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Showing 100 Latest Publications
TitleDate Created
Five-Year Antibody Persistence and Booster Response to a Single Dose of Meningococcal A, C, W, and Y Tetanus Toxoid Conjugate Vaccine in Adolescents and Young Adults: An Open, Randomized Trial.Monday, August 03, 2015
Baxter R, Baine Y, Kolhe D, Baccarini CI, Miller JM, Van der Wielen M,
The Pediatric infectious disease journal. 1-Aug-2015
Before the booster dose administration at Year 5, hSBA-MenC, -MenW and -MenY antibody persistence was observed in most participants. However, only ≥37.5% of MenACWY-TT and 44.4% of MenACWY-DT recipients retained hSBA-MenA titers ≥1:8. MenACWY-TT booster doses elicited robust anamnestic responses, irrespective of the priming vaccine, and were well-tolerated.
Cdk5 promotes DNA replication stress checkpoint activation through RPA-32 phosphorylation, and impacts on metastasis free survival in breast cancer patients.Monday, August 03, 2015
Chiker S, Pennaneach V, Loew D, Dingli F, Biard D, Cordelières FP, Gemble S, Vacher S, Bieche I, Hall J, Fernet M,
Cell cycle (Georgetown, Tex.). 3-Aug-2015
Cyclin dependent kinase 5 (Cdk5) is a determinant of PARP inhibitor and ionizing radiation (IR) sensitivity. Here we show that Cdk5-depleted (Cdk5-shRNA) HeLa cells show higher sensitivity to S-phase irradiation, chronic hydroxyurea exposure, and 5-fluorouracil and 6-thioguanine treatment, with hydroxyurea and IR sensitivity also seen in Cdk5-depleted U2OS cells. As Cdk5 is not directly implicated in DNA strand break repair we investigated in detail its proposed role in the intra-S checkpoint activation. Whilst Cdk5-shRNA HeLa cells showed altered basal S-phase dynamics with slower replication velocity and fewer active origins per DNA megabase, checkpoint activation was impaired after a hydroxyurea block. Cdk5 depletion was associated with reduced priming phosphorylations of RPA32 serines 29 and 33 and SMC1-Serine 966 phosphorylation, lower levels of RPA serine 4 and 8 phosphorylation and DNA damage measured using the alkaline Comet assay, gamma-H2AX signal intensity, RPA and Rad51 foci, and sister chromatid exchanges resulting in impaired intra-S checkpoint activation and subsequently higher numbers of chromatin bridges. In vitro kinase assays coupled with mass spectrometry demonstrated the Cdk5 can carry out the RPA32 priming phosphorylations on serines 23, 29, and 33 necessary for this checkpoint activation. In addition we found an association between lower Cdk5 levels and with longer metastasis free survival in breast cancer patients and survival in Cdk5-depleted breast tumor cells after treatment with IR and a PARP inhibitor. Taken together, these results show that Cdk5 is necessary for basal replication and replication stress checkpoint activation and highlight clinical opportunities to enhance tumor cell killing.
A Universal Strategy to Engineer Catalytic DNA Hairpin Assemblies for Protein Analysis.Monday, August 03, 2015
Tang Y, Lin Y, Yang X, Wang Z, Le XC, Li F,
Analytical chemistry. 3-Aug-2015
Nucleic acids can be programmed into enzyme-free catalytic DNA circuits (CDCs) to carry out various functions ranging from DNA computing to signal amplifications for biosensing. Catalytic hairpin assembly (CHA), the accelerated hybridization between two DNA hairpins catalyzed by a DNA input, is one of the most widely studied and used CDCs for amplified detection of nucleic acids and small molecules. So far, it is still challenging to expand CHAs to proteins largely due to the lack of a universal strategy to construct protein-responsive CHAs. To address this challenge, we demonstrate that rationally designed protein-DNA binding complex can be used as an effective catalyst to accelerate CHA reactions. Based on this principle, we developed specific CHAs for a number of important protein biomarkers, including human α-thrombin, human prostate specific antigen, and human epidermal growth factor receptor 2. Upon establishing this panel of protein-responsive CHAs, we further explore their potential applications to detect specific protein biomarkers from human serum samples and cancer cells.
Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease.Monday, August 03, 2015
Tremoulet AH, Dutkowski J, Sato Y, Kanegaye JT, Ling XB, Burns JC,
Pediatric research. 3-Aug-2015
After prospective validation, this 8-biomarker panel may improve the recognition of KD.Pediatric Research (2015); doi:10.1038/pr.2015.137.
Proton MR Spectroscopy for Diagnosis and Evaluation of Treatment Efficacy in Parkinson Disease.Monday, August 03, 2015
Mazuel L, Chassain C, Jean B, Pereira B, Cladière A, Speziale C, Durif F,
Radiology. 4-Aug-2015
Purpose To assess the neurochemical profile in the putamen of patients with parkinsonian syndromes undergoing L-3,4-dihydroxyphenylalanine (L-DOPA) treatment (drug-on) or after withdrawal of L-DOPA medication (drug-off) compared with healthy volunteers to identify dopaminergic therapy-sensitive biomarkers of Parkinson disease. Materials and Methods The local institutional review board approved the study, and all participants gave informed consent. A short echo-time (29 msec) single-voxel (1-cm(3)) proton (hydrogen 1 [(1)H]) magnetic resonance (MR) spectroscopic approach was used at 3 T to explore the metabolic profile in the putamen of patients with Parkinson disease. Spectra obtained from 20 healthy volunteers were blindly compared with spectra obtained from 20 patients with parkinsonian syndromes in drug-on and drug-off conditions in a randomized permuted block study to assess the accuracy of diagnostic biomarkers for Parkinson disease and efficacy of L-DOPA therapy. The statistical tests were two sided, with a type-I error set at α of .05. Random-effects models were used to compare healthy subjects and patients with parkinsonian syndromes in drug-on or drug-off conditions. Results Measured concentrations of putaminal total N-acetylaspartate (tNAA) (8.1 ± 0.2 vs 9.4 ± 0.4; P < .01), total creatine (tCr) (7.5 ± 0.2 vs 8.3 ± 0.3; P < .01), and myo-inositol (m-Ins) (3.8 ± 0.3 vs 5.6 ± 0.4; P < .001) were significantly lower in patients with parkinsonian syndromes in drug-off condition than in healthy volunteers. Moreover, L-DOPA therapy restored tNAA (9.1 ± 0.4 vs 8.1 ± 0.2; P < .01) and tCr (8.1 ± 0.3 vs 7.5 ± 0.2; P < .01) levels, whereas m-Ins levels remained unchanged. The combined glutamate and glutamine and choline showed no changes in drug-off or drug-on condition compared with those in control subjects. Conclusion tNAA, tCr, and m-Ins were identified as putative biomarkers of Parkinson disease in the putamen of patients. tNAA and tCr levels are responsive to L-DOPA therapy. (©) RSNA, 2015.
Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer.Monday, August 03, 2015
Zhao J, Liu Y, Zhang W, Zhou Z, Wu J, Cui P, Zhang Y, Huang G,
Cell cycle (Georgetown, Tex.). 3-Aug-2015
Gastric cancer remains a serious threat to public health with high incidence and mortality worldwide. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) play important roles in regulating gene expression and are involved in various pathological processes, including gastric cancer. To investigate the possible role of dysregulated lncRNAs in gastric cancer development, we performed lncRNA microarray and identified 3141 significantly differentially expressed lncRNAs in gastric cancer tissues. Next, some of deregulated lncRNAs were validated among about 60 paired gastric cancer specimens such as Linc00261, DKFZP434K028, RPL34-AS1, H19, HOTAIR and Linc00152. Our results found that the decline of DKFZP434K028 and RPL34-AS1, and the increased expression of Linc00152 positively correlated with larger tumor size. The high expression levels of HOTAIR were associated with lymphatic metastasis and poor differentiation. Since the biological roles of Linc00152 are largely unknown in gastric cancer pathogenesis, we assessed its functions by silencing its up-regulation in gastric cancer cells. We found that Linc00152 knockdown could inhibit cell proliferation and colony formation, promote cell cycle arrest at G1 phase, trigger late apoptosis, reduce the epithelial to mesenchymal transition (EMT) program, and suppress cell migration and invasion. Taken together, we delineate the gastric cancer lncRNA signature and demonstrate the oncogenic functions of Linc00152. These findings may have implications for developing lncRNA-based biomarkers for diagnosis and therapeutics for gastric cancer.
Culture and Isolation of Brain Tumor Initiating Cells.Tuesday, August 04, 2015
Vora P, Venugopal C, McFarlane N, Singh SK,
Current protocols in stem cell biology. 2015
Brain tumors are typically composed of heterogenous cells that exhibit distinct phenotypic characteristics and proliferative potentials. Only a relatively small fraction of cells in the tumor with stem cell properties, termed brain tumor initiating cells (BTICs), possess an ability to differentiate along multiple lineages, self-renew, and initiate tumors in vivo. This unit describes protocols for the culture and isolation BTICs. We applied culture conditions and assays originally used for normal neural stem cells (NSCs) in vitro to a variety of brain tumors. Using fluorescence-activated cell sorting for the neural precursor cell surface marker CD133/CD15, BTICs can be isolated and studied prospectively. Isolation of BTICs from GBM bulk tumor will enable examination of dissimilar morphologies, self-renewal capacities, tumorigenicity, and therapeutic sensitivities. As cancer is also considered a disease of unregulated self-renewal and differentiation, an understanding of BTICs is fundamental to understanding tumor growth. Ultimately, it will lead to novel drug discovery approaches that strategically target the functionally relevant BTIC population. © 2015 by John Wiley & Sons, Inc.
Adipose-Derived Mesenchymal Stem Cells Ameliorate Ulcerative Colitis Through miR-1236 Negatively Regulating the Expression of Retinoid-Related Orphan Receptor Gamma.Monday, August 03, 2015
Zhang Y, Jin Y, Lin Y, Lin LJ, Cao Y, Wang DX, Zheng CQ,
DNA and cell biology. 3-Aug-2015
Mesenchymal stem cells (MSCs) were reported to accelerate the curing of ulcerative colitis (UC). Altered expression of microRNAs (miRNAs) has recently revealed association with UC. However, the effect of adipose-derived MSCs (ASCs) on UC and the mechanism of how miRNAs regulate UC remain unclear. We investigated the effect of ASCs on 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced UC in rat colon tissues. qRT-PCR and immunofluorescence analyses were performed to monitor the expression of miR-1236 and its target molecule, retinoid-related orphan receptor γ (RORγ). Regulation of the expression of RORγ by miR-1236 was assessed using luciferase reporter construct assays and miR-1236 mimic transfection. The relationship between miR-1236 and RORγ was further investigated in HT29 cells induced by TNF-α. ASCs highly ameliorated UC and decreased the inflammation markers in rats with TNBS-induced UC. In addition, ASCs upregulated the expression of miR-1236 and decreased the expression of RORγ in the TNBS-induced rat model of UC. The luciferase reporter assay and bioinformatic analysis demonstrated that the expression of RORγ was directly targeted and regulated by miR-1236. Specifically, the expression of RORγ was suppressed by miR-1236 mimic and enhanced by miR-1236 inhibitor. Furthermore, we demonstrated that exogenous miR-1236 mimic could inhibit the expression of RORγ in HT29 cell induced by TNF-α. ASCs effectively alleviated UC in rats with the expression of miR-1236 alteration, and miR-1236 may play important roles in UC by downregulating the expression of RORγ.
Identification of novel putative-binding proteins for cellular prion protein and a specific interaction with the STIP1 homology and U-Box-containing protein 1.Monday, August 03, 2015
Gimenez AP, Richter LM, Atherino MC, Beirão BC, Fávaro C, Costa MD, Zanata SM, Malnic B, Mercadante AF,
Prion. 3-Aug-2015
Prion diseases involve the conversion of the endogenous cellular prion protein, PrP(C), into a misfolded infectious isoform, PrP(Sc). Several functions have been attributed to PrP(C), and its role has also been investigated in the olfactory system. PrP(C) is expressed in both the olfactory bulb (OB) and olfactory epithelium (OE) and the nasal cavity is an important route of transmission of diseases caused by prions. Moreover, Prnp-/- mice showed impaired behavior in olfactory tests. Given the high PrP(C) expression in OE and its putative role in olfaction, we screened a mouse OE cDNA library to identify novel PrP(C)-binding partners. Ten different putative PrP(C) ligands were identified, which were involved in functions such as cellular proliferation and apoptosis, cytoskeleton and vesicle transport, ubiquitination of proteins, stress response, and other physiological processes. In vitro binding assays confirmed the interaction of PrP(C) with STIP1 homology and U-Box containing protein 1 (Stub1) and are reported here for the first time. Stub1 is a co-chaperone with ubiquitin E3-ligase activity, which is associated with neurodegenerative diseases characterized by protein misfolding and aggregation. Physiological and pathological implications of PrP(C)-Stub1 interaction are under investigation. The PrP(C)-binding proteins identified here are not exclusive to the OE, suggesting that these interactions may occur in other tissues and play general biological roles. These data corroborate the proposal that PrP(C) is part of a multiprotein complex that modulates several cellular functions and provide a platform for further studies on the physiological and pathological roles of prion protein.
