Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex.

Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.

Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Although host responses to the ancestral SARS-CoV-2 strain are well described, those to the new Omicron variants are less resolved. We profiled the clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoires of >1,000 blood cell or plasma specimens from SARS-CoV-2 Omicron patients. Using in-depth integrated multi-omics, we dissected the host response dynamics during multiple disease phases to reveal the molecular and cellular landscapes in the blood. Specifically, we detected enhanced interferon-mediated antiviral signatures of platelets in Omicron-infected patients, and platelets preferentially formed widespread aggregates with leukocytes to modulate immune cell functions. In addition, patients who were re-tested positive for viral RNA showed marked reductions in B cell receptor clones, antibody generation, and neutralizing capacity against Omicron. Finally, we developed a machine learning model that accurately predicted the probability of re-positivity in Omicron patients. Our study may inspire a paradigm shift in studying systemic diseases and emerging public health concerns.

Rice false smut virulence protein subverts host chitin perception and signaling at lemma and palea for floral infection.

The flower-infecting fungus Ustilaginoidea virens causes rice false smut, which is a severe emerging disease threatening rice (Oryza sativa) production worldwide. False smut not only reduces yield, but more importantly produces toxins on grains, posing a great threat to food safety. U. virens invades spikelets via the gap between the 2 bracts (lemma and palea) enclosing the floret and specifically infects the stamen and pistil. Molecular mechanisms for the U. virens-rice interaction are largely unknown. Here, we demonstrate that rice flowers predominantly employ chitin-triggered immunity against U. virens in the lemma and palea, rather than in the stamen and pistil. We identify a crucial U. virens virulence factor, named UvGH18.1, which carries glycoside hydrolase activity. Mechanistically, UvGH18.1 functions by binding to and hydrolyzing immune elicitor chitin and interacting with the chitin receptor CHITIN ELICITOR BINDING PROTEIN (OsCEBiP) and co-receptor CHITIN ELICITOR RECEPTOR KINASE1 (OsCERK1) to impair their chitin-induced dimerization, suppressing host immunity exerted at the lemma and palea for gaining access to the stamen and pistil. Conversely, pretreatment on spikelets with chitin induces a defense response in the lemma and palea, promoting resistance against U. virens. Collectively, our data uncover a mechanism for a U. virens virulence factor and the critical location of the host-pathogen interaction in flowers and provide a potential strategy to control rice false smut disease.

Double-helical assembly of heterodimeric nanoclusters into supercrystals.

DNA has long been used as a template for the construction of helical assemblies of inorganic nanoparticles1-5. For example, gold nanoparticles decorated with DNA (or with peptides) can create helical assemblies6-9. But without such biological ligands, helices are difficult to achieve and their mechanism of formation is challenging to understand10,11. Atomically precise nanoclusters that are protected by ligands such as thiolate12,13 have demonstrated hierarchical structural complexity in their assembly at the interparticle and intraparticle levels, similar to biomolecules and their assemblies14. Furthermore, carrier dynamics can be controlled by engineering the structure of the nanoclusters15. But these nanoclusters usually have isotropic structures16,17 and often assemble into commonly found supercrystals18. Here we report the synthesis of homodimeric and heterodimeric gold nanoclusters and their self-assembly into superstructures. While the homodimeric nanoclusters form layer-by-layer superstructures, the heterodimeric nanoclusters self-assemble into double- and quadruple-helical superstructures. These complex arrangements are the result of two different motif pairs, one pair per monomer, where each motif bonds with its paired motif on a neighbouring heterodimer. This motif pairing is reminiscent of the paired interactions of nucleobases in DNA helices. Meanwhile, the surrounding ligands on the clusters show doubly or triply paired steric interactions. The helical assembly is driven by van der Waals interactions through particle rotation and conformational matching. Furthermore, the heterodimeric clusters have a carrier lifetime that is roughly 65 times longer than that of the homodimeric clusters. Our findings suggest new approaches for increasing complexity in the structural design and engineering of precision in supercrystals.

Barley yellow dwarf virus-GAV 17K protein disrupts thiamine biosynthesis to facilitate viral infection in plants.

