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Stress granules (SGs) are cytoplasmic aggregates formed upon stress when untranslated messenger ribonucleoproteins accumulate in the cells. In a green fluorescent protein library screening of the fission yeast SG proteins, Puf2 of the PUF family of RNA-binding proteins was identified that is required for SG formation after deprivation of glucose. Accordingly, the puf2 mutant is defective in recovery from glucose starvation with a much longer lag to reenter the cell cycle. In keeping with these results, Puf2 contains several low-complexity and intrinsically disordered protein regions with a tendency to form aggregates and, when overexpressed, it represses translation to induce aggregation of poly(A) binding protein Pabp, the signature constituent of SGs. Intriguingly, overexpression of Puf2 also enhances the structure of processing bodies (PBs), another type of cytoplasmic RNA granule, a complex of factors involved in mRNA degradation. In this study, we demonstrate a function of the fission yeast PB in SG formation and show Puf2 may provide a link between these two structures. [ABSTRACT FROM AUTHOR]

Aminoacyl-tRNA synthetase cofactors play important roles in coordinating aminoacylation and translation. In this study, we describe an additional function of the fission yeast aminoacyl-tRNA synthetase cofactor 1 (Asc1) in translation. We found that Asc1 directly binds and stabilizes the interaction between small ribosomal protein Rps0A/uS2 and eukaryotic initiation factor 3a (eIF3a). In the absence of Asc1, the interaction between eIF3a and Rps0A/uS2 was compromised. The interaction between Rps0A/uS2 and eIF3a mediated the 40S ribosomal subunit binding of eIF3 in 43S preinitiation complex formation to stimulate translation initiation. Keeping with this idea, in an asc1 mutant, the association of mRNA with the 40S ribosomal subunit was defective and protein synthesis was compromised. To show that Asc1 is directly involved in translation, we demonstrate that the addition of recombinant Asc1 is able to rescue the translation defect of the asc1 mutant in a cellfree system. Furthermore, this function of Asc1 is likely to be evolutionarily conserved, as a similar interaction with eIF3a and Rps0A/uS2 could be identified in the budding yeast Saccharomyces cerevisiae and human aminoacyl-tRNA synthetase cofactors. Together, these results identify a function of aminoacyl-tRNA synthetase cofactors in translation preinitiation complex formation, which adds significantly to the expanded functions associated with aminoacyl-tRNA synthetases and their cofactors. [ABSTRACT FROM AUTHOR]

VEGF stimulates the formation of new blood vessels by inducing endothelial cell (EC) proliferation and migration. Brefeldin A (BFA)-inhibited guanine nucleotide-exchange protein (BIG)1 and 2 accelerate the replacement of bound GDP with GTP to activate ADP-ribosylation factor (Arf)1, which regulates vesicular transport between the Golgi and plasma membrane. Although it has been reported that treating cells with BFA interferes with Arf1 activation to inhibit VEGF secretion, the role of BIG1 and BIG2 in VEGF trafficking and expression, EC migration and proliferation, and vascular development remains unknown. Here, we found that inactivation of Arf1 reduced VEGF secretion but did not affect the levels of VEGF protein. Interestingly, however, BIG1 and BIG2 knockdown significantly decreased the levels of VEGF mRNA and protein in glioblastoma U251 cells and HUVECs. Furthermore, depletion of BIG1 and BIG2 inhibited HUVEC angiogenesis by diminishing cell migration. Angioblast migration and intersegmental vessel sprouting were also impaired when the BIG2 homolog, Arf guanine nucleotide exchange factor (arfgef)2, was knocked down in zebrafish with endothelial expression of green fluorescent protein (GFP). Depletion of arfgef2 by clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) also caused defects in vascular development of zebrafish embryos. Taken together, these data reveal that BIG1 and BIG2 participate in endothelial cell angiogenesis. [ABSTRACT FROM AUTHOR]

Autophagy is essential for maintaining cellular homeostasis and survival under various stress conditions. Autophagy-related gene 9 (Atg9) encodes a multipass transmembrane protein thought to act as a membrane carrier for forming autophagosomes. However, the molecular regulation and physiological importance of Atg9 in animal development remain largely unclear. Here, we generated Atg9 null mutant flies and found that loss of Atg9 led to shortened lifespan, locomotor defects, and increased susceptibility to stress. Atg9 loss also resulted in aberrant adult midgut morphology with dramatically enlarged enterocytes. Interestingly, inhibiting the TOR signaling pathway rescued the midgut defects of the Atg9 mutants. In addition, Atg9 interacted with PALS1-associated tight junction protein (Patj), which associates with TSC2 to regulate TOR activity. Depletion of Atg9 caused a marked decrease in TSC2 levels. Our findings revealed an antagonistic relationship between Atg9 and TOR signaling in the regulation of cell growth and tissue homeostasis. [ABSTRACT FROM AUTHOR]