Challenges in the classification of fibrotic ILD.Monday, August 03, 2015
Bendstrup E, Maher TM, Manali ED, Wijsenbeek M,
Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG / World Association of Sarcoidosis and Other Granulomatous Disorders. 3-8-2015
According to current international guidelines the idiopathic interstitial pneumonias (IIPs) are grouped into three categories; major, rare, and unclassifiable. Idiopathic pulmonary fibrosis (IPF) is one of the major IIPs and has been recognised as a distinct clinical entity since 2001. This has led to significant advances in our understanding and treatment of the disease and to the identification of new therapeutic targets. While multidisciplinary team assessment yields a definite diagnosis in many cases of interstitial lung disease (ILD), 15-25% of patients remain unclassifiable. This can be due to inadequate clinical, pathological, or radiological data (e.g., where a biopsy is not performed) or because results of investigations show major discrepancies, overlapping features, or mixed patterns. Patients with unclassifiable disease tend to be of similar age to those with IPF and older than those with connective tissue disorders. Survival of patients with unclassifiable disease is intermediate between IPF and non-IPF ILD. There is no single recommended treatment for patients with unclassifiable disease. However, the ILD-GAP index has recently been validated in this group and can risk-stratify patients based on four easily measurable variables. "Disease behaviour classification" (DBC) is an alternative, pragmatic approach to managing patients with unclassifiable disease. The ILD-GAP index has been shown to provide strong prognostic information in these hard-to-treat patients. In the future, new diagnostic tools such as protein biomarkers may become available to help guide therapeutic decisions. (Sarcoidosis Vasc Diffuse Lung Dis 2015; 32; Suppl 1: 4-9).
Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma.Monday, August 03, 2015
Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PD, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dȩbniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze HJ, Dunning AM, Bishop JA, Demenais F, Amos CI, MacGregor S, Iles MM,
Nature genetics. 3-Aug-2015
Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.
Generation of Functional Cardiomyocytes from Efficiently Generated Human iPSCs and a Novel Method of Measuring Contractility.Monday, August 03, 2015
Rajasingh S, Thangavel J, Czirok A, Samanta S, Roby KF, Dawn B, Rajasingh J,
PloS one. 03-8-2015
Human induced pluripotent stem cells (iPSCs) derived cardiomyocytes (iCMCs) would provide an unlimited cell source for regenerative medicine and drug discoveries. The objective of our study is to generate functional cardiomyocytes from human iPSCs and to develop a novel method of measuring contractility of CMCs. In a series of experiments, adult human skin fibroblasts (HSF) and human umbilical vein endothelial cells (HUVECs) were treated with a combination of pluripotent gene DNA and mRNA under specific conditions. The iPSC colonies were identified and differentiated into various cell lineages, including CMCs. The contractile activity of CMCs was measured by a novel method of frame-by-frame cross correlation (particle image velocimetry-PIV) analysis. Our treatment regimen transformed 4% of HSFs into iPSC colonies at passage 0, a significantly improved efficiency compared with use of either DNA or mRNA alone. The iPSCs were capable of differentiating both in vitro and in vivo into endodermal, ectodermal and mesodermal cells, including CMCs with >88% of cells being positive for troponin T (CTT) and Gata4 by flow cytometry. We report a highly efficient combination of DNA and mRNA to generate iPSCs and functional iCMCs from adult human cells. We also report a novel approach to measure contractility of iCMCs.
Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques.Monday, August 03, 2015
Santra S, Tomaras GD, Warrier R, Nicely NI, Liao HX, Pollara J, Liu P, Alam SM, Zhang R, Cocklin SL, Shen X, Duffy R, Xia SM, Schutte RJ, Pemble Iv CW, Dennison SM, Li H, Chao A, Vidnovic K, Evans A, Klein K, Kumar A, Robinson J, Landucci G, Forthal DN, Montefiori DC, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber BT, Moog C, Shattock RJ, Letvin NL, Schmitz JE, Moody MA, Gao F, Ferrari G, Shaw GM, Haynes BF,
PLoS pathogens. Aug-2015
HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Thus, some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.
Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry (LC MS/MS).Monday, August 03, 2015
Hill RC, Oman TJ, Shan G, Schafer B, Eble J, Chen C,
Journal of agricultural and food chemistry. 3-Aug-2015
Currently, traditional immunochemistry technologies such as Enzyme-Linked Immunosorbent Assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices due to increasing numbers of transgenic proteins being co-expressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide tolerant proteins in soybean tissues; aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation observed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.
Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays.Monday, August 03, 2015
Laborde C, Pittino F, Verhoeven HA, Lemay SG, Selmi L, Jongsma MA, Widdershoven FP,
Nature nanotechnology. 3-Aug-2015
Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.
Plant Seed Species Identification from Chemical Fingerprints-A High-Throughput Application of Direct Analysis in Real Time Mass Spectrometry.Monday, August 03, 2015
Lesiak AD, Cody RB, Dane AJ, Musah RA,
Analytical chemistry. 3-Aug-2015
Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometric (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.Monday, August 03, 2015
O'Hurley G, Busch C, Fagerberg L, Hallström BM, Stadler C, Tolf A, Lundberg E, Schwenk JM, Jirström K, Bjartell A, Gallagher WM, Uhlén M, Pontén F,
PloS one. 3-8-2015
To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL.
The impact of gonadal hormones on cannabinoid dependence.Tuesday, August 04, 2015
Marusich JA, Craft RM, Lefever TW, Wiley JL,
Experimental and clinical psychopharmacology. Aug-2015
Cannabis is the most widely used illicit substance in the United States. Women report greater positive subjective effects of cannabis, and greater cannabis withdrawal compared to men. Female rodents are more sensitive than males to some acute effects of Δ⁹-tetrahydrocannabinol (THC), and females also develop greater tolerance to THC in some assays. The purpose of this study was to determine whether gonadal hormones modulate THC dependence in rats. Adult rats were gonadectomized (GDX) or sham-GDX, and hormone was replaced in half of the GDX rats of each sex (testosterone in males; estradiol and/or progesterone in females). THC (30 mg/kg) or vehicle was administered twice daily for 6.5 days, followed on the seventh day by vehicle or rimonabant challenge and assessment for withdrawal-related behaviors. Sham-GDX females developed greater tolerance than males to THC-induced hypothermia, and GDX females given progesterone showed greater tolerance to THC-induced locomotor suppression. Rimonabant precipitated withdrawal, as evidenced by increased somatic signs (forepaw tremors, licking) and increased startle amplitude. Testosterone in GDX males decreased withdrawal-induced licking. Estradiol and progesterone in GDX females increased withdrawal-induced chewing, and progesterone increased withdrawal-induced sniffing. These results suggest that estradiol and progesterone may promote the development of dependence, whereas testosterone may protect against dependence. While the present study indicates that testosterone and estradiol produce opposite effects on THC-induced behavior, estradiol appears to play a broader role than testosterone in modulating THC's behavioral effects. (PsycINFO Database Record
Serum Cardiac Troponin-I is Superior to Troponin-T as a Marker for Left Ventricular Dysfunction in Clinically Stable Patients with End-Stage Renal Disease.Monday, August 03, 2015
Buiten MS, de Bie MK, Rotmans JI, Dekker FW, van Buren M, Rabelink TJ, Cobbaert CM, Schalij MJ, van der Laarse A, Jukema JW,
PloS one. 4-8-2015
In the present cohort, serum cTnI levels showed a stronger association with LVMI and LVEF than cTnT. However, cTnT was significantly associated with CAD and residual renal function, unlike cTnI. Therefore, cTnI seems to be superior to cTnT as a marker of left ventricular dysfunction in asymptomatic dialysis patients, while cTnT might be better suited to detect CAD in these patients.
Desmosine and Isodesmosine as a Novel Biomarker for Pulmonary Arterial Hypertension: A Pilot Study.Monday, August 03, 2015
Minkin R, Sandhu G, Grosu H, Tartell L, Ma S, Lin YY, Eden E, Turino GM,
American journal of therapeutics. 31-Jul-2015
Delayed diagnosis is common in patients with pulmonary arterial hypertension (PAH). Right-sided heart catheterization, the gold standard for diagnosis, is invasive and cannot be applied for routine screening. Some biomarkers have been looked into; however, due to the lack of a clear pathological mechanism linking the marker to PAH, the search for an ideal one is still ongoing. Elastin is a significant structural constituent of blood vessels. Its synthesis involves cross-linking of monomers by 2 amino acids, desmosine and isodesmosine (D&I). Being extremely stable, elastin undergoes little metabolic turnover in healthy individuals resulting in very low levels of D&I amino acids in the human plasma, urine, or sputum. We hypothesized that in PAH patients, the elastin turnover is high; which in turn should result in elevated levels of D&I in plasma and urine. Using mass spectrometry, plasma and urine levels of D&I were measured in 20 consecutive patients with PAH confirmed by cardiac catheterization. The levels were compared with 13 healthy controls. The mean level of total plasma D&I in patients with PAH was 0.47 ng/mL and in controls was 0.19 ng/mL (P = 0.001). The mean levels of total D&I in the urine of PAH patients was 20.55 mg/g creatinine and in controls was 12.78 mg/g creatinine (P = 0.005). The mean level of free D&I in the urine of PAH patients was 10.34 mg/g creatinine and in controls was 2.52 mg/g creatinine (P < 0.001). This is the first study highlighting that the serum and urine D&I has a potential to be a novel screening biomarker for patients with PAH. It paves the way for larger studies to analyze its role in assessing for disease severity and response to treatment.
Molecular biomarkers in colorectal carcinoma.Monday, August 03, 2015
Puerta-García E, Cañadas-Garre M, Calleja-Hernández MÁ,
Pharmacogenomics. 3-Aug-2015
Colorectal cancer is a tumor with increasing incidence which represents one of the first leading causes of death worldwide. Gene alterations described for colorectal cancer include genome instability (microsatellite and chromosomal instability), CpG islands methylator phenotype, microRNA, histone modification, protein biomarkers, gene mutations (RAS, BRAF, PI3K, TP53, PTEN) and polymorphisms (APC, CTNNB1, DCC). In this article, biomarkers with prognostic value commonly found in colorectal cancer will be reviewed.
Whole slide image cytometry: a novel method to detect abnormal DNA content in Barrett's esophagus.Monday, August 03, 2015
Wang Y, McManus DT, Arthur K, Johnston BT, Kennedy AJ, Coleman HG, Murray LJ, Hamilton PW,
Laboratory investigation; a journal of technical methods and pathology. 3-Aug-2015
Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma (EAC). Both low-grade dysplasia (LGD) and high-grade dysplasia (HGD) are associated with an increased risk of progression to EAC. However, histological interpretation and grading of dysplasia (particularly LGD) is subjective and poorly reproducible. This study has combined whole slide imaging with DNA image cytometry to provide a novel method for the detection of abnormal DNA content through image analysis of tissue sections. A total of 20 cases were evaluated, including 8 negative for dysplasia (NFD), 6 LGD, and 6 HGD. Feulgen-stained esophageal sections were scanned in their entirety. Barrett's mucosa was interactively chosen for automatic nuclei segmentation where irrelevant cell types were ignored. The combined DNA content histogram for all nuclei within selected image regions was then obtained. In addition, three histogram measurements were computed, including xER-5C, 2cDI, and DNA-MG. Visual evaluation suggested the shape of DNA content histograms from NFD, LGD, and HGD cases exhibiting identifiable differences. The histogram measurements, xER-5C, 2cDI, and DNA-MG, were shown to be effective in differentiating metaplastic from dysplastic cases with statistical significance. Moreover, they also successfully separated NFD, LGD, and HGD patients with statistical significance. Whole slide image cytometry is a novel and effective method for the detection of abnormal DNA content in BE. Compared with histological review, it is more objective. Compared with flow cytometry and cytology-preparation image cytometry, it is low cost, simple to use, only requires a single 1 μm section, and facilitates selection of tissue and topographical correlation. Whole slide image cytometry can detect differences in DNA content between NFD, LGD, and HGD patients in this cross-sectional study. Abnormal DNA content detection by whole slide image cytometry is a promising biomarker of progression that could affect future diagnostics in BE.Laboratory Investigation advance online publication, 3 August 2015; doi:10.1038/labinvest.2015.98.
Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells.Monday, August 03, 2015
Paull D, Sevilla A, Zhou H, Hahn AK, Kim H, Napolitano C, Tsankov A, Shang L, Krumholz K, Jagadeesan P, Woodard CM, Sun B, Vilboux T, Zimmer M, Forero E, Moroziewicz DN, Martinez H, Malicdan MC, Weiss KA, Vensand LB, Dusenberry CR, Polus H, Sy KT, Kahler DJ, Gahl WA, Solomon SL, Chang S, Meissner A, Eggan K, Noggle SA,
Nature methods. 3-Aug-2015
Induced pluripotent stem cells (iPSCs) are an essential tool for modeling how causal genetic variants impact cellular function in disease, as well as an emerging source of tissue for regenerative medicine. The preparation of somatic cells, their reprogramming and the subsequent verification of iPSC pluripotency are laborious, manual processes limiting the scale and reproducibility of this technology. Here we describe a modular, robotic platform for iPSC reprogramming enabling automated, high-throughput conversion of skin biopsies into iPSCs and differentiated cells with minimal manual intervention. We demonstrate that automated reprogramming and the pooled selection of polyclonal pluripotent cells results in high-quality, stable iPSCs. These lines display less line-to-line variation than either manually produced lines or lines produced through automation followed by single-colony subcloning. The robotic platform we describe will enable the application of iPSCs to population-scale biomedical problems including the study of complex genetic diseases and the development of personalized medicines.
ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.Monday, August 03, 2015
Cozen AE, Quartley E, Holmes AD, Hrabeta-Robinson E, Phizicky EM, Lowe TM,
Nature methods. 3-Aug-2015
High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA methylation sequencing (ARM-seq), which uses pretreatment with Escherichia coli AlkB to demethylate N(1)-methyladenosine (m(1)A), N(3)-methylcytidine (m(3)C) and N(1)-methylguanosine (m(1)G), all commonly found in tRNAs. Comparative methylation analysis using ARM-seq provides the first detailed, transcriptome-scale map of these modifications and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-seq demonstrates that tRNA fragments accurately recapitulate the m(1)A modification state for well-characterized yeast tRNAs and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state and may reveal new roles for tRNA fragments as biomarkers or signaling molecules.
Diverse Ways of Perturbing the Human Arachidonic Acid Metabolic Network To Control Inflammation.Monday, August 03, 2015
Meng H, Liu Y, Lai L,
Accounts of chemical research. 3-Aug-2015
Inflammation and other common disorders including diabetes, cardiovascular disease, and cancer are often the result of several molecular abnormalities and are not likely to be resolved by a traditional single-target drug discovery approach. Though inflammation is a normal bodily reaction, uncontrolled and misdirected inflammation can cause inflammatory diseases such as rheumatoid arthritis and asthma. Nonsteroidal anti-inflammatory drugs including aspirin, ibuprofen, naproxen, or celecoxib are commonly used to relieve aches and pains, but often these drugs have undesirable and sometimes even fatal side effects. To facilitate safer and more effective anti-inflammatory drug discovery, a balanced treatment strategy should be developed at the biological network level. In this Account, we focus on our recent progress in modeling the inflammation-related arachidonic acid (AA) metabolic network and subsequent multiple drug design. We first constructed a mathematical model of inflammation based on experimental data and then applied the model to simulate the effects of commonly used anti-inflammatory drugs. Our results indicated that the model correctly reproduced the established bleeding and cardiovascular side effects. Multitarget optimal intervention (MTOI), a Monte Carlo simulated annealing based computational scheme, was then developed to identify key targets and optimal solutions for controlling inflammation. A number of optimal multitarget strategies were discovered that were both effective and safe and had minimal associated side effects. Experimental studies were performed to evaluate these multitarget control solutions further using different combinations of inhibitors to perturb the network. Consequently, simultaneous control of cyclooxygenase-1 and -2 and leukotriene A4 hydrolase, as well as 5-lipoxygenase and prostaglandin E2 synthase were found to be among the best solutions. A single compound that can bind multiple targets presents advantages including low risk of drug-drug interactions and robustness regarding concentration fluctuations. Thus, we developed strategies for multiple-target drug design and successfully discovered several series of multiple-target inhibitors. Optimal solutions for a disease network often involve mild but simultaneous interventions of multiple targets, which is in accord with the philosophy of traditional Chinese medicine (TCM). To this end, our AA network model can aptly explain TCM anti-inflammatory herbs and formulas at the molecular level. We also aimed to identify activators for several enzymes that appeared to have increased activity based on MTOI outcomes. Strategies were then developed to predict potential allosteric sites and to discover enzyme activators based on our hypothesis that combined treatment with the projected activators and inhibitors could balance different AA network pathways, control inflammation, and reduce associated adverse effects. Our work demonstrates that the integration of network modeling and drug discovery can provide novel solutions for disease control, which also calls for new developments in drug design concepts and methodologies. With the rapid accumulation of quantitative data and knowledge of the molecular networks of disease, we can expect an increase in the development and use of quantitative disease models to facilitate efficient and safe drug discovery.
Psychological and social resources relate to biomarkers of allostasis in newly admitted nursing home residents.Monday, August 03, 2015
Meeks S, Van Haitsma K, Mast BT, Arnold S, Streim JE, Sephton S, Smith PJ, Kleban M, Rovine M,
Aging & mental health. 3-Aug-2015
Although these results are based on a small sample, the effect sizes were large enough to confer some confidence in the value of pursuing further research relating biomarkers of allostasis to psychological and physical resources and well-being.
A novel covalent mTOR inhibitor, DHM25, shows in vivo anti-tumor activity against triple-negative breast cancer cells.Monday, August 03, 2015
Amélie F, Delalande O, Jean M, Castellano R, Josselin E, Malleter M, Shoji K, Mac DH, Rampanarivo H, Collette Y, van de Weghe P, Legembre P,
Journal of medicinal chemistry. 3-Aug-2015
Constitutive activation of the PI3K/mTOR signaling pathway contributes to carcinogenesis and metastasis in most, if not all, breast cancers. From a chromene backbone reported to inhibit class I PI3K catalytic subunits, several rounds of chemical syntheses led to the generation of a new collection of chromologs that showed enhanced ability to kill PI3K-addicted cancer cells and to inhibit Akt phosphorylation at serine 473, a hallmark of PI3K/mTOR activation. This initial screen uncovered a chromene designated DHM25 that exerted potent anti-tumor activity against breast tumor cell lines. Strikingly, DHM25 was shown to be a selective and covalent inhibitor of mTOR using biochemical and cellular analyses, modeling, and a large panel of kinase activity assays spanning the human kinome (243 kinases). Finally, in vivo, this novel drug was an efficient inhibitor of growth and metastasis of triple-negative breast cancer cells, paving the way for its clinical application in oncology.
Liquid Chromatography Enantioseparations of Halogenated Compounds on Polysaccharide-Based Chiral Stationary Phases: Role of Halogen Substituents in Molecular Recognition.Monday, August 03, 2015
Peluso P, Mamane V, Cossu S,
Chirality. 3-Aug-2015
Halogenated chiral molecules have become important in several fields of science, industry, and society as drugs, natural compounds, agrochemicals, environmental pollutants, synthetic products, and chiral supports. Meanwhile, the perception of the halogen moiety in organic compounds and its role in recognition processes changed. Indeed, the recognition of the halogen bond as an intermolecular interaction occurring when the halogen acts as a Lewis acid had a strong impact, particularly in crystal engineering and medicinal chemistry. Due to this renewed interest in the potentialities of chiral organohalogens, here we focus on selected recent applications dealing with enantioseparations of halogenated compounds on polysaccharide-based chiral stationary phases (CSPs), widely used in liquid chromatography (LC). In particular, recently the first case of halogen bonding-driven high-performance LC (HPLC) enantioseparation was reported on a cellulose-based CSP. Along with enantioseparations performed under conventional HPLC, representative applications using supercritical fluid chromatography (SFC) are reported. Chirality 00:000-000, 2015. © 2015 Wiley Periodicals, Inc.
Production of Furin-Cleaved Papillomavirus Pseudovirions and Their Use for In Vitro Neutralization Assays of L1- or L2-Specific Antibodies.Tuesday, August 04, 2015
Wang JW, Matsui K, Pan Y, Kwak K, Peng S, Kemp T, Pinto L, Roden RB,
Current protocols in microbiology. 2015
Immunization with Human Papillomavirus (HPV) L1 virus-like particles or L2 capsid protein elicits neutralizing antibodies that mediate protection. A high-throughput and sensitive in vitro neutralization assay is therefore valuable for prophylactic HPV vaccine studies. Over several hours during infection of the genital tract, virions take on a distinct intermediate conformation, including a required furin cleavage of L2 at its N-terminus. This intermediate is an important target for neutralization by L2-specific antibody, but it is very transiently exposed during in vitro infection of most cell lines resulting in insensitive measurement for L2, but not L1-specific neutralizing antibodies. To model this intermediate, we describe a protocol to generate furin-cleaved HPV pseudovirions (fc-PsV), which deliver an encapsidated reporter plasmid to facilitate infectivity measurements. We also describe a protocol for use of fc-PsV in a high-throughput in vitro neutralization assay for the sensitive measurement of both L1 and L2-specific neutralizing antibodies. © 2015 by John Wiley & Sons, Inc.
Molecular Mechanisms of Alzheimer's Biomarker FDDNP Binding to Aβ Amyloid Fibril.Monday, August 03, 2015
Parikh ND, Klimov DK,
The journal of physical chemistry. B. 3-Aug-2015
Using isobaric-isothermal replica exchange molecular dynamics and all-atom explicit water model we examined binding of FDDNP biomarkers to Abeta amyloid fibril fragment. Our results can be summarized as follows. First, FDDNP ligands bind with high affinity to Abeta fibril and hydrophobic effect together with pi-stacking interactions are the dominant factors governing FDDNP binding. In comparison, electrostatic interactions and hydrogen bonding play minor role. Second, our simulations reveal strong tendency of bound FDDNP molecules for self-aggregation. Accordingly, about two-third of all bound ligands form aggregated clusters of various sizes and ligand-ligand interactions make considerable contribution to FDDNP binding. Third, FDDNP ligands bind to two distinct sites on Abeta fibril. Primary binding sites (NT) are located at the N-terminals of Abeta10-40 peptides, whereas secondary ones (CE) occur on the concave fibril edge near fibril channels. The NT sites are characterized by strong hydrophobic and pi-stacking interactions, favorable binding entropy resulting from multiple FDDNP binding orientations and propensity for self-aggregation, but relatively weak van-der-Waals interactions. In contrast, the CE sites offer stronger van-der-Waals binding interactions, but weaker hydrophobic and aromatic interactions and less favorable binding entropy. By comparing our data with previous studies we suggest that the primary binding locations identified by us are likely to occur in other Abeta fibril polymorphic structures. We also show that FDDNP binds via distinct mechanisms to Abeta fibrils and monomers. We argue that FDDNP binds with stronger affinity to benign Abeta monomers than to the fibrils raising questions about FDDNP ability to selectively label amyloid deposits.
Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia.Tuesday, August 04, 2015
Gabriel AS, Lafta FM, Schwalbe EC, Nakjang S, Cockell SJ, Iliasova A, Enshaei A, Schwab C, Rand V, Clifford SC, Kinsey SE, Mitchell CD, Vora A, Harrison CJ, Moorman AV, Strathdee G,
Epigenetics. 3-Aug-2015
Although children with acute lymphoblastic leukemia (ALL) generally have a good outcome, some patients do relapse and survival following relapse is poor. Altered DNA methylation is highly prevalent in ALL and raises the possibility that DNA methylation-based biomarkers could predict patient outcome. In this study, genome-wide methylation analysis, using the Illumina Infinium HumanMethylation450 BeadChip platform, was carried out on 52 diagnostic patient samples from 4 genetic subtypes [ETV6-RUNX1, high hyperdiploidy (HeH), TCF3-PBX1 and dic(9;20)(p11-13;q11)] in a 1:1 case-control design with patients who went on to relapse (as cases) and patients achieving long-term remission (as controls). Pyrosequencing assays for selected loci were used to confirm the array-generated data. Non-negative matrix factorization consensus clustering readily clustered samples according to genetic subgroups and gene enrichment pathway analysis suggested that this is in part driven by epigenetic disruption of subtype specific signaling pathways. Multiple bioinformatics approaches (including bump hunting and individual locus analysis) were used to identify CpG sites or regions associated with outcome. However, no associations with relapse were identified. Our data revealed that ETV6-RUNX1 and dic(9;20) subtypes were mostly associated with hypermethylation; conversely, TCF3-PBX1 and HeH were associated with hypomethylation. We observed significant enrichment of the neuroactive ligand-receptor interaction pathway in TCF3-PBX1 as well as an enrichment of genes involved in immunity and infection pathways in ETV6-RUNX1 subtype. Taken together, our results suggest that altered DNA methylation may have differential impacts in distinct ALL genetic subtypes.
An In silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents.Monday, August 03, 2015
Verma S, Debnath U, Agarwal P, Srivastava K, Prabhakar YS,
Journal of chemical information and modeling. 3-Aug-2015
A strategy is described to identify new antimalarial agents to overcome the drug resistance and/or failure issues through in silico screening of multiple biological targets. As a part of this, three enzymes namely CTPS, CK and GST were selected, from among 56 drug targets of P. falciparum, and used them in virtual screening of ZINC database entries which led to the design and synthesis of arylsulfonyloxy acetimidamides as their consensus inhibitors. From these, two compounds showed good activity against sensitive (3D7; IC50, 1.10 and 1.45µM) and resistant (K1; IC50, 2.10 and 2.13µM) strains of the parasite, and further investigated through docking and molecular dynamics simulations. The findings of this study collectively paved the way for arylsulfonyloxy acetimidamides as new class of antimalarial agents.
MicroRNA-486 as a Biomarker for Early Diagnosis and Recurrence of Non-Small Cell Lung Cancer.Monday, August 03, 2015
Li W, Wang Y, Zhang Q, Tang L, Liu X, Dai Y, Xiao L, Huang S, Chen L, Guo Z, Lu J, Yuan K,
PloS one. 3-8-2015
The results suggest that miR-486 and miR-150 could be potential blood-based biomarkers for early diagnosis of NSCLC. Monitoring change of miR-486 expression in plasma might be an effective and non-invasive method for recurrence prediction of early-staged NSCLC patients.
Biofluid Biomarkers of Mild Traumatic Brain Injury: Whither Plasma Tau.Monday, August 03, 2015
Peskind ER, Kraemer B, Zhang J,
JAMA neurology. 3-Aug-2015
Detection of Intracellular Cytokines by Flow Cytometry.Tuesday, August 04, 2015
Yin Y, Mitson-Salazar A, Prussin C,
Current protocols in immunology / edited by John E. Coligan ... [et al.]. 2015
Intracellular cytokine staining (ICCS), employing fluorescently labeled MAbs detected by flow cytometry, has emerged as the premier technique for studying cytokine expression at the single-cell level. Advances in polychromatic flow cytometry have dramatically enhanced the sophistication of ICCS investigations. ICCS can simultaneously measure multiple cytokines within a single cell, allowing the detection of complex cytokine phenotypes. Additionally, cytokines can be measured with a variety of other analytes, including transcription factors, proliferation dilution dyes, activation markers, and viability dyes. This capability, combined with the high throughput inherent in the instrumentation, gives ICCS an enormous advantage over other single-cell techniques such as ELISPOT, limiting dilution, and T cell cloning. The unit describes intracellular staining of cells that have already been stimulated in vitro and fixed. Methods for in vitro activation by PMA and ionomycin or antigens, fixation of cell suspensions, and cell surface staining are also described. © 2015 by John Wiley & Sons, Inc.