Thiamine functions as a crucial activator modulating plant health and broad-spectrum stress tolerances. However, the role of thiamine in regulating plant virus infection is largely unknown. Here, we report that the multifunctional 17K protein encoded by barley yellow dwarf virus-GAV (BYDV-GAV) interacted with barley pyrimidine synthase (HvTHIC), a key enzyme in thiamine biosynthesis. HvTHIC was found to be localized in chloroplast via an N-terminal 74-amino acid domain. However, the 17K-HvTHIC interaction restricted HvTHIC targeting to chloroplasts and triggered autophagy-mediated HvTHIC degradation. Upon BYDV-GAV infection, the expression of the HvTHIC gene was significantly induced, and this was accompanied by accumulation of thiamine and salicylic acid. Silencing of HvTHIC expression promoted BYDV-GAV accumulation. Transcriptomic analysis of HvTHIC silenced and non-silenced barley plants showed that the differentially expressed genes were mainly involved in plant-pathogen interaction, plant hormone signal induction, phenylpropanoid biosynthesis, starch and sucrose metabolism, photosynthesis-antenna protein, and MAPK signaling pathway. Thiamine treatment enhanced barley resistance to BYDV-GAV. Taken together, our findings reveal a molecular mechanism underlying how BYDV impedes thiamine biosynthesis to uphold viral infection in plants.

ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction.

The latent features extracted from the multiple sequence alignments (MSAs) of homologous protein families are useful for identifying residue-residue contacts, predicting mutation effects, shaping protein evolution, etc. Over the past three decades, a growing body of supervised and unsupervised machine learning methods have been applied to this field, yielding fruitful results. Here, we propose a novel self-supervised model, called encoder-transformation layer-decoder (ETLD) architecture, capable of capturing protein sequence latent features directly from MSAs. Compared to the typical autoencoder model, ETLD introduces a transformation layer with the ability to learn inter-site couplings, which can be used to parse out the two-dimensional residue-residue contacts map after a simple mathematical derivation or an additional supervised neural network. ETLD retains the process of encoding and decoding sequences, and the predicted probabilities of amino acids at each site can be further used to construct the mutation landscapes for mutation effects prediction, outperforming advanced models such as GEMME, DeepSequence and EVmutation in general. Overall, ETLD is a highly interpretable unsupervised model with great potential for improvement and can be further combined with supervised methods for more extensive and accurate predictions.

The shorter a man is, the more he defends fairness: relative height disadvantage promoting third-party punishment-evidence from inter-brain synchronization.

Third-party punishment occurs in interpersonal interactions to sustain social norms, and is strongly influenced by the characteristics of the interacting individuals. During social interactions, height is the striking physical appearance features first observed, height disadvantage may critically influence men's behavior and mental health. Herein, we explored the influence of height disadvantage on third-party punishment through time-frequency analysis and electroencephalography hyperscanning. Two participants were randomly designated as the recipient and third party after height comparison and instructed to complete third-party punishment task. Compared with when the third party's height is higher than the recipient's height, when the third party's height is lower, the punishment rate and transfer amount were significantly higher. Only for highly unfair offers, the theta power was significantly greater when the third party's height was lower. The inter-brain synchronization between the recipient and the third party was significantly stronger when the third party's height was lower. Compared with the fair and medium unfair offers, the inter-brain synchronization was strongest for highly unfair offers. Our findings indicate that the height disadvantage-induced anger and reputation concern promote third-party punishment and inter-brain synchronization. This study enriches research perspective and expands the application of the theory of Napoleon complex.

Romantic relationships attenuated competition between lovers: evidence from brain synchronization.