Background: Ribonuclease-L (RNase-L) was known to be a ubiquitous enzyme involved in several cellular functions, especially innate immunity. It was recently shown to participate in adipogenesis in rodents. Here, we developed a method to measure serum levels of RNase-L and analyzed the relationship between RNase-L and metabolic syndrome (MetS). Methods: A total of 396 subjects were recruited from a health check-up program. An in-house RNase-L immunoassay was developed. The serum RNase-L levels of these subjects were measured, and the association of MetS-related factors with RNase-L levels was assessed. Results: The mean serum level of RNase-L of the subjects with MetS were lower than those without (16.5 ± 6.4 vs. 18.4 ± 8.0 µg/ml, P = 0.018). The subjects with central obesity, elevated blood pressure, or impaired fasting glucose also had lower serum RNase-L levels in comparison to those without. In multivariate linear regression analysis, diastolic blood pressure (β = -0.129, P = 0.024) and high-density lipoprotein cholesterol (HDL-C) (β = 0.127, P = 0.036) were related to serum RNase-L. For every 5 μg/ml increase in serum RNase-L levels, it is associated with a reduced risk of MetS (OR 0.83, 95% CI 0.71-0.98, P = 0.028), central obesity (OR 0.82, 95% CI 0.71-0.94, P = 0.005), or low HDL-C (OR 0.86, 95% CI 0.74-1.00, P = 0.042). Moreover, age is inversely related to serum RNase-L levels in various analyses. Conclusions: The serum RNase-L levels were inversely associated with MetS, unfavorable metabolic profiles, and age. [ABSTRACT FROM AUTHOR]

Background: A computationally efficient tool is required for a genome-wide gene-gene interaction analysis that tests an extremely large number of single-nucleotide polymorphism (SNP) interaction pairs in genome-wide association studies (GWAS). Current tools for GWAS interaction analysis are mainly developed for unrelated case-control samples. Relatively fewer tools for interaction analysis are available for complex disease studies with family-based design, and these tools tend to be computationally expensive. Results: We developed a fast gene-gene interaction test, GCORE-sib, for discordant sib pairs and implemented the test into an efficient tool. We used simulations to demonstrate that the GCORE-sib has correct type I error rates and has comparable power to that of the regression-based interaction test. We also showed that the GCORE-sib can run more than 10 times faster than the regression-based test. Finally, the GCORE-sib was applied to a GWAS dataset with approximately 2,000 discordant sib pairs, and the GCORE-sib finished testing 19,368,078,382 pairs of SNPs within 6 days. Conclusions: An efficient gene-gene interaction tool for discordant sib pairs was developed. It will be very useful for genome-wide gene-gene interaction analysis in GWAS using discordant sib pairs. The tool can be downloaded for free at http://gcore-sib.sourceforge.net. [ABSTRACT FROM AUTHOR]

Motivation: Several efficient gene-gene interaction tests have been developed for unrelated case- control samples in genome-wide association studies (GWAS), making it possible to test tens of billions of interaction pairs of single-nucleotide polymorphisms (SNPs) in a reasonable timeframe. However, current family-based gene-gene interaction tests are computationally expensive and are not applicable to genome-wide interaction analysis. Results: We developed an efficient family-based gene-gene interaction test, GCORE, for trios (i.e. two parents and one affected sib). The GCORE compares interlocus correlations at two SNPs between the transmitted and non-transmitted alleles. We used simulation studies to compare the statistical properties such as type I error rates and power for the GCORE with several other family-based interaction tests under various scenarios. We applied the GCORE to a family-based GWAS for autism consisting of approximately 2000 trios. Testing a total of 22 471 383 013 interaction pairs in the GWAS can be finished in 36 h by the GCORE without large-scale computing resources, demonstrating that the test is practical for genome-wide gene-gene interaction analysis in trios. [ABSTRACT FROM AUTHOR]

Background: Genome-wide association studies (GWAS) have become a common approach to identifying single nucleotide polymorphisms (SNPs) associated with complex diseases. As complex diseases are caused by the joint effects of multiple genes, while the effect of individual gene or SNP is modest, a method considering the joint effects of multiple SNPs can be more powerful than testing individual SNPs. The multi-SNP analysis aims to test association based on a SNP set, usually defined based on biological knowledge such as gene or pathway, which may contain only a portion of SNPs with effects on the disease. Therefore, a challenge for the multi-SNP analysis is how to effectively select a subset of SNPs with promising association signals from the SNP set. Results: We developed the Optimal P-value Threshold Pedigree Disequilibrium Test (OPTPDT). The OPTPDT uses general nuclear families. A variable p-value threshold algorithm is used to determine an optimal p-value threshold for selecting a subset of SNPs. A permutation procedure is used to assess the significance of the test. We used simulations to verify that the OPTPDT has correct type I error rates. Our power studies showed that the OPTPDT can be more powerful than the set-based test in PLINK, the multi-SNP FBAT test, and the p-value based test GATES. We applied the OPTPDT to a family-based autism GWAS dataset for gene-based association analysis and identified MACROD2-AS1 with genome-wide significance (p-value= 2.5 × 10-6). Conclusions: Our simulation results suggested that the OPTPDT is a valid and powerful test. The OPTPDT will be helpful for gene-based or pathway association analysis. The method is ideal for the secondary analysis of existing GWAS datasets, which may identify a set of SNPs with joint effects on the disease. [ABSTRACT FROM AUTHOR]

