that ubiquitinates Notch ligands, a necessary step for induction of Notch signaling. The structural basis for binding of the JAG1 ligand by the N-terminal region of MIB1 is known, yet how the ankyrin (ANK) and RING domains of MIB1 cooperate to catalyze ubiquitin transfer from E2[~]Ub to Notch ligands remains unclear. Here, we show that the third RING domain and adjacent coiled coil region of MIB1 (ccRING3) drives MIB1 dimerization and that ubiquitin transfer activity of MIB1 relies solely on RING3. We report x-ray crystal structures of a UbcH5B-ccRING3 complex as a fusion protein and of the ANK region. Directly tethering the N-terminal region to ccRING3 forms a minimal MIB1 protein, which is sufficient to induce a Notch response in receiver cells. Together, these studies define the functional elements of an E3 ligase needed for ligands to induce a Notch signaling response.

biochemistry↗

bioRxiv2024

Dark-based Optical Sectioning assists Background Removal in Fluorescence Microscopy

A fundamental challenge in fluorescence microscopy is the defocused background caused by scattering light, optical aberration, or limited axial resolution. Severe defocus backgrounds will submerge the in-focus information and cause artifacts in the following processing. Here, we leverage a priori knowledge about dark channels of biological structures and dual frequency separation to develop a single-frame defocus removal algorithm. It stably improves the signal-to-background ratio and structural similarity index measure of images by approximately 10-fold, and recovers in-focus signal with 85% accuracy, even when the defocus background is 50 times larger than in-focus information. Our Dark-based optical sectioning approach (Dark sectioning) is fully compatible with various microscopy techniques, such as wide-filed microscopy, polarized microscopy, laser-scanning / spinning-disk confocal microscopy, stimulated emission depletion microscopy, lightsheet microscopy, and light-field microscopy. It also complements reconstruction or processing algorithms such as deconvolution, structure illumination microscopy, and super-resolution optical fluctuation imaging.

bioinformatics↗

bioRxiv2024

Ramping cells in rodent mPFC encode time to past and future events via real Laplace transform

In interval reproduction tasks, animals must remember the event starting the interval and anticipate the time of the planned response to terminate the interval. The interval reproduction task thus allows for studying both memory for the past and anticipation of the future. We analyzed previously published recordings from rodent mPFC (Henke et al., 2021) during an interval reproduction task and identified two cell groups by modeling their temporal receptive fields using hierarchical Bayesian models. The firing in the "past cells" group peaked at the start of the interval and relaxed exponentially back to baseline. The firing in the "future cells" group increased exponentially and peaked right before the planned action at the end of the interval. Contrary to the previous assumption that timing information in the brain has one or two time scales for a given interval, we found strong evidence for a continuous distribution of the exponential rate constants for both past and future cell populations. The real Laplace transformation of time predicts exponential firing with a continuous distribution of rate constants across the population. Therefore, the firing pattern of the past cells can be identified with the Laplace transform of time since the past event while the firing pattern of the future cells can be identified with the Laplace transform of time until the planned future event.

neuroscience↗

bioRxiv2024

Genome-wide CRISPR screen identifies AC9 as a key regulator of ER calcium homeostasis involved in neuronal differentiation.

Endoplasmic reticulum (ER) calcium (Ca2+) homeostasis is essential for maintaining normal cellular physiological functions. Its disturbance is strongly linked to the onset and progression of human diseases, including cancer, developmental defects, and neurodegenerative disorders. The lack of sensitive ratiometric ER Ca2+ indicators, nevertheless, hinders systematic investigation of ER Ca2+ modulators and the underlying mechanisms. Capitalizing on two ultra-sensitive ER Ca2+ indicators and CRISPR-based genome-wide screening, we identified a set of proteins capable of reducing the ER Ca2+ content. Further comparative analysis and qPCR validation pinpointed adenylate cyclase 9 (AC9), which is upregulated during neuronal differentiation, as a key ER-Ca2+-reducing regulator. Mechanistically, AC9-mediated production of cAMP is not essential for its ability to reduce ER Ca2+ content. Instead, AC9 inhibits store operated calcium entry (SOCE) by acting on Orai1, ultimately causing attenuation of ER Ca2+ level. More physiologically relevant, upregulation of AC9 in neurons is essential for reducing ER Ca2+ levels during Drosophila brain development. Collectively, this study lays a solid groundwork for further in-depth exploration of the regulatory mechanisms dictating ER Ca2+ homeostasis during neuronal differentiation and brain development.

cell biology↗

bioRxiv2024

Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems

Computational imaging reconstructions from multiple measurements that are captured sequentially often suffer from motion artifacts if the scene is dynamic. We propose a neural space-time model (NSTM) that jointly estimates the scene and its motion dynamics. Hence, we can both remove motion artifacts and resolve sample dynamics. We demonstrate NSTM in three computational imaging systems: differential phase contrast microscopy, 3D structured illumination microscopy, and rolling-shutter DiffuserCam. We show that NSTM can recover subcellular motion dynamics and thus reduce the misinterpretation of living systems caused by motion artifacts.