Competition is an essential component of social interaction and is influenced by interpersonal relationships. This study is based on social exchange theory and explores the relationship between brain synchronization and competition in the binary system of romantic relationships through electroencephalogram hyperscanning technology. The results found that females had a greater win rate in the romantic and friend groups. During the early stage (0-200 ms), when the competitive target appeared, the stranger group exhibited greater interbrain synchronicity in the Alpha frequency band. However, during the later stage (600-800 ms), the romantic group showed higher Alpha band interbrain synchrony when the competitive target appeared. Significant interbrain synchronizations were observed in the Theta frequency band of the stranger and friend groups at 400-600 ms and 800-1000 ms. Moreover, these interbrain synchronizations were significantly positively correlated with the winning rates of females in the competition. These findings suggest a close relationship between interpersonal coordination and interbrain synchronization. Furthermore, romantic relationships reduce participants' willingness to compete, affecting their attention regulation, emotional processing, and goal orientation, thus influencing competition. This study investigated the impact of romantic relationships on competition, providing a theoretical foundation for promoting the positive and healthy development of romantic relationships.

Who takes the lead in consumer choices within romantic relationships: the evidence from electroencephalography hyperscanning and granger causality analysis.

In real-life scenarios, joint consumption is common, particularly influenced by social relationships such as romantic ones. However, how romantic relationships affect consumption decisions and determine dominance remains unclear. This study employs electroencephalography hyperscanning to examine the neural dynamics of couples during joint-consumption decisions. Results show that couples, compared to friends and strangers, prefer healthier foods, while friends have significantly faster reaction times when selecting food. Time-frequency analysis indicates that couples exhibit significantly higher theta power, reflecting deeper emotional and cognitive involvement. Strangers show greater beta1 power, indicating increased cognitive effort and alertness due to unfamiliarity. Friends demonstrate higher alpha2 power when choosing unhealthy foods, suggesting increased cognitive inhibition. Inter-brain phase synchrony analysis reveals that couples display significantly higher inter-brain phase synchrony in the beta1 and theta bands across the frontal-central, parietal, and occipital regions, indicating more coordinated cognitive processing and stronger emotional bonds. Females in couples may be more influenced by emotions during consumption decisions, with detailed sensory information processing, while males exhibit higher cognitive control and spatial integration. Granger-causality analysis shows a pattern of male dominance and female dependence in joint consumption within romantic relationships. This study highlights gender-related neural synchronous patterns during joint consumption among couples, providing insights for further research in consumer decision-making.

Intimate relationships regulate female brain activity in a competitive context: evidence from EEG and functional connectivity analysis.

Competition is common in life, and intimate relationships are essential. Understanding how intimate relationships impact an individual's competitive process is crucial. This study explored the impact of competitor gender on female competition using electroencephalography analysis. The results revealed that females exhibited a smaller median of the absolute value of reaction time difference (DRT) between their partners and their competitors when their partners were absent compared to when their partners were present. Additionally, females showed greater average amplitudes of N2 posterior contralateral component (N2pc) and Late Positive Potential (LPP), increased activation of the alpha frequency band, and enhanced theta frequency band functional connectivity between the central parietal lobe and occipital lobe. Furthermore, when competing with individuals of the same gender as opposed to individuals of the opposite gender, females exhibited greater average amplitudes of percentage of wins and N2pc. A significant negative correlation was noted between the DRT and the average wave amplitudes of N2pc and LPP. These findings suggest that females are more engaged in competitive tasks when partners are not present and have improved decision-making when competing with same-gender individuals. This study provides evidence for the influence of lovers on female competition, helping females adapt to social competition and promoting healthy relationships.

Favoritism or bias? Cooperation and competition under different intergroup relationships: evidence from EEG hyperscanning.

Cooperation and competition are the most common forms of social interaction in various social relationships. Intergroup relationships have been posited to influence individuals' interpersonal interactions significantly. Using electroencephalography hyperscanning, this study aimed to establish whether intergroup relationships influence interpersonal cooperation and competition and the underlying neural mechanisms. According to the results, the in-group Coop-index is better than the out-group, whereas the out-group Comp-index is stronger than the in-group. The in-group functional connectivity between the frontal-central region and the right temporoparietal junction in the ß band was stronger in competition than cooperation. The out-group functional connectivity between the frontal-central region and the left temporoparietal junction in the α band was stronger in cooperation than competition. In both cooperation and competition, the in-group exhibited higher interbrain synchronization between the prefrontal cortex and parietal region in the θ band, as well as between the frontal-central region and frontal-central region in the α band, compared to the out-group. The intrabrain phase-locking value in both the α and ß bands can effectively predict performance in competition tasks. Interbrain phase-locking value in both the α and θ bands can be effectively predicted in a performance cooperation task. This study offers neuroscientific evidence for in-group favoritism and out-group bias at an interpersonal level.

