Phage display-derived alpaca nanobodies as potential therapeutics for Naja atra snake envenomation.

Naja atra, the Chinese cobra, is a major cause of snake envenomation in Asia, causing hundreds of thousands of clinical incidents annually. The current treatment, horse serum-derived antivenom, has unpredictable side effects and presents manufacturing challenges. This study focused on developing new-generation snake venom antidotes by using microbial phage display technology to derive nanobodies from an alpaca immunized with attenuated N. atra venom. Following confirmation of the immune response in the alpaca, we amplified VHH genes from isolated peripheral blood mononuclear cells and constructed a phage display VHH library of 1.0 × 107 transformants. After four rounds of biopanning, the enriched phages exhibited increased binding activity to N. atra venom. Four nanobody clones with high binding affinities were selected: aNAH1, aNAH6, aNAH7, and aNAH9. Specificity testing against venom from various snake species, including two Southeast Asian cobra species, revealed nanobodies specific to the genus Naja. An in vivo mouse venom neutralization assay demonstrated that all nanobodies prolonged mouse survival and aNAH6 protected 66.6% of the mice from the lethal dosage. These findings highlight the potential of phage display-derived nanobodies as valuable antidotes for N. atra venom, laying the groundwork for future applications in snakebite treatment.IMPORTANCEChinese cobra venom bites present a formidable medical challenge, and current serum treatments face unresolved issues. Our research applied microbial phage display technology to obtain a new, effective, and cost-efficient treatment approach. Despite interest among scientists in utilizing this technology to screen alpaca antibodies against toxins, the available literature is limited. This study makes a significant contribution by introducing neutralizing antibodies that are specifically tailored to Chinese cobra venom. We provide a comprehensive and unbiased account of the antibody construction process, accompanied by thorough testing of various nanobodies and an assessment of cross-reactivity with diverse snake venoms. These nanobodies represent a promising avenue for targeted antivenom development that bridges microbiology and biotechnology to address critical health needs.

Recent advances in LC-MS-based metabolomics for clinical biomarker discovery.

The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.

Coupling capillary electrophoresis with mass spectrometry for the analysis of oxidized phospholipids in human high-density lipoproteins.

The oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (ox-PAPC) products in human high-density lipoproteins (HDLs) were investigated by low-flow capillary electrophoresis-mass spectrometry (low-flow CE-MS). To accelerate the optimization, native PAPC (n-PAPC) standard was first analyzed by a commercial CE instrument with a photodiode array detector. The optimal separation buffer contained 60% (v/v) acetonitrile, 40% (v/v) methanol, 20 mM ammonium acetate, 0.5% (v/v) formic acid, and 0.1% (v/v) water. The selected separation voltage and capillary temperature were 20 kV and 23°C. The optimal CE separation buffer was then used for the low-flow CE-MS analysis. The selected MS conditions contained heated capillary temperature (250°C), capillary voltage (10 V), and injection time (1 s). No sheath gas was used for MS. The linear range for n-PAPC was 2.5-100.0 µg/mL. The coefficient of determination (R2 ) was 0.9918. The concentration limit of detection was 1.52 µg/mL, and the concentration limit of quantitation was 4.60 µg/mL. The optimal low-flow CE-MS method showed good repeatability and sensitivity. The ox-PAPC products in human HDLs were determined based on the in vitro ox-PAPC products of n-PAPC standard. Twenty-one ox-PAPC products have been analyzed in human HDLs. Uremic patients showed significantly higher levels of 15 ox-PAPC products than healthy subjects.

Online 2D High-pH and Low-pH Reversed-Phase Nano-LC-MS/MS System for Deep Proteome Analysis.

