msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease.

SUMMARY: Identification and quantification of phosphorylation sites are essential for biological interpretation of a phosphoproteomics experiment. For data independent acquisition mass spectrometry-based (DIA-MS) phosphoproteomics, extracting a site-level report from the output of current processing software is not straightforward as multiple peptides might contribute to a single site, multiple phosphorylation sites can occur on the same peptides, and protein isoforms complicate site specification. Currently only limited support is available from a commercial software package via a platform-specific solution with a rather simple site quantification method. Here, we present sitereport, a software tool implemented in an extendable Python package called msproteomics to report phosphosites and phosphopeptides from a DIA-MS phosphoproteomics experiment with a proven quantification method called MaxLFQ. We demonstrate the use of sitereport for downstream data analysis at site level, allowing benchmarking different DIA-MS processing software tools. AVAILABILITY AND IMPLEMENTATION: sitereport is available as a command line tool in the Python package msproteomics, released under the Apache License 2.0 and available from the Python Package Index (PyPI) at https://pypi.org/project/msproteomics and GitHub at https://github.com/tvpham/msproteomics.

Secretome processing for proteomics: A methods comparison.

The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment with high detectability in biofluids. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: (1) Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); (2) Acetone protein precipitation coupled to IGD; (3) MWCO filter-based protein concentration followed by to in-solution digestion (ISD); (4) Acetone protein precipitation coupled to ISD; (5) Direct ISD; (6) Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines, and growth factors. Our findings revealed that acetone protein precipitation coupled to ISD outperformed the other methods in terms of the number of identified proteins (2246) and method reproducibility (correlation coefficient between replicates (r = 0.94, CV = 19%). Overall, especially small proteins such as those from the classes mentioned above were better identified using ISD workflows. Concluding, herein we report that secretome protein precipitation coupled to ISD is the method of choice for high-throughput secretome proteomics via single shot nanoLC-MS/MS.

A study of genetic variants associated with skin traits in the Vietnamese population.

BACKGROUND: Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. OBJECTIVES: We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health. METHODS: Vietnamese cohorts of whole-genome sequencing (WGS) of 1008 healthy individuals for the reference and 96 genotyping samples (which do not have any skin cutaneous issues) by Infinium Asian Screening Array-24 v1.0 BeadChip were employed to predict skin-associated genetic variants of 25 skin-related and micronutrient requirement traits in population analysis and correlation analysis. Simultaneously, we compared the landscape of cutaneous issues of Vietnamese people with other populations by assessing their genetic profiles. RESULTS: The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst = 0.036, CHB: Fst = 0.031, CHS: Fst = 0.027, CDX: Fst = 0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p = 1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)). CONCLUSION: This is the first investigation in Vietnam to explore genetic variants of facial skin. These findings could improve inadequate skin-related genetic diversity in the currently published database.

A new R,R-RvD6 isomer with protective actions following corneal nerve injury.

The transparent cornea is the most densely innervated tissue in the body, primarily by sensory nerves originating from the trigeminal ganglia (TG). Damage to corneal nerves reduces sensitivity and tear secretion and results in dry eye. Consequently, ocular pain, for which no satisfactory therapies exist, arises in many cases. Treatment of injured corneas with pigment epithelium-derived factor (PEDF) combined with docosahexaenoic acid (DHA) stimulates nerve regeneration in models of refractive surgery, which damages nerves. The mechanism involves the synthesis of a stereoisomer of resolvin D6 (R,R-RvD6) formed after incorporating DHA into membrane lipids. Activation of a PEDF receptor (PEDF-R) with phospholipase activity releases DHA to synthesize the new resolvin isomer, which is secreted via tears. Topical treatment of mice corneas with R,R-RvD6 shows higher bioactivity in regenerating nerves and increasing sensitivity compared to PEDF+DHA. It also stimulates a transcriptome in the TG that modulates genes involved in ocular pain. Our studies suggest an important therapeutic role for R,R-RvD6 in regenerating corneal nerves and decreasing pain resulting from dry eye.

Injecting drug use increases the risk of death in HIV patients on antiretroviral therapy in Vietnam.