Identifying Patients With Rapid Progression From Hormone-Sensitive to Castration-Resistant Prostate Cancer: A Retrospective Study.

Prostate cancer (PCa) is the second most prevalent malignancy and the fifth cause of cancer-related deaths in men. A crucial challenge is identifying the population at risk of rapid progression from hormone-sensitive prostate cancer (HSPC) to lethal castration-resistant prostate cancer (CRPC). We collected 78 HSPC biopsies and measured their proteomes using pressure cycling technology and a pulsed data-independent acquisition pipeline. We quantified 7355 proteins using these HSPC biopsies. A total of 251 proteins showed differential expression between patients with a long- or short-term progression to CRPC. Using a random forest model, we identified seven proteins that significantly discriminated long- from short-term progression patients, which were used to classify PCa patients with an area under the curve of 0.873. Next, one clinical feature (Gleason sum) and two proteins (BGN and MAPK11) were found to be significantly associated with rapid disease progression. A nomogram model using these three features was generated for stratifying patients into groups with significant progression differences (p-value = 1.3×10-4). To conclude, we identified proteins associated with a fast progression to CRPC and an unfavorable prognosis. Based on these proteins, our machine learning and nomogram models stratified HSPC into high- and low-risk groups and predicted their prognoses. These models may aid clinicians in predicting the progression of patients, guiding individualized clinical management and decisions.

Copper Single-Atom-Based Metal-Organic Framework for Ultrasound-Enhanced Nanocatalytic Therapy.

Chemodynamic therapy (CDT) is an emerging therapeutic modality triggered by endogenous substances in the tumor microenvironment (TME) to generate reactive oxygen species. However, the mild acid pH, low H2O2 concentration, and overexpressed glutathione can suppress the CDT efficiency. Herein, ultrasound (US)-triggered Cu2+-based single-atom nanoenzymes (FA-NH2-UiO-66-Cu, FNUC) are constructed with the performance of target and glutathione depletion. In the TME, the single-atom Cu sites of FNUC consume glutathione and the FNUC:Cu+ generates •OH via peroxidase-like activity. The US-activated FNUC exhibits a fast •OH generation rate, a low Michaelis constant, and a large •OH concentration, indicating the cavitation effect of US promotes the •OH generation. Meanwhile, the tumor target of FNUC is confirmed by NIR-II fluorescence imaging, in which it is modified with IR-1061. Combined with the antitumor performance of FNUC in vitro and in vivo, the novel Cu-based SAzymes can achieve efficient and precise cancer treatment.

High Spatial Resolution 2D Imaging of Current Density and Pressure for Graphene Devices under High Pressure Using Nitrogen-Vacancy Centers in Diamond.

Current density imaging is helpful for discovering interesting electronic phenomena and understanding carrier dynamics, and by combining pressure distributions, several pressure-induced novel physics may be comprehended. In this work, noninvasive, high-resolution two-dimensional images of the current density and pressure gradient for graphene ribbon and hBN-graphene-hBN devices are explored using nitrogen-vacancy (NV) centers in diamond under high pressure. The two-dimensional vector current density is reconstructed by the vector magnetic field mapped by the near-surface NV center layer in the diamond. The current density images accurately and clearly reproduce the complicated structure and current flow of graphene under high pressure. Additionally, the spatial distribution of the pressure is simultaneously mapped, rationalizing the nonuniformity of the current density under high pressure. The current method opens a significant new avenue to investigate electronic transport and conductance variations in two-dimensional materials and electrical devices under high pressure as well as for nondestructive evaluation of semiconductor circuits.

Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy.

Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32 patients with CCOC (H1 cohort) and characterized 8697 proteins using data-independent acquisition mass spectrometry (DIA-MS). We then performed proteomic analysis of 28 fresh frozen (FF) CCOC tissue specimens from an independent cohort of 24 patients with CCOC (H2 cohort), leading to the identification of 9409 proteins with DIA-MS. After bioinformatics analysis, we narrowed our focus to 15 proteins significantly correlated with the recurrence free survival (RFS) in both cohorts. These proteins are mainly involved in DNA damage response, extracellular matrix (ECM), and mitochondrial metabolism. Parallel reaction monitoring (PRM)-MS was adopted to validate the prognostic potential of the 15 proteins in the H1 cohort and an independent confirmation cohort (H3 cohort). Interferon-inducible transmembrane protein 1 (IFITM1) was observed as a robust prognostic marker for CCOC in both PRM data and immunohistochemistry (IHC) data. Taken together, this study presents a CCOC proteomic data resource and a single promising protein, IFITM1, which could potentially predict the recurrence and survival of CCOC.

The promoting effect of the absence of second-party's punishment power on third-party punishment in maintaining social fairness norms: An EEG hyper-scanning study.

Third-party punishment (TPP) plays an irreplaceable role in maintaining social fairness. Punishment power is a significant area of study within economic games. However, the impact of whether or not the second-party possesses punishment power on TPP remains unexplored. The present study utilizes the high temporal resolution of EEG and time-frequency analysis, intra-barin functional connectivity analysis, inter-brain synchronization (IBS) analysis, and granger causality analysis(GCA) to comprehensively explore the neural mechanism of TPP from the perspective of third-party individual's decision-making and IBS in the real-time social interaction. Time-frequency results found that, the absence of the punishment power activated more theta-band and alpha-band power compare to when second-party has punishment power. When second-party has no punishment power, functional connection results observed stronger functional connectivity in theta band for medium unfair offers between rTPJ and PFC. Dual-brain analysis revealed that when the second-party has no punishment power, there is a significantly higher IBS in the alpha band between the frontal and frontal-central lobes of the second-party and the parietal and parietal occipital lobes of the third-party. GCA results further showed that the direction of IBS from third-party to second-party was significantly stronger than from second-party to third-party. This study demonstrates that the absence of the second-party's punishment power promote TPP, and similar cognitive process of thinking on how to maintain social fairness enhances IBS. The current study emphasizes the influence of punishment power on TPP, broadens the research perspective and contributes crucial insights into maintain social fairness.

Homotopic functional connectivity disruptions in schizophrenia and their associated gene expression.

It has been revealed that abnormal voxel-mirrored homotopic connectivity (VMHC) is present in patients with schizophrenia, yet there are inconsistencies in the relevant findings. Moreover, little is known about their association with brain gene expression profiles. In this study, transcription-neuroimaging association analyses using gene expression data from Allen Human Brain Atlas and case-control VMHC differences from both the discovery (meta-analysis, including 9 studies with a total of 386 patients and 357 controls) and replication (separate group-level comparisons within two datasets, including a total of 258 patients and 287 controls) phases were performed to identify genes associated with VMHC alterations. Enrichment analyses were conducted to characterize the biological functions and specific expression of identified genes, and Neurosynth decoding analysis was performed to examine the correlation between cognitive-related processes and VMHC alterations in schizophrenia. In the discovery and replication phases, patients with schizophrenia exhibited consistent VMHC changes compared to controls, which were correlated with a series of cognitive-related processes; meta-regression analysis revealed that illness duration was negatively correlated with VMHC abnormalities in the cerebellum and postcentral/precentral gyrus. The abnormal VMHC patterns were stably correlated with 1287 genes enriched for fundamental biological processes like regulation of cell communication, nervous system development, and cell communication. In addition, these genes were overexpressed in astrocytes and immune cells, enriched in extensive cortical regions and wide developmental time windows. The present findings may contribute to a more comprehensive understanding of the molecular mechanisms underlying VMHC alterations in patients with schizophrenia.

Microstructural and functional substrates underlying dispositional greed and its link with trait but not state impulsivity.