Viral proteins assemble into homopolymers in the infected cells and have a role as diffusion-amplifier for ions across subcellular membranes. The homopolymer of hepatitis C virus, protein p7 of strain 1a, which is known to form channels, is used to investigate the dynamics of physiological relevant ions, Na+, K+, Cl- and Ca2+ in the vicinity of the protein bundle. The protein bundle is generated by a combination of docking approach and molecular dynamics (MD) simulations. Ion dynamics are recorded during multiple 200 ns MD simulations of 1 M solutions. His-17 is found to point into the lumen of the pore. Protonation of this residue allows Cl-ions to enter the pore while in its unprotonated state Ca-ions are found within the pore as well. Applied voltage identifies large Cl-ion currents from the site of the loop passing through the pore. Rectification of the current of the Cl-ions is observed. [ABSTRACT FROM AUTHOR]

Labile Zn fingers (Zfs) in proteins contain Zn-bound thiolates that can react with electrophilic agents, causing Zn2+ ejection and protein unfolding. Such labile Zfs have been shown to be Cys4 or Cys3His cores whose Zn-bound Cys have no hydrogen bonds. Our aim here is to identify labile Zfs in proteins that are promising drug targets using these features. To prove the strategy used, we showed that five proteins with predicted labile Zfs reacted with Zn-ejecting agents, whereas five proteins with no or inert Zfs did not. The comprehensive set of labile Zfs provides new drug targets and guidelines to redesign Znejecting compounds with improved specificity. [ABSTRACT FROM AUTHOR]

TDP-43 is the major pathological protein identified in the cellular inclusions in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The pathogenic forms of TDP-43 are processed C-terminal fragments containing a truncated RNA-recognition motif (RRM2) and a glycine-rich region. Although extensive studies have focused on this protein, it remains unclear how the dimeric full-length TDP-43 is folded and assembled and how the processed C-terminal fragments are misfolded and aggregated. Here, using size-exclusion chromatography, pulldown assays, and small angle x-ray scattering, we show that the C-terminal-deleted TDP-43 without the glycine-rich tail is sufficient to form a head-to-head homodimer primarily via its N-terminal domain. The truncated RRM2, as well as two β-strands within the RRM2, form fibrils in vitro with a similar amyloid-negative staining property to those of TDP-43 pathogenic fibrils in diseases. In addition to the glycine-rich region, the truncated RRM2, but not the intact RRM2, plays a key role in forming cytoplasmic inclusions in neuronal cells. Our data thus suggest that the process that disrupts the dimeric structure, such as the proteolytic cleavage of TDP-43 within the RRM2 that removes the N-terminal dimerization domain, may produce unassembled truncated RRM2 fragments with abnormally exposed β-strands, which can oligomerize into high-order inclusions. [ABSTRACT FROM AUTHOR]

Background: Systemic lupus erythematosus (SLE) is a complex chronic autoimmune disease with no known cure. However, the regulatory mechanism of immunity-related genes is not fully understood in SLE. In order to explore new therapeutic targets, we used bioinformatical methods to analyze a series of data. Methods: After downloading and processing the data from Gene Expression Omnibus database, the differentially expressed genes of SLE were analyzed. CIBERSORT algorithm was used to analyze the immune infiltration of SLE. Based on single-cell RNA-sequencing data, the role of immune-related genes in SLE and its target organ (kidney) were analyzed. Key transcription factors affecting immune-related genes were identified. Cell-cell communication networks in SLE were analyzed. Results: In total, 15 hub genes and 4 transcription factors were found in the bulk data. Monocytes and macrophages in GSE81622 (SLE) showed more infiltration. There were four cell types were annotated in scRNA sequencing dataset (GSE135779), as follows T cells, monocyte, NK cells and B cells. Immunity-related genes were overexpressed in monocytes. Conclusion: The present study shows that immune-related genes affect SLE through monocytes and play an important role in target organ renal injury. [ABSTRACT FROM AUTHOR]

Cellular supply of deoxythymidine triphosphate (dTTP) is crucial for DNA replication and repair. Thymidylate kinase (TMPK) catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, which is an essential step for dTTP synthesis. Despite their major cellular localization in cytosol, TMPK and ribonucleotide reductase (RNR) are detected at DNA damage sites for local dNDP formation. Because deoxyuridine diphosphate is synthesized by RNR, the simultaneous recruitment of TMPK and RNR to DNA damage sites is critical for preventing deoxyuridine triphosphate-mediated toxic repair. This study investigates the mechanism responsible for the recruitment of TMPK to DNA damage sites. Our data demonstrate the requirement of ataxia telangiectasia mutated (ATM) kinase activity for TMPK recruitment to DNA lesion sites. Moreover, we find that TMPK is able to form the complex with histone acetyltransferase Tip60 and RNR. Inhibition of ATM kinase reduces the complex formation and TMPK phosphorylation. Our analysis further shows the presence of TMPK phosphorylation at serine 88, which is an ATM kinase consensus site. A phosphorylation-defective mutation at this site suppresses TMPK recruitment to DNA damage sites and the complex formation with Tip60. Finally, we provide evidence that this site is critical for the function of TMPK in DNA repair but not for catalytic activity. Together, these findings suggest that Tip60-ATM signaling has a functional contribution to the recruitment of TMPK to DNA damage sites, thereby increasing local dTTP synthesis for DNA repair. [ABSTRACT FROM AUTHOR]