In bottom-up proteomic profiling, the complexity of proteome composition and wide dynamic range has created challenges on the limited number of protein identification and proteome coverage, especially in sample input-limited nanoflow (nano) LC-MS/MS analysis. Herein, we developed a fully automatic online 2D nano-LC-MS/MS system using both high-pH and low-pH reverse phase (RP) LCs on a single LC instrument toward comprehensive proteomics analysis. Compared to conventional microflow 2D-LC, the high-pH RP trapping column demonstrated a low sample requirement of cellular protein digest at the µg level with good fractionation resolution of >90% peptides in a single fraction. Compared to the offline 2D RP-RP nano-LC-QTOF using C18-HPLC column and C18-Stage Tip, and 1D nano-LC-QTOF system, superior coverage was observed on the higher number of identified protein groups/unique peptides by 1.35-/1.68-, 1.46-/1.75-, and 3.21-/4.35-fold, respectively, using an online 2D RP-RP nano-LC-QTOF mass spectrometer. On the evolution of quantitation performance, the online 2D high-/low-pH RP data-independent acquisition (DIA) showed a higher reproducibility in protein groups intensity (R2 > 0.977) and more quantified proteins than that obtained using the offline 2D high-/low-pH RP DIA approach. Using an advanced Orbitrap Exploris 480 mass spectrometer, ∼1.9-fold higher proteome coverage was also observed in our 2D online RP-RP system (6039 protein groups) compared to the 1D nano-LC system (3133 protein groups). In summary, the online 2D nano-LC-MS/MS platform can be a sensitive and robust approach compatible with conventional nano-LC instruments for deep proteome coverage of trace amounts of samples.

Elucidating the Mechanisms of Sodium Benzoate in Alzheimer Disease: Insights from Quantitative Proteomics Analysis of Serum Samples.

BACKGROUND: N-methyl-D-aspartate receptors (NMDARs) are crucial components of brain function involved in memory and neurotransmission. Sodium benzoate is a promising NMDAR enhancer and has been proven to be a novel, safe, and efficient therapy for patients with Alzheimer disease (AD). However, in addition to the role of sodium benzoate as an NMDA enhancer, other mechanisms of sodium benzoate in treating AD are still unclear. To elucidate the potential mechanisms of sodium benzoate in Alzheimer disease, this study employed label-free quantitative proteomics to analyze serum samples from AD cohorts with and without sodium benzoate treatment. METHODS: The serum proteins from each patient were separated into 24 fractions using an immobilized pH gradient, digested with trypsin, and then subjected to nanoLC‒MS/MS to analyze the proteome of all patients. The nanoLC‒MS/MS data were obtained with a label-free quantitative proteomic approach. Proteins with fold changes were analyzed with STRING and Cytoscape to find key protein networks/processes and hub proteins. RESULTS: Our analysis identified 861 and 927 protein groups in the benzoate treatment cohort and the placebo cohort, respectively. The results demonstrated that sodium benzoate had the most significant effect on the complement and coagulation cascade pathways, amyloidosis disease, immune responses, and lipid metabolic processes. Moreover, Transthyretin, Fibrinogen alpha chain, Haptoglobin, Apolipoprotein B-100, Fibrinogen beta chain, Apolipoprotein E, and Alpha-1-acid glycoprotein 1 were identified as hub proteins in the protein‒protein interaction networks. CONCLUSIONS: These findings suggest that sodium benzoate may exert its influence on important pathways associated with AD, thus contributing to the improvement in the pathogenesis of the disease.

Influence of confirmed viral infection on adult acute fulminant myocarditis supported with extracorporeal membrane oxygenation.