The Human Immunodeficiency Virus (HIV) epidemic remains a major public health issue worldwide. In Vietnam, the HIV epidemic is essentially driven by people who inject drugs (PWID). This study aims to compare mortality and loss to follow-up (LTFU) between PWID and other patients. From June 2017 to April 2018, HIV-infected adults were enrolled in a prospective cohort from time of ART initiation in six provinces of North Vietnam. The end date was July 2020. Mortality and LTFU were described using competing-risk survival models. Factors associated with mortality and with LTFU were identified using Cox models with a competing-risk approach. Of the 578 participants, 261 (45.2%) were PWID and almost exclusively male. 49 patients died, corresponding to a mortality rate (95% confidence interval (CI)) of 3.7 (2.8-4.9) per 100 person-months, and 79 were lost to follow-up, corresponding to a rate (95% CI) of 6.0 (4.8-7.4) per 100 person-months. PWID were at higher risk of death but not of LTFU. Overall, LTFU was high in both groups. Latecomers to clinical visits were more at risk of both death and LTFU. Therefore, this should be a warning to clinical teams and preventive actions taken in these patients.Trial registration: ClinicalTrials.gov identifier: NCT03249493..

Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines.

In Birt-Hogg-Dubé (BHD) syndrome, germline loss-of-function mutations in the Folliculin (FLCN) gene lead to an increased risk of renal cancer. To address how FLCN inactivation affects cellular kinase signaling pathways, we analyzed comprehensive phosphoproteomic profiles of FLCNPOS and FLCNNEG human renal tubular epithelial cells (RPTEC/TERT1). In total, 15,744 phosphorylated peptides were identified from 4329 phosphorylated proteins. INKA analysis revealed that FLCN loss alters the activity of numerous kinases, including tyrosine kinases EGFR, MET, and the Ephrin receptor subfamily (EPHA2 and EPHB1), as well their downstream targets MAPK1/3. Validation experiments in the BHD renal tumor cell line UOK257 confirmed that FLCN loss contributes to enhanced MAPK1/3 and downstream RPS6K1/3 signaling. The clinically available MAPK inhibitor Ulixertinib showed enhanced toxicity in FLCNNEG cells. Interestingly, FLCN inactivation induced the phosphorylation of PIK3CD (Tyr524) without altering the phosphorylation of canonical Akt1/Akt2/mTOR/EIF4EBP1 phosphosites. Also, we identified that FLCN inactivation resulted in dephosphorylation of TFEB Ser109, Ser114, and Ser122, which may be linked to increased oxidative stress levels in FLCNNEG cells. Together, our study highlights differential phosphorylation of specific kinases and substrates in FLCNNEG renal cells. This provides insight into BHD-associated renal tumorigenesis and may point to several novel candidates for targeted therapies.

A national program to advance dementia research in Vietnam.

BACKGROUND: As Vietnam and other low- and middle-income countries (LMIC) experience a rapid increase in the number of people living with dementia, an acute need exists to strengthen research capacity to inform policy, improve care and support, and develop national dementia plans. We describe the development and early outcomes of an National Institutes of Health (NIH)/National Institute on Aging (NIA)-funded national dementia research capacity building program in Vietnam. METHODS: The research capacity building program commenced in 2019 and has three components: (1) Vietnam Alzheimer's and other dementias research Network (VAN), (2) a mentored pilot grant program, and (3) research training, networking, and dissemination activities. The pilot grant program funds Vietnamese researchers for one to two years to conduct research focusing on Alzheimer's Disease and Alzheimer's Disease Related Dementias (AD/ADRD). Grants are reviewed and scored using NIH criteria, and priority is given to pilot grants with policy relevance and potential for future funding. An international pool of high-income country (e.g., United States, Australia, and United Kingdom) mentors has been engaged and mentors paired with each funded project. Training and networking activities include workshops on AD/ADRD research topics and regular meetings in conjunction with Vietnam's annual national dementia/geriatric conferences. Dissemination is facilitated through targeted outreach and the creation of a national network of institutions. RESULTS: Over four years (2019-2023), we received 62 applications, reviewed 58 applications, and funded 21 projects (4-5 per year). Funded investigators were from diverse disciplines and institutions across Vietnam with projects on a range of topics, including biomarkers, prevention, diagnosis, neuropsychological assessment, family caregiver support, dementia education, and clinical trials. A network of 12 leading academic and research institutions nationwide has been created to facilitate dissemination. Six research training workshops have been organized and included presentations from international speakers. Grantees have published or presented their studies at both national and international levels. The mentoring program has helped grantees to build their research skills and expand their research network. CONCLUSION: This research capacity building program is the first of its kind in Vietnam and may serve as a useful model for other LMIC.

VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells.

The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to oxidative stress. which alters the nuclear pattern of histone epigenetic modifications and phosphoproteome pathways. The early effect of oxidative stress on chromatin was studied by determining the levels of 8-oxoG lesions and the alteration of the epigenetic modification of histones. Oxidative stress caused an accumulation of 8-oxoG DNA lesions that were increased by VRK1 depletion, causing a significant accumulation of DNA strand breaks detected by labeling free 3'-DNA ends. In addition, oxidative stress altered the pattern of chromatin epigenetic marks and the nuclear phosphoproteome pathways that were impaired by VRK1 depletion. Oxidative stress induced the acetylation of H4K16ac and H3K9 and the loss of H3K4me3. The depletion of VRK1 altered all these modifications induced by oxidative stress and resulted in losses of H4K16ac and H3K9ac and increases in the H3K9me3 and H3K4me3 levels. All these changes were induced by the oxidative stress in the epigenetic pattern of histones and impaired by VRK1 depletion, indicating that VRK1 plays a major role in the functional reorganization of chromatin in the response to oxidative stress. The analysis of the nuclear phosphoproteome in response to oxidative stress detected an enrichment of the phosphorylated proteins associated with the chromosome organization and chromatin remodeling pathways, which were significantly decreased by VRK1 depletion. VRK1 depletion alters the histone epigenetic pattern and nuclear phosphoproteome pathways in response to oxidative stress. The enzymes performing post-translational epigenetic modifications are potential targets in synthetic lethality strategies for cancer therapies.

Care needs assessment of older adults with dementia in a semi-rural district in Vietnam: A community-based cross-sectional study.

BACKGROUND: The increasing needs of people living with dementia (PLWD) in Vietnam present an enormous public health challenge. Vietnam is an understudied country, and little is known regarding the overall unmet needs of caregivers or the demographic risk factors associated with unmet caregiving needs. This study aimed to determine the burden of unmet care needs of community-dwelling PLWD and identify sociodemographic risks associated with unmet care needs. METHODS: A cross-sectional study in a rural area facing urbanisation in Hanoi, Vietnam recruited PWLD-caregiver dyads with multistage sampling. We utilised the Camberwell Assessment of Need for the Elderly (CANE) instrument to evaluate care needs across four domains. Caregivers rated PLWD needs, with higher scores indicating greater unmet needs. The Mann-Whitney test was employed for comparing two groups, while the Kruskal-Wallis test was used for comparisons involving more than two groups in the analysis, and a P-value of less than 0.05 was considered statistically significant. RESULTS: Among 90 PLWD participating in the study, the overall mean care needs score was 11.6 ± 4.3, with only 16.2% of PLWD having their care needs met. Environmental and physical needs were more frequently met than psychological or social needs. Only 48.0% and 43.9% of environmental and physical needs were met respectively, and a meagre 20.9% and 23.6% for psychological and social needs. Unmet care needs were more frequent for PWLD who were female, single or divorced, had lower monthly household income, or who were in more advanced stages of dementia, as indicated by Clinical Dementia Rating scores ≥1. CONCLUSIONS: Unmet needs for PWLD are common. Increased caregiver education, resources, and services in Vietnam are urgently required to improve the quality of life for this population.

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics.

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.

Unraveling the Role of Entropy in Thermoelectrics: Entropy-Stabilized Quintuple Rock Salt PbGeSnCdxTe3+x.

Entropy-engineered materials are garnering considerable attention owing to their excellent mechanical and transport properties, such as their high thermoelectric performance. However, understanding the effect of entropy on thermoelectrics remains a challenge. In this study, we used the PbGeSnCdxTe3+x family as a model system to systematically investigate the impact of entropy engineering on its crystal structure, microstructure evolution, and transport behavior. We observed that PbGeSnTe3 crystallizes in a rhombohedral structure at room temperature with complex domain structures and transforms into a high-temperature cubic structure at ∼373 K. By alloying CdTe with PbGeSnTe3, the increased configurational entropy lowers the phase-transition temperature and stabilizes PbGeSnCdxTe3+x in the cubic structure at room temperature, and the domain structures vanish accordingly. The high-entropy effect results in increased atomic disorder and consequently a low lattice thermal conductivity of 0.76 W m-1 K-1 in the material owing to enhanced phonon scattering. Notably, the increased crystal symmetry is conducive to band convergence, which results in a high-power factor of 22.4 µW cm-1 K-1. As a collective consequence of these factors, a maximum ZT of 1.63 at 875 K and an average ZT of 1.02 in the temperature range of 300-875 K were obtained for PbGeSnCd0.08Te3.08. This study highlights that the high-entropy effect can induce a complex microstructure and band structure evolution in materials, which offers a new route for the search for high-performance thermoelectrics in entropy-engineered materials.