A novel zwitterionic polymer ionic liquid functionalized magnetic nanospheres, shortly as Fe3O4@PCL-PILs, is synthesized by grafting ionic liquid VimCOOHBr onto polymer ε-caprolactone (PCL) modified magnetic nanospheres via esterification and surface-initiated free radical polymerization. This established synthesis strategy offers the obtained magnetic nanospheres with well-defined core-corona structure, compact grafting layer, favorable zwitterionic and negative-charged surface, and high magnetic susceptibility. The as-prepared Fe3O4@PCL-PILs nanospheres exhibit typical "zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC)" behaviors toward protein binding, and selectively adsorption of glycoprotein is achieved. The adsorption capacity of the magnetic nanospheres toward Immunoglobulin G is high up to 1136.4 mg g-1, and the captured Immunoglobulin G could be efficiently recovered by using 0.5% NH3 H2O (v/v) as stripping reagent, providing a recovery of 80.5%. Fe3O4@PCL-PILs nanospheres are then employed as sorbent for the selective isolation of Immunoglobulin G from human whole blood, obtaining high-purity Immunoglobulin G as demonstrated by polyacrylamide gel electrophoresis assays. [ABSTRACT FROM AUTHOR]

The article presents animal studies suggesting that the apolipoprotein E ε4 (APOEε4) allele as a culprit of early microglial activation in Alzheimer's disease (AD). It mentions the testing of the association between APOEε4 status and microglial activation in living individuals across the aging and AD spectrum.

Sp1 is a ubiquitously expressed transcription factor that plays important role in the regulation of mamy GC-rich genes encoding for housekeeping proteins. The transcriptional activity of Sp1 is mainly determined by three elements: transcriptional activity, DNA binding ability and its protein stability. Previous studies, including our laboratory, have shown that the posttranslational modification are implicated in the regulation of Sp1 activity and modulates the expression of Sp1-target genes. The posttranslational modifications of Sp1 include phosphorylation, glycosylation, acetylation, ubiquitination and sumoylation. Our study has shown that the sumoylation site of Sp1 is located in the lysine 9 of Sp1 (778 amino acids). Moreover its target genes such as p21 and 12(S)-Lox were negatively regulated upon the sumoylation of Sp1. However, the underlying mechanism is still unclear. Our preliminary data showed that the protein level of sumoylation-deficient Sp1 (K9R) was higher compared to Sp1 wild type. However, the RNA and ubiquitination level of sumoylation-deficient Sp1 did not change. Therefore, we infer that sumoylation of Sp1 is involved with its degradation mechanism. The protein level of Sp1 decreased and negatively regulated target genes through the sumoylation of Sp1. At present, we will focus in elucidating the mechanism how the sumoylation-deficient Sp1 could increase its protein stability without affecting its ubiquitination level. Our preliminary results show that sumoylation of S11 increases the interaction with proteasome subunit Rpt6 and induces its degradation. [ABSTRACT FROM AUTHOR]

We previous reported that Sp1 recruits c-Jun to the promoter of the 12(S)-lipoxygenase gene in 12-myristate 13-acetate-treated cells. We now show that Sp1 that recruited HDAC1 to the Sp1/cJun complex was constitutively acetylated when cells were exposed to phorbol 12-myristate 13-acetate (PMA) (3 h). Prolonged stimulation of the cells with PMA (9 h), however, caused the dissociation of histone deacetylase 1 (HDAC1) and the deacetylation of Sp1, with the latter being able to recruit p300 that in turn caused the acetylation and dissociation of histone 3, thus enhancing the expression of 12(S)-lipoxygenase. We also overexpressed an Sp1 mutant (K703/A, lacking acetylation sites) in the cell and found that cells recruited more p300 and expressed more 12(S)-lipoxygenase. Taken together, our results indicated that Sp1 recruits HDAC1 together with c-Jun to the gene promoter, followed by deacetylation of Sp1 upon PMA treatment. p300 is then recruited to the gene promoter through the interaction with deacetylated Sp1 to acetylate histone 3, leading to the enhancement of the expression of 12(S)-lipoxygenase. [ABSTRACT FROM AUTHOR]

Central blood pressure may be more closely associated with cardiovascular events than peripheral blood pressure. The aim of the present study was to investigate central blood pressure responses to exercise. Apparently healthy 18 subjects were enrolled in the study (38±6 years) and changes in central and brachial blood pressure were recorded in response to ergometer and hand-grip exercises. Central blood pressure was estimated using an automated device (Omron HEM-9000AI). Systolic brachial blood pressure was increased after both ergometer (from 119±10 to 172±16 mmHg;P<0.001) and hand-grip (from 118±8 to 122±9 mmHg; P=0.001) exercises, but central systolic blood pressure was increased only after hand-grip exercise (from 117±11 to 121±12 mmHg; P=0.002). The radial augmentation index was increased after hand-grip exercise, whereas ergometer exercise reduced this index. Heart rate was increased only after ergometer exercise. Thus, isometric, but not isotonic, exercise may increase central blood pressure in overall healthy subjects. The response of central blood pressure, which is a better index of cardiac load than peripheral blood pressure, to hand-grip exercise may be useful in evaluating cardiovascular risk. [ABSTRACT FROM AUTHOR]

