Supplementary Material for: MiR-129-5p Inhibits Proliferation and Invasion of Chondrosarcoma Cells by Regulating SOX4/Wnt/β-Catenin Signaling Pathway

<i>Background/Aims:</i> Recently, microRNAs (miRNA) have been identified as novel regulators in Chondrosarcoma (CHS). This study was aimed to identify the roles of miR-129-5p-5p in regulation of SOX4 and Wnt/β-catenin signaling pathway, as well as cell proliferation and apoptosis in chondrosarcomas. <i>Materials and Methods:</i> Tissue samples were obtained from chondrosarcoma patients. Immunohistochemistry, real-time quantitative RT-PCR (RT-qPCR) and western blot analysis were performed to detect the expressions of miR-129-5p and SOX4. Luciferase assay was conducted to confirm that miR-129-5p directly targeted SOX4 mRNA. Manipulations of miR-129-5p and SOX4 expression were achieved through cell transfection. Cell proliferation, migration and apoptosis were evaluated by CCK-8 assay, colony forming assay, wound healing assay and flow cytometry <i>in vitro</i>. For <i>in vivo</i> experiment, the tumor xenograft model was established to evaluate the effects of miR-129-5p and SOX4 on chondrosarcomas. <i>Results:</i> The expression of miR-129-5p was significantly down-regulated in chondrosarcoma tissues as well as cells in comparison with normal ones, while SOX4 was over-activated. Further studies suggested that miR-129-5p suppressed cell proliferation, migration and promoted apoptosis by inhibiting SOX4 and Wnt/β-catenin pathway. <i>Conclusion:</i> MiR-129-5p inhibits the Wnt/β-catenin signaling pathway by targeting SOX4 and further suppresses cell proliferation, migration and promotes apoptosis in chondrosarcomas

Supplementary Material for: Potential Regulators Driving the Transition in Nonalcoholic Fatty Liver Disease: a Stage-Based View

<i>Background and Aim:</i> The incidence of nonalcoholic fatty liver disease (NAFLD), ranging from mild steatosis to hepatocellular injury and inflammation, increases with the rise of obesity. However, the implications of transcription factors network in progressive NAFLD remain to be determined. <i>Methods:</i> A co-regulatory network approach by combining gene expression and transcription influence was utilized to dissect transcriptional regulators in different NAFLD stages. <i>In vivo</i>, mice models of NAFLD were used to investigate whether dysregulated expression be undertaken by transcriptional regulators. <i>Results:</i> Through constructing a large-scale co-regulatory network, sample-specific regulator activity was estimated. The combinations of active regulators that drive the progression of NAFLD were identified. Next, top regulators in each stage of NAFLD were determined, and the results were validated using the different experiments and bariatric surgical samples. In particular, Adipocyte enhancer-binding protein 1 (AEBP1) showed increased transcription activity in nonalcoholic steatohepatitis (NASH). Further characterization of the AEBP1 related transcription program defined its co-regulators, targeted genes, and functional organization. The dynamics of AEBP1 and its potential targets were verified in an animal model of NAFLD. <i>Conclusions:</i> This study identifies putative functions for several transcription factors in the pathogenesis of NAFLD and may thus point to potential targets for therapeutic interventions

Supplementary Material for: Dietary Elimination of Soybean Components Enhances Allergic Immune Response to Peanuts in BALB/c Mice

<b><i>Background:</i></b> Food allergy research is hampered by a lack of animal models that consistently mimic human food allergic responses. Laboratory mice are generally fed grain-based chow made with large amounts of soybeans rich in immunomodulatory isoflavones. We tested the role of dietary soy components in the induction of food allergic responses in the BALB/c mouse strain, which is known to be resistant to anaphylaxis when orally challenged by food allergens. <b><i>Methods:</i></b> Mice were fed a soy-free diet for 2 generations. After weaning, mice were maintained on the same diet or fed a diet containing soy isoflavones, i.e. genistein and daidzein, followed by weekly oral sensitizations with crude peanut extract plus cholera toxin and finally challenged at week 7. The anaphylactic symptoms, body temperature, peanut-specific antibodies and mast cell degranulation were assessed. <b><i>Results:</i></b> Soy-free diet mice showed significantly higher anaphylactic symptom scores and mast cell degranulation after challenge and higher peanut-specific antibody levels than mice fed regular chow. Introduction of a regular soy diet or an isoflavone diet to soy-free diet mice significantly suppressed the allergic reactions compared to the soy-free diet. <b><i>Conclusion:</i></b> Rodent diet is an important variable and needs to be taken into consideration when designing experiments involving animal models. Our results indicate that elimination of soy components from the diet enhances peanut sensitization in BALB/c mice. In addition to serving as a valuable tool to mimic human food allergy, the dietary influence on the immune response could have far-reaching consequences in research involving animal models

Supplementary Material for: Improvement of Spinosad Production upon Utilization of Oils and Manipulation of β-Oxidation in a High-Producing <b><i>Saccharopolyspora spinosa</i></b> Strain