Enzyme-Linked Immunosorbent Assays.Tuesday, August 04, 2015
Hornbeck PV,
Current protocols in immunology / edited by John E. Coligan ... [et al.]. 2015
This unit describes six different ELISA systems for the detection of specific antibodies, soluble antigens, or cell-surface antigens. In all six systems, soluble reactants are removed from solution after specifically binding to solid-phase reactants. In the first four protocols, solid-phase reactants are prepared by adsorbing an antigen or antibody onto plastic microtiter plates; in the next two protocols, the solid-phase reactants are cell-associated molecules. In all protocols, the solid-phase reagents are incubated with secondary or tertiary reactants covalently coupled to an enzyme. Unbound conjugates are washed out and a chromogenic or fluorogenic substrate is added. As the substrate is hydrolyzed by the bound enzyme conjugate, a colored or fluorescent product is generated. Finally, the product is detected visually or with a microtiter plate reader. The amount of product generated is proportional to the amount of analysate in the test mixture. One of the support protocols can be used to optimize the different ELISAs. A second support protocol presents a method for preparing alkaline phosphatase conjugates. © 2015 by John Wiley & Sons, Inc.
Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality.Monday, August 03, 2015
Tse A, Verkhivker GM,
Journal of chemical information and modeling. 3-Aug-2015
The Abl and Src tyrosine kinases play a fundamental regulatory role in orchestrating functional processes in cellular networks and represent an important class of therapeutic targets. Crystallographic studies of these kinases have revealed a similar structural organization of multi-domain complexes that confers salient features of their regulatory mechanisms. Molecular characterization of the interaction networks and regulatory residues by which the SH3 and SH2 domains act cooperatively with the catalytic domain to suppress or promote kinase activation presents an active area of structural, biochemical and computational investigations. In this work, we combine biophysical simulations with computational modeling of the residue interaction networks to characterize allosteric mechanisms of kinase regulation and gain insight into differential sensitivity of c-Abl and c-Src kinases to specific drug binding. Using these approaches, we examine dynamics of cooperative rearrangements in the residue interaction networks and elucidate structural role of regulatory residues responsible for modulation of kinase activity. We have found that global network parameters such as residue centrality can unambiguously distinguish functional sites that are responsible for mediating allosteric interactions in the regulatory assemblies. This study has revealed mechanistic aspects of allosteric mechanisms and communication pathways by which the SH3 and SH2 domains may exert their regulatory influence on the catalytic domain and kinase activity. We have also found that high centrality residues can be linked to each other to form efficient and robust routes that transmit allosteric signals between spatially separated regulatory regions. The presented results have demonstrated that global features of the residue interaction networks may serve as transparent and robust indicators of kinase regulatory mechanisms and accurately pinpoint key functional residues.
Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms.Monday, August 03, 2015
Ueoka R, Uria AR, Reiter S, Mori T, Karbaum P, Peters EE, Helfrich EJ, Morinaka BI, Gugger M, Takeyama H, Matsunaga S, Piel J,
Nature chemical biology. 3-Aug-2015
Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.
[Effect of aquaporin 9 on proliferation, apoptosis, invasiveness and migration of HepG2 cells].Monday, August 03, 2015
Li CF, Chen XF, Zhang WG, Liu J, Lyu L, Mei ZC,
Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology. 20-Jun-2015
In HepG2 cells, AQP9 significantly reduces the migrative and invasive capabilities, induces cell apoptosis, and inhibits cell proliferation via cell cycle arrest at the G1/S phases.
Content Analysis of Trends in Print Magazine Tobacco Advertisements.Monday, August 03, 2015
Banerjee S, Shuk E, Greene K, Ostroff J,
Tobacco regulatory science. Jul-2015
This study has implications for tobacco product marketing regulation, particularly around limiting tobacco advertising in publications with a large youth readership and prohibiting false or misleading labels, labeling, and advertising for tobacco products, such as modified risk (unless approved by the FDA) or therapeutic claims.
Update on biomarkers in neuromyelitis optica.Monday, August 03, 2015
Melamed E, Levy M, Waters PJ, Sato DK, Bennett JL, John GR, Hooper DC, Saiz A, Bar-Or A, Kim HJ, Pandit L, Leite MI, Asgari N, Kissani N, Hintzen R, Marignier R, Jarius S, Marcelletti J, Smith TJ, Yeaman MR, Han MH, Aktas O, Apiwattanakul M, Banwell B, Bichuetti D, Broadley S, Cabre P, Chitnis T, De Seze J, Fujihara K, Greenberg B, Hellwig K, Iorio R, Jarius S, Klawiter E, Kleiter I, Lana-Peixoto M, Nakashima O'Connor K, Palace J, Paul F, Prayoonwiwat N, Ruprecht K, Stuve O, Tedder T, Tenembaum S, Garrahan JP, Aires B, van Herle K, van Pelt D, Villoslada P, Waubant E, Weinshenker B, Wingerchuk D, Würfel J, Zamvil S,
Neurology® neuroimmunology & neuroinflammation. Aug-2015
Neuromyelitis optica (NMO) (and NMO spectrum disorder) is an autoimmune inflammatory disease of the CNS primarily affecting spinal cord and optic nerves. Reliable and sensitive biomarkers for onset, relapse, and progression in NMO are urgently needed because of the heterogeneous clinical presentation, severity of neurologic disability following relapses, and variability of therapeutic response. Detecting aquaporin-4 (AQP4) antibodies (AQP4-IgG or NMO-IgG) in serum supports the diagnosis of seropositive NMO. However, whether AQP4-IgG levels correlate with disease activity, severity, response to therapy, or long-term outcomes is unclear. Moreover, biomarkers for patients with seronegative NMO have yet to be defined and validated. Collaborative international studies hold great promise for establishing and validating biomarkers that are useful in therapeutic trials and clinical management. In this review, we discuss known and potential biomarkers for NMO.
NKG2D Signaling Leads to NK Cell Mediated Lysis of Childhood AML.Monday, August 03, 2015
Schlegel P, Ditthard K, Lang P, Mezger M, Michaelis S, Handgretinger R, Pfeiffer M,
Journal of immunology research. 2015
Natural killer cells have been shown to be relevant in the recognition and lysis of acute myeloid leukemia. In childhood acute lymphoblastic leukemia, it was shown that HLA I expression and KIR receptor-ligand mismatch significantly impact ALL cytolysis. We characterized 14 different primary childhood AML blasts by flow cytometry including NKG2D ligands. Further HLA I typing of blasts was performed and HLA I on the AML blasts was quantified. In two healthy volunteer NK cell donors HLA I typing and KIR genotyping were done. Blasts with high NKG2D ligand expression had significantly higher lysis by isolated NK cells. Grouping the blasts by NKG2D ligand expression led to a significant inverse correlation of HLA I expression and cytolysis in NKG2D low blasts. Furthermore, a significant positive correlation of NKG2D ligand expression and blast cytolysis was shown. No impact of KIR ligand-ligand mismatch was found but a significantly increased lysis of homozygous C2 blasts by KIR2DL1 negative NK cells (donor B) was revealed. In conclusion, NKG2D signaling leads to NK cell mediated lysis of childhood AML despite high HLA I expression.
GHK Peptide as a Natural Modulator of Multiple Cellular Pathways in Skin Regeneration.Monday, August 03, 2015
Pickart L, Vasquez-Soltero JM, Margolina A,
BioMed research international. 2015
GHK (glycyl-L-histidyl-L-lysine) is present in human plasma, saliva, and urine but declines with age. It is proposed that GHK functions as a complex with copper 2+ which accelerates wound healing and skin repair. GHK stimulates both synthesis and breakdown of collagen and glycosaminoglycans and modulates the activity of both metalloproteinases and their inhibitors. It stimulates collagen, dermatan sulfate, chondroitin sulfate, and the small proteoglycan, decorin. It also restores replicative vitality to fibroblasts after radiation therapy. The molecule attracts immune and endothelial cells to the site of an injury. It accelerates wound-healing of the skin, hair follicles, gastrointestinal tract, boney tissue, and foot pads of dogs. It also induces systemic wound healing in rats, mice, and pigs. In cosmetic products, it has been found to tighten loose skin and improve elasticity, skin density, and firmness, reduce fine lines and wrinkles, reduce photodamage, and hyperpigmentation, and increase keratinocyte proliferation. GHK has been proposed as a therapeutic agent for skin inflammation, chronic obstructive pulmonary disease, and metastatic colon cancer. It is capable of up- and downregulating at least 4,000 human genes, essentially resetting DNA to a healthier state. The present review revisits GHK's role in skin regeneration in the light of recent discoveries.
An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.Monday, August 03, 2015
Shang J, Sun Y, Li S, Liu JX, Zheng CH, Zhang J,
BioMed research international. 2015
SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.
A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets.Monday, August 03, 2015
Zhang Y, Wang P,
BioMed research international. 2015
New high-throughput technique ChIP-seq, coupling chromatin immunoprecipitation experiment with high-throughput sequencing technologies, has extended the identification of binding locations of a transcription factor to the genome-wide regions. However, the most existing motif discovery algorithms are time-consuming and limited to identify binding motifs in ChIP-seq data which normally has the significant characteristics of large scale data. In order to improve the efficiency, we propose a fast cluster motif finding algorithm, named as FCmotif, to identify the (l,  d) motifs in large scale ChIP-seq data set. It is inspired by the emerging substrings mining strategy to find the enriched substrings and then searching the neighborhood instances to construct PWM and cluster motifs in different length. FCmotif is not following the OOPS model constraint and can find long motifs. The effectiveness of proposed algorithm has been proved by experiments on the ChIP-seq data sets from mouse ES cells. The whole detection of the real binding motifs and processing of the full size data of several megabytes finished in a few minutes. The experimental results show that FCmotif has advantageous to deal with the (l,  d) motif finding in the ChIP-seq data; meanwhile it also demonstrates better performance than other current widely-used algorithms such as MEME, Weeder, ChIPMunk, and DREME.
Animal Models and "Omics" Technologies for Identification of Novel Biomarkers and Drug Targets to Prevent Heart Failure.Monday, August 03, 2015
Hou Y, Adrian-Segarra JM, Richter M, Kubin N, Shin J, Werner I, Walther T, Schönburg M, Pöling J, Warnecke H, Braun T, Kostin S, Kubin T,
BioMed research international. 2015
It is now accepted that heart failure (HF) is a complex multifunctional disease rather than simply a hemodynamic dysfunction. Despite its complexity, stressed cardiomyocytes often follow conserved patterns of structural remodelling in order to adapt, survive, and regenerate. When cardiac adaptations cannot cope with mechanical, ischemic, and metabolic loads efficiently or become chronically activated, as, for example, after infection, then the ongoing structural remodelling and dedifferentiation often lead to compromised pump function and patient death. It is, therefore, of major importance to understand key events in the progression from a compensatory left ventricular (LV) systolic dysfunction to a decompensatory LV systolic dysfunction and HF. To achieve this, various animal models in combination with an "omics" toolbox can be used. These approaches will ultimately lead to the identification of an arsenal of biomarkers and therapeutic targets which have the potential to shape the medicine of the future.
Depot-Based Delivery Systems for Pro-Angiogenic Peptides: A Review.Monday, August 03, 2015
Van Hove AH, Benoit DS,
Frontiers in bioengineering and biotechnology. 2015
Insufficient vascularization currently limits the size and complexity for all tissue engineering approaches. Additionally, increasing or re-initiating blood flow is the first step toward restoration of ischemic tissue homeostasis. However, no FDA-approved pro-angiogenic treatments exist, despite the many pre-clinical approaches that have been developed. The relatively small size of peptides gives advantages over protein-based treatments, specifically with respect to synthesis and stability. While many pro-angiogenic peptides have been identified and shown promising results in vitro and in vivo, the majority of biomaterials developed for pro-angiogenic drug delivery focus on protein delivery. This narrow focus limits pro-angiogenic therapeutics as peptides, similar to proteins, suffer from poor pharmacokinetics in vivo, necessitating the development of controlled release systems. This review discusses pro-angiogenic peptides and the biomaterials delivery systems that have been developed, or that could easily be adapted for peptide delivery, with a particular focus on depot-based delivery systems.
Production of poly(3-hydroxybutyrate) by Halomonas boliviensis in an air-lift reactor.Monday, August 03, 2015
Rivera-Terceros P, Tito-Claros E, Torrico S, Carballo S, Van-Thuoc D, Quillaguamán J,
Journal of biological research (Thessalonikē, Greece). Dec-2015
This study showed that the production of PHB by H. boliviensis using cheap substrates such as starch hydrolysate in a simple production system involving an ALR is feasible. Both maltose and glucose in the hydrolysate induce cell growth and PHB synthesis; most likely the cells balance adequately CoA and NAD(P)H during the assimilation of these carbohydrates. The combination of cheap substrates, simple production systems and the use of non-strict sterile conditions by the halophile H. boliviensis are desirable traits for large scale production of PHB, and should lead to a competitive bioprocess.
