Linking chromatin acylation mark-defined proteome and genome in living cells.

A generalizable strategy with programmable site specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and ß-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation and established linkages for chromatin acylation mark-defined proteome, genome, and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the "metabolites-modification-regulation" axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.

A domain-general frontoparietal network interacts with domain-preferential intermediate pathways to support working memory task.

Working memory (WM) is essential for cognition, but the underlying neural mechanisms remain elusive. From a hierarchical processing perspective, this paper proposed and tested a hypothesis that a domain-general network at the top of the WM hierarchy can interact with distinct domain-preferential intermediate circuits to support WM. Employing a novel N-back task, we first identified the posterior superior temporal gyrus (pSTG), middle temporal area (MT), and postcentral gyrus (PoCG) as intermediate regions for biological motion and shape motion processing, respectively. Using further psychophysiological interaction analyses, we delineated a frontal-parietal network (FPN) as the domain-general network. These results were further verified and extended by a delayed match to sample (DMS) task. Although the WM load-dependent and stimulus-free activations during the DMS delay phase confirm the role of FPN as a domain-general network to maintain information, the stimulus-dependent activations within this network during the DMS encoding phase suggest its involvement in the final stage of the hierarchical processing chains. In contrast, the load-dependent activations of intermediate regions in the N-back task highlight their further roles beyond perception in WM tasks. These results provide empirical evidence for a hierarchical processing model of WM and may have significant implications for WM training.

Proanthocyanidins inhibited colorectal cancer stem cell characteristics through Wnt/ß-catenin signaling.

BACKGROUND: Cancer stem cells (CSCs) play a key role in tumor cell growth, drug resistance, recurrence, and metastasis. Proanthocyanidins (PC) is widely existed in plants and endowed with powerful antioxidant and anti-aging effects. Interestingly, recent studies have found that PC exhibits the inhibitory effect on tumor growth. However, the role of PC in CSCs of colorectal cancer (CRC) and molecular mechanism remain unclear. METHODS: CCK-8, colony, and tumorsphere formation assay were used to evaluate cancer cell viability and stemness, respectively. Western blotting was used to detect the protein expression. Tumor xenograft experiments were employed to examine the tumorigenicity of CRC cells in nude mice. RESULTS: PC decreased the proliferation of CRC cells (HT29 and HCT-116), and improved the sensitivity of CRC cells to oxaliplatin (L-OHP), as well as inhibited tumor growth in nude mice. Further studies showed that PC also down-regulated CSCs surface molecular and stemness transcriptional factors, while suppressed the formations of tumorspheres and cell colony in CRC. In addition, PC-impaired proteins expressions of p-GSK3ß, ß-catenin and DVL1-3. LiCl, an activator of the Wnt/ß-catenin signaling, rescued PC-induced downregulation of CSCs markers, and reduction of tumorspheres and cell colony formation abilities in CRC cells. Furthermore, the effects of PC on inhibiting cell proliferation and enhancing L-OHP sensitivity were impaired by LiCl. CONCLUSIONS: PC exerted an inhibitory effect on CSCs via Wnt/ß-catenin in CRC, and may be a potential new class of natural drug for CRC treatment.

Dihydroartemisinin inhibited stem cell-like properties and enhanced oxaliplatin sensitivity of colorectal cancer via AKT/mTOR signaling.

Colorectal cancer (CRC) is a common tumor with high morbidity and mortality. The use of oxaliplatin (L-OHP) as a first-line treatment for CRC is limited due to chemoresistance. Growing evidence have revealed that the existence of cancer stem-like cells (CSLCs) is one of the important reasons for drug resistance and recurrence of cancers. Dihydroartemisinin (DHA), a derivative of artemisinin, has showed anticancer effects on a variety of malignancies, in addition to its antimalarial effects. However, the effect and mechanism of DHA on CSLCs and chemosensitivity in CRC cells remains unclear. In this study, we found that DHA inhibited cell viability in HCT116 and SW620 cells. Moreover, DHA decreased cell clonogenicity, and improved L-OHP sensitivity. Furthermore, DHA treatment attenuated tumor sphere formation, and the expressions of stem cell surface marker (CD133 and CD44) and stemness-associated transcription factor (Nanog, c-Myc, and OCT4). Mechanistically, the present findings showed that DHA inhibited of AKT/mTOR signaling pathway. The activation of AKT/mTOR signaling reversed DHA-decreased cell viability, clonogenicity, L-OHP resistance, tumor sphere, and expressions of stemness-associated protein in CRC. The inhibitory effect of DHA on tumorigenicity of CRC cells has also been demonstrated in BALB/c nude mice. In conclusion, this study revealed that DHA inhibited CSLCs properties in CRC via AKT/mTOR signaling, suggesting that DHA may be used as a potential therapeutic agent for CRC.