Spinosad, a member of polyketide-derived macrolides produced in the actinomycete <i>Saccharopolyspora spinosa</i>, has been developed as a broad-spectrum and effective insecticide. The β-oxidation pathway could be an important source of building blocks for the biosynthesis of spinosad, thus the effect of vegetable oils on the production of spinosad in a high-yield strain was investigated. The spinosad production increased significantly with the addition of strawberry seed oil (511.64 mg/L) and camellia oil (520.07 mg/L) compared to the control group without oil (285.76 mg/L) and soybean oil group (398.11 mg/L). It also revealed that the addition of oils would affect the expression of genes involved in fatty acid metabolism, precursor supply, and oxidative stress. The genetically engineered strain, in which <i>fadD1</i> and <i>fadE</i> genes of <i>Streptomyces coelicolor</i> were inserted, produced spinosad up to 784.72 mg/L in the medium containing camellia oil, while a higher spinosad production level (843.40 mg/L) was detected with the addition of 0.01 mM of thiourea

Supplementary Material for: Roles of HDAC2 and HDAC8 in Cardiac Remodeling in Renovascular Hypertensive Rats and the Effects of Valproic Acid Sodium

<p>Recent studies indicate that histone deacetylases (HDACs) activity is associated with the development and progression of cardiac hypertrophy. In this study, we investigated the effects of a HDACs inhibitor, valproic acid sodium (VPA), on cardiac remodeling and the differential expression of HDACs in left ventricles (LVs) of renovascular hypertensive rats. Renovascular hypertension was induced in rats by the two-kidney two-clip (2K2C) method. Cardiac remodeling, heart function and the differential expression of HDACs were examined at different weeks after 2K2C operation. The effects of VPA on cardiac remodeling, the expressions of HDACs, transforming growth factor-beta 1 (TGF-β1) and connective tissue growth factor (CTGF) in LV were investigated. The expressions of atrial natriuretic factor, β-myosin heavy chain, HDAC2 and HDAC8 increased in LV of 2K2C rats at 4, 8, 12 weeks after operation. Cardiac dysfunction, cardiac hypertrophy and fibrosis were markedly attenuated by VPA treatment in 2K2C rats. Further studies revealed that VPA inhibited the expressions of HDAC2, HDAC8, TGF-β1 and CTGF in LV of 2K2C rats. In summary, these data indicate that HDAC2 and HDAC8 play a key role in cardiac remodeling in renovascular hypertensive rats and that VPA attenuates hypertension and cardiac remodeling. The effect of VPA is possibly exerted via decreasing HDAC2, HDAC8, TGF-β1 and CTGF expressions in LV of 2K2C rats.</p

Supplementary Material for: Heterologous Expression of Spinosyn Biosynthetic Gene Cluster in Streptomyces Species Is Dependent on the Expression of Rhamnose Biosynthesis Genes

<p>Spinosyns are a group of macrolide insecticides produced by <i>Saccharopolyspora spinosa</i>. Although <i>S. spinosa</i> can be used for industrial-scale production of spinosyns, this might suffer from several limitations, mainly related to its long growth cycle, low fermentation biomass, and inefficient utilization of starch. It is crucial to generate a robust strain for further spinosyn production and the development of spinosyn derivatives. A BAC vector, containing the whole biosynthetic gene cluster for spinosyn (74 kb) and the elements required for conjugal transfer and site-specific integration, was introduced into different <i>Streptomyces</i> hosts in order to obtain heterologous spinosyn-producing strains. The exconjugants of different <i>Streptomyces</i> strains did not show spinosyn production unless the rhamnose biosynthesis genes from <i>S. spinosa</i> genomic DNA were present and expressed under the control of a strong constitutive <i>ermE</i>*<i>p</i> promoter. Using this heterologous expression system resulted in yields of 1 μg/mL and 1.5 μg/mL spinosyns in <i>Streptomyces coelicolor</i> and <i>Streptomyces lividans</i>, respectively. This report demonstrates spinosyn production in 2 <i>Streptomyces</i> strains and stresses the essential role of rhamnose in this process. This work also provides a potential alternative route for producing spinosyn analogs by means of genetic manipulation in the heterologous hosts.</p

Supplementary Material for: Gross Hematuria Is More Common in Male and Older Patients with Renal Tuberculosis in China: A Single-Center 15-Year Clinical Experience

<p><b><i>Objectives:</i></b> This study aimed to investigate the clinical features of renal tuberculosis and identify the age- and gender-related differences. <b><i>Methods:</i></b> A total of 419 patients at the Peking University First Hospital from January 2000 to July 2015 were retrospectively reviewed. Data on demographic characteristics, clinical presentation, complications, laboratory results, radiologic imaging, surgical procedures, and pathology features were collected and compared between genders and 3 different age groups (under 40 years, 41-60, years and over 60 years). <b><i>Results:</i></b> The most common local presentations were lower urinary tract symptoms (65.2%), flank pain (37.9%), and gross hematuria (26.3%). Constitutional symptoms were also observed in 38.9% of the patients. Gross hematuria was more common in male patients (32.2%) and older patients (45.5%). Flank pain was more common in female patients (43.6%). Patients younger than 40 years of age had lower frequencies of calcification of the urinary tract (22.2%) and kidney atrophy (4.2%) in CT. In the postoperative pathological reports, atrophy (35.9%) and fibrosis (38.5%) were found to be significantly more common in older patients. <b><i>Conclusions:</i></b> While gross hematuria is more prevalent in older patients and male patients, flank pain is more common in female patients. Radiological and pathological features including calcification of the urinary tract, fibrosis, and kidney atrophy are more common in older patients.</p