Increased P-35, EBI3 Transcripts and Other Treg Markers in Peripheral Blood Mononuclear Cells of Breast Cancer Patients with Different clinical Stages.Monday, August 03, 2015
Hamidinia M, Ghafourian Boroujerdnia M, Talaiezadeh A, Solgi G, Roshani R, Iranprast S, Khodadadi A,
Advanced pharmaceutical bulletin. Jun-2015
The data suggests that the immune system is suppressed in breast cancer patients, which may be due to elevated Treg cells population. These results may be useful for diagnostic or therapeutic purposes. However it may require more investigations.
Cloning and Stable Expression of cDNA Coding For Platelet Endothelial Cell Adhesion Molecule -1 (PECAM-1, CD31) in NIH-3T3 Cell Line.Monday, August 03, 2015
Salehi-Lalemarzi H, Shanehbandi D, Shafaghat F, Abbasi-Kenarsari H, Baradaran B, Movassaghpour AA, Kazemi T,
Advanced pharmaceutical bulletin. Jun-2015
Due to murine origin of NIH-3T3 cell line, CD31-expressing NIH-3T3 cells could be useful as immunogen in production of diagnostic monoclonal antibodies against human CD31, with no need for purification of recombinant proteins.
Solid Lipid Nanoparticles as Efficient Drug and Gene Delivery Systems: Recent Breakthroughs.Monday, August 03, 2015
Ezzati Nazhad Dolatabadi J, Valizadeh H, Hamishehkar H,
Advanced pharmaceutical bulletin. Jun-2015
In recent years, nanomaterials have been widely applied as advanced drug and gene delivery nanosystems. Among them, solid lipid nanoparticles (SLNs) have attracted great attention as colloidal drug delivery systems for incorporating hydrophilic or lipophilic drugs and various macromolecules as well as proteins and nucleic acids. Therefore, SLNs offer great promise for controlled and site specific drug and gene delivery. This article includes general information about SLN structures and properties, production procedures, characterization. In addition, recent progress on development of drug and gene delivery systems using SLNs was reviewed.
Outlining the limits of partial nephrectomy.Monday, August 03, 2015
Chopra S, Satkunasivam R, Kundavaram C, Liang G, Gill IS,
Translational andrology and urology. Jun-2015
Amongst nephron-sparing modalities, partial nephrectomy (PN) is the standard of care in the treatment of renal cell carcinoma (RCC). Despite the increasing utilization of PN, particularly propagated by robot-assisted, minimally invasive approaches for small renal masses (SRMs), the limits of PN appear to be also evolving. In this review, we sought to address the tumour stage beyond which PN may be oncologically perilous. While the evidence supports PN in the treatment of tumours < pT2a, PN may have a role in advanced or metastatic RCC. Other scenarios wherein PN has limited utility are also explored, including anatomical or surgical factors that dictate the difficulty of the case, such as prior renal surgery. Lastly, we discuss the emerging role of molecular biomarkers, specifically epigenetics, to aid in the risk stratification of SRMs and to select tumours optimally suited for PN.
Multispectral photoacoustic microscopy based on an optical-acoustic objective.Monday, August 03, 2015
Cao R, Kilroy JP, Ning B, Wang T, Hossack JA, Hu S,
Photoacoustics. Jun-2015
We have developed reflection-mode multispectral photoacoustic microscopy (PAM) based on a novel optical-acoustic objective that integrates a customized ultrasonic transducer and a commercial reflective microscope objective into one solid piece. This technical innovation provides zero chromatic aberration and convenient confocal alignment of the optical excitation and acoustic detection. With a wavelength-tunable optical-parametric-oscillator laser, we have demonstrated multispectral PAM over an ultrabroad spectral range of 270-1300 nm. A near-constant lateral resolution of ∼2.8 μm is achieved experimentally. Capitalizing on the consistent performance over the ultraviolet, visible, and near-infrared range, multispectral PAM enables label-free concurrent imaging of cell nucleus (DNA/RNA contrast at 270 nm), blood vessel (hemoglobin contrast at 532 nm), and sebaceous gland (lipid contrast at 1260 nm) at the same spatial scale in a living mouse ear.
An in vitro iron superoxide dismutase inhibitor decreases the parasitemia levels of Trypanosoma cruzi in BALB/c mouse model during acute phase.Monday, August 03, 2015
Olmo F, Urbanová K, Rosales MJ, Martín-Escolano R, Sánchez-Moreno M, Marín C,
International journal for parasitology. Drugs and drug resistance. Dec-2015
In order to identify new compounds to treat Chagas disease during the acute phase with higher activity and lower toxicity than the reference drug benznidazole (Bz), two hydroxyphthalazine derivative compounds were prepared and their trypanocidal effects against Trypanosoma cruzi were evaluated by light microscopy through the determination of IC50 values. Cytotoxicity was determined by flow cytometry assays against Vero cells. In vivo assays were performed in BALB/c mice, in which the parasitemia levels were quantified by fresh blood examination; the assignment of a cure was determined by reactivation of blood parasitemia levels after immunosuppression. The mechanism of action was elucidated at metabolic and ultra-structural levels, by (1)H NMR and TEM studies. Finally, as these compounds are potentially capable of causing oxidative damage in the parasites, the study was completed, by assessing their activity as potential iron superoxide dismutase (Fe-SOD) inhibitors. High-selectivity indices observed in vitro were the basis of promoting one of the tested compounds to in vivo assays. The tests on the murine model for the acute phase of Chagas disease showed better parasitemia inhibition values than those found for Bz. Compound 2 induced a remarkable decrease in the reactivation of parasitemia after immunosuppression. Compound 2 turned out to be a great inhibitor of Fe-SOD. The high antiparasitic activity and low toxicity together with the modest costs for the starting materials render this compound an appropriate molecule for the development of an affordable anti-Chagas agent.
Sirtuin 1 and Aging Theory for Chronic Obstructive Pulmonary Disease.Monday, August 03, 2015
Conti V, Corbi G, Manzo V, Pelaia G, Filippelli A, Vatrella A,
Analytical cellular pathology (Amsterdam). 2015
Chronic Obstructive Pulmonary disease (COPD) is an inflammatory syndrome that represents an increasing health problem, especially in the elderly population. Drug therapies are symptomatic and inadequate to contrast disease progression and mortality. Thus, there is an urgent need to clarify the molecular mechanisms responsible for this condition in order to identify new biomarkers and therapeutic targets. Processes including oxidant/antioxidant, protease/antiprotease, and proliferative/antiproliferative balance and control of inflammatory response become dysfunctional during aging as well as in COPD. Recently it was suggested that Sirtuin 1 (SIRT1), an antiaging molecule involved in the response to oxidative stress and chronic inflammation, is implicated in both development and progression of COPD. The present review focuses on the involvement of SIRT1 in the regulation of redox state, inflammation, and premature senescence, all crucial characteristics of COPD phenotypes. Recent evidence corroborating the statement of the "aging theory for COPD" was also discussed.
Infection, Inflammation and Healing in Zebrafish: Intestinal Inflammation.Monday, August 03, 2015
Marjoram L, Bagnat M,
Current pathobiology reports. 1-Jun-2015
Inflammatory bowel diseases (IBD), which include Crohn's disease and ulcerative colitis, contribute to significant morbidity and mortality globally. Despite an increase in incidence, IBD onset is still poorly understood. Mouse models of IBD recapitulate several aspects of human disease, but limited accessibility for live imaging and the lack of forward genetics highlight the need for new model systems for disease onset characterization. Zebrafish represent a powerful platform to model IBD using forward and reverse genetics, live imaging of transgenic lines and physiological assays. In this review, we address current models of IBD in zebrafish and newly developed reagents available for future studies.
Helping to drive the robustness of preclinical research - the assay capability tool.Monday, August 03, 2015
Gore K, Stanley P,
Pharmacology research & perspectives. Aug-2015
Numerous articles in Nature, Science, Pharmacology Research and Perspectives, and other biomedical research journals over the past decade have highlighted that research is plagued by findings that are not reliable and cannot be reproduced. Poor experiments can occur, in part, as a consequence of inadequate statistical thinking in the experimental design, conduct and analysis. As it is not feasible for statisticians to be involved in every preclinical experiment many of the same journals have published guidelines on good statistical practice. Here, we outline a tool that addresses the root causes of irreproducibility in preclinical research in the pharmaceutical industry. The Assay Capability Tool uses 13 questions to guide scientists and statisticians during the development of in vitro and in vivo assays. It promotes the absolutely essential experimental design and analysis strategies and documents the strengths, weaknesses, and precision of an assay. However, what differentiates it from other proposed solutions is the emphasis on how the resulting data will be used. An assay can be assigned a low, medium, or high rating to indicate the level of confidence that can be afforded when making important decisions using data from that assay. This provides transparency on the appropriate interpretation of the assay's results in the light of its current capability. We suggest that following a well-defined process during assay development and use such as that laid out within the Assay Capability Tool means that whatever the results, positive or negative, a researcher can have confidence to make decisions upon and publish their findings.
Pharmacological properties of acid N-thiazolylamide FFA2 agonists.Monday, August 03, 2015
Brown AJ, Tsoulou C, Ward E, Gower E, Bhudia N, Chowdhury F, Dean TW, Faucher N, Gangar A, Dowell SJ,
Pharmacology research & perspectives. Jun-2015
FFA2 is a receptor for short-chain fatty acids. Propionate (C3) and 4-chloro-α-(1-methylethyl)-N-2-thiazolyl-benzeneacetamide (4-CMTB), the prototypical synthetic FFA2 agonist, evoke calcium mobilization in neutrophils and inhibit lipolysis in adipocytes via this G-protein-coupled receptor. 4-CMTB contains an N-thiazolylamide motif but no acid group, and 4-CMTB and C3 bind to different sites on FFA2 and show allosteric cooperativity. Recently, FFA2 agonists have been described that contain both N-thiazolylamide and carboxylate groups, reminiscent of bitopic ligands. These are thought to engage the carboxylate-binding site on FFA2, but preliminary evidence suggests they do not bind to the same site as 4-CMTB even though both contain N-thiazolylamide. Here, we describe the characterization of four FFA2 ligands containing both N-thiazolylamide and carboxylate. (R)-3-benzyl-4-((4-(2-chlorophenyl)thiazol-2-yl)(methyl)amino)-4-oxobutanoic acid (compound 14) exhibits allosteric agonism with 4-CMTB but not C3. Three other compounds agonize FFA2 in [(35)S]GTPγS-incorporation or cAMP assays but behave as inverse agonists in yeast-based gene-reporter assays, showing orthosteric antagonism of C3 responses but allosteric antagonism of 4-CMTB responses. Thus, the bitopic-like FFA2 ligands engage the orthosteric site but do not compete at the site of 4-CMTB binding on an FFA2 receptor molecule. Compound 14 activates FFA2 on human neutrophils and mouse adipocytes, but appears not to inhibit lipolysis upon treatment of human primary adipocytes in spite of the presence of a functional FFA2 receptor in these cells. Hence, these new ligands may reveal differences in coupling of FFA2 between human and rodent adipose tissues.
The discovery of a selective and potent A2a agonist with extended lung retention.Monday, August 03, 2015
Åstrand AB, Lamm Bergström E, Zhang H, Börjesson L, Söderdahl T, Wingren C, Jansson AH, Smailagic A, Johansson C, Bladh H, Shamovsky I, Tunek A, Drmota T,
Pharmacology research & perspectives. Jun-2015
Although the anti-inflammatory role of the A2a receptor is well established, controversy remains with regard to the therapeutic value for A2a agonists in treatment of inflammatory lung diseases, also as a result of unwanted A2a-mediated cardiovascular effects. In this paper, we describe the discovery and characterization of a new, potent and selective A2a agonist (compound 2) with prolonged lung retention and limited systemic exposure following local administration. To support the lead optimization chemistry program with compound selection and profiling, multiple in vitro and in vivo assays were used, characterizing compound properties, pharmacodynamics (PD), and drug concentrations. Particularly, pharmacokinetic-PD modeling was applied to quantify the effects on the cardiovascular system, and an investigative toxicology study in rats was performed to explore potential myocardial toxicities. Compound 2, in comparison to a reference A2a agonist, UK-432,097, demonstrated higher solubility, lower lipophilicity, lower plasma protein binding, high rat lung retention (28% remaining after 24 h), and was efficacious in a lung inflammatory rat model following intratracheal dosing. Despite these properties, compound 2 did not provide a sufficient therapeutic index, that is, separation of local anti-inflammatory efficacy in the lung from systemic side effects in the cardiovascular system. The plasma concentration that resulted in induction of hypotension (half maximal effective concentration; EC50 0.5 nmol/L) correlated to the in vitro A2a potency (rIC50 0.6 nmol/L). Histopathological lesions in the heart were observed at a dose level which is threefold above the efficacious dose level in the inflammatory rat lung model. In conclusion, compound 2 is a highly potent and selective A2a agonist with significant lung retention after intratracheal administration. Despite its local anti-inflammatory efficacy in rat lung, small margins to the cardiovascular effects suggested limited therapeutic value of this compound for treatment of inflammatory lung disease by the inhaled route.
Sperm DNA fragmentation after radioiodine treatment for differentiated thyroid cancer.Monday, August 03, 2015
Esquerré-Lamare C, Isus F, Moinard N, Bujan L,
Basic and clinical andrology. 2015
Treatment with (131)I induces alterations in sperm chromatin as well as in sperm parameters a short time (3 months) after a first dose of (131)I with persistence of sperm alterations until 12 months after a second dose. Sperm banking should be recommended before treatment.
Standardizing metadata and taxonomic identification in metabarcoding studies.Monday, August 03, 2015
Tedersoo L, Ramirez KS, Nilsson RH, Kaljuvee A, Kõljalg U, Abarenkov K,
GigaScience. 2015
High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.