Development of information integration in the visual working memory of preschoolers.

Visual working memory (WM) plays a pivotal role in integrating fragments into meaningful units, but no study has addressed how visual WM integration takes place in children. The current study examined whether WM integration emerges once preschoolers master Gestalt cue and can retain two representations in WM (automatic integration hypothesis), or still needs time to mature (maturation-of-integration hypothesis). Four experiments (N = 168, 81 females, 4- to 6-year-olds, Chinese, in Hangzhou, China, from 2016.10 to 2021.11) were conducted. Although 4-year-olds can retain two objects in WM and benefit from Gestalt cues in simultaneous display (Cohen's ds >1.00), they failed when memory arrays were presented sequentially. Meanwhile, 5- and 6-year-olds consistently demonstrated WM integration ability (all Cohen's ds >0.69), supporting the maturation-of-integration hypothesis.

Object-based attention in retaining binding in working memory: Influence of activation states of working memory.

It has been suggested that retaining bindings in working memory (WM) requires more object-based attention than retaining constituent features. Recent studies have found that when memorized stimuli are presented sequentially, the most recent stimulus is in a highly accessible privileged state such that it is retained in a relatively automatic and resource-free manner, whereas the other stimuli are in a non-privileged state. The current study investigated whether the activation states of WM modulate the role of object-based attention in retaining bindings in WM. To address this question, we presented three colored shapes sequentially and added a transparent-motion task (Experiment 1) or a mental rotation task (Experiment 2) into the WM maintenance phase to consume object-based attention. We consistently found that consuming object-based attention led to a larger impairment to bindings relative to constituent features, which is independent of the WM activation states, suggesting that object-based attention is critical in retaining bindings in WM across activation states of WM.

Copper-Triggered Bioorthogonal Cleavage Reactions for Reversible Protein and Cell Surface Modifications.

Temporal and reversible control over protein and cell conjugations holds great potential for traceless release of antibody-drug conjugates (ADCs) on tumor sites as well as on-demand altering or removal of targeting elements on cell surface. We herein developed a bioorthogonal and traceless releasable reaction on proteins and intact cells to fulfill such purposes. A systematic survey of transition metals in catalyzing the bioorthogonal cleavage reactions revealed that copper complexes such as Cu(I)-BTTAA and dual-substituted propargyl (dsPra) or propargyloxycarbonyl (dsProc) moieties offered a bioorthogonal releasable pair for reversible blockage and rescue of primary amines and phenol alcohols on small molecule drugs, protein side chains, as well as intact cell surface. For proof-of-concept, we employed such Cu(I)-BTTAA/dsProc and Cu(I)-BTTAA/dsPra pairs as a "traceless linker" strategy to construct cleavable ADCs to unleash cytotoxic compounds on cancer cells in situ and as a "reversible modification" strategy for cell surface engineering. Furthermore, by coupling with the genetic code expansion strategy, we site-specifically modulated ligand-receptor interactions on live cell membranes. Together, our work expanded the transition-metal-mediated bioorthogonal cleavage tool kit from terminal decaging to internal-linker breakage, which offered a temporal and reversible conjugation strategy on therapeutic proteins and cells.

Saturation and brightness modulate the effect of depth on visual working memory.

Although previous studies show inconsistent results regarding the effect of depth perception on visual working memory (VWM), a recent finding shows that perceptually closer-in-depth items are better remembered than farther items when combining the congruent disparity and relative size cues. In this study, we employed a similar change detection paradigm to investigate the effects of saturation and brightness, alone or in combination with binocular disparity, on VWM. By varying the appearance of the memory items, we aimed to manipulate the visual salience as well as to simulate the aerial perspective cue that induces depth perception. We found that the change detection accuracy was significantly improved for brighter and more saturated items, but not for items solely with higher saturation. Additionally, combining saturation with the congruent disparity cue significantly improved memory performance for perceptually closer items over farther items. Conflicting the disparity cue with saturation eliminated the memory benefit for the closer items. These results indicate that saturation and brightness could modulate the effect of depth on VWM, and both visual salience and depth perception affect VWM possibly through a common underlying mechanism of setting priority for attentional selection.