Atrial epicardial adipose tissue abundantly secretes myeloperoxidase and activates atrial fibroblasts in patients with atrial fibrillation.

BACKGROUND: Epicardial adipose tissue (EAT) secretome induces fibrosis. Fibrosis, primarily extracellular matrix (ECM) produced by fibroblasts, creates a substrate for atrial fibrillation (AF). Whether the EAT secretome from patients with AF activates human atrial fibroblasts and through which components, remains unexplored. RESEARCH AIMS: (a) To investigate if the EAT secretome from patients with versus without AF increases ECM production in atrial fibroblasts. (b) To identify profibrotic proteins and processes in the EAT secretome and EAT from patients with, who will develop (future onset), and without AF. METHODS: Atrial EAT was obtainded during thoracoscopic ablation (AF, n = 20), or open-heart surgery (future onset and non-AF, n = 35). ECM gene expression of human atrial fibroblasts exposed to the EAT secretome and the proteomes of EAT secretome and EAT were assessed in patients with and without AF. Myeloperoxidase and neutrophil extracellular traps (NETs) were assessed immunohistochemically in patients with paroxysmal, persistent, future onset, and those who remain free of AF (non-AF). RESULTS: The expression of COL1A1 and FN1 in fibroblasts exposed to secretome from patients with AF was 3.7 and 4.7 times higher than in patients without AF (p < 0.05). Myeloperoxidase was the most increased protein in the EAT secretome and EAT from patients with versus without AF (FC 18.07 and 21.57, p < 0.005), as was the gene-set neutrophil degranulation. Immunohistochemically, myeloperoxidase was highest in persistent (FC 13.3, p < 0.0001) and increased in future onset AF (FC 2.4, p = 0.02) versus non-AF. Myeloperoxidase aggregated subepicardially and around fibrofatty infiltrates. NETs were increased in patients with persistent versus non-AF (p = 0.03). CONCLUSION: In AF, the EAT secretome induces ECM gene expression in atrial fibroblasts and contains abundant myeloperoxidase. EAT myeloperoxidase was increased prior to AF onset, and both myeloperoxidase and NETs were highest in persistent AF, highlighting the role of EAT neutrophils in the pathophysiology of AF.

Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications.

Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry-based phosphoproteomic experiments nowadays routinely allow identification and quantitation of >10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM-SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase-substrate databases, and user-friendliness is presented. The most widely-used tools are compared in-depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM-SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.

Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics.

The tyrosine kinase inhibitor sunitinib is an effective first-line treatment for patients with advanced renal cell carcinoma (RCC). Hypothesizing that a functional read-out by mass spectrometry-based (phospho, p-)proteomics will identify predictive biomarkers for treatment outcome of sunitinib, tumor tissues of 26 RCC patients were analyzed. Eight patients had primary resistant (RES) and 18 sensitive (SENS) RCC. A 78 phosphosite signature (p < 0.05, fold-change > 2) was identified; 22 p-sites were upregulated in RES (unique in RES: BCAR3, NOP58, EIF4A2, GDI1) and 56 in SENS (35 unique). EIF4A1/EIF4A2 were differentially expressed in RES at the (p-)proteome and, in an independent cohort, transcriptome level. Inferred kinase activity of MAPK3 (p = 0.026) and EGFR (p = 0.045) as determined by INKA was higher in SENS. Posttranslational modifications signature enrichment analysis showed that different p-site-centric signatures were enriched (p < 0.05), of which FGF1 and prolactin pathways in RES and, in SENS, vanadate and thrombin treatment pathways, were most significant. In conclusion, the RCC (phospho)proteome revealed differential p-sites and kinase activities associated with sunitinib resistance and sensitivity. Independent validation is warranted to develop an assay for upfront identification of patients who are intrinsically resistant to sunitinib.

Epigenetic Modification of the von Willebrand Factor Promoter Drives Platelet Aggregation on the Pulmonary Endothelium in Chronic Thromboembolic Pulmonary Hypertension.