Carqueja (Baccharis trimera) Protects against Oxidative Stress and β-Amyloid-Induced Toxicity in Caenorhabditis elegans.Monday, August 03, 2015
Aparecida Paiva F, de Freitas Bonomo L, Ferreira Boasquivis P, Borges Raposo de Paula IT, Guerra JF, Mendes Leal W, Silva ME, Pedrosa ML, Oliveira Rde P,
Oxidative medicine and cellular longevity. 2015
Carqueja (Baccharis trimera) is a native plant found throughout South America. Several studies have shown that Carqueja has antioxidant activity in vitro, as well as anti-inflammatory, antidiabetic, analgesic, antihepatotoxic, and antimutagenic properties. However, studies regarding its antioxidant potential in vivo are limited. In this study, we used Caenorhabditis elegans as a model to examine the antioxidant effects of a Carqueja hydroalcoholic extract (CHE) on stress resistance and lifespan and to investigate whether CHE has a protective effect in a C. elegans model for Alzheimer's disease. Here, we show for the first time, using in vivo assays, that CHE treatment improved oxidative stress resistance by increasing survival rate and by reducing ROS levels under oxidative stress conditions independently of the stress-related signaling pathways (p38, JNK, and ERK) and transcription factors (SKN-1/Nrf and DAF-16/Foxo) tested here. CHE treatment also increased the defenses against β-amyloid toxicity in C. elegans, in part by increasing proteasome activity and the expression of two heat shock protein genes. Our findings suggest a potential neuroprotective use for Carqueja, supporting the idea that dietary antioxidants are a promising approach to boost the defensive systems against stress and neurodegeneration.
Closely related fungi employ diverse enzymatic strategies to degrade plant biomass.Monday, August 03, 2015
Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CP, El-Bushari HB, Coutinho PM, Gruben BS, Hildén KS, Houbraken J, Barboza LA, Levasseur A, Majoor E, Mäkelä MR, Narang HM, Trejo-Aguilar B, van den Brink J, vanKuyk PA, Wiebenga A, McKie V, McCleary B, Tsang A, Henrissat B, de Vries RP,
Biotechnology for biofuels. 2015
These data demonstrate that Aspergillus species and possibly also other related fungi employ significantly different approaches to degrade plant biomass. This makes sense from an ecological perspective where mixed populations of fungi together degrade plant biomass. The results of this study indicate that combining the approaches from different species could result in improved enzyme mixtures for industrial applications, in particular saccharification of plant biomass for biofuel production. Such an approach may result in a much better improvement of saccharification efficiency than adding specific enzymes to the mixture of a single fungus, which is currently the most common approach used in biotechnology.
Induction of Thioredoxin Reductase 1 by Korean Red Ginseng Water Extract Regulates Cytoprotective Effects on Human Endothelial Cells.Monday, August 03, 2015
Park HR, Lee SE, Yang H, Son GW, Jin YH, Park YS,
Evidence-based complementary and alternative medicine : eCAM. 2015
Korean Red Ginseng is a popular herbal medicine and is widely used in many food products. KRG has biological benefits related to vascular diseases including diabetes, hypertension, atherosclerosis, and other cardiac diseases and KRG has antioxidant and anti-hyperlipidemic actions. KRG decreases the level of oxidative stress and suppresses proinflammatory cytokines and cell adhesion molecules, thus protecting endothelial dysfunction. Mammalian Thioredoxin reductase 1 is an NADPH-dependent selenoprotein, essential for antioxidant defense and DNA synthesis and repair, that regulates the redox system by modulating redox-sensitive transcription factors and thiol-containing proteins. Here, we show that KRG water extract increases the expression of TrxR1 in human umbilical vein endothelial cells via the p38 and PKC-δ signaling pathways. The induction of TrxR1 expression by KRG was confirmed by Western blot analysis and reverse transcription polymerase chain reaction. However, the increase in TrxR1 expression was abolished by specific silencing of the p38 and PKC-δ genes. In addition, we demonstrated that auranofin, a TrxR1 inhibitor, weakens the protective effect of KRG against H2O2-induced cell death as measured by the terminal transferase dUTP nick end labeling assay. These results suggest that KRG may have protective effects in vascular diseases by upregulating TrxR1 in endothelial cells, thereby inhibiting the generation of reactive oxygen species and cell death.
Apoptosis-Inducing Activity of Marine Sponge Haliclona sp. Extracts Collected from Kosrae in Nonsmall Cell Lung Cancer A549 Cells.Monday, August 03, 2015
Bae W, Lim HK, Kim KM, Cho H, Lee SY, Jeong CS, Lee HS, Jung J,
Evidence-based complementary and alternative medicine : eCAM. 2015
Although various anticancer drugs have been developed for the treatment of nonsmall cell lung cancer, chemotherapeutic efficacy is still limited. Natural products such as phytochemicals have been screened as novel alternative materials, but alternative funds such as marine bioresources remain largely untapped. Of these resources, marine sponges have undergone the most scrutiny for their biological activities, including antiinflammatory, antiviral, and anticancer properties. However, the biological mechanisms of the activities of these marine sponges are still unclear. We investigated the anticancer activity of marine sponges collected from Kosrae in Micronesia and examined their mechanisms of action using nonsmall cell lung cancer A549 cells as a model system. Of 20 specimens, the Haliclona sp. (KO1304-328) showed both dose- and time-dependent cytotoxicity. Further, methanol extracts of Haliclona sp. significantly inhibited cell proliferation and cell viability. A549 cells treated with Haliclona sp. demonstrated induced expression of c-Jun N-terminal kinase (JNK), p53, p21, caspase-8, and caspase-3. The percentage of apoptotic cells significantly increased in A549 cultures treated with Haliclona sp. These results indicate that Haliclona sp. induces apoptosis via the JNK-p53 pathway and caspase-8, suggesting that this marine sponge is a good resource for the development of drugs for treatment of nonsmall cell lung cancer.
Maslinic Acid, a Triterpene from Olive, Affects the Antioxidant and Mitochondrial Status of B16F10 Melanoma Cells Grown under Stressful Conditions.Monday, August 03, 2015
Mokhtari K, Rufino-Palomares EE, Pérez-Jiménez A, Reyes-Zurita FJ, Figuera C, García-Salguero L, Medina PP, Peragón J, Lupiáñez JA,
Evidence-based complementary and alternative medicine : eCAM. 2015
Maslinic acid (MA) is a natural compound whose structure corresponds to a pentacyclic triterpene. It is abundant in the cuticular lipid layer of olives. MA has many biological and therapeutic properties related to health, including antitumor, anti-inflammatory, antimicrobial, antiparasitic, antihypertensive, and antioxidant activities. However, no studies have been performed to understand the molecular mechanism induced by this compound in melanoma cancer. The objective of this study was to examine the effect of MA in melanoma (B16F10) cells grown in the presence or absence of fetal bovine serum (FBS). We performed cell proliferation measurements, and the reactive oxygen species (ROS) measurements using dihydrorhodamine 123 (DHR 123) and activities of catalase, glucose 6-phosphate dehydrogenase, glutathione S-transferase, and superoxide dismutase. These changes were corroborated by expression assays. FBS absence reduced cell viability decreasing IC50 values of MA. The DHR 123 data showed an increase in the ROS level in the absence of FBS. Furthermore, MA had an antioxidant effect at lower assayed levels measured as DHR and antioxidant defense. However, at higher dosages MA induced cellular damage by apoptosis as seen in the results obtained.
MicroRNAs as clinical biomarkers?Monday, August 03, 2015
Angelini TG, Emanueli C,
Frontiers in genetics. 2015
Eradication of high viable loads of Listeria monocytogenes contaminating food-contact surfaces.Monday, August 03, 2015
de Candia S, Morea M, Baruzzi F,
Frontiers in microbiology. 2015
This study demonstrates the efficacy of cold gaseous ozone treatments at low concentrations in the eradication of high Listeria monocytogenes viable cell loads from glass, polypropylene, stainless steel, and expanded polystyrene food-contact surfaces. Using a step by step approach, involving the selection of the most resistant strain-surface combinations, 11 Listeria sp. strains resulted inactivated by a continuous ozone flow at 1.07 mg m(-3) after 24 or 48 h of cold incubation, depending on both strain and surface evaluated. Increasing the inoculum level to 9 log CFU coupon(-1), the best inactivation rate was obtained after 48 h of treatment at 3.21 mg m(-3) ozone concentration when cells were deposited onto stainless steel and expanded polystyrene coupons, resulted the most resistant food-contact surfaces in the previous assays. The addition of naturally contaminated meat extract to a high load of L. monocytogenes LMG 23775 cells, the most resistant strain out of the 11 assayed Listeria sp. strains, led to its complete inactivation after 4 days of treatment. To the best of our knowledge, this is the first report describing the survival of L. monocytogenes and the effect of ozone treatment under cold storage conditions on expanded polystyrene, a commonly used material in food packaging. The results of this study could be useful for reducing pathogen cross-contamination phenomena during cold food storage.
Plant hairy root cultures as plasmodium modulators of the slime mold emergent computing substrate Physarum polycephalum.Monday, August 03, 2015
Ricigliano V, Chitaman J, Tong J, Adamatzky A, Howarth DG,
Frontiers in microbiology. 2015
Roots of the medicinal plant Valeriana officinalis are well-studied for their various biological activities. We applied genetically transformed V. officinalis root biomass to exert control of Physarum polycephalum, an amoeba-based emergent computing substrate. The plasmodial stage of the P. polycephalum life cycle constitutes a single, multinucleate cell visible by unaided eye. The plasmodium modifies its network of oscillating protoplasm in response to spatial configurations of attractants and repellents, a behavior that is interpreted as biological computation. To program the computing behavior of P. polycephalum, a diverse and sustainable library of plasmodium modulators is required. Hairy roots produced by genetic transformation with Agrobacterium rhizogenes are a metabolically stable source of bioactive compounds. Adventitious roots were induced on in vitro V. officinalis plants following infection with A. rhizogenes. A single hairy root clone was selected for massive propagation and the biomass was characterized in P. polycephalum chemotaxis, maze-solving, and electrical activity assays. The Agrobacterium-derived roots of V. officinalis elicited a positive chemotactic response and augmented maze-solving behavior. In a simple plasmodium circuit, introduction of hairy root biomass stimulated the oscillation patterns of slime mold's surface electrical activity. We propose that manipulation of P. polycephalum with the plant root culture platform can be applied to the development of slime mold microfluidic devices as well as future models for engineering the plant rhizosphere.
Quality of Smartphone Apps Related to Panic Disorder.Monday, August 03, 2015
Van Singer M, Chatton A, Khazaal Y,
Frontiers in psychiatry. 2015
Quality of smartphone apps related to panic: smartphone apps have a growing role in health care. This study assessed the quality of English-language apps for panic disorder (PD) and compared paid and free apps. Keywords related to PD were entered into the Google Play Store search engine. Apps were assessed using the following quality indicators: accountability, interactivity, self-help score (the potential of smartphone apps to help users in daily life), and evidence-based content quality. The Brief DISCERN score and the criteria of the "Health on the Net" label were also used as content quality indicators as well as the number of downloads. Of 247 apps identified, 52 met all inclusion criteria. The content quality and self-help scores of these PD apps were poor. None of the assessed indicators were associated with payment status or number of downloads. Multiple linear regressions showed that the Brief DISCERN score significantly predicted the content quality and self-help scores. Poor content quality and self-help scores of PD smartphone apps highlight the gap between their technological potential and the overall quality of available products.
Predicting individual brain maturity using dynamic functional connectivity.Monday, August 03, 2015
Qin J, Chen SG, Hu D, Zeng LL, Fan YM, Chen XP, Shen H,
Frontiers in human neuroscience. 2015
Neuroimaging-based functional connectivity (FC) analyses have revealed significant developmental trends in specific intrinsic connectivity networks linked to cognitive and behavioral maturation. However, knowledge of how brain functional maturation is associated with FC dynamics at rest is limited. Here, we examined age-related differences in the temporal variability of FC dynamics with data publicly released by the Nathan Kline Institute (NKI; n = 183, ages 7-30) and showed that dynamic inter-region interactions can be used to accurately predict individual brain maturity across development. Furthermore, we identified a significant age-dependent trend underlying dynamic inter-network FC, including increasing variability of the connections between the visual network, default mode network (DMN) and cerebellum as well as within the cerebellum and DMN and decreasing variability within the cerebellum and between the cerebellum and DMN as well as the cingulo-opercular network. Overall, the results suggested significant developmental changes in dynamic inter-network interaction, which may shed new light on the functional organization of typical developmental brains.
Promoting the translation of intentions into action by implementation intentions: behavioral effects and physiological correlates.Monday, August 03, 2015
Wieber F, Thürmer JL, Gollwitzer PM,
Frontiers in human neuroscience. 2015
The present review addresses the physiological correlates of planning effects on behavior. Although intentions to act qualify as predictors of behavior, accumulated evidence indicates that there is a substantial gap between even strong intentions and subsequent action. One effective strategy to reduce this intention-behavior gap is the formation of implementation intentions that specify when, where, and how to act on a given goal in an if-then format ("If I encounter situation Y, then I will initiate action Z!"). It has been proposed that implementation intentions render the mental representation of the situation highly accessible and establish a strong associative link between the mental representations of the situation and the action. These process assumptions have been examined in behavioral research, and in physiological research, a field that has begun to investigate the temporal dynamics of and brain areas involved in implementation intention effects. In the present review, we first summarize studies on the cognitive processes that are central to the strategic automation of action control by implementation intentions. We then examine studies involving critical samples with impaired self-regulation. Lastly, we review studies that have applied physiological measures such as heart rate, cortisol level, and eye movement, as well as electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) studies on the neural correlates of implementation intention effects. In support of the assumed processes, implementation intentions increased goal attainment in studies on cognitive processes and in critical samples, modulated brain waves related to perceptual and decision processes, and generated less activity in brain areas associated with effortful action control. In our discussion, we reflect on the status quo of physiological research on implementation intentions, methodological and conceptual issues, related research, and propose future directions.
