Chi-Jen Lo

The GXXXG motif, also called the glycine zipper, is a common sequence pattern that facilitates tight packing of secondary structures, especially through helix–helix interactions in both membrane and soluble proteins. However, its overall distribution, sequence variation, and structural preferences depending on context are not fully understood. Here, we offer a detailed, large-scale analysis of GXXXG motifs, examining over 25,000 unique UniProt sequences with structural data. We classified the motifs as transmembrane (TM), non-transmembrane (non-TM), or shared, based on their TM coverage, and analyzed them via statistical models, diversity measures, and compositional profiling. Our findings show that ≥60% TM coverage is a reliable cutoff to distinguish TM-specific motifs, which tend to have less sequence diversity, lower entropy, more hydrophobic residues (notably leucine, isoleucine, and valine), and rank–frequency distributions that follow a heavy-tailed pattern, indicating strong selective pressure. Conversely, non-TM motifs are more varied, with higher entropy and a preference for polar or flexible residues. Shared motifs have intermediate features, reflecting their functional versatility. Power-law and Zipfian analyses support the distinct statistical signatures of TM and non-TM motifs at the 60% coverage threshold. These results enhance our understanding of the structural and evolutionary roles of the GXXXG motif, setting clear standards for identifying TM-specific motifs and offering insights into membrane protein biology, synthetic design, and functional annotation.

This study evaluated chemical safety indicators in 38 commercial fish sauces from Thailand, South Korea, Taiwan, and Vietnam sold in Taiwan. We quantified key nitrogenous compounds, biogenic amines, preservatives, and sodium levels, and further characterized metabolite profiles using untargeted ¹H nuclear magnetic resonance (¹H-NMR) spectroscopy. Vietnamese fish sauces exhibited the highest total nitrogen content and lowest pH, indicating superior fermentation quality. Sodium concentrations ranged from 5037 to 12,637 mg/100 mL, and nearly 40% of products, particularly Thai and Korean, exceeded the permitted labeling tolerance (≤120%), highlighting substantial labeling inaccuracies. Preservative analysis revealed the unauthorized or excessive use of benzoates and sorbates in several samples, indicating regulatory non-compliance. Preservative analysis revealed that three of seven Taiwanese samples contained dehydroacetic acid above the regulatory limit of 1 g/kg, with sample C6 both mislabeled and showing the highest concentration (3.22 g/kg). Among the ten Vietnamese samples, two exceeded the permissible limits for combined preservative use, and samples D2–D5 contained triacetin, a non-listed food additive, in violation of current regulations. Notably, South Korean fish sauces contained histamine concentrations up to 539.85 ± 318.88 ppm, with several samples surpassing the Taiwanese regulatory limit of 400 ppm, raising significant food safety concerns. Metabolomic analysis differentiated products by country, with formic acid, acetate, branched-chain amino acids, and alanine contributing to the distinct profiles of Thai and Taiwanese fish sauces. Collectively, our results provide critical insights into the quality and safety of fish sauce products, highlighting the importance of monitoring biogenic amines and ensuring accurate labeling to comply with food safety regulations.

Introduction: The influence of deranged body composition on stage I/II hepatocellular carcinoma (HCC) after surgery remains undetermined. The current study aimed to investigate the impact of low skeletal muscle bulk and disturbed body fat mass on the recurrence outcome of stage I/II HCC patients undergoing liver resection. The associated metabolomic alterations were also assessed. Methods: From 2012 to 2021, stage I and II HCC patients who underwent liver resection at our institute were retrospectively reviewed. Their preoperative body composition including skeletal muscle mass and body fat volume was measured by computed tomography (CT). The recurrence outcome was recorded and analyzed. The preoperative serum was collected and subjected to metabolomic analysis. Results: A total of 450 stage I and II HCC patients were included in the current study. Among them, 76% were male and around 60% had HBV infection. After stratified by normal cut-off values obtained from a healthy cohort, 6.4% of stage I/II HCC patients were found to have a low psoas muscle index (PMI), 17.8% a high subcutaneous adipose tissue (SAT) index, and 27.8% a high visceral adipose tissue (VAT) index. Cox regression multivariate analysis further demonstrated that low PMI and high SAT index were independent prognostic factors for time-to-recurrence (TTR) after surgery. Metabolomic analysis discovered that free fatty acid β-oxidation was enhanced in patients with low PMI or high SAT index. Conclusion: The current study demonstrated that reduced psoas muscle mass may impair while elevated SAT may prolong the TTR of stage I/II HCC patients undergoing liver resections. VAT, on the other hand, was not associated with recurrence outcomes after surgery. Further studies are warranted to validate our findings.