BACKGROUND: The impact of etiologies of acute fulminant myocarditis (AFM), which requires extracorporeal membrane oxygenation (ECMO), on clinical outcomes remains unknown. This study aimed to investigate the risk factors for ECMO weaning and mortality among patients with AFM due to viral etiologies in a tertiary referral medical center. METHODS: We included 33 adults with AFM who received ECMO and were admitted between January 2002 and January 2021. General demographics, laboratory data, echocardiography findings, and long-term outcomes were analyzed for confirmed viral etiology and unconfirmed etiology groups. RESULTS: The overall hospital survival rate was 54.5%. The age, sex, severity of the hemodynamic condition, and cardiac rhythm were similar between the two groups. Multivariate Cox regression analysis revealed that a confirmed viral etiology (HR 4.201, 95% CI 1.061-16.666), peri-ECMO renal replacement therapy (RRT) (HR 9.804, 1.140-83.333) and a high positive end-expiratory pressure (PEEP) in the ventilator settings at 24 h after ECMO (HR 1.479, 1.020-2.143) were significant prognostic factors for in-hospital mortality. Peri-ECMO RRT was also a significant negative prognostic factor for successful ECMO weaning (OR 0.061, 0.006-0.600) in the multivariate logistic model. CONCLUSIONS: Among AFM patients receiving ECMO support, RRT use was associated with a decreased chance of survival to ECMO weaning. Multiple organ dysfunction and a high PEEP were also predictive of a lower chance of hospital survival. Those with a confirmed diagnosis of viral myocarditis may require more medical attention due to the higher risk of hospital mortality than those without a definite diagnosis.

l-lactic acidosis confers insensitivity to PKC inhibitors by competing for uptake via monocarboxylate transporters.

Targeting protein kinase C (PKC) family was found to repress the migration and resistance of non-small cell lung cancer cells to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). However, none of the PKC inhibitors has been approved for anticancer therapy yet due to the limited efficacy in clinical trials, and the underlying mechanisms remain unclear. l-lactic acidosis, a common condition comprising high l-lactate concentration and acidic pH in the tumor microenvironment, has been known to induce tumor metastasis and drug resistance. In this study, l-lactic acid was found to reverse the inhibitory effects of pan-PKC inhibitors GO6983 on PKC activity, cell migration, and EGFR-TKI resistance, but these effects were not affected by the modulators of lactate receptor GPR81. Interestingly, blockade of lactate transporters, monocarboxylate transporter-1 and -4 (MCT1 and MCT4), attenuated the intracellular level of GO6983, and its inhibitory effect on PKC activity, suggesting that lactic acid promotes the resistance to PKC inhibitors by competing for the uptake through these transporters rather than by activating its receptor, GPR81. Our findings explain the underlying mechanisms of the limited response of PKC inhibitors in clinical trials.

Anodal transcutaneous DC stimulation enhances learning of dynamic balance control during walking in humans with spinal cord injury.

Deficits in locomotor function, including impairments in walking speed and balance, are major problems for many individuals with incomplete spinal cord injury (iSCI). However, it remains unclear which type of training paradigms are more effective in improving balance, particularly dynamic balance, in individuals with iSCI. The purpose of this study was to determine whether anodal transcutaneous spinal direct current stimulation (tsDCS) can facilitate learning of balance control during walking in individuals with iSCI. Fifteen individuals with iSCI participated in this study and were tested in two sessions (i.e., tsDCS and sham conditions). Each session consisted of 1 min of treadmill walking without stimulation or perturbation (baseline), 10 min of walking with either anodal tsDCS or sham stimulation, paired with bilateral pelvis perturbation (adaptation), and finally 2 min of walking without stimulation and perturbation (post-adaptation). The outcome measures were the dynamic balance, assessed using the minimal margin of stability (MoS), and electromyography of leg muscles. Participants demonstrated a smaller MoS during the late adaptation period for the anodal tsDCS condition compared to sham (p = 0.041), and this MoS intended to retain during the early post-adaptation period (p = 0.05). In addition, muscle activity of hip abductors was greater for the anodal tsDCS condition compared to sham during the late adaptation period and post-adaptation period (p < 0.05). Results from this study suggest that anodal tsDCS may modulate motor adaptation to pelvis perturbation and facilitate learning of dynamic balance control in individuals with iSCI.

Development of a high-pH reversed-phase well plate for peptide fractionation and deep proteome analysis of cells and exosomes.

