Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.

Anemia in inflammatory bowel disease course is associated with patients' worse outcome.

BACKGROUND: Purpose: Anemia affects the life quality of inflammatory bowel disease (IBD) patients, but no report from Asian about anemia screening and its impact previously. We aimed to explore the prevalence and impact of anemia among the IBD patients in Taiwan. METHODS: A retrospective study was conducted from January 2006 to February 2018 at National Taiwan University Hospital. Clinical characteristics and outcomes were analyzed. RESULTS: A total of 1604 IBD patients were enrolled [494 Crohn's disease (CD) and 1110 ulcerative colitis (UC)]. Overall, 95.3% (471/494) of CD and 87.9% (976/1110) of UC patients underwent anemia screening. Anemia screening rate in IBD patients significantly increased from 62.6% (162/259) in 2006 to 77.2% (838/1086) in 2017. The mean time from IBD diagnosis to anemia screening was 122.4 days in CD patients and even longer in UC patients at 216.2 days. Persistent anemia was found in 47.3% (548/1158) of the screened patients. Risk factors of persistent anemia included low body mass index [odds ratio (OR) = 1.96, p < 0.01], steroid [OR = 2.96, p < 0.01], thiopurine [OR = 2.62, p < 0.01], colectomy [OR = 6.3, p < 0.01], and small bowel resection [OR = 3.21, p < 0.05)] after IBD diagnosis. Compared with those without anemia, anemic IBD patients had higher admission (p < 0.01) and mortality rates (p < 0.01). CONCLUSION: The anemia screening rate was acceptable and increased over time in Taiwan. Since anemia is associated with worse outcomes, earlier survey and treatment of anemia in IBD patients is recommended.

Clinical Outcomes of Metastatic Breast Cancer in Patients Having Imaging Liver Pseudocirrhosis with or without Evident Varices.

BACKGROUND: Pseudocirrhosis is an imaging finding of malignancies with liver metastasis with or without clinical liver cirrhosis-related portal hypertension (pHTN). This study defined evident pHTN by the presence of esophageal or gastric varices and compared patients' outcomes of metastatic breast cancer with imaging-diagnosed pseudocirrhosis with or without varices. METHODS: The medical records from patients with metastatic breast cancer and pseudocirrhosis between 2005 and 2017 were retrospectively analyzed. Survival outcomes were compared based on endoscopic evidence of esophageal or gastric varices. RESULTS: Among 106 patients with pseudocirrhosis, 33 (31%) had de novo stage IV disease, and 66 (62%) had hormone receptor (HR)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. Eighty-one (76%) had initial metastases in both hepatic lobes, and 32 (30%) had esophageal or gastric varices. The median overall survival (OS) was 5 and 13 months in patients with and without varices (P = .002). The median OS in patients with HER2-positive, HR-positive/HER2-negative, and triple-negative subtype was 16, 9, and 2 months, respectively (P = .001). Patients with varices usually had cirrhotic complications, including gastrointestinal bleeding, hyperbilirubinemia, hyperammonemia, and coagulopathy. Despite their challenging clinical conditions, 7 patients with varices had OS exceeding 1 year. In multivariate analysis, evident varices (P = .007) and triple-negative subtype (P = .013) were associated with poor OS. CONCLUSIONS: Patients with pseudocirrhosis and evident varices had a significantly shorter median OS, and were usually associated with clinical cirrhosis-related complications. To maximize OS, early identification and meticulous supportive care are warranted.

A Case Report of MODY3 Combined with Intestinal Neuroendocrine Tumor.

Maturity-onset diabetes of the young 3 (MODY3) is an autosomal dominant monogenic diabetes mellitus characterized by defective ß-cell function and non-insulin-dependent early-onset diabetes mellitus. The facts that patients with MODY3 are often misdiagnosed as type 1 and type 2 diabetes mellitus and genetic diagnosis is expensive, make its diagnosis very challenging. In this study, we reported a case of MODY3, which was verified to be caused by a mutation in hepatocyte nuclear factor 1α gene (c.598C>T, p.Arg200Trp). In addition, the patient had a neuroendocrine tumor simultaneously, and a KMT2D gene mutation (c.5587C>G, p.Pro1863Ala) might be associated with this leson.

Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat.

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.

The catalytic triad of rice NARROW LEAF1 involves H234.

NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

Effect of smoking on the development and outcomes of inflammatory bowel disease in Taiwan: a hospital-based cohort study.

