Multiplexed Antibody Glycosylation Profiling Using Dual Enzyme Digestion and Liquid Chromatography-Triple Quadrupole Mass Spectrometry Method.

Antibody glycosylation plays a crucial role in the humoral immune response by regulating effector functions and influencing the binding affinity to immune cell receptors. Previous studies have focused mainly on the immunoglobulin G (IgG) isotype owing to the analytical challenges associated with other isotypes. Thus, the development of a sensitive and accurate analytical platform is necessary to characterize antibody glycosylation across multiple isotypes. In this study, we have developed an analytical workflow using antibody-light-chain affinity beads to purify IgG, IgA, and IgM from 16 µL of human plasma. Dual enzymes, trypsin and Glu-C, were used during on-bead digestion to obtain enzymatic glycopeptides and protein-specific surrogate peptides. Ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry was used in order to determine the sensitivity and specificity. Our platform targets 95 glycopeptides across the IgG, IgA, and IgM isotypes, as well as eight surrogate peptides representing total IgG, four IgG classes, two IgA classes, and IgM. Four stable isotope-labeled internal standards were added after antibody purification to calibrate the preparation and instrumental bias during analysis. Calibration curves constructed using serially diluted plasma samples showed good curve fitting (R2 > 0.959). The intrabatch and interbatch precision for all the targets had relative standard deviation of less than 29.6%. This method was applied to 19 human plasma samples, and the glycosylation percentages were calculated, which were comparable to those reported in the literature. The developed method is sensitive and accurate for Ig glycosylation profiling. It can be used in clinical investigations, particularly for detailed humoral immune profiling.

Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2.

SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2-S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.

Effects of Different Extraction Methods on Vanilla Aroma.

To establish the analytic conditions for examining the aroma quality of vanilla pods, we compared different extraction methods and identified a suitable option. We utilized headspace solid-phase microextraction (HS-SPME), steam distillation (SD), simultaneous steam distillation (SDE) and alcoholic extraction combined with gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) to identify volatile components of vanilla pods. A total of 84 volatile compounds were identified in this experiment, of which SDE could identify the most volatile compounds, with a total of 51 species, followed by HS-SPME, with a total of 28 species. Ten volatile compounds were identified by extraction with a minimum of 35% alcohol. HS-SPME extraction provided the highest total aroma peak areas, and the peak areas of aldehydes, furans, alcohols, monoterpenes and phenols compounds were several times higher than those of the other extraction methods. The results showed that the two technologies, SDE and HS-SPME, could be used together to facilitate analysis of vanilla pod aroma.

New Insights on Volatile Components of Vanilla planifolia Cultivated in Taiwan.

Vanilla (Vanilla planifolia) is a precious natural flavoring that is commonly used throughout the world. In the past, all vanilla used in Taiwan was imported; however, recent breakthroughs in cultivation and processing technology have allowed Taiwan to produce its own supply of vanilla. In this study, headspace solid-phase microextraction (HS-SPME) combined with GC-FID and GC-MS was used to analyze the volatile components of vanilla from different origins produced in Taiwan under different cultivation and processing conditions. The results of our study revealed that when comparing different harvest maturities, the composition diversity and total volatile content were both higher when the pods were matured for more than 38 weeks. When comparing different killing conditions, we observed that the highest vanillin percentage was present after vanilla pods were killed three times in 65 °C treatments for 1 min each. From the experiment examining the addition of different strains, the PCA results revealed that the volatiles of vanilla that was processed with Dekkera bruxellensis and Bacillus subtilis was clearly distinguished from which obtained by processing with the other strains. Vanilla processed with B. subtilis contained 2-ethyl-1-hexanol, and this was not detected in other vanillas. Finally, when comparing the vanillin percentage from seven different regions in Taiwan, vanilla percentage from Taitung and Taoyuan Longtan were the highest.

Hepatitis C Virus NS3 Protein Plays a Dual Role in WRN-Mediated Repair of Nonhomologous End Joining.