Stock trading activities are always very popular in many countries. Generally, investors with various backgrounds have different preferences over the stocks they trade. In literature, a number of studies examine the institutions' holding preferences for certain stock characteristics when choosing the security portfolio. However, very few studies investigate the stock trading preferences of individual investors. In this paper, we focus on two factors which affect the portfolio choices of investors, which are stock characteristics and investor features. In particular, a self-organizing map (SOM) is used to group a certain number of clusters based on a chosen dataset. Then, the decision tree model is used to extract useful rules from the clusters which contain the most trading records in the sample. We find that if the investors are females, less wealthy, and make stock trades with lower frequencies, they will be more careful and conservative. On the other hand, if the investors are males, having a high level of wealth, and make stock trades very often, they tend to choose stocks with high EPS, high market-to-book, and high prices. [ABSTRACT FROM AUTHOR]

ATP-binding cassette transporter A1 (ABCA1), which promotes cholesterol efflux from cells and inhibits inflammatory responses, is highly expressed in the kidney. Research has shown that exendin-4, a glucagon-like peptide-1 receptor (GLP-1R) agonist, promotes ABCA1 expression in multiple tissues and organs; however, the mechanisms underlying exendin-4 induction of ABCA1 expression in glomerular endothelial cells are not fully understood. In this study we investigated the effect of exendin-4 on ABCA1 in glomerular endothelial cells of diabetic kidney disease (DKD) and the possible mechanism. We observed a marked increase in glomerular lipid deposits in tissues of patients with DKD and diabetic apolipoprotein E knock-out (apoE-/-) mice by Oil Red O staining and biochemical analysis of cholesterol. We found significantly decreased ABCA1 expression in glomerular endothelial cells of diabetic apoE-/- mice and increased renal lipid, cholesterol, and inflammatory cytokine levels. Exendin-4 decreased renal cholesterol accumulation and inflammation and increased cholesterol efflux by up-regulating ABCA1. In human glomerular endothelial cells, GLP-1R-mediated signaling pathways (e.g. Ca2+/ calmodulin-dependent protein kinase, cAMP/PKA, PI3K/AKT, and ERK1/2) were involved in cholesterol efflux and inflammatory responses by regulating ABCA1 expression. We propose that exendin-4 increases ABCA1 expression in glomerular endothelial cells, which plays an important role in alleviating renal lipid accumulation, inflammation, and proteinuria in mice with type 2 diabetes. [ABSTRACT FROM AUTHOR]

Rhodiola rosea L. (RRL) possesses a wide range of pharmacological properties, including lung-protective activity, and has been utilized in folk medicine for several 100 years. However, the lung-protective mechanism remains unclear. This study investigated the possible lung-protective activity mechanism of RRL in a pulmonary fibrosis (PF) rat model. Lung fibrotic injury was induced in Sprague-Dawley rats by single intratracheal instillation of saline containing bleomycin (BLM; 5 mg/kg). The rats were administered 125, 250, or 500 mg/kg of a 95% ethanol extract of RRL for 28 days. The animals were killed to detect changes in body weight, serum levels of glutathione (GSH) and total superoxide dismutase (T-SOD), as well as lung tissue hydroxyproline (HYP) content. Tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), and interleukin 6 (IL-6) levels were measured in bronchoalveolar lavage fluid (BALF) by enzyme-linked immunosorbent assay. Hematoxylin and eosin, Masson's trichrome, and immunohistochemical staining were performed to observe the histopathological changes in lung tissues. Additionally, target-related proteins were measured by Western blotting. RRL alleviated the loss of body weight induced by instilling BLM in PF rats, particularly at the 500 mg/kg per day dose. RRL reduced HYP (p < 0.01) and increased GSH and T-SOD contents. BALF levels of TNF-α, TGF-β1, and IL-6 decreased significantly in the RRL-treated groups. Expression levels of matrix metalloproteinase-9 (MMP-9) and -smooth muscle actin decreased significantly in a dose-dependent manner in response to RRL. Moreover, the levels of TGF-β1 and tissue inhibitor of metalloproteinase-1 in lung tissues also decreased in the RRL-treated groups. RRL alleviated BLM-induced PF in rats. Our results reveal that the protective effects of RRL against fibrotic lung injury in rats are correlated with its anti-inflammatory, antioxidative, and anti-fibrotic properties. MMP-9 may play important roles in BLM-induced PF. [ABSTRACT FROM AUTHOR]

Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 μg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (~15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 μg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression. [ABSTRACT FROM AUTHOR]

Background: Thyroid-stimulating hormone (TSH) and free thyroxine (FT4) reference intervals are essential for screening and diagnosing thyroid dysfunction during pregnancy. The aim of this study was to establish method- and trimester-specific TSH and FT4 reference intervals in pregnant Chinese women using the Beckman Coulter UniCel™ DxI 600. Methods: A cross-sectional dataset analysis was performed. A total of 3507 participants were recruited, and 2743 were eligible for analysis to set reference intervals. TSH, FT4, and thyroid peroxidase antibody (TPOAb) levels were analyzed with the Beckman Coulter UniCel ™ DxI 600 Access® immunoassay system. Ranges between the 2.5th and 97.5th percentiles were defined as reference intervals for TSH and FT4. Results: The calculated reference intervals for the first, second, and third trimesters were TSH: 0.06-3.13, 0.07-4.13 and 0.15-5.02 mIU/L, respectively, and FT4: 8.72-15.22, 7 .10-13.55 and 6.16-12.03 pmol/L, respectively. Conclusions: Our reference intervals for TSH and FT4 are distinct from the ranges reported in the DxI 600 instruction manual and previously reported data, confirming the importance of method-specific reference intervals. [ABSTRACT FROM AUTHOR]