Smoking influences the risks of inflammatory bowel disease (IBD). A hospital-based cohort was conducted to evaluate the effect of smoking on the development and outcomes of IBD, with age, sex and comorbidities matched non-IBD controls from the National Health Interview Survey database of Taiwan. 700 IBD patients (360 ulcerative colitis (UC), 340 Crohn's disease (CD)) were analyzed for outcomes; and 575 patients (297 UC, 278 CD) were analyzed for prevalence. Smoking prevalence was significantly lower in UC patients than controls (20.9% vs. 30.4%, p < 0.01), but no difference between CD patients and controls (19.8% vs. 22.1%, p = 0.60). UC smokers had fewer admissions (1.6 vs. 2.5, p < 0.05) but higher rates of new cancer development (16% vs. 6.7%, p < 0.05) and mortality (16% vs. 4.9%, p < 0.01) than nonsmokers. CD smokers tended to have higher rates of stricturing and penetrating diseases (p < 0.05), and higher surgery risk (60.3% vs. 38.3%, p < 0.01) than nonsmokers. Smoking prevents UC occurrence and is associated with fewer hospitalization but increases risks of cancer and mortality. By contrast, smoking does not affect CD occurrence but is related to more aggressive behavior which results in a higher surgical rate.

Characteristics and Resource Utilization Associated with Frequent Users of Emergency Departments.

Background: Frequent emergency department (ED) users place a huge influence and burden on healthcare systems and medical costs. In Taiwan, citizens have very easy access to medical services and the national health insurance (NHI) puts very few restrictions on the frequency and facilities which the patients go to. However, there is still a certain percentage of frequent ED users in Taiwan, and yet, there are few research studies investigating the features of such users and their impact on the healthcare system. We conducted this study to investigate the prevalence and characteristics of the repeated ED users in a tertiary care medical center with more than 80000 emergency visits in a year and hypothesized that frequent ED users have unique medical and social characteristics and results in increased medical expense. Methods: We searched the integrated medical database of an urban tertiary medical center in 2017. We compared frequent ED users (≧4 visits/year) with nonfrequent users (<4 visits/year) with regards to the medical history, distance from home to the hospital, main visiting purposes, whether patients had used outpatient care or other medical resources at the same time, and the charge to the patients for each visit. Results: In 2017, 2191 patients (3.37%) were listed as frequent users and accounted for 12166 visits (14.20%). Most of the frequent users were over 65 years old (53.1%) and more than half of them had suffered from cancer (55.1%). The most significant features of frequent ED users were male, educational attainment below university, low-income households, drug or food allergies, terminal stage of illness, possession of IC Cards for Severe Illness, hospitalization in the past year, multiple outpatient visits in same year, and with certain medical history including anemia, cerebrovascular accident, congestive heart failure, peptic ulcer disease, ileus, cirrhosis, chronic obstructive pulmonary disease, and psychiatric disease. There were significant differences between frequent and nonfrequent users in disposition and median charge per visit (US$137 vs. $117, p < 0.001). Conclusions: Frequent users of ED are a heterogeneous group who usually suffer from multiple chronic diseases. There were higher rates of hospital admission and medical costs among frequent ED users compared to nonfrequent users. In addition to emergency services, frequent users also utilized outpatient resources heavily.

A Toolbox for Site-Specific Labeling of RecQ Helicase With a Single Fluorophore Used in the Single-Molecule Assay.

Fluorescently labeled proteins can improve the detection sensitivity and have been widely used in a variety of biological measurements. In single-molecule assays, site-specific labeling of proteins enables the visualization of molecular interactions, conformational changes in proteins, and enzymatic activity. In this study, based on a flexible linker in the Escherichia coli RecQ helicase, we established a scheme involving a combination of fluorophore labeling and sortase A ligation to allow site-specific labeling of the HRDC domain of RecQ with a single Cy5 fluorophore, without inletting extra fluorescent domain or peptide fragment. Using single-molecule fluorescence resonance energy transfer, we visualized that Cy5-labeled HRDC could directly interact with RecA domains and could bind to both the 3' and 5' ends of the overhang DNA dynamically in vitro for the first time. The present work not only reveals the functional mechanism of the HRDC domain, but also provides a feasible method for site-specific labeling of a domain with a single fluorophore used in single-molecule assays.

miR-503/Apelin-12 mediates high glucose-induced microvascular endothelial cells injury via JNK and p38MAPK signaling pathway.