Hepatitis C virus (HCV) NS3 protein possesses protease and helicase activities and is considered an oncoprotein in virus-derived hepatocellular carcinoma. The NS3-associated oncogenesis has been studied but not fully understood. In this study, we have identified novel interactions of the NS3 protein with DNA repair factors, Werner syndrome protein (WRN) and Ku70, in both an HCV subgenomic replicon system and Huh7 cells expressing NS3. HCV NS3 protein inhibits WRN-mediated DNA repair and reduces the repair efficiency of nonhomologous end joining. It interferes with Ku70 recruitment to the double-strand break sites and alters the nuclear distribution of WRN-Ku repair complex. In addition, WRN is a substrate of the NS3/4A protease; the level of WRN protein is regulated by both the proteasome degradation pathway and HCV NS3/4A protease activity. The dual role of HCV NS3 and NS3/4A proteins in regulating the function and expression level of the WRN protein intensifies the effect of impairment on DNA repair. This may lead to an accumulation of DNA mutations and genome instability and, eventually, tumor development.IMPORTANCE HCV infection is a worldwide problem of public health and a major contributor to hepatocellular carcinoma. The single-stranded RNA virus with RNA-dependent RNA polymerase experiences a high error rate and develops strategies to escape the immune system and hepatocarcinogenesis. Studies have revealed the involvement of HCV proteins in the impairment of DNA repair. The present study aimed to further elucidate mechanisms by which the viral NS3 protein impairs the repair of DNA damage. Our results clearly indicate that HCV NS3/4A protease targets WRN for degradation, and, at the same time, diminishes the repair efficiency of nonhomologous end joining by interfering with the recruitment of Ku protein to the DNA double-strand break sites. The study describes a novel mechanism by which the NS3 protein influences DNA repair and provides new insight into the molecular mechanism of HCV pathogenesis.

Evaluation of ensemble strategy on the development of multiple view ankle fracture detection algorithm.

OBJECTIVE: To identify the feasibility and efficiency of deep convolutional neural networks (DCNNs) in the detection of ankle fractures and to explore ensemble strategies that applied multiple projections of radiographs.Ankle radiographs (AXRs) are the primary tool used to diagnose ankle fractures. Applying DCNN algorithms on AXRs can potentially improve the diagnostic accuracy and efficiency of detecting ankle fractures. METHODS: A DCNN was trained using a trauma image registry, including 3102 AXRs. We separately trained the DCNN on anteroposterior (AP) and lateral (Lat) AXRs. Different ensemble methods, such as "sum-up," "severance-OR," and "severance-Both," were evaluated to incorporate the results of the model using different projections of view. RESULTS: The AP/Lat model's individual sensitivity, specificity, positive-predictive value, accuracy, and F1 score were 79%/84%, 90%/86%, 88%/86%, 83%/85%, and 0.816/0.850, respectively. Furthermore, the area under the receiver operating characteristic curve (AUROC) of the AP/Lat model was 0.890/0.894 (95% CI: 0.826-0.954/0.831-0.953). The sum-up method generated balanced results by applying both models and obtained an AUROC of 0.917 (95% CI: 0.863-0.972) with 87% accuracy. The severance-OR method resulted in a better sensitivity of 90%, and the severance-Both method obtained a high specificity of 94%. CONCLUSION: Ankle fracture in the AXR could be identified by the trained DCNN algorithm. The selection of ensemble methods can depend on the clinical situation which might help clinicians detect ankle fractures efficiently without interrupting the current clinical pathway. ADVANCES IN KNOWLEDGE: This study demonstrated different ensemble strategies of AI algorithms on multiple view AXRs to optimize the performance in various clinical needs.

Structural and functional insights into ABHD5, a ligand-regulated lipase co-activator.

Alpha/beta hydrolase domain-containing protein 5 (ABHD5) is a highly conserved protein that regulates various lipid metabolic pathways via interactions with members of the perilipin (PLIN) and Patatin-like phospholipase domain-containing protein (PNPLA) protein families. Loss of function mutations in ABHD5 result in Chanarin-Dorfman Syndrome (CDS), characterized by ectopic lipid accumulation in numerous cell types and severe ichthyosis. Recent data demonstrates that ABHD5 is the target of synthetic and endogenous ligands that might be therapeutic beneficial for treating metabolic diseases and cancers. However, the structural basis of ABHD5 functional activities, such as protein-protein interactions and ligand binding is presently unknown. To address this gap, we constructed theoretical structural models of ABHD5 by comparative modeling and topological shape analysis to assess the spatial patterns of ABHD5 conformations computed in protein dynamics. We identified functionally important residues on ABHD5 surface for lipolysis activation by PNPLA2, lipid droplet targeting and PLIN-binding. We validated the computational model by examining the effects of mutating key residues in ABHD5 on an array of functional assays. Our integrated computational and experimental findings provide new insights into the structural basis of the diverse functions of ABHD5 as well as pathological mutations that result in CDS.

Predicting Oncogenic Missense Mutations.

With the rapid progress of cancer genome studies, many missense mutations in populations of somatic cells of different cancer types and at different stages have been identified. However, it is challenging to understand the implications of these cancer-related variants. We have developed a computational method that integrates structural, topographical, and evolutionary information for assessments of biochemical effects and the extent of deleteriousness of the cancer-related variants. We have mapped somatic missense mutations from the Catalogue of Somatic Mutations In Cancer (COSMIC) to 3D structures in the Protein Data Bank (PDB). Our results show that a large portion of these missense mutations is located on protein surface pockets, which often serve as a structural and functional unit of cancer variants. We provide detailed analysis of several examples and assessment on the importance of these variants, including prediction of previously unreported cancer-variants, along with independent evidence from the literature. Furthermore, we show our predictions can inform on the functional roles and the mechanism of predicted cancer variants.