The complexity of the proteome often limits the number of identified proteins in the nanoflow LC-MS (nanoLC-MS) analysis of samples. Therefore, peptide fractionation is essential for reducing the sample complexity and improving the proteome coverage. In this study, to achieve high-pH reversed-phase (RP)-well plate fractionation for high-throughput proteomics analysis, C18 particles were coated on a 96-well plate, and the sample-loading processes were optimized for high-pH fractionation. The sample capacity of the high-pH RP-well plate was estimated to be ~6 µg of protein. There were 1.85- and 1.71-fold increases in the number of protein groups and peptides identified, respectively, with high-pH RP-well plate fractionation, compared to those without fractionation. In addition, with alkaline C18 well plate fractionation, exosome markers could be detected using ~1 µg of a protein digest of exosomes by microflow LC-MS (microLC-MS). These results illustrate that high-pH RP-well plate fractionation has superior sensitivity and effectiveness in preparing trace amounts of proteins for deep proteome analysis.

Protein Biomarker Discovery for Methicillin-Sensitive, Heterogeneous Vancomycin-Intermediate and Vancomycin-Intermediate Staphylococcus aureus Strains Using Label-Free Data-Independent Acquisition Proteomics.

Rapid identification of methicillin-sensitive Staphylococcus aureus (MSSA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-intermediate S. aureus (VISA) is important for accurate treatment, timely intervention, and prevention of outbreaks. Here, 90 S. aureus isolates were analyzed for protein biomarker discovery, including MSSA, vancomycin-susceptible S. aureus (VSSA), hVISA, and VISA strains. Label-free data-independent acquisition proteomics was used to identify protein biomarkers that allow for discrimination among MSSA, hVISA, and VISA strains. There were 8786 nonredundant peptides identified, corresponding to 418 different annotated nonredundant proteins. Two VISA protein biomarkers, two hVISA protein biomarkers, and one MSSA protein biomarker with high sensitivities and specificities were discovered and verified. Data are available via MassIVE with identifier MSV000085776.

Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics.

Urothelial carcinoma (UC) is the ninth most prevalent malignancy worldwide. Noninvasive and efficient biomarkers with high accuracy are imperative for the surveillance and diagnosis of UC. CKD patients were enrolled as a control group in this study for the discovery of highly specific urinary protein markers of UC. An iTRAQ-labeled quantitative proteomic approach was used to discover novel potential markers. These markers were further validated with 501 samples by ELISA assay, and their diagnostic accuracies were compared to those of other reported UC markers. BRDT, CYBP, GARS, and HDGF were identified as novel urinary UC biomarkers with a high discrimination ability in a population comprising CKD and healthy subjects. The diagnostic values of the four novel UC markers were better than that of a panel of well-known or FDA-approved urinary protein markers CYFR21.1, Midkine, and NUMA1. Three of our discovered markers (BRDT, HDGF, GARS) and one well-known marker (CYFR21.1) were finally selected and combined as a marker panel having AUC values of 0.962 (95% CI, 0.94-0.98) and 0.860 (95% CI, 0.83-0.89) for the discrimination between UC and normal groups and UC and control (healthy + CKD) groups, respectively.

Increased motor variability facilitates motor learning in weight shift toward the paretic side during walking in individuals post-stroke.

The purpose of this study was to determine whether applying "varied" versus constant pelvis assistance force mediolaterally toward the paretic side of stroke survivors during walking would result in short-term improvement in weight shift toward the paretic side. Twelve individuals post-stroke (60.4 ± 6.2 years; gait speed: 0.53 ± 0.19 m/s) were tested under two conditions (varied vs. constant). Each condition was conducted in a single separate session, which consisted of (a) treadmill walking with no assistance force for 1 min (baseline), pelvis assistance toward the paretic side for 9 min (adaptation), and then no force for additional 1 min (post-adaptation), and (b) overground walking. In the "varied" condition, the magnitude of force was randomly changed across steps between 30% and 100% of the predetermined amount. In the abrupt condition, the magnitude of force was kept constant at 100% of the predetermined amount. Participants exhibited greater improvements in weight shift toward the paretic side (p < 0.01) and in muscle activity of plantar flexors and hip adductors of the paretic leg (p = 0.02) from baseline to late post-adaptation period for the varied condition than for the constant condition. Motor variability of the peak pelvis displacement at baseline was correlated with improvement in weight shift toward the paretic side after training for the varied (R2  = 0.64, p = 0.01) and the constant condition (R2  = 0.39, p = 0.03). These findings suggest that increased motor variability, induced by applying the varied pelvis assistance, may facilitate motor learning in weight shift and gait symmetry during walking in individuals post-stroke.