Preliminary analysis using multi-atlas labeling algorithms for tracing longitudinal change.Monday, August 03, 2015
Kim RE, Lourens S, Long JD, Paulsen JS, Johnson HJ,
Frontiers in neuroscience. 2015
Multicenter longitudinal neuroimaging has great potential to provide efficient and consistent biomarkers for research of neurodegenerative diseases and aging. In rare disease studies it is of primary importance to have a reliable tool that performs consistently for data from many different collection sites to increase study power. A multi-atlas labeling algorithm is a powerful brain image segmentation approach that is becoming increasingly popular in image processing. The present study examined the performance of multi-atlas labeling tools for subcortical identification using two types of in-vivo image database: Traveling Human Phantom (THP) and PREDICT-HD. We compared the accuracy (Dice Similarity Coefficient; DSC and intraclass correlation; ICC), multicenter reliability (Coefficient of Variance; CV), and longitudinal reliability (volume trajectory smoothness and Akaike Information Criterion; AIC) of three automated segmentation approaches: two multi-atlas labeling tools, MABMIS and MALF, and a machine-learning-based tool, BRAINSCut. In general, MALF showed the best performance (higher DSC, ICC, lower CV, AIC, and smoother trajectory) with a couple of exceptions. First, the results of accumben, where BRAINSCut showed higher reliability, were still premature to discuss their reliability levels since their validity is still in doubt (DSC < 0.7, ICC < 0.7). For caudate, BRAINSCut presented slightly better accuracy while MALF showed significantly smoother longitudinal trajectory. We discuss advantages and limitations of these performance variations and conclude that improved segmentation quality can be achieved using multi-atlas labeling methods. While multi-atlas labeling methods are likely to help improve overall segmentation quality, caution has to be taken when one chooses an approach, as our results suggest that segmentation outcome can vary depending on research interest.
Blood-sampling collection prior to surgery may have a significant influence upon biomarker concentrations measured.Monday, August 03, 2015
Kahn N, Riedlinger J, Roeßler M, Rabe C, Lindner M, Koch I, Schott-Hildebrand S, Herth FJ, Schneider MA, Meister M, Muley TR,
Clinical proteomics. 2015
In this study we show the unexpectedly marked influence of blood withdrawal timing (before vs. after anesthesia) and procedure (venous versus arterial vessel puncture) has on the concentration of the protein biomarker SCC and to a less extent upon CYFRA21-1. The potential causes for these effects remain to be elucidated in subsequent studies, however these findings highlight the importance of a standardized, controlled blood collection protocol for biomarker detection.
ATP-Binding Pocket-Targeted Suppression of Src and Syk by Luteolin Contributes to Its Anti-Inflammatory Action.Monday, August 03, 2015
Lee JO, Jeong D, Kim MY, Cho JY,
Mediators of inflammation. 2015
Luteolin is a flavonoid identified as a major anti-inflammatory component of Artemisia asiatica. Numerous reports have demonstrated the ability of luteolin to suppress inflammation in a variety of inflammatory conditions. However, its exact anti-inflammatory mechanism has not been fully elucidated. In the present study, the anti-inflammatory mode of action in activated macrophages of luteolin from Artemisia asiatica was examined by employing immunoblotting analysis, a luciferase reporter gene assay, enzyme assays, and an overexpression strategy. Luteolin dose-dependently inhibited the secretion of nitric oxide (NO) and prostaglandin E2 (PGE2) and diminished the levels of mRNA transcripts of inducible NO synthase (iNOS), tumor necrosis factor- (TNF-) α, and cyclooxygenase-2 (COX-2) in lipopolysaccharide- (LPS-) and pam3CSK-treated macrophage-like RAW264.7 cells without displaying cytotoxicity. Luteolin displayed potent NO-inhibitory activity and also suppressed the nuclear translocation of NF-κB (p65 and p50) via blockade of Src and Syk, but not other mitogen-activated kinases. Overexpression of wild type Src and point mutants thereof, and molecular modelling studies, suggest that the ATP-binding pocket may be the luteolin-binding site in Src. These results strongly suggest that luteolin may exert its anti-inflammatory action by suppressing the NF-κB signaling cascade via blockade of ATP binding in Src and Syk.
Effect of a barley-vegetable soup on plasma carotenoids and biomarkers of cardiovascular disease.Monday, August 03, 2015
Bacchetti T, Tullii D, Masciangelo S, Gesuita R, Skrami E, Brugè F, Silvestri S, Orlando P, Tiano L, Ferretti G,
Journal of clinical biochemistry and nutrition. Jul-2015
Functional foods that provide benefits beyond their traditional nutritional value have attracted much interest. Aim of the study was to evaluate the nutritional and the functional properties of a frozen ready-to-eat soup containing barley and pigmented vegetables. Both glycaemic index and the glyceamic load of ready-to-eat soup were evaluated in vivo. Moreover the bioavailability of carotenoids (lutein and beta-carotene) and the effect on lipid profile and lipid peroxidation were studied in 38 volunteers whose diet was supplemented for two weeks with a daily portion (250 g) of the ready-to-eat soup. Plasma levels of carotenoids (lutein and beta-carotene) and plasma total antioxidant capacity significantly increased after 2 weeks of treatment. Furthermore, we observed a decrease in the levels of lipids (total cholesterol and low density lipoprotein-cholesterol) and of markers of lipid peroxidation (oxidized low density lipoprotein and lipid hydroperoxides) in plasma of all subjects. The glyceamic index of the product was 36, therefore it could be considered a low glyceamic index food. An accurate selection of vegetable foods results in a palatable and healthy product that provides benefits on plasma lipids and lipid peroxidation (Protocol number 211525).
Risk Classification with an Adaptive Naive Bayes Kernel Machine Model.Monday, August 03, 2015
Minnier J, Yuan M, Liu JS, Cai T,
Journal of the American Statistical Association. 22-Apr-2015
Genetic studies of complex traits have uncovered only a small number of risk markers explaining a small fraction of heritability and adding little improvement to disease risk prediction. Standard single marker methods may lack power in selecting informative markers or estimating effects. Most existing methods also typically do not account for non-linearity. Identifying markers with weak signals and estimating their joint effects among many non-informative markers remains challenging. One potential approach is to group markers based on biological knowledge such as gene structure. If markers in a group tend to have similar effects, proper usage of the group structure could improve power and efficiency in estimation. We propose a two-stage method relating markers to disease risk by taking advantage of known gene-set structures. Imposing a naive bayes kernel machine (KM) model, we estimate gene-set specific risk models that relate each gene-set to the outcome in stage I. The KM framework efficiently models potentially non-linear effects of predictors without requiring explicit specification of functional forms. In stage II, we aggregate information across gene-sets via a regularization procedure. Estimation and computational efficiency is further improved with kernel principle component analysis. Asymptotic results for model estimation and gene set selection are derived and numerical studies suggest that the proposed procedure could outperform existing procedures for constructing genetic risk models.
Studies on a biomimetic oxidative dimerization approach to the hibarimicins.Monday, August 03, 2015
Romaine IM, Sulikowski GA,
Tetrahedron letters. 3-Jun-2015
Nature utilizes dimerization as a method of producing structurally complex metabolites. The microbial metabolites known collectively as the hibarimicins are one example of complex natural products produced biosynthetically by dimerization of a phenolic aromatic polyketide. Described in this communication are model studies aimed at demonstrating regiocontrolled oxidative dimerization of phenolic ring systems related to the biosynthetic precursor of the hibarimicin family of natural products.
Functional brain network changes associated with clinical and biochemical measures of the severity of hepatic encephalopathy.Monday, August 03, 2015
Jao T, Schröter M, Chen CL, Cheng YF, Lo CZ, Chou KH, Patel AX, Lin WC, Lin CP, Bullmore ET,
NeuroImage. 31-Jul-2015
Functional properties of the brain may be associated with changes in complex brain networks. However, little is known about how properties of large-scale functional brain networks may be altered stepwise in patients with disturbance of consciousness, e.g. an encephalopathy. We used resting-state fMRI data on patients suffering from various degrees of hepatic encephalopathy (HE) to explore how topological and spatial network properties of functional brain networks changed at different cognitive and consciousness states. Severity of HE was measured clinically and by neuropsychological tests. 58 non-alcoholic liver cirrhosis patients and 62 normal controls were studied. Patients were subdivided into liver cirrhosis with no outstanding HE (NoHE, n = 23), minimal HE with cognitive impairment only detectable by neuropsychological tests (MHE, n = 28), and clinically overt HE (OHE, n = 7). From the earliest stage, the NoHE, functional brain networks were progressively more random, less clustered, and less modular. Since the intermediate stage (MHE), increased ammonia level was accompanied by concomitant exponential decay of mean connectivity strength, especially in the primary cortical areas and midline brain structures. Finally, at the OHE stage, there were radical reorganization of the topological centrality-i.e. the relative importance-of the hubs and reorientation of functional connections between nodes. In summary, this study illustrated progressively greater abnormalities in functional brain network organization in patients with clinical and biochemical evidence of more severe hepatic encephalopathy. The early-than-expected brain network dysfunction in cirrhotic patients suggests that brain functional connectivity and network analysis may provide useful and complementary biomarkers for more aggressive and earlier intervention of hepatic encephalopathy. Moreover, the stepwise deterioration of functional brain networks in HE patients may suggest that hierarchical network properties are necessary for normal brain function.
Mechanistic Evidence of Viscum schimperi (Viscaceae) Antihyperglycemic Activity: From a Bioactivity-guided Approach to Comprehensive Metabolite Profiling.Monday, August 03, 2015
Abdallah HM, Farag MA, Abdel-Naim AB, Ghareib SA, Abdel-Sattar EA,
Phytotherapy research : PTR. 3-Aug-2015
Diabetes mellitus is possibly the world's largest growing metabolic disorder. Effective treatment of diabetes is increasingly dependent on active constituents of medicinal plants capable of controlling hyperglycemia as well as its secondary complications. Viscum schimperi Engl. is a plant growing in Saudi Arabia and known for its antidiabetic activity. The potential antidiabetic activity of its methanol extract as well as its chloroform, n-butanol, and the remaining water fractions was evaluated in streptozotocin-induced diabetic rats at two dose levels. The antidiabetic activity was assessed through the determination of fasting blood glucose level, insulin levels, area under the curve (AUC) in oral glucose tolerance test, glucose absorption in isolated rat gut assay, and glucose uptake by psoas muscle. Moreover, large-scale untargeted metabolite profiling of methanol extract was performed via UPLC-PDA and qTOF-MS (ultra-performance liquid chromatography photodiode array detection and quadrupole time-of-flight mass spectrometry) respectively, to explore its chemical composition and standardization of its extract. Multivariate statistical analysis including principal component analysis and orthogonal projection to latent structures discriminant analysis was used to determine bioactives in its fractions. In conclusion, oleanane triterpenes and O-caffeoyl quinic acid conjugates were the major compounds that might account for antihyperglycemic effect of the plant. Copyright © 2015 John Wiley & Sons, Ltd.
Brazilian group of flow cytometry (GBCFLUX) panels for acute leukemia: Some insights.Monday, August 03, 2015
Mazza Matos D,
Cytometry. Part B, Clinical cytometry. 31-Jul-2015
Interfacial inhibitors.Monday, August 03, 2015
Pommier Y, Kiselev E, Marchand C,
Bioorganic & medicinal chemistry letters. 18-Jul-2015
Targeting macromolecular interface is a general mechanism by which natural products inactivate macromolecular complexes by stabilizing normally transient intermediates. Demonstrating interfacial inhibition mechanism ultimately relies on the resolution of drug-macromolecule structures. This review focuses on medicinal drugs that trap protein-DNA complexes by binding at protein-DNA interfaces. It provides proof-of-concept and detailed structural and mechanistic examples for topoisomerase inhibitors and HIV integrase inhibitors. Additional examples of recent interfacial inhibitors for protein-DNA interfaces are provided, as well as prospects for targeting previously 'undruggable' targets including transcription, replication and chromatin remodeling complexes. References and discussion are included for interfacial inhibitors of protein-protein interfaces.
Synthesis and evaluation of novel 2,4-diaminopyrimidines bearing bicyclic aminobenzazepines for anaplastic lymphoma kinase (ALK) inhibitor.Monday, August 03, 2015
Kang GA, Lee M, Song D, Lee HK, Ahn S, Park CH, Lee CO, Yun CS, Jung H, Kim P, Ha JD, Cho SY, Kim HR, Hwang JY,
Bioorganic & medicinal chemistry letters. 17-Jul-2015
A series of novel 2,4-diaminopyrimidine compounds bearing bicyclic aminobenzazepine were synthesized and evaluated for their anti-ALK activities. The activities of these compounds were confirmed in both enzyme- and cell-based ALK assays. Amongst compounds synthesized, KRCA-0445 showed very promising results in pharmacokinetic study and in vivo efficacy study with H3122 xenograft mouse model.