Supplementary Material for: Cyclic Mechanical Stretch Induced Smooth Muscle Cell Changes in Cerebral Aneurysm Progress by Reducing Collagen Type IV and Collagen Type VI Levels

<b><i>Background/Aims:</i></b> Cerebral aneurysm growth is characterized by continuous structural weakness of local smooth muscle cells, though the mechanism is unclear. In this study, we examine protein changes in cerebral aneurysm and human brain vascular smooth muscle cells after cyclic mechanical stretch. We further explore the relationship between the smooth muscle cell changes and reductions in the levels of collagen types IV and VI. <b><i>Methods:</i></b> Saccular cerebral aneurysms (n=10) were collected, and temporal artery samples were used as controls. Quantitative proteomics were analyzed and histopathological changes were examined. Smooth muscle cells were cultured in a flexible silicone chamber and subjected to 15% cyclic mechanical stretch. The effect of stretch on the cell viability, function, gene and protein expression were further studied for the understanding the molecular mechanism of aneurysm development. <b><i>Results:</i></b> Proteomics analysis revealed 92 proteins with increased expression and 88 proteins with decreased expression compared to the controls (<i>p</i><0.05). KEGG pathway analysis showed that the change in focal adhesion and extracellular matrix-receptor interaction, suggesting the involvement of collagen type IV and VI. The aneurysm tissue exhibited fewer smooth muscle cells and lower levels of collagen type IV and VI. Human brain vascular smooth muscle cell culture showed spindle-like cells and obvious smooth muscle cell layer. Cell proteomics analysis showed that decreased expression of 118 proteins and increased expression of 32 proteins in smooth muscle cells after cyclic mechanical stretch. KEGG pathway analysis indicated that focal adhesion and ECM-receptor interaction were involved. After cyclic mechanical stretch, collagen type IV and IV expression were decreased. Moreover, the stretch induced MMP-1 and MMP-3 expression elevation. <b><i>Conclusion:</i></b> We demonstrated that collagen type IV and VI were decreased in cerebral aneurysms and continuous cyclic mechanical stretch induced smooth muscle cell changes. Smooth muscle cell protection provides an additional therapeutic option to prevent the growth of cerebral aneurysms

Supplementary Material for: ‘a’-Position-Mutated and G4-Mutated Hemagglutinin-Neuraminidase Proteins of Newcastle Disease Virus Impair Fusion and Hemagglutinin-Neuraminidase-Fusion Interaction by Different Mechanisms

<b><i>Objectives:</i></b> To determine the effects of heptad repeat regions (HRs) and N-linked carbohydrate sites of the Newcastle disease virus hemagglutinin-neuraminidase (HN) protein on fusion of HN and fusion (F) proteins and HN-F interaction. <b><i>Methods:</i></b> We mutated six ‘a’ residues in the HRs and four asparagines in N-linked carbohydrate sites to alanine in the HN protein. A vaccinia-T7 RNA polymerase expression system was used to express HN cDNAs in BHK-21 cells to determine the HN functions. Deglycosylation was treated with PGNase F digestion. The formation of HN-F protein complexes was determined by the coimmunoprecipitation assay. <b><i>Results:</i></b> Each HR-mutated protein interfered with fusion and the HN-F interaction. The G4-mutated protein not only impaired fusion and HN-F interaction but also decreased activities in cell fusion promotion, hemadsorption and neuraminidase. <b><i>Conclusions:</i></b> It is assumed that two different mechanisms for mutations in these two regions are responsible for the decreased fusion promotion activity and the reduced ability of interaction with F protein. Mutations in the HRs impair fusion and HN-F interaction by altering the transmission of a signal from the globular domain to the F-specific region in the stalk, but the G4 mutation modulates fusion and HN-F interaction by the misfolding of some important structures

Supplementary Material for: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31

<p>To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide single nucleotide polymorphism array. Palau has unique features advantageous for this study: due to its population history, Palauans are substantially interrelated; affected individuals often, but not always, cluster in families; and we have essentially complete ascertainment of affected individuals. To localize risk variants to genomic regions, we evaluated long-shared haplotypes, ≥10 Mb, identifying clusters of affected individuals who share such haplotypes. This extensive sharing, typically identical by descent, was significantly greater in cases than population controls, even after controlling for relatedness. Several regions of the genome exhibited substantial excess of shared haplotypes for affected individuals, including 3p21, 3p12, 4q28, and 5q23-q31. Two of these regions, 4q28 and 5q23-q31, showed significant linkage by traditional LOD score analysis and could harbor variants of more sizeable risk for psychosis or a multiplicity of risk variants. The pattern of haplotype sharing in 4q28 highlights <i>PCDH10</i>, encoding a cadherin-related neuronal receptor, as possibly involved in risk.</p