Heterologous Hsp90 promotes phenotypic diversity through network evolution.

Biological processes in living cells are often carried out by gene networks in which signals and reactions are integrated through network hubs. Despite their functional importance, it remains unclear to what extent network hubs are evolvable and how alterations impact long-term evolution. We investigated these issues using heat shock protein 90 (Hsp90), a central hub of proteostasis networks. When native Hsp90 in Saccharomyces cerevisiae cells was replaced by the ortholog from hypersaline-tolerant Yarrowia lipolytica that diverged from S. cerevisiae about 270 million years ago, the cells exhibited improved growth in hypersaline environments but compromised growth in others, indicating functional divergence in Hsp90 between the two yeasts. Laboratory evolution shows that evolved Y. lipolytica-HSP90-carrying S. cerevisiae cells exhibit a wider range of phenotypic variation than cells carrying native Hsp90. Identified beneficial mutations are involved in multiple pathways and are often pleiotropic. Our results show that cells adapt to a heterologous Hsp90 by modifying different subnetworks, facilitating the evolution of phenotypic diversity inaccessible to wild-type cells.

Gradual adaptation to pelvis perturbation during walking reinforces motor learning of weight shift toward the paretic side in individuals post-stroke.

The purpose of this study was to determine whether the gradual versus abrupt adaptation to lateral pelvis assistance force improves weight shift toward the paretic side and enhance forced use of the paretic leg during walking. Sixteen individuals who had sustained a hemispheric stroke participated in two experimental sessions, which consisted of (1) treadmill walking with the application of lateral pelvis assistance force (gradual vs. abrupt condition) and (2) overground walking. In the "gradual" condition, during treadmill walking, the assistance force was gradually increased from 0 to 100% of the predetermined force step by step. In the abrupt condition, the force was applied at 100% of the predetermined force throughout treadmill walking. Participants exhibited significant improvements in hip abductor and adductor, ankle dorsiflexor, and knee extensor muscle activities, weight shift toward the paretic side, and overground walking speed in the gradual condition (P < 0.05), but showed no significant changes in the abrupt condition (P > 0.20). Changes in weight shift toward the paretic side were statistically different between conditions (P < 0.001), although changes in muscle activities were not (P > 0.11). In the gradual condition, the error amplitude was proportional to the improvement in weight shift during the late post-adaptation (R2 = 0.32, P = 0.03), but not in the abrupt condition (R2 = 0.001, P = 0.93). In conclusion, the "gradual adaptation" inducing "small errors" during constraint-induced walking may improve weight shift and enhance forced use of the paretic leg in individuals post-stroke. Applying gradual pelvis assistance force during walking may be used as an intervention strategy to improve walking in individuals post-stroke.

Enhanced error facilitates motor learning in weight shift and increases use of the paretic leg during walking at chronic stage after stroke.

The purpose of this study was to determine whether the application of lateral pelvis pulling force toward the non-paretic side during the stance phase of the paretic leg would enhance forced use of the paretic leg and increase weight shift toward the paretic side in stroke survivors. Eleven chronic stroke survivors participated in two experimental sessions, which consisted of (1) treadmill walking with the application of "pelvis resistance" or "pelvis assistance" and (2) overground walking. During the treadmill walking, the laterally pulling force was applied during the stance phase of the paretic leg toward the non-paretic side for the "pelvis resistance" condition or toward the paretic side for the "pelvis assistance" condition during the stance phase of the paretic leg. After force release, the "pelvis resistance" condition exhibited greater enhancement in muscle activation of hip ABD, ADD, and SOL and greater improvement in lateral weight shift toward the paretic side, compared with the effect of the "pelvis assistance" condition (P < 0.03). This improved lateral weight shift was associated with the enhanced muscle activation of hip ABD and ADD (R2 = 0.67, P = 0.01). The pelvis resistance condition also improved overground walking speed and stance phase symmetry when measured 10 min after the treadmill walking (P = 0.004). In conclusion, applying pelvis resistance forces to increase error signals may facilitate motor learning of weight shift toward the paretic side and enhance use of the paretic leg in chronic stroke survivors. Results from this study may be utilized to develop an intervention approach to improve walking in stroke survivors.