Rationale: von Willebrand factor (vWF) mediates platelet adhesion during thrombosis. While chronic thromboembolic pulmonary hypertension (CTEPH) is associated with increased plasma levels of vWF, the role of this protein in CTEPH has remained enigmatic. Objectives: To identify the role of vWF in CTEPH. Methods: CTEPH-specific patient plasma and pulmonary endarterectomy material from patients with CTEPH were used to study the relationship between inflammation, vWF expression, and pulmonary thrombosis. Cell culture findings were validated in human tissue, and proteomics and chromatin immunoprecipitation were used to investigate the underlying mechanism of CTEPH. Measurements and Main Results: vWF is increased in plasma and the pulmonary endothelium of CTEPH patients. In vitro, the increase in vWF gene expression and the higher release of vWF protein upon endothelial activation resulted in elevated platelet adhesion to CTEPH endothelium. Proteomic analysis revealed that nuclear factor (NF)-κB2 was significantly increased in CTEPH. We demonstrate reduced histone tri-methylation and increased histone acetylation of the vWF promoter in CTEPH endothelium, facilitating binding of NF-κB2 to the vWF promoter and driving vWF transcription. Genetic interference of NFκB2 normalized the high vWF RNA expression levels and reversed the prothrombotic phenotype observed in CTEPH-pulmonary artery endothelial cells. Conclusions: Epigenetic regulation of the vWF promoter contributes to the creation of a local environment that favors in situ thrombosis in the pulmonary arteries. It reveals a direct molecular link between inflammatory pathways and platelet adhesion in the pulmonary vascular wall, emphasizing a possible role of in situ thrombosis in the development or progression of CTEPH.

Experiences and perceptions of dementia in Vietnam and among the Vietnamese diaspora: a systematic review of qualitative studies.

Objectives: This paper aimed to review and synthesise the qualitative research evidence on the experiences and perceptions of dementia in Vietnam and among the Vietnamese diaspora.Methods: Systematic searches were conducted in June 2019 using Medline, Embase, Emcare, PsycINFO and Cochrane electronic databases, as well as grey literature. Keywords and Medical Subject Headings [MeSH terms] for dementia and associated terms were combined with keywords for Vietnam and its provinces. Qualitative research articles published in English or Vietnamese were included to examine evidence on the life experiences of Vietnamese people with dementia using thematic analysis.Results: Our searches resulted in 3,940 papers, from which 21 qualitative research studies were included for final analysis. The majority of research has not been undertaken in Vietnam but with the Vietnamese diaspora in Western countries and has taken a cultural perspective to analyses. Research in Western countries has focused on the need for culturally adapted and culturally sensitive models of care. Emerging themes about the life experiences of Vietnamese people with dementia identified from the studies included: many people do not have diagnostic terms for dementia but use the descriptive language of symptoms; stigma was a reported problem and on occasions can be observed in the descriptive language used for people with dementia; cultural and traditional values create both an opportunity and a barrier, supporting compassion, family care and relaxation, but creating barriers to accessing health services or long-term residential care.Conclusions: This is the first systematic review reporting qualitative evidence on the life experiences of people with dementia in Vietnam and among the Vietnamese diaspora. Future research is needed on the voice of people with dementia themselves and their caregivers particularly in Vietnam, and low and middle-income countries with regards to living with dementia, pathways to care from diagnosis, treatment, care and support, additional social care and preparedness for end of life care for people with dementia.

Mechanisms of Quasi van der Waals Epitaxy of Three-Dimensional Metallic Nanoislands on Suspended Two-Dimensional Materials.

Understanding structure at the interface between two-dimensional (2D) materials and 3D metals is crucial for designing novel 2D/3D heterostructures and improving the performance of many 2D material devices. Here, we quantify and discuss the 2D/3D interface structure and the 3D morphology in several materials systems. We first deposit faceted Au nanoislands on graphene and transition metal dichalcogenides, using measurements of the equilibrium island shape to determine values for the 2D/Au interface energy and examining the role of surface reconstructions, chemical identity, and defects on the grown structures. We then deposit the technologically relevant metals Ti and Nb under conditions where kinetic rather than thermodynamic factors govern growth. We describe a transition from dendritic to faceted islands as a function of growth temperature and discuss the factors determining island shape in these materials systems. Finally, we show that suspended 2D materials enable the fabrication of a novel type of 3D/2D/3D heterostructure and discuss the growth mechanism. We suggest that emerging nanodevices will utilize versatile fabrication of 2D/3D heterostructures with well-characterized interfaces and morphologies.