Epidermal growth factor receptor (EGFR) is a heavily glycosylated transmembrane receptor tyrosine kinase. Upon EGF-binding, EGFR undergoes conformational changes to dimerize, resulting in kinase activation and autophosphorylation and downstream signaling. Tyrosine kinase inhibitors (TKIs) have been used to treat lung cancer by inhibiting EGFR phosphorylation. Previously, we demonstrated that EGFR sialylation suppresses its dimerization and phosphorylation. In this report, we further investigated the effect of sialylation on the phosphorylation profile of EGFR in TKIsensitive and TKI-resistant cells. Sialylation was induced in cancer progression to inhibit the association of EGFR with EGF and the subsequent autophosphorylation. In the absence of EGF the TKIresistant EGFR mutant (L858R/T790M) had a higher degree of sialylation and phosphorylation at Y1068, Y1086, and Y1173 than the TKI-sensitive EGFR. In addition, although sialylation in the TKIresistant mutants suppresses EGFR tyrosine phosphorylation, with the most significant effect on the Y1173 site, the sialylation effect is not strong enough to stop cancer progression by inhibiting the phosphorylation of these three sites. These findings were supported further by the observation that the L858R/T790M EGFR mutant, when treated with sialidase or sialyltransferase inhibitor, showed an increase in tyrosine phosphorylation, and the sensitivity of the corresponding resistant lung cancer cells to gefitinib was reduced by desialylation and was enhanced by sialylation. [ABSTRACT FROM AUTHOR]

We study interference and interactions in an InAs/InAsSb two-dimensional electron system. In such a system, spin-orbit interactions are shown to be strong, which result in weak antilocalization (WAL) and thereby positive magnetoresistance around zero magnetic field. After suppressing WAL by the magnetic field, we demonstrate that classical positive magnetoresistance due to spin-orbit coupling plays a role. With further increasing the magnetic field, the system undergoes a direct insulator-quantum Hall transition. By analyzing the magnetotransport behavior in different field regions, we show that both electron-electron interactions and spin-related effects are essential in understanding the observed direct transition. [ABSTRACT FROM AUTHOR]

Methodologies to enrich heterogeneous types of phosphopeptides are critical for comprehensive mapping of the under-explored phosphoproteome. Taking advantage of the distinct binding affinities of Ga3+ and Fe3+ for phosphopeptides, we designed a metal-directed immobilized metal ion affinity chromatography for the sequential enrichment of phosphopeptides. In Raji B cells, the sequential Ga3+-Fe3+-immobilized metal affinity chromatography (IMAC) strategy displayed a 1.5-3.5- fold superior phosphoproteomic coverage compared to single IMAC (Fe3+, Ti4+, Ga3+, and Al3+). In addition, up to 92% of the 6283 phosphopeptides were uniquely enriched in either the first Ga3+-IMAC (41%) or second Fe3+-IMAC (51%). The complementary properties of Ga3+ and Fe3+ were further demonstrated through the exclusive enrichment of almost all of 1214 multiply phosphorylated peptides (99.4%) in the Ga3+- IMAC, whereas only 10% of 5069 monophosphorylated phosphopeptides were commonly enriched in both fractions. The application of sequential Ga3+-Fe3+-IMAC to human lung cancer tissue allowed the identification of 2560 unique phosphopeptides with only 8% overlap. In addition to the above-mentioned mono- and multiply phosphorylated peptides, this fractionation ability was also demonstrated on the basic and acidic phosphopeptides: acidophilic phosphorylation sites were predominately enriched in the first Ga3+-IMAC (72%), while Pro-directed (85%) and basophilic (79%) phosphorylation sites were enriched in the second Fe3+-IMAC. This strategy provided complementary mapping of different kinase substrates in multiple cellular pathways related to cancer invasion and metastasis of lung cancer. Given the fractionation ability and ease of tip preparation of this Ga3+-Fe3+-IMAC, we propose that this strategy allows more comprehensive characterization of the phosphoproteome both in vitro and in vivo. [ABSTRACT FROM AUTHOR]

Four H7N3 avian influenza viruses (AIVs) were isolated from domestic ducks in live-poultry markets in Zhejiang Province, Eastern China, in 2011. All viruses were characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight viral genes showed that the viruses clustered in the Eurasian lineage of influenza viruses. The hemagglutinin cleavage site of all viruses indicated that the four strains were low-pathogenic avian influenza viruses. [ABSTRACT FROM AUTHOR]

This study describes the characterization of seven H5N1 avian influenza viruses from domestic ducks in Eastern China in 2011. Phylogenetic analysis showed these viruses were closely related to an H5N1 virus circulating in wild birds in Hong Kong. Some characteristics of these viruses were similar to those of an H5N1 strain that circulated in China and Vietnam (2003-2004). The virulence of three isolates was examined in chickens and mice, and they were found to be highly pathogenic in chickens but showed low pathogenicity in mice. These results suggest that continued H5N1 surveillance in poultry should be used as an early warning system for avian influenza outbreaks. [ABSTRACT FROM AUTHOR]