Tuliposides H-J and Bioactive Components from the Bulb of Amana edulis.

Three new tuliposides H-J (1-3) and 11 known compounds were obtained from the methanolic extracts of the bulbs of Amana edulis for the first time. Their structures were elucidated by NMR, MS, and IR spectroscopic data, optical rotation, and Mosher's method. The melanogenesis properties of all the isolates were evaluated in B16 melanoma cells. Consequently, tributyl citrate (9) had anti-melanogenesis activity but was cytotoxic toward B16. (+)-Pyroglutamic acid (4), (+)-butyl 5-oxopyrrolidine-2-carboxylate (6), (-)-3-hydroxy-2-methylbutyrolactone (10), and 5-(hydroxymethyl)furfural (12) had increased melanin productions and tyrosinase activities. Those active components could be further studied as the candidates against melanoma and vitiligo for skin diseases or whitening/hypopigmentation for hair.

Misfolding-prone proteins are reversibly sequestered to an Hsp42-associated granule upon chronological aging.

Alteration of protein localization is an important strategy for cells to regulate protein homeostasis upon environmental stresses. In the budding yeast Saccharomyces cerevisiae, many proteins relocalize and form cytosolic granules during chronological aging. However, the functions and exact components of these protein granules remain uncharacterized in most cases. In this study, we performed a genome-wide analysis of protein localization in stationary phase cells, leading to the discovery of 307 granule-forming proteins and the identification of new components in the Hsp42-stationary phase granule (Hsp42-SPG), P-bodies, Ret2 granules and actin bodies. We further characterized the Hsp42-SPG, which contains the largest number of protein components, including many molecular chaperones, metabolic enzymes and regulatory proteins. Formation of the Hsp42-SPG efficiently downregulates the activities of sequestered components, which can be differentially released from the granule based on environmental cues. We found a similar structure in the pre-whole genome duplication yeast species, Lachancea kluyveri, suggesting that the Hsp42-SPG is a common machinery allowing chronologically aged cells to contend with changing environments when available energy is limited. This article has an associated First Person interview with the first author of the paper.

Protection from hydrogen peroxide stress relies mainly on AhpCF and KatA2 in Stenotrophomonas maltophilia.

BACKGROUND: Aerobically-grown bacteria can be challenged by hydrogen peroxide stress from endogenous aerobic metabolism and exogenously generated reactive oxygen species. Catalase (Kat), alkyl hydroperoxidase (Ahp), and glutathione peroxidase (Gpx) systems are major adaptive responses to H2O2 stress in bacteria. Stenotrophomonas maltophilia is a ubiquitous Gram-negative bacterium equipped with four Kats (KatA1, KatA2, KatMn, and KatE), one Ahp (AhpCF), and three Gpxs (Gpx1, Gpx2, and Gpx3). Here, we systematically investigated how the eight H2O2 scavenging genes differentially contribute to the low-micromolar levels of H2O2 generated from aerobic metabolism and high-millimolar levels of H2O2 from exogenous sources. METHODS: Gene expression was assessed and quantified by reverse transcription-PCR (RT-PCR) and real time quantitative PCR (qRT-PCR), respectively. The contribution of these enzymes to H2O2 stress was assessed using mutant construction and functional investigation. RESULTS: Of the eight genes, katA2, ahpCF, and gpx3 were intrinsically expressed in response to low-micromolar levels of H2O2 from aerobic metabolism, and the expression of katA2 and ahpCF was regulated by OxyR. AhpCF and KatA2 were responsible for alleviating aerobic growth-mediated low concentration H2O2 stress and AhpCF played a critical role for stationary-phase cells. KatA2 was upregulated to compensate for AhpCF in the case of ahpCF inactivation. After exposure to millimolar levels of H2O2, katA2 and ahpCF were upregulated in an OxyR-dependent manner. KatA2 was the critical enzyme for dealing with high concentration H2O2. Loss-of-function of KatA2 increased bacterial susceptibility to high concentration H2O2. CONCLUSIONS: AhpCF and KatA2 are key enzymes protecting S. maltophilia from hydrogen peroxide stress.