In this work, we demonstrated an off-chip capacitance array biosensor with limit of detection 1 μM of TMAO to diagnose chronic metabolism disease in urine. Based on the improved cole-cole model, the parameters of R _catalyzed and C _catalyzed and R _{p catalyzed} can predict the catalytic resistance of enzyme and redox effects of the analyte, and identify the AC properties of ion strength due to enzymatic catalysis. With the investigation of the off-chip capacitance biosensor electrical field change with respect to pixel geometry and associated driving and sensing electrode width in a pixel, the proposed off-chip biosensor with readout SoC exhibits high sensitivity of 21 ADC counts/μM (or 25 mV/μM), response time of 0.1 s, repetition of 98.9%, and drift over time of 0.5 mV. The proposed off-chip biosensor can distinguish TMAO in phosphate buffered saline (PBS) solution from the tiny capacitance change of TMAO induced by enzyme TorA with a difference of 2.15%, and the measurements has been successful verified with traditional cyclic-voltammetry (CV) method, which shows a difference of only 0.024%. The off-chip biosensor is designed to specifically detect TMAO by excluding the redox reactions of TMAO-specific enzyme TorA with creatine and creatinine in urine. This exclusion ensures that the biosensor focuses solely on TMAO, enhancing its specificity for accurate and reliable TMAO detection.

Plasma lipid levels are commonly measured using traditional methods such as triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and cholesterol (CH). However, the use of newer technologies, such as nuclear magnetic resonance (NMR) with post-analysis platforms, has made it easier to assess lipoprotein profiles in research. In this study involving ApoE-deficient mice that were fed high-fat diets, significant changes were observed in TG, CH, free cholesterol (FC), and phospholipid (PL) levels within the LDL fraction. The varied proportions of TG in wild-type mice and CH, FC, and PL in ApoE^-/- mice were strikingly different in very low-density lipoproteins (VLDL), LDL, intermediate-density lipoprotein (IDL), and HDL. This comprehensive analysis expands our understanding of lipoprotein subfractions and the impacts of the APOE protein and high-fat diet in mouse models. The new testing method allows for a complete assessment of plasma lipids and their correlation with genetic background and diet in mice.

The coming of the hyper-aged society in Taiwan prompts us to investigate the relationship between the metabolic status of sarcopenic patients and their most adverse outcome–death. We studied the association between any plasma metabolites and the risk for mortality among older Taiwanese sarcopenic patients. We applied a targeted metabolomic approach to study the plasma metabolites of adults aged ≥65 years, and identified the metabolic signature predictive of the mortality of sarcopenic patients who died within a 5.5-year follow-up period. Thirty-five sarcopenic patients who died within the follow-up period (Dead cohort) had shown a specific plasma metabolic signature, as compared with 54 patients who were alive (Alive cohort). Only 10 of 116 non-sarcopenic individuals died during the same period. After multivariable adjustment, we found that sex, hypertension, tetradecanoyl-carnitine (C14-carnitine), and docosahexaenoic acid (DHA)-containing phosphatidylcholine diacyl (PCaa) C38:6 and C40:6 were important risk factors for the mortality of sarcopenic patients. Low PCaa C38:6 levels and high C14-carnitine levels correlated with an increased mortality risk; this was even the same for those patients with hypertension (HTN). Our findings suggest that plasma PCaa C38:6 and acylcarnitine C14-carnitine, when combined, can be a better early biomarker for evaluating the mortality risk of sarcopenia patients.