Endonuclease G (EndoG) is a mitochondrial protein that traverses to the nucleus and participates in chromosomal DNA degradation during apoptosis in yeast, worms, flies, and mammals. However, it remains unclear how EndoG binds and digests DNA. Here we show that the Caenorhabditis elegans CPS-6, a homolog of EndoG, is a homodimeric Mg2+-dependent nuclease, binding preferentially to G-tractDNAin the optimum low salt buffer at pH 7. The crystal structure of CPS-6 was determined at 1.8 Å resolution, revealing a mixed αβ topology with the two ββα-metal finger nuclease motifs located distantly at the two sides of the dimeric enzyme. A structural model of the CPS-6-DNA complex suggested a positively charged DNAbinding groove near the Mg2+-bound active site. Mutations of four aromatic and basic residues: Phe122, Arg146, Arg156, and Phe166, in the protein-DNA interface significantly reduced the DNA binding and cleavage activity of CPS-6, confirming that these residues are critical for CPS-6-DNA interactions. In vivo transformation rescue experiments further showed that the reduced DNase activity of CPS-6 mutants was positively correlated with its diminished cell killing activity in C. elegans. Taken together, these biochemical, structural, mutagenesis, and in vivo data reveal a molecular basis of how CPS-6 binds and hydrolyzes DNA to promote cell death. [ABSTRACT FROM AUTHOR]

Background: Neurons and astrocytes are generated from common neural precursors, yet neurogenesis precedes astrocyte formation during embryogenesis. The mechanisms of neural development underlying suppression and de-suppression of differentiation- related genes for cell fate specifications are not well understood. Methodology/Principal Findings: By using an in vitro system in which NTera-2 cells were induced to differentiate into an astrocyte-like lineage, we revealed a novel role for Sin3A in maintaining the suppression of GFAP in NTera-2 cells. Sin3A coupled with MeCP2 bound to the GFAP promoter and their occupancies were correlated with repression of GFAP transcription. The repression by Sin3A and MeCP2 may be an essential mechanism underlying the inhibition of cell differentiation. Upon commitment toward an astrocyte-like lineage, Sin3A- MeCP2 departed from the promoter and activated STAT3 simultaneously bound to the promoter and exon 1 of GFAP; meanwhile, olig2 was exported from nuclei to the cytoplasm. This suggested that a three-dimensional or higher-order structure was provoked by STAT3 binding between the promoter and proximal coding regions. STAT3 then recruited CBP/p300 to exon 1 and targeted the promoter for histone H3K9 and H3K14 acetylation. The CBP/p300-mediated histone modification further facilitates chromatin remodeling, thereby enhancing H3K4 trimethylation and recruitment of RNA polymerase II to activate GFAP gene transcription. Conclusions/Significance: These results provide evidence that exchange of repressor and activator complexes and epigenetic modifications are critical strategies for cellular differentiation and lineage-specific gene expression. [ABSTRACT FROM AUTHOR]

There has been considerable progress in second language (L2) research at the syntax—semantics interface addressing how syntax can inform phrasal semantics, in terms of interpretive correlates of word order (Slabakova, 2008). This article provides evidence of a flow of information ostensibly in the opposite direction, from meaning to grammar, at the interface between lexical semantics and syntax. It is argued that there is a functional hierarchy of modifiers in the domain of adpositions, which enables the linguistic elaboration of trajectories, but that not all languages lexicalize all types. This study examines whether L2 learners of English are able to overcome the poverty of the stimulus and recruit the relevant functional categories despite their absence in the first language (L1). Modifiers were taught to learners individually, but never in combination. A computer-animated narrative was designed in order to create felicitous contexts for combinations of modifiers, and preference and grammaticality judgment tasks were administered to 121 students from various L1 backgrounds, as well as 20 native speakers. Accuracy scores were remarkably targetlike on binary combinations of modifiers (1) across proficiency levels, (2) across L1s, and (3) across the two tasks, revealing that with the semantics of modifiers in place, the syntactic hierarchy is naturally manifested. [ABSTRACT FROM AUTHOR]

Background: Ras is frequently mutated in a variety of human cancers, including lung cancer, leading to constitutive activation of MAPK signaling. Despite decades of research focused on the Ras oncogene, Ras-targeted phosphorylation events and signaling pathways have not been described on a proteome-wide scale. Methodology/Principal Findings: By functional phosphoproteomics, we studied the molecular mechanics of oncogenic Ras signaling using a pathway-based approach. We identified Ras-regulated phosphorylation events (n = 77) using label-free comparative proteomics analysis of immortalized human bronchial epithelial cells with and without the expression of oncogenic Ras. Many were newly identified as potential targets of the Ras signaling pathway. A majority (∼60%) of the Rastargeted events consisted of a [pSer/Thr]-Pro motif, indicating the involvement of proline-directed kinases. By integrating the phosphorylated signatures into the Pathway Interaction Database, we further inferred Ras-regulated pathways, including MAPK signaling and other novel cascades, in governing diverse functions such as gene expression, apoptosis, cell growth, and RNA processing. Comparisons of Ras-regulated phosphorylation events, pathways, and related kinases in lung cancer-derived cells supported a role of oncogenic Ras signaling in lung adenocarcinoma A549 and H322 cells, but not in large cell carcinoma H1299 cells. Conclusions/Significance: This study reveals phosphorylation events, signaling networks, and molecular functions that are regulated by oncogenic Ras. The results observed in this study may aid to extend our knowledge on Ras signaling in lung cancer. [ABSTRACT FROM AUTHOR]