Urine metabolomics signatures in reversible cerebral vasoconstriction syndrome.

BACKGROUND: The pathophysiology of reversible cerebral vasoconstriction syndrome is unclear. An unbiased systems-based approach might help to illustrate the metabolite profiling and underlying pathophysiology. METHODS: Urine samples were collected from reversible cerebral vasoconstriction syndrome patients and matched controls recruited in Taipei Veterans General Hospital. 1H-Nuclear magnetic resonance was used to initially explore the metabolic profile, and liquid chromatography tandem mass spectrometry was then used to identify metabolic alterations in reversible cerebral vasoconstriction syndrome. Untargeted metabolite screening was randomly performed on 10 reversible cerebral vasoconstriction syndrome patients and 10 control subjects in the discovery phase. The selected untargeted metabolites were further validated on 47 reversible cerebral vasoconstriction syndrome patients during their ictal stage (with 40 of them having remission samples) and 47 controls in the replication phase. RESULTS AND CONCLUSION: Six metabolites-hippurate, citrate, 1,3,7-trimethyluric acid, ascorbic acid, D-glucurono-6,3-lactone, and D-threo-isocitric acid-with t-test derived p-value < 0.05 and VIP score >1, were identified as potential urine signatures that can well distinguish reversible cerebral vasoconstriction syndrome subjects at ictal stage from controls. Among them, citrate, hippurate, ascorbic acid, and D-glucurono-6,3-lactone were significantly lower, and 1,3,7-trimethyluric acid and D-threo-isocitric acid were higher in reversible cerebral vasoconstriction syndrome patients. Of these, four selected metabolites, citrate, D-glucurono-6,3-lactone, ascorbic acid, and 1,3,7-trimethyluric acid, returned to normal levels in remission. These metabolites are related to pathways associated with free radical scavenging, with the hub molecules being associated with endothelial dysfunction or sympathetic overactivity. Whether these metabolites and their implicated networks play a role in the pathogenesis of reversible cerebral vasoconstriction syndrome remains to be confirmed.

Analytically validated protein biomarkers of chronic pancreatitis and pancreatic cancer for potential clinical diagnosis with mass spectrometry.

RATIONALE: Chronic pancreatitis (CP) is a pancreatic disease with poor prognosis and pancreatic cancer (PC) is one of the most lethal types of cancer that is symptomless in the early stage. Because the clinical and image findings of CP can overlap that of pancreatic cancer (PC) which leads to confusion in the diagnosis and treatment of PC, discovery/verification/validation of more accurate protein biomarkers to diagnose CP and PC is in urgent need. METHODS: The PubMed, Web of Science, and Google Scholar were searched using the keywords: 'biomarker', 'marker', 'chronic pancreatitis', "pancreatic cancer" or "proteomics" for highly related researches. We focused on the articles published after the year 2005 in this review. RESULTS: We introduce the background to CP and PC and summarize the diagnosis of CP and PC, analytically validated protein biomarkers, and proteomic approaches for discovery/verification/validation. The potential use of mass spectrometry (MS) in clinical diagnosis is also discussed. CONCLUSIONS: Continuously improving sensitivity of MS can provide deeper proteome for new marker discovery and high reliability for protein marker verification, validation, and clinical diagnosis. The analytically validated protein markers could be considered as targeted protein biomarkers for developing a MS platform in the clinical validation process or clinical diagnosis of CP and PC.