The interplay between personality traits and impulsivity has long been a central theme in psychology and psychiatry. However, the potential association between Greed Personality Traits (GPT) and impulsivity, encompassing both trait and state impulsivity and future time perspective, remains largely unexplored. To address these issues, we employed questionnaires and an inter-temporal choice task to estimate corresponding trait/state impulsivity and collected multi-modal neuroimaging data (resting-state functional imaging: n = 430; diffusion-weighted imaging: n = 426; task-related functional imaging: n = 53) to investigate the underlying microstructural and functional substrates. Behavioral analyses revealed that GPT mediated the association between time perspective (e.g., present fatalism) and trait impulsivity (e.g., motor impulsivity). Functional imaging analyses further identified that brain activation strengths and patterns related to delay length, particularly in the dorsomedial prefrontal cortex, superior parietal lobule, and cerebellum, were associated with GPT. Moreover, individuals with similar levels of greed exhibited analogous spontaneous brain activity patterns, predominantly in the Default Mode Network (DMN), Fronto-Parietal Network (FPN), and Visual Network (VIS). Diffusion imaging analysis observed specific microstructural characteristics in the spinocerebellar/pontocerebellar fasciculus, internal/external capsule, and corona radiata that support the formation of GPT. Furthermore, the corresponding neural activation pattern, spontaneous neural activity pattern, and analogous functional couplings among the aforementioned brain regions mediated the relationships between time perspective and GPT and between GPT and motor impulsivity. These findings provide novel insights into the possible pathway such as time perspective → dispositional greed → impulsivity and uncover their underlying microstructural and functional substrates.

Happy people are always similar: The evidence from brain morphological and functional inter-subject correlations.

A fundamental question in the study of happiness is whether there is neural evidence to support a well-known hypothesis that happy people are always similar while unfortunate people have their own misfortunes. To investigate this, we employed several happiness-related questionnaires to identify potential components of happiness, and further investigated and confirmed their associations with personality, mood, aggressive behaviors, and amygdala reactivity to fearful faces within a substantial sample size of college students (n = 570). Additionally, we examined the functional and morphological similarities and differences among happy individuals using the inter-subject representational similarity analysis (IS-RSA). IS-RSA emphasizes the geometric properties in a high-dimensional space constructed by brain or behavioral patterns and focuses on individual subjects. Our behavioral findings unveiled two factors of happiness: individual and social, both of which mediated the effect of personality traits on individual aggression. Subsequently, mood mediated the impact of happiness on aggressive behaviors across two subgroup splits. Functional imaging data revealed that individuals with higher levels of happiness exhibited reduced amygdala reactivity to fearful faces, as evidenced by a conventional face-matching task (n = 104). Moreover, IS-RSA demonstrated that these participants manifested similar neural activation patterns when processing fearful faces within the visual pathway, but not within the emotional network (e.g., amygdala). Morphological observations (n = 425) indicated that individuals with similar high happiness levels exhibited comparable gray matter volume patterns within several networks, including the default mode network, fronto-parietal network, visual network, and attention network. Collectively, these findings offer early neural evidence supporting the proposition that happy individuals may share common neural characteristics.

Bottom-Up Construction of Metal-Organic Framework Loricae on Metal Nanoclusters with Consecutive Single Nonmetal Atom Tuning for Tailored Catalysis.

The introduction of single or multiple heterometal atoms into metal nanoparticles is a well-known strategy for altering their structures (compositions) and properties. However, surface single nonmetal atom doping is challenging and rarely reported. For the first time, we have developed synthetic methods, realizing "surgery"-like, successive surface single nonmetal atom doping, replacement, and addition for ultrasmall metal nanoparticles (metal nanoclusters, NCs), and successfully synthesized and characterized three novel bcc metal NCs Au38I(S-Adm)19, Au38S(S-Adm)20, and Au38IS(S-Adm)19 (S-Adm: 1-adamantanethiolate). The influences of single nonmetal atom replacement and addition on the NC structure and optical properties (including absorption and photoluminescence) were carefully investigated, providing insights into the structure (composition)-property correlation. Furthermore, a bottom-up method was employed to construct a metal-organic framework (MOF) on the NC surface, which did not essentially alter the metal NC structure but led to the partial release of surface ligands and stimulated metal NC activity for catalyzing p-nitrophenol reduction. Furthermore, surface MOF construction enhanced NC stability and water solubility, providing another dimension for tunning NC catalytic activity by modifying MOF functional groups.