In this paper, we report on a new dataset based on expert surveys carried out in nearly 90 countries around the world. This dataset helps to overcome the limited existence of cross-national data on democratic linkage mechanisms between citizens and politicians, especially with regard to contingent exchange of targeted goods for electoral support as most studies that have examined democratic accountability have a narrow geographic focus or are single-case studies. The report outlines the various methodological challenges faced in implementing the survey and in interpreting its results, as well as steps taken to determine the quality of the data. This preliminary analysis of results from the survey lends support that the various indicators developed from the survey are reliable and valid measures of political parties' actual organizational practices, linkage mechanisms, and policy orientations. [ABSTRACT FROM AUTHOR]

Infecting about one-half of the global human population, Helicobacter pylori is well established as the primary cause of gastritis, duodenal ulcer, and gastric cancer. Currently there is no clear information regarding if and how host cells interact with H. pylori, and if such interactions are dependent on the type of gastric disease. Using fluorescently labeled fucose-containing glycoconjugates, we provide evidence observing both the uptake of l-fucose from gastric cancer cells to H. pylori and that human α-l-fucosidase 2 (FUCA2) is secreted only under coculture conditions (i.e., host cells infected with H. pylori). Upon depletion of FUCA2 by RNA interference and detection of translocated CagA (a virulence factor of H. pylori) in host cells, FUCA2 was found to be essential for H. pylori adhesion, in particular to the gastric cancer- and duodenal ulcer-specific strains. Additionally FUCA2 was shown to significantly enhance the expression of Lewis x antigen in H. pylori, which is critical for bacterial cell adhesion in the pathogenesis and defense strategy to escape host surveillance. These findings not only demonstrate an important connection between FUCA2 and the adhesion, growth, and pathogenicity of H. pylori, but also support the idea that FUCA2 is a potential target for clinical diagnosis and therapeutic intervention of H. pylori-related diseases. [ABSTRACT FROM AUTHOR]

The Giardia lamblia cyst wall is required for survival outside the host and infection. Three cyst wall protein (cwp) genes identified to date are highly up-regulated during encystation. However, little is known of the molecular mechanisms governing their gene regulation. Messenger RNAs containing premature stop codons are rapidly degraded by a nonsensemediated mRNA decay (NMD) system to avoid production of non-functional proteins. In addition to RNA surveillance, NMD also regulates thousands of naturally occurring transcripts through a variety of mechanisms. It is interesting to know the NMD pathway in the primitive eukaryotes. Previously, we have found that the giardial homologue of a conserved NMD factor, UPF1, may be functionally conserved and involved in NMD and in preventing nonsense suppression. In this study, we tested the hypothesis that NMD factors can regulate some naturally occurring transcripts in G. lamblia. We found that overexpression of UPF1 resulted in a significant decrease of the levels of CWP1 and cyst formation and of the endogenous cwp1-3, and myb2 mRNA levels and stability. This indicates that NMD could contribute to the regulation of the cwp1-3 and myb2 transcripts, which are key to G. lamblia differentiation into cyst. Interestingly, we also found that UPF1 may be involved in regulation of eight other endogenous genes, including up-regulation of the translation elongation factor gene, whose product increases translation which is required for NMD. Our results indicate that NMD factor could contribute to the regulation of not only nonsense containing mRNAs, but also mRNAs of the key encystation-induced genes and other endogenous genes in the early-diverging eukaryote, G. lamblia. [ABSTRACT FROM AUTHOR]

A methodology is presented for assessing the toxicity of chemical substances through their inhibitory action toward the Pseudomonas initial oxygen uptake (PIOU) rate. The current studies reveal that the PIOU assay is rapid, cost-efficient, and easy to perform. The oxygen uptake rate was found to be associated with a putative benzoate transporter and highly dependent on benzoate concentration. The putative benzoate transporter has been shown to follow Michaelis-Menten kinetics. Most phenols were found to be noncompetitive inhibitors of the benzoate transporter. The inhibition constant (Ki) of these noncompetitive inhibitors can be related to the concentration causing 50% oxygen uptake inhibition in Pseudomonas putida. Modeling these data by using the response--surface approach leads to the development of a quantitative structure--activity relationship (QSAR) for the toxicity of phenols ((1/Ki) = -0.435 (±0.038) lowest-unoccupied-molecular orbital + 0.517 (±0.027)log KOW - 2.340 (±0.068), n = 49, r² = 0.930, s = 0.107, radj⊃2 = 0.926, F = 303.1 ). A comparison of QSAR models derived from the Ki data of the PIOU method and the toxicity data of 40-h Tetrahymena pyrifomis growth inhibition assay (Tetratox) indicated that there was a high correlation between the two approaches (r² = 0.925). [ABSTRACT FROM AUTHOR]