Palladium-Triggered Chemical Rescue of Intracellular Proteins via Genetically Encoded Allene-Caged Tyrosine.

Chemical de-caging has emerged as an attractive strategy for gain-of-function study of proteins via small-molecule reagents. The previously reported chemical de-caging reactions have been largely centered on liberating the side chain of lysine on a given protein. Herein, we developed an allene-based caging moiety and the corresponding palladium de-caging reagents for chemical rescue of tyrosine (Tyr) activity on intracellular proteins. This bioorthogonal de-caging pair has been successfully applied to unmask enzymatic Tyr sites (e.g., Y671 on Taq polymerase and Y728 on Anthrax lethal factor) as well as the post-translational Tyr modification site (Y416 on Src kinase) in vitro and in living cells. Our strategy provides a general platform for chemical rescue of Tyr-dependent protein activity inside cells.

Holding the product of visual working memory integration: The role of attention.

The involuntary integration of discrete fragments into meaningful units (e.g., Gestalt) within visual working memory (VWM) is a crucial process in mind. However, the mechanisms governing the maintenance of these integrated products within VWM have remained largely unexplored. The current study sought to address this gap by investigating whether maintaining such VWM integration products places a greater demand on attention resources compared to discrete representations. We hypothesized that maintenance may be costless or require additional attention, which may be domain-specific or domain-general. To examine these hypotheses, we tested whether the emerged Gestalts by VWM integration can be abolished by an attention consumption task. Participants were required to memorize a sequence of oriented disks with or without Gestalt cues, alongside a secondary task during maintenance, consuming a specific type of attention. We found that a task consuming spatial attention impaired the VWM Gestalts of bar contours (Experiments 1 and 3), but not the Gestalts of square contours (Experiment 2). Moreover, a task consuming domain-general attention did not affect the VWM Gestalts of bar contours (Experiment 4). These findings provide evidence suggesting that maintaining VWM integration products requires more attention than discrete representations and that the type of attention required is domain-specific.

Involuntary and voluntary processes compete for entering the focus of attention of working memory.

Representations in the focus of attention (FoA) of working memory (WM) have the highest activation state and processing privilege among representations in WM. There are two distinct processes for representations entering the FoA: involuntary and voluntary. The former is an automatic attentional response to stimuli, while the latter is directed by the central executive. Although extensive WM research has examined these processes individually, their interaction, particularly in competitive scenarios, remains poorly understood. To address this, we conducted experiments by displaying memorized stimuli that contain a color singleton to trigger an involuntary process, followed by a retro-cue in the WM maintenance phase to initiate a voluntary process. By manipulating the retro-cue validity, we probed how the singleton effect was modulated when the two processes had distinct targets. Our findings indicated that when the retro-cue validity was low, the singleton effect remained unaffected by a retro-cue directing to a nonsingleton target. However, when the retro-cue validity was high, the singleton effect was eliminated on reaction time, suggesting that involuntary and voluntary processes compete for a limited capacity of the FoA, with the stronger one prevailing in this competition. These findings illuminate the intricate interplay between involuntary and voluntary attentional processes in WM and offer critical insights into the nature and allocation mechanisms of the FoA. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Diverting the focus of attention in working memory through a perceptual task.

Working memory (WM) has a limited capacity; however, this limitation can be mitigated by selecting individual items from the set currently held in WM for prioritization. The selection mechanism underlying this prioritization ability is referred to as the focus of attention (FOA) in WM. Although impressive progress has been achieved in recent years, a fundamental question remains unclear: Do perception and WM share one FOA? In the current study, we investigated the hypothesis that only a perceptual task tapping object-based attention can divert the FOA in WM. We adopted a retro-cue WM paradigm and inserted a perceptual task after the offset of the cue. Critically, we manipulated the type of attention (object-based attention in Experiments 1-3, feature-based attention in Experiment 4, and spatial attention in Experiment 5) consumed by the perceptual task. We found that participants were able to prioritize a retro-cued representation in WM, and the retro-cue benefit on memory accuracy was intact regardless of the perceptual task. Critically, the retro-cue benefit on the response time of WM task was significantly reduced only after an object-based attention perceptual task (Experiments 1, 2, 3a, and 3b), while remaining constant after a feature-based attention (Experiment 4) or spatial attention (Experiment 5) perceptual task. These results suggest that WM and perception share an object-based FOA, and an object-based attention perceptual task can divert the FOA in WM. Meanwhile, the current study further confirms that sustained attention is not necessary for selective maintenance in WM. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction.