biophysics↗

bioRxiv2023

Task-Dependent Representation of Features within the Same Dimension in Visual Working Memory

Working memory (WM) serves as a neurocognitive system responsible for temporarily storing and manipulating information when its source has disappeared. Previous investigations into whether features within the same dimension were stored separately or conjoined into objects have yielded conflicting findings. Based on increasing evidence on the adaptivity of the working memory system, we conjectured that the format in which objects from the same dimension are stored in Visual Working Memory (VWM) might be contingent on the specific task demands, and subtle distinctions across experiments may account for the disparities in results. In the current study, we introduced modifications to the paradigm used by Luck and Vogel (1997) and Wheeler and Treisman (2002), where the same paradigm led to different conclusions, to assess whether implicit task requirements could influence the storage format of objects in visual working memory. In two conditions, we manipulated the relevance of conjunction between two colors by varying the proportions of Mis-conjunct probes, a probe type depending on conjunction information for accurate responses. The results showed that in both conditions, performance was primarily determined by the number of features rather than the number of objects, aligning with the results of Wheeler and Treisman. Nevertheless, we observed that Mis-conjunct probes, which require conjunction information, exhibited improved performance when tested more frequently. This suggests that the format of retention in working memory, whether in separate or conjoined form, is influenced by the task demands.

animal behavior and cognition↗

bioRxiv2023

High-speed Auto-Polarization Synchronization Modulation Three-dimensional Structured Illumination Microscopy

In recent years, notable progress has been achieved in both the hardware and algorithms of structured illumination microscopy (SIM). Nevertheless, the advancement of 3DSIM has been impeded by challenges arising from the speed and intricacy of polarization modulation. In this study, we introduce a high-speed modulation 3DSIM system, leveraging the polarization maintaining and modulation capabilities of a digital micro-mirror device (DMD) in conjunction with an electro-optic modulator. The DMD-3DSIM system yields a 2-fold enhancement in both lateral (133 nm) and axial (300 nm) resolution compared to wide-field imaging, and can acquire a data set comprising 29 sections of 1024x1024 pixels, with 15 ms exposure time and 6.75 s per volume. The versatility of the DMD-3DSIM approach was exemplified through the imaging of various specimens, including fluorescent beads, nuclear pores, microtubules, actin filaments, and mitochondria within cells, as well as plant and animal tissues. Notably, polarized 3DSIM elucidated the orientation of actin filaments. Furthermore, the implementation of diverse deconvolution algorithms further enhances three-dimensional resolution. The DMD-based 3DSIM system presents a rapid and reliable methodology for investigating biomedical phenomena, boasting capabilities encompassing 3D superresolution, fast temporal resolution, and polarization imaging.

cell biology↗

bioRxiv2023

Binding in visual working memory is task-dependent

Working memory is a neurocognitive system for maintaining and manipulating information online for a short period after the source of information disappears. The information held in working memory has been shown to flexibly match current functional goals. Considering this, we revisited the question of whether information is held in WM as separate features or as bound objects. We conjectured that rather than having a fixed answer, the format in which information is maintained in working memory is also task dependent. In two separate experiments, we investigated the binding between features when the location was not (Experiment 1, color and orientation binding) or was (Experiment 2, color and location binding) a task-relevant feature in a delayed (yes/no) recognition task by manipulating the relative relevance of conjunctions and separate features. Each experiment included two conditions, Binding dominant (BD), which emphasizes the retention of binding between features, and Feature dominant (FD), which emphasizes the retention of individual features. In both experiments, we found that memory for conjunctions was better in the BD condition and that memory for separate features was better in the FD condition. These patterns suggested that the formats of objects in VWM could be shaped by the tasks they serve. Additionally, we found that the memory of location was impaired when conjunction between location and color was task-irrelevant, while memory of color and orientation was relatively independent of each other. We conclude that the representation format of objects in working memory is influenced by task requirements.

neuroscience↗

bioRxiv2023

Honey varietals differentially impact Bifidobacterium animalis ssp lactis survivability in yogurt through simulated in vitro digestion

