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.
Fused Deposition Modeling (FDM) can be used to manufacture any complex geometry and internal structures, and it has been widely applied in many industries, such as the biomedical, manufacturing, ...aerospace, automobile, industrial, and building industries. The purpose of this research is to characterize the polylactic acid (PLA) and polyethylene terephthalate glycol (PETG) materials of FDM under four loading conditions (tension, compression, bending, and thermal deformation), in order to obtain data regarding different printing temperatures and speeds. The results indicated that PLA and PETG materials exhibit an obvious tensile and compression asymmetry. It was observed that the mechanical properties (tension, compression, and bending) of PLA and PETG are increased at higher printing temperatures, and that the effect of speed on PLA and PETG shows different results. In addition, the mechanical properties of PLA are greater than those of PETG, but the thermal deformation is the opposite. The above results will be a great help for researchers who are working with polymers and FDM technology to achieve sustainability.
Blood–brain barrier (BBB) disruption contributes to neurodegenerative diseases. Loss of tight junction (TJ) proteins in cerebral endothelial cells (ECs) is a leading cause of BBB breakdown. We ...recently reported that miR‐195 provides vasoprotection, which urges us to explore the role of miR‐195 in BBB integrity. Here, we found cerebral miR‐195 levels decreased with age, and BBB leakage was significantly increased in miR‐195 knockout mice. Furthermore, exosomes from miR‐195‐enriched astrocytes increased endothelial TJ proteins and improved BBB integrity. To decipher how miR‐195 promoted BBB integrity, we first demonstrated that TJ proteins were metabolized via autophagic–lysosomal pathway and the autophagic adaptor p62 was necessary to promote TJ protein degradation in cerebral ECs. Next, proteomic analysis of exosomes revealed miR‐195‐suppressed thrombospondin‐1 (TSP1) as a major contributor to BBB disruption. Moreover, TSP1 was demonstrated to activate selective autophagy of TJ proteins by increasing the formation of claudin‐5‐p62 and ZO1‐p62 complexes in cerebral ECs while TSP1 impaired general autophagy. Delivering TSP1 antibody into the circulation showed dose‐dependent reduction of BBB leakage by 20%–40% in 25‐month‐old mice. Intravenous or intracerebroventricular injection of miR‐195 rescued TSP1‐induced BBB leakage. Dementia patients with BBB damage had higher levels of serum TSP1 compared to those without BBB damage (p = 0.0015), while the normal subjects had the lowest TSP1 (p < 0.0001). Taken together, the study implies that TSP1‐regulated selective autophagy facilitates the degradation of TJ proteins and weakens BBB integrity. An adequate level of miR‐195 can suppress the autophagy–lysosome pathway via a reduction of TSP1, which may be important for maintaining BBB function.
The present study revealed that thrombospondin‐1 (TSP1) is a key factor for BBB leakage and miR‐195 protects BBB integrity. We showed that cerebral miR‐195 reduces with age and blood‐brain barrier (BBB) leakage is increased in miR‐195 knockout mice. miR‐195‐regulated thrombospondin‐1 impairs BBB via selective autophagy of tight junctions. Furthermore, circulating TSP1 was higher in BBB‐damaged patients, which implied TSP1 as a new biomarker of BBB damage.
Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase ...(cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.
Frailty is associated with major health outcomes. However, the relationships between frailty and frailty symptoms haven't been well studied. This study aims to show the associations between frailty ...and frailty symptoms. The Health and Retirement Study (HRS) is an ongoing longitudinal biannual survey in the United States. Three of the most used frailty diagnoses, defined by the Functional Domains Model, the Burden Model, and the Biologic Syndrome Model, were reproduced according to previous studies. The associations between frailty statuses and input symptoms were assessed using odds ratios and correlation coefficients. The sample sizes, mean ages, and frailty prevalence matched those reported in previous studies. Frailty statuses were weakly correlated with each other (coefficients = 0.19 to 0.38, p 0.05 for all). One to six symptoms defined by the other two models were not significantly correlated with each of the three frailty statuses (p > 0.05 for all). Frailty statuses were significantly correlated with their own bias variables (p < 0.05 for all). Frailty diagnoses lack significant correlations with some of their own frailty symptoms and some of the frailty symptoms defined by the other two models. This finding raises questions like whether the frailty symptoms lacking significant correlations with frailty statuses could be included to diagnose frailty and whether frailty exists and causes frailty symptoms.