Determination of Pyruvate Metabolic Fates Modulates Head and Neck Tumorigenesis.

Even with increasing evidence for roles of glycolytic enzymes in controlling cancerous characteristics, the best target of candidate metabolic enzymes for lessening malignancy remains under debate. Pyruvate is a main glycolytic metabolite that could be mainly converted into either lactate by Lactate Dehydrogenase A (LDHA) or acetyl-CoA by Pyruvate Dehydrogenase E1 component α subunit (PDHA1) catalytic complex. In tumor cells, accumulating lactate is produced whereas the conversion of pyruvate into mitochondrial acetyl-CoA is less active compared with their normal counterparts. This reciprocal molecular association makes pyruvate metabolism a potential choice of anti-cancer target. Cellular and molecular changes were herein assayed in Head and Neck Squamous Cell Carcinoma (HNSCC) cells in response to LDHA and PDHA1 loss in vitro, in vivo and in clinic. By using various human cancer databases and clinical samples, LDHA and PDHA1 levels exhibit reversed prognostic roles. In vitro analysis demonstrated that decreased cell growth and motility accompanied by an increased sensitivity to chemotherapeutic agents was found in cells with LDHA loss whereas PDHA1-silencing exhibited opposite phenotypes. At the molecular level, it was found that oncogenic Protein kinase B (PKB/Akt) and Extracellular signal-regulated kinase (ERK) singling pathways contribute to pyruvate metabolism mediated HNSCC cell growth. Furthermore, LDHA/PDHA1 changes in HNSCC cells resulted in a broad metabolic reprogramming while intracellular molecules including polyunsaturated fatty acids and nitrogen metabolism related metabolites underlie the malignant changes. Collectively, our findings reveal the significance of pyruvate metabolic fates in modulating HNSCC tumorigenesis and highlight the impact of metabolic plasticity in HNSCC cells.

Age- and disease-related features of task-related brain oscillations by using mutual information.

The aim of this study was to investigate changes in task-related brain oscillations and corticocortical connections in patients with mild cognitive impairment (MCI) and those with normal aging using cross-mutual information (CMI) analysis. We hypothesized that task-related brain oscillations and corticocortical connections were affected by age- and disease-related changes, which could be reflected in the CMI analysis. Electroencephalogram (EEG) recordings were measured in 16 MCI patients, 15 healthy age-matched controls, and 16 healthy younger individuals. The frequencies and interhemispheric CMI data were estimated in all groups. The specific EEG rhythms measured were delta (δ), theta (θ), alpha (α), beta (ß), and gamma (γ) bands. Significant differences in δ, θ, α, and ß bands were observed between the younger and elderly groups. However, only the θ band was significantly different between the elderly and MCI groups. Moreover, this study used EEG recordings to investigate age- and disease-related changes in the corticocortical connections of the brain. This study proves that the θ-band frequency of the connection between the parietal and occipital lobes for the age- and disease-related changes can be depicted using the CMI analysis.

Age-related changes of task-specific brain activity in normal aging.

An important question in healthcare for older patients is whether age-related changes in cortical reorganization can be measured with advancing age. This study investigated the factors behind such age-related changes, using time-frequency analysis of event-related potentials (ERPs). We hypothesized that brain rhythms was affected by age-related changes, which could be reflected in the ERP indices. An oddball task was conducted in two experimental groups, namely young participants (N=15; mean age 23.7±2.8 years) and older participants (N=15; mean age 70.1±7.9 years). Two types of stimuli were used: the target (1 kHz frequency) and standard (2 kHz frequency). We scrutinized three ERP indices: event-related spectral power (ERPSP), inter-trial phase-locking (ITPL), and event-related cross-phase coherence (ERPCOH). Both groups performed equally well for correct response rate. However, the results revealed a statistically significant age difference for inter-trial comparison. Compared with the young, the older participants showed the following age-related changes: (a) power activity decreased; however, an increase was found only in the late (P3, 280-450 ms) theta (4-7 Hz) component over the bilateral frontal and temporo-frontal areas; (b) low phase-locking in the early (N1, 80-140 ms) theta band over the parietal/frontal (right) regions appeared; (c) the functional connections decreased in the alpha (7-13 Hz) and beta (13-30 Hz) bands, but no difference emerged in the theta band between the two groups. These results indicate that age-related changes in task-specific brain activity for a normal aging population can be depicted using the three ERP indices.