C1q is increased in cerebrospinal fluid-derived extracellular vesicles in Alzheimer's disease: A multi-cohort proteomics and immuno-assay validation study.

INTRODUCTION: Extracellular vesicles (EVs) may propagate and modulate Alzheimer's disease (AD) pathology. We aimed to comprehensively characterize the proteome of cerebrospinal fluid (CSF) EVs to identify proteins and pathways altered in AD. METHODS: CSF EVs were isolated by ultracentrifugation (Cohort 1) or Vn96 peptide (Cohort 2) from non-neurodegenerative controls (n = 15, 16) and AD patients (n = 22, 20, respectively). EVs were subjected to untargeted quantitative mass spectrometry-based proteomics. Results were validated by enzyme-linked immunosorbent assay (ELISA) in Cohorts 3 and 4, consisting of controls (n = 16, n = 43, (Cohort3, Cohort4)), and patients with AD (n = 24, n = 100). RESULTS: We found > 30 differentially expressed proteins in AD CSF EVs involved in immune-regulation. Increase of C1q levels in AD compared to non-demented controls was validated by ELISA (∼ 1.5 fold, p (Cohort 3) = 0.03, p (Cohort 4) = 0.005). DISCUSSION: EVs may be utilized as a potential biomarker and may play a so far unprecedented role in immune-regulation in AD.

Creating Optimal Pockets in a Clathrochelate-Based Metal-Organic Framework for Gas Adsorption and Separation: Experimental and Computational Studies.

The rational design and synthesis of robust metal-organic frameworks (MOFs) based on novel organic building blocks are fundamental aspects of reticular chemistry. Beyond simply fabricating new organic linkers, however, it is important to elucidate structure-property relationships at the molecular level to develop high-performing materials. In this work, we successfully targeted a highly porous and robust cage-type MOF (NU-200) with an nbo-derived fof topology through the deliberate assembly of a cyclohexane-functionalized iron(II)-clathrochelate-based meta-benzenedicarboxylate linker with a Cu2(CO2)4 secondary building unit (SBU). NU-200 exhibited an outstanding adsorption capacity of xenon and a high ideal adsorbed solution theory (IAST) predicted selectivity for a 20/80 v/v mixture of xenon (Xe)/krypton (Kr) at 298 K and 1.0 bar. Our extensive computational simulations with grand canonical Monte Carlo (GCMC) and density functional theory (DFT) on NU-200 indicated that the MOF's hierarchical bowl-shaped nanopockets surrounded by custom-designed cyclohexyl groups─instead of the conventionally believed open metal sites (OMSs)─played a crucial role in reinforcing Xe-binding affinity. The optimally sized pockets firmly trapped Xe through numerous supramolecular interactions including Xe···H, Xe···O, and Xe···π. Additionally, we validated the unique pocket confinement effect by experimentally and computationally employing the similarly sized probe, sulfur dioxide (SO2), which provided significant insights into the molecular underpinnings of the high uptake of SO2 (11.7 mmol g-1), especially at a low pressure of 0.1 bar (8.5 mmol g-1). This work therefore can facilitate the judicious design of organic building blocks, producing MOFs featuring tailor-made pockets to boost gas adsorption and separation performances.

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

Recent data showed that cancer cells from different tumor subtypes with distinct metastatic potential influence each other's metastatic behavior by exchanging biomolecules through extracellular vesicles (EVs). However, it is debated how small amounts of cargo can mediate this effect, especially in tumors where all cells are from one subtype, and only subtle molecular differences drive metastatic heterogeneity. To study this, we have characterized the content of EVs shed in vivo by two clones of melanoma (B16) tumors with distinct metastatic potential. Using the Cre-LoxP system and intravital microscopy, we show that cells from these distinct clones phenocopy their migratory behavior through EV exchange. By tandem mass spectrometry and RNA sequencing, we show that EVs shed by these clones into the tumor microenvironment contain thousands of different proteins and RNAs, and many of these biomolecules are from interconnected signaling networks involved in cellular processes such as migration. Thus, EVs contain numerous proteins and RNAs and act on recipient cells by invoking a multi-faceted biological response including cell migration.