The adrenal gland responds to heat stress by epinephrine and glucocorticoid release to alleviate the adverse effects. This study investigated the effect of acute heat stress on the protein profile ...and histone modification in the adrenal gland of layer-type country chickens. A total of 192 roosters were subject to acute heat stress and thereafter classified into a resistant or susceptible group according to body temperature change. The iTRAQ analysis identified 80 differentially expressed proteins, in which the resistant group had a higher level of somatostatin and hydroxy-δ-5-steroid dehydrogenase but a lower parathymosin expression in accordance with the change of serum glucocorticoid levels. Histone modification analysis identified 115 histone markers. The susceptible group had a higher level of tri-methylation of histone H3 lysine 27 (H3K27me3) and showed a positive crosstalk with K36me and K37me in the H3 tails. The differential changes of body temperature projected in physiological regulation at the hypothalamus-pituitary-adrenal axis suggest the genetic heterogeneity in basic metabolic rate and efficiency for heat dissipation to acclimate to thermal stress and maintain body temperature homeostasis. The alteration of adrenal H3K27me3 level was associated with the endocrine function of adrenal gland and may contribute to the thermotolerance of chickens.
Frailty is a geriatric syndrome that has been defined differently with various indices. Without a uniform definition, it remains unclear how to interpret and compare different frailty indices (FIs). ...With the advances in index mining, we find it necessary to review the implicit assumptions about the creation of FIs. We are concerned the processing of frailty data may introduce measurement error and bias. We aim to review the assumptions, interpretability and predictive power of FIs regarding mortality.
Three FIs, the Functional Domains Model proposed by Strawbridge et al. (1998), the Burden Model by Rockwood et al. (2007) and the Biologic Syndrome Model by Fried et al. (2004), were directly compared using the data from the Health and Retirement Study (HRS), a longitudinal study since 1996 mainly following up Americans aged 50 years and over. The FIs were reproduced according to Cigolle et al. (2009) and interpreted with their input variables through forward-stepwise regression. Biases were the residuals of the FIs that could not be explained by own input variables. Any four of the input variables were used to create alternative indices. Discrete-time survival analysis was conducted to compare the predictive power of FIs, input variables and alternative indices on mortality.
We found frailty a syndrome not unique to the elderly. The FIs were produced with different degrees of bias. The FIs could not be fully interpreted with the theory-based input variables. The bias induced by the Biological Syndrome Model better predicted mortality than frailty status. A complicated FI, the Burden Model, could be simplified. The input variables better predicted mortality than the FIs. The continuous FIs predicted mortality better than the frailty statuses. At least 6865 alternative indices better predicted mortality than the FIs.
FIs have been used as outcome in clinical trials and need to be reviewed for adequacy based on our findings. The three FIs are not closely linked to the theories because of bias introduced by data manipulation and excessive numbers of input variables. We are developing new algorithms to develop and validate innovative indices.
Mango is widely grown in Taiwan and anthracnose is one of the most important diseases of this crop. The aim of this study was to investigate
Colletotrichum
species associated with mango and the ...pathogenicity of these fungal species. From 2006 to 2017, mango tissue from 33 mango orchards were collected. Eighty-seven isolates associated with mango were analyzed preliminarily by comparing partial glyceraldehyde-3-phosphate dehydrogenase sequences. Four species belonging to
C. gloeosporioides
complex were preliminarily identified, namely
C. asianum
(68 isolates),
C. fructicola
(four isolates),
C. siamense
(eight isolates) and
C. tropicale
(two isolates). The other five isolates were identified as belonging to the
C. acutatum
complex. Ten isolates, belonging to different
Colletotrichum
species according to glyceraldehyde-3-phosphate dehydrogenase sequences prediction, were used for further morphology and multi-gene phylogenetic analysis. Five species were identified, namely
C. asianum
,
C. fructicola
,
C. siamense
,
C. tropicale
and
C. scovillei
. All five species showed pathogenicity on fruit, and
C. asianum
isolates C-1076 and C-1646 as well as
C. siamense
isolate C-526 caused larger lesions than the other isolates. On mango leaves,
C. asianum
,
C. fructicola
,
C. siamense
and
C. scovillei
isolates were pathogenic, while
C. tropicale
isolates, C-141 and C-303, failed to cause significant foliar lesions. In addition,
C. siamense
isolates C-526 and C-848 caused significantly larger lesions on leaves than other isolates. This study reports the identification and pathogenicity of
Colletotrichum
species related to mango anthracnose in Taiwan.
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 (R 2 > 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.
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.
PDF