Atherosclerosis is an inflammatory disease of the arteries associated with alterations in lipid and other metabolism and is a major cause of cardiovascular disease (CVD). LDL consists of several subclasses with different sizes, densities, and physicochemical compositions. Small dense LDL (sd-LDL) is a subclass of LDL. There is growing evidence that sd-LDL-C is associated with CVD risk, metabolic dysregulation, and several pathophysiological processes. In this study, we present a straightforward membrane device filtration method that can be performed with simple laboratory methods to directly determine sd-LDL in serum without the need for specialized equipment. The method consists of three steps: first, the precipitation of lipoproteins with magnesium harpin; second, the collection of effluent from a 100 nm filter; and third, the quantification of sd-LDL-ApoB in the effluent with an SH-SAW biosensor. There was a good correlation between ApoB values obtained using the centrifugation (y = 1.0411x + 12.96, r = 0.82, n = 20) and filtration (y = 1.0633x + 15.13, r = 0.88, n = 20) methods and commercially available sd-LDL-C assay values. In addition to the filtrate method, there was also a close correlation between sd-LDL-C and ELISA assay values (y = 1.0483x − 4489, r = 0.88, n = 20). The filtration treatment method also showed a high correlation with LDL subfractions and NMR spectra ApoB measurements (y = 2.4846x + 4.637, r = 0.89, n = 20). The presence of sd-LDL-ApoB in the effluent was also confirmed by ELISA assay. These results suggest that this filtration method is a simple and promising pretreatment for use with the SH-SAW biosensor as a rapid in vitro diagnostic (IVD) method for predicting sd-LDL concentrations. Overall, we propose a very sensitive and specific SH-SAW biosensor with the ApoB antibody in its sensitive region to monitor sd-LDL levels by employing a simple delay-time phase shifted SH-SAW device. In conclusion, based on the demonstration of our study, the SH-SAW biosensor could be a strong candidate for the future measurement of sd-LDL.

Background: During biological aging, significant metabolic dysregulation in the central nervous system may lead to cognitive decline and neurodegeneration. However, the metabolomics of the aging process in cerebrospinal fluid (CSF) has not been thoroughly explored. Methods: In this cohort study of CSF metabolomics using liquid chromatography-mass spectrometry (LC–MS), fasting CSF samples collected from 92 cognitively unimpaired adults aged 20–87 years without obesity or diabetes were analyzed. Results: We identified 37 metabolites in these CSF samples with significant positive correlations with aging, including cysteine, pantothenic acid, 5-hydroxyindoleacetic acid (5-HIAA), aspartic acid, and glutamate; and two metabolites with negative correlations, asparagine and glycerophosphocholine. The combined alterations of asparagine, cysteine, glycerophosphocholine, pantothenic acid, sucrose, and 5-HIAA showed a superior correlation with aging (AUC = 0.982). These age-correlated changes in CSF metabolites might reflect blood–brain barrier breakdown, neuroinflammation, and mitochondrial dysfunction in the aging brain. We also found sex differences in CSF metabolites with higher levels of taurine and 5-HIAA in women using propensity-matched comparison. Conclusions: Our LC–MS metabolomics of the aging process in a Taiwanese population revealed several significantly altered CSF metabolites during aging and between the sexes. These metabolic alterations in CSF might provide clues for healthy brain aging and deserve further exploration.

Alterations in lipid composition and disturbed lipoprotein metabolism are involved in the pathomechanism of Huntington’s disease (HD). Here, we measured 112 lipoprotein subfractions and components in the plasma of 20 normal controls, 24 symptomatic (sympHD) and 9 presymptomatic (preHD) HD patients. Significant changes were found in 30 lipoprotein subfractions and components in all HD patients. Plasma levels of total cholesterol (CH), apolipoprotein (Apo)B, ApoB-particle number (PN), and components of low-density lipoprotein (LDL) were lower in preHD and sympHD patients. Components of LDL4, LDL5, LDL6 and high-density lipoprotein (HDL)4 demonstrated lower levels in preHD and sympHD patients compared with controls. Components in LDL3 displayed lower levels in sympHD compared with the controls, whereas components in very low-density lipoprotein (VLDL)5 were higher in sympHD patients compared to the controls. The levels of components in HDL4 and VLDL5 demonstrated correlation with the scores of motor assessment, independence scale or functional capacity of Unified Huntington’s Disease Rating Scale. These findings indicate the potential of components of VLDL5, LDL3, LDL4, LDL5 and HDL4 to serve as the biomarkers for HD diagnosis and disease progression, and demonstrate substantial evidence of the involvement of lipids and apolipoproteins in HD pathogenesis.