Formaldehyde (FA) has long been considered as a toxin and carcinogen due to its damaging effects to biological macromolecules, but its beneficial roles have been increasingly appreciated lately. Real-time monitoring of this reactive molecule in living systems is highly desired in order to decipher its physiological and/or pathological functions, but a genetically encoded FA sensor is currently lacking. We herein adopt a structure-based study of the underlying mechanism of the FA-responsive transcription factor HxlR from Bacillus subtilis, which shows that HxlR recognizes FA through an intra-helical cysteine-lysine crosslinking reaction at its N-terminal helix α1, leading to conformational change and transcriptional activation. By leveraging this FA-induced intra-helical crosslinking and gain-of-function reorganization, we develop the genetically encoded, reaction-based FA sensor-FAsor, allowing spatial-temporal visualization of FA in mammalian cells and mouse brain tissues.

Evidence for the beneficial effect of perceptual grouping on visual working memory: an empirical study on illusory contour and a meta-analytic study.

The capacity of visual working memory (VWM) is found to be extremely limited. Past research shows that VWM can be facilitated by Gestalt principles of grouping, however, it remains controversial whether factors like the type of Gestalt principles, the characteristics of stimuli and the nature of experimental design could affect the beneficial effect of grouping. In particular, studies have shown that perceptual grouping could improve memory performance for a feature that is relevant for grouping, but it is unclear whether the same improvement exists for a feature that is irrelevant for grouping. In this article, an empirical study and a meta-analytic study were conducted to investigate the effect of perceptual grouping on VWM. In the empirical study, we examined the grouping effect by employing a Kanizsa illusion in which memory items were grouped by illusory contour. We found that the memory performance was improved for the grouped items even though the tested feature was grouping irrelevant, and the improvement was not significantly different from the effect of grouping by physical connectedness or by solid occlusion. In the meta-analytic study, we systematically and quantitatively examined the effect of perceptual grouping on VWM by pulling the results from all eligible studies, and found that the beneficial grouping effect was robust but the magnitude of the effect can be affected by several moderators. Factors like the types of grouping methods, the duration and the layout of the memory display, and the characteristics of the tested feature moderated the grouping effect, whereas whether employing a cue or a verbal suppression task did not. Our study suggests that the underlying mechanism of the grouping benefit may be distinct with regard to grouping relevancy of the to-be-stored feature. The grouping effect on VWM may be independent of attention for a grouping relevant feature, but may rely on attentional prioritization for a grouping irrelevant feature.

Evidence for the effect of depth on visual working memory.

Visual working memory (VWM) is a cognitive memory buffer for temporarily holding, processing, and manipulating visual information. Previous studies have demonstrated mixed results of the effect of depth perception on VWM, with some showing a beneficial effect while others not. In this study, we employed an adapted change detection paradigm to investigate the effects of two depth cues, binocular disparity and relative size. The memory array consisted of a set of pseudo-randomly positioned colored items, and the task was to judge whether the test item was changed compared to the memory item after a retention interval. We found that presenting the items in stereoscopic depth alone hardly affected VWM performance. When combining the two coherent depth cues, a significant larger VWM capacity of the perceptually closer-in-depth items was observed than that of the farther items, but the capacity for the two-depth-planes condition was not significantly different from that for the one-plane condition. Conflicting the two depth cues resulted in cancelling the beneficial effect of presenting items at a closer depth plane. The results indicate that depth perception could affect VWM, and the visual system may have an advantage in maintaining closer-in-depth objects in working memory.

Paired Design of dCas9 as a Systematic Platform for the Detection of Featured Nucleic Acid Sequences in Pathogenic Strains.

We developed an in vitro DNA detection system using a pair of dCas9 proteins linked to split halves of luciferase. Luminescence was induced upon colocalization of the reporter pair to a ∼44 bp target sequence defined by sgRNAs. We used the system to detect Mycobacterium tuberculosis DNA with high specificity and sensitivity. The reprogrammability of dCas9 was further leveraged in an array design that accesses sequence information across the entire genome.