INTRODUCTION: Diabetic patients are often accompanied by complications of diabetic vascular disease, which could lead to heart failure or stroke. In this work, we explored the role of miR-503/Apelin-12 in diabetic angiopathy (DA) in vitro. METHODS: ELISA and qPCR were applied to assess the expression of miR-503 and Apelin-12 in high glucose (HG)-treated microvascular endothelial cells (HMEC-1). The effects of miR-503 on apoptosis, inflammation and oxidative stress were assessed by flow cytometry, western blotting, qPCR, and ELISA. The interaction between miR-503 and Apelin-12 was evaluated by dual-luciferase reporter assay, qPCR and ELISA, respectively. Western blotting was performed to examine the function of miR-503/Apelin-12 on JNK and p38MAPK activation. RESULTS: MiR-503 was markedly increased and Apelin-12 was decreased in HG-treated HMEC-1 cells. MiR-503 inhibitor significantly assuaged apoptosis, inflammation and oxidative stress in HMEC-1 cells. MiR-503 could specifically bind to the 3'UTR of Apelin and inversely downregulate Apelin-12 expression. Furthermore, Apelin-12 suppressed apoptosis, inflammation and oxidative stress. Inhibition of Apelin-12 could partially reverse the decrease of p-JNK and p-p38 expression levels induced by miR-503 suppression. CONCLUSION: In HG-induced microvascular cells injury, miR-503/Apelin-12 enhances inflammation and oxidative stress by regulating JNK and p38MAPK pathway, suggesting a potential therapeutic target for DA.

Protein profile of human lung squamous carcinoma cell line NCI-H226.

OBJECTIVE: To construct a database of human lung squamous carcinoma cell line NCI-H226 and to facilitate discovery of novel subtypes markers of lung cancer. METHOD: Proteomic technique was used to analyze human lung squamous carcinoma cell line NCI-H226. The proteins of the NCI-H226 cells were separated by two-dimensional gel electrophoresis and identified by mass spectrometry. RESULTS: The results showed that a good reproducibility of the 2-D gel pattern was attained. The position deviation of matched spots among three 2-D gels was 1.95 +/- 0.53 mm in the isoelectric focusing direction, and 1.73 +/- 0.45 mm in the sodium dodecyl sulfate-polyacrylamide gel electrophoresis direction. One hundred and twenty-seven proteins, including enzymes, signal transduction proteins, structure proteins, transport proteins, etc. were characterized, of which, 29 identified proteins in NCI-H226 cells were reported for the first time to be involved in lung cancer carcinogenesis. CONCLUSION: The information obtained from this study could provide some valuable clues for further study on the carcinogenetic mechanism of different types of lung cancer, and may help us to discover some potential subtype-specific biomarkers of lung cancer.

[Identification and clinical evaluation of lung cancer serum biomarker L-lactate dehydrogenase B].

OBJECTIVE: To identify potential biomarkers related with lung cancer metastasis. METHODS: Conditional media proteins collected from a primary non-small cell lung cancer cell line (NSCLC) NCI-H226 and its brain metastatic subline H226Br were analyzed by SDS-PAGE and MALDI-TOF-MS. Twelve biomarkers were identified, of which LDHB was significantly up-regulated in H226Br cell and was further validated using ELISA in sera including 105 lung cancer samples, 41 pneumonia and pulmonary tuberculosis samples and 65 healthy samples. RESULTS: The levels of LDHB were specifically elevated in NSCLC sera [A value 0.485 (0 - 1.415)] compared with pneumonia and pulmonary tuberculosis [A value 0.187 (0 - 0.609), P < 0.01] and healthy group [A value, 0.159 (0 - 0.524), P < 0.01] and were progressively increased with the clinical stage. At the cutoff point 0.260 (A value) on the ROC curve, the sensitivity, specificity and total accuracy of LDHB were 81%, 70% and 76% respectively. CONCLUSION: These findings demonstrated that secretome could open up a possibility to identify novel biomarkers related with cancer occurrence and metastasis.

[A new automatic quasars recognition technique based on PCA and Hough transform].

The main purpose of quasar recognition is to determine the observed quasar spectrum's redshift value. Previously the template of quasar rest frame in the literature was basically constructed based on astronomers' hypotheses. Due to the inaccuracy of such a template, it is hard to determine the redshift value by matching the observed quasar spectrum with the template directly. This paper's main contributions are two-fold: Firstly, the template in our paper is constructed by the principal component analysis (PCA) method from some selected spectra with known redshift values, hence the obtained template is more realistic. Secondly, a 2D standard Hough transform, rather than a 1D Hough transform, is used. This is because although only redshift needs to be determined in our system, based on our observations, the magnitude of emission peak is also changed, hence a new parameter, namely scale parameter, is also introduced to the Hough transform to enhance the reliability of the recognition. The experiments show that the proposed technique is workable and the correct recognition rate can reach about as high as 90%.