BackgroundBifidobacterium animalis ssp. lactis DN-173 010/CNCM I-2494 (B. animalis) is a probiotic strain commonly added to yogurt. Yogurt and honey are a popular culinary pairing. Honey improves bifidobacteria survival in vitro. However, probiotic survival in yogurt with honey during in vitro digestion has not been investigated. ObjectiveThe study aimed to evaluate the effects of different honey varietals and concentrations on B. animalis survivability in yogurt through in vitro digestion. MethodsYogurt with honey or control-treated samples underwent in vitro simulated oral, gastric, and intestinal digestion. B. animalis cells were enumerated on MRS medium followed by an overlay with a modified selective MRS medium; all underwent anaerobic incubation. B. animalis were enumerated pre-digestion and after oral, gastric, and intestinal digestion. There were two study phases: phase 1 tested four honey varietals at 20% w/w per 170g yogurt, and phase 2 tested seven dosages of clover honey (20, 14, 10, 9, 8, 6, and 4% w/w) per 170g yogurt. ResultsSimilar B. animalis counts were observed between all treatments after oral and gastric digestion (<1 Log CFU/g probiotic reduction). Higher B. animalis survivability was observed in yogurt with clover honey after exposure to simulated intestinal fluids ([~]3.5 Log CFU/g reduction; P < 0.05) compared to all control treatments ([~]5.5 Log CFU/g reduction; P < 0.05). Yogurt with 10 to 20% w/w clover honey increased B. animalis survivability after simulated in vitro digestion (up to [~]4.7 Log CFU/g survival; P < 0.05). ConclusionYogurt with added honey improves probiotic survivability during in vitro digestion. The effective dose of clover honey in yogurt was 10 to 20% w/w per serving (1 - 2 tablespoons per 170g yogurt) for increased probiotic survivability during in vitro digestion.

microbiology↗

bioRxiv2023

Molecular Mechanism of PP2A/B55α Inhibition by IER5

PP2A serine/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, FAM122A, and IER5. Here, we report the cryoelectron microscopy structure of a complex of PP2A/B55 with the N-terminal structured region of IER5 (IER5-N50), which occludes a surface on B55 used for substrate recruitment, and show that IER5-N50 inhibits PP2A/B55 catalyzed dephosphorylation of pTau in biochemical assays. Mutations of full-length IER5 that disrupt its PP2A/B55 interface interfere with co-immunoprecipitation of PP2A/B55. These mutations and deletions that remove the nuclear localization sequence of IER5 suppress cellular events such as KRT1 expression that depend on association of IER5 with PP2A/B55. Querying the Alphafold2 predicted structure database identified SERTA domain proteins as high-confidence PP2A/B55-binding structural homologs of IER5-N50. These studies define the molecular basis of PP2A/B55 inhibition by IER5-family proteins and suggest a roadmap for selective pharmacologic modulation of PP2A/B55 complexes.

biochemistry↗

bioRxiv2023

Protein Structure Refinement via DeepTracer and AlphaFold2

Understanding the structures of proteins has numerous applications, such as vaccine development. It is a slow and labor-intensive task to manually build protein structures from experimental electron density maps, therefore, machine learning approaches have been proposed to automate this process. However, most of the experimental maps are not atomic resolution, so they are insufficient for computer vision-based machine learning methods to precisely determine the protein structure. On the other hand, methods that utilize evolutionary information from protein sequences to predict structures, like AlphaFold2, have recently achieved groundbreaking accuracy but often require manual effort to refine the results. We propose DeepTracer-Refine, an automated method to refine AlphaFold structures by aligning them to DeepTracers predicted structure. We tested our method on 39 multi-domain proteins and we improved the average residue coverage from 78.2% to 90.0% and average lDDT score from 0.67 to 0.71. We also compared DeepTracer-Refine against another method, Phenixs AlphaFold refinement, to demonstrate that our method not only performs better when the initial AlphaFold model is less precise but also exceeds Phenix in run-time performance.

bioinformatics↗

bioRxiv2023

Melatonin alleviates valproic acid-induced neural tube defects by modulating Src/PI3K/ERK signaling and oxidative stress

Neural tube defects (NTDs) represent a developmental disorder of the nervous system that can lead to significant disability in children and impose substantial social burdens. Valproic acid (VPA), a widely prescribed first-line antiepileptic drug for epilepsy and various neurological conditions, has been associated with a fourfold increase in the risk of NTDs when used during pregnancy. Consequently, urgent efforts are required to identify innovative prevention and treatment approaches for VPA-induced NTDs. Studies have demonstrated that the disruption in the delicate balance between cell proliferation and apoptosis is a crucial factor contributing to NTDs induced by VPA. Encouragingly, our current data reveal that melatonin (MT) exerts significant inhibition on apoptosis while promoting the restoration of neuroepithelial cells proliferation impaired by VPA. Moreover, further investigations demonstrate that MT substantially reduces the incidence of neural tube malformations resulting from VPA exposure, primarily achieved by suppressing apoptosis through the modulation of intracellular reactive oxygen species levels. In addition, the Src/PI3K/ERK signaling pathway appears to play a pivotal role in VPA-induced NTDs, with a significant inhibition observed in the affected samples. Notably, MT treatment successfully reinstates the Src/PI3K/ERK signals, thereby offering a potential underlying mechanism for MTs protective effects against VPA-induced NTDs. In summary, our current study substantiates the considerable protective potential of MT in mitigating VPA-triggered NTDs, thereby offering valuable strategies for the clinical management of VPA-related birth defects.

developmental biology↗