Pharmacological Activities and Hydrolysis by Peptidases of [Phospho-Ser(6)]-Bradykinin (pS(6)-BK).Monday, August 03, 2015
Assis DM, Juliano L, Paschoalin T, Kouyoumdjian M, Calixto JB, Santos RA, Pertinhez TA, Gauthier F, Moreau T, Blaber M, Juliano MA,
Biochemical pharmacology. 30-Jul-2015
Phosphorylated kininogen and some of its fragments containing serine phosphorylated bradykinin ([pS(6)]-Bk) were identified in human serum and plasma by a phosphoproteomic approach. We report the kininogenase ability of human tissue and plasma kallikreins and tryptase to generate [pS(6)]-Bk or Lys-[pS(6)]-Bk having as substrate the synthetic human kininogen fluorescent fragment Abz-MISLMKRPPGF[pS(386)]PFRSSRI-NH2. The pharmacological assays of [pS(6)]-Bk showed it as a full B2 bradykinin receptor agonist in smooth muscle, it produces a portal liver hypertensive response in rat and mouse paw edema that lasts longer than Bk. The rat hypotensive response to infusions of Bk is greater than that of [pS(6)]Bk, both if injected through femoral vein or aorta. [pS(6)]-Bk was more resistant than Bk to kininase digestion performed with angiotensin converting enzyme, neprilysin, thimet oligopeptidase, aminopeptidase P and carboxypeptidase M. (1)H-NMR experiments indicated that [pS(6)]-Bk has lower flexibility, with the pS(6)-P(7) bond restricted to the trans conformation, and can explain [pS(6)]-Bk resistance to hydrolysis. In conclusion, [pS(6)]-Bk presenting lower activity than Bk, with longer lasting effects and being slowly released by kininogenases from synthetic Abz-MISLMKRPPGF[pS(386)]PFRSSRI-NH2, suggests that phosphorylation of the kininogens can be an efficient kallikrein-kinin system regulator.
Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet.Monday, August 03, 2015
Moraes C, Fouque D, Amaral AC, Mafra D,
Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation. 31-Jul-2015
Low-protein diet is the recommended nutritional intervention for nondialysis chronic kidney disease (CKD) patients because excess protein intake can damage kidney function and produce uremic toxins. Some of these toxins are generated from amino acids breakdown by gut microbiota as p-cresyl sulfate and indoxyl sulfate that have been clearly associated with cardiovascular mortality in CKD patients. Another uremic toxin, trimethylamine N-oxide (TMAO), a degradation product of choline and L-carnitine (which come mainly from animal protein such as red meat and eggs) is now considered as a proatherogenic metabolite. In the present review, we will highlight the relationship between TMAO, diet and cardiovascular aspects, and the potential concerns about TMAO in nondialysis CKD patients.
Current and emerging modalities for detection of cardiotoxicity in cardio-oncology.Monday, August 03, 2015
Khouri MG, Klein MR, Velazquez EJ, Jones LW,
Future cardiology. 3-Aug-2015
Advancements in diagnostic tools and curative-intent therapies have improved cancer-specific survival. With prolonged survival, patients are now subject to increased aging and development of cardiovascular risk factors such that further improvements in cancer-specific mortality are at risk of being offset by increased cardiovascular mortality. Moreover, established and novel adjuvant therapies used in cancer treatment are associated with unique and varying degrees of direct as well as indirect myocardial and cardiovascular injury (i.e., cardiotoxicity). Current approaches for evaluating anticancer therapy-induced injury have limitations, particularly lack of sensitivity for early detection of subclinical cardiac and cardiovascular dysfunction. With emerging evidence suggesting early prevention and treatment can mitigate the degree of cardiotoxicity and limit interruption of life-saving cancer therapy, the importance of early detection is increasingly paramount. Newer imaging modalities, functional capacity testing and blood biomarkers have the potential to improve early detection of cardiotoxicity and reduce cardiovascular morbidity and mortality.
Multimeric xanthates as carbonic anhydrase inhibitors.Monday, August 03, 2015
Abellán-Flos M, Tanç M, Supuran CT, Vincent SP,
Journal of enzyme inhibition and medicinal chemistry. 3-Aug-2015
The field of multivalent inhibition of enzymes is growing exponentially from the first reported multivalent effect on a glycosidase enzyme. However, the investigations have generally remained restricted to carbohydrate-processing enzymes. Carbonic anhydrases are ubiquitous metallo-enzymes involved in many key biological processes, that catalyze the reversible hydration/dehydration of [Formula: see text]. This study reports the first synthesis of multimeric xanthates addressing the selectivity and potency of CA multivalent inhibition. Six multivalent compounds containing three, four, and six xanthate moieties were prepared and assayed against four relevant CA isoforms together with their monovalent analogues. Some of the multimers were stronger inhibitors than the monomeric species. For hCA I, the two best molecules 18 and 20 showed an improvement of the ligand affinity of 4.8 and 2.3 per xanthate units (valence-corrected values), respectively, which corresponds to a clear multivalent effect. Moreover, the biochemical assays demonstrated that the multimeric presentation of xanthates, also affected the selectivity of the relative inhibition among the four CAs assayed.
Beneficial effects of vitamin E supplementation against the oxidative stress on Cylindrospermopsin-exposed tilapia (Oreochromis niloticus).Monday, August 03, 2015
Guzmán-Guillén R, Prieto Ortega AI, Martín-Caméan A, Cameán AM,
Toxicon : official journal of the International Society on Toxinology. 30-Jul-2015
Cylindrospermopsin (CYN) is known to produce changes in some oxidative stress biomarkers in fish acutely and subchronically exposed to the toxin. The present study investigated the effects of vitamin E supplementation against the oxidative stress induced by pure CYN in tilapia (Oreochromis niloticus). Fish were pretreated with 700 mg vitamin E/kg fish body weight (bw)/day for 7 days by oral route, and on day seven, they received a single oral dose of 400 μg pure CYN/kg fish bw, and were killed after 24 hours. The biomarkers evaluated included lipid peroxidation (LPO), protein and DNA oxidation, glutathione-S-transferase (GST), glutathione peroxidase (GPx), superoxide dismutase (SOD), catalase (CAT) and γ-glutamyl-cysteine synthetase (γ-GCS) activities, and ratio of reduced glutathione-oxidized glutathione (GSH/GSSG). This is the first study showing that vitamin E supplementation is effective at reducing the toxicity induced by CYN, recovering the biomarkers assayed to basal levels. Therefore, vitamin E can be considered a useful chemoprotectant that reduces hepatic and renal oxidative stress and can be used in the prophylaxis and treatment of CYN-related intoxication in fish.
α-5 Laminin Synthesized by Human Pluripotent Stem Cells Promotes Self-Renewal.Monday, August 03, 2015
Laperle A, Hsiao C, Lampe M, Mortier J, Saha K, Palecek SP, Masters KS,
Stem cell reports. 29-Jul-2015
Substrate composition significantly impacts human pluripotent stem cell (hPSC) self-renewal and differentiation, but relatively little is known about the role of endogenously produced extracellular matrix (ECM) components in regulating hPSC fates. Here we identify α-5 laminin as a signature ECM component endogenously synthesized by undifferentiated hPSCs cultured on defined substrates. Inducible shRNA knockdown and Cas9-mediated disruption of the LAMA5 gene dramatically reduced hPSC self-renewal and increased apoptosis without affecting the expression of pluripotency markers. Increased self-renewal and survival was restored to wild-type levels by culturing the LAMA5-deficient cells on exogenous laminin-521. Furthermore, treatment of LAMA5-deficient cells with blebbistatin or a ROCK inhibitor partially restored self-renewal and diminished apoptosis. These results demonstrate that endogenous α-5 laminin promotes hPSC self-renewal in an autocrine and paracrine manner. This finding has implications for understanding how stem cells dynamically regulate their microenvironment to promote self-renewal and provides guidance for efforts to design substrates for stem cell bioprocessing.
The anti-esophageal cancer cell activity by a novel tyrosine/phosphoinositide kinase inhibitor PP121.Monday, August 03, 2015
Peng Y, Zhou Y, Cheng L, Hu D, Zhou X, Wang Z, Xie C, Zhou F,
Biochemical and biophysical research communications. 30-Jul-2015
Here we explored the potential effect of PP121, a novel dual inhibitor of tyrosine and phosphoinositide kinases, against human esophageal cancer cells. We showed that PP121 exerted potent cytotoxic effect in primary (patient-derived) and established (Eca-109, TE-1 and TE-3 lines) esophageal cancer cells, possibly through activating caspase-3-dependnent apoptosis. PP121 was, however, non-cytotoxic to the normal human esophageal epithelial cells (EECs). At the molecular level, we showed that PP121 blocked Akt-mTOR (mammalian target of rapamycin) activation in esophageal cancer cells, which was restored by introducing a constitutively-active Akt (CA-Akt). Yet, CA-Akt only partly inhibited cytotoxicity by PP121 in Eca-109 cells. Importantly, we showed that PP121 inhibited nuclear factor kappa B (NFκB) signaling activation in esophageal cancer cells, which appeared independent of Akt-mTOR blockage. In vivo, oral administration of PP121 remarkably inhibited Eca-109 xenograft growth in nude mice, and significantly improved mice survival. Further, the immunohistochemistry (IHC) and Western blot assays analyzing xenografted tumors showed that PP121 inhibited Akt-mTOR and NFκB activations in vivo. Together, we demonstrate that PP121 potently inhibits esophageal cancer cells in vitro and in vivo, possibly through concurrently inhibiting Akt-mTOR and NFκB signalings.
Do Anti-Bredt Natural Products Exist? Olefin Strain Energy as a Predictor of Isolability.Monday, August 03, 2015
Krenske EH, Williams CM,
Angewandte Chemie (International ed. in English). 29-Jul-2015
Bredt's rule holds a special place in the realm of physical organic chemistry, but its application to natural products chemistry-the field in which the rule was originally formulated-is not well defined. Herein, the use of olefin strain (OS) energy as a readily calculated predictor of the stability of natural products containing a bridgehead alkene is introduced. Schleyer first used OS energies to classify parent bridgehead alkenes into "isolable", "observable", and "unstable" classes. OS calculations on natural products, using contemporary forcefield methods, unequivocally predict all structurally verified bridgehead alkene natural products to be "isolable". Thus, when one assigns the structure of a putative bridgehead alkene natural product, an OS in the "observable" or "unstable" ranges is a red flag for error.
Circulating microparticles from diabetic rats impair endothelial function and regulate endothelial protein expression.Monday, August 03, 2015
Ishida K, Taguchi K, Hida M, Watanabe S, Kawano K, Matsumoto T, Hattori Y, Kobayashi T,
Acta physiologica (Oxford, England). 3-Aug-2015
Circulating MPs isolated from STZ-induced diabetic rats induce endothelial dysfunction in carotid arteries and regulate protein expressions of eNOS and caveolin-1. These data advance our understanding of the deleterious effects of circulating MPs observed in disorders with diabetic complications. This article is protected by copyright. All rights reserved.
Filter paper-based insulin-like growth factor assay.Monday, August 03, 2015
Jensen AK, Coleman C, Stokes D, Ying GS, Huang J, Kuhn I, Binenbaum G,
Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus / American Association for Pediatric Ophthalmology and Strabismus. 30-Jul-2015
This study assessed validity, reliability, and feasibility of a filter paper blood spot insulin-like growth factor 1 (IGF-1) assay for retinopathy of prematurity (ROP) research. Blood samples were collected from 45 healthy children. Half of each sample was spun to obtain serum; half was applied to filter cards and stored for varying times and at different temperatures. IGF-1 assays were performed using a commercially available kit. Intraclass correlation between blood spot and serum IGF-1 values was high (0.97) for validity, and the mean differences were low for test-retest reliability. Time (up to 25 days) and temperature (4° C to 37° C) had no significant effect on sample stability. Feasibility was further assessed in a second cohort study of 74 premature infants being screened for ROP. A total of 817 filter card samples were successfully collected and transported to a central lab, where IGF-1 assays were successfully performed.
Reversible and Selective Fluorescence Detection of Histidine Using a Naphthalimide-based Chemosensing Ensemble.Monday, August 03, 2015
Zhang R, Meng Q, Jia H, Gao X, Wang Y, Wang R, Zhang Z,
Chemistry, an Asian journal. 31-Jul-2015
We described a new ensemble approach-based chemosensor, NCH-Cu2+, for highly selective and reversible detection of histidine (His) in aqueous solution and live cells. The ligand NCH exhibited specific binding with Cu2+ ions over other metal ions, accompanied with a 92.2% fluorescence quenching. The decomplexation of NCH-Cu2+ ensemble by His led to the liberation of the fluorophore, NCH, and thus the fluorescence was recovered. The specific fluorescence enhancement of NCH-Cu2+ towards His showed a good linearity with a detection of limit at 70 nM. Quantification of intracellular His at single cell level was achieved by microscopy and flow cytometry. Besides the UV-vis and emission titration, reversibility of the NCH-Cu2+ towards His was further confirmed by the imaging and cytometry analysis. In adition, microscopy studies revealed that NCH-Cu2+ was distributed in lysosome of live cells, where it could be employed as the fluorescent biosensor for imaging of His at subcellular level.
Differential expression of plasma miRNAs in patients with unprovoked venous thromboembolism and healthy control individuals.Monday, August 03, 2015
Starikova I, Jamaly S, Sorrentino A, Blondal T, Latysheva N, Sovershaev M, Hansen JB,
Thrombosis research. 15-Jul-2015
The results of this pilot study indicate that plasma miRNAs profiling can provide novel biomarkers of unprovoked VTE.
Stratification of resectable lung adenocarcinoma by molecular and pathological risk estimators.Monday, August 03, 2015
Rakha E, Pajares MJ, Ilie M, Pio R, Echeveste J, Hughes E, Soomro I, Long E, Idoate MA, Wagner S, Lanchbury JS, Baldwin DR, Hofman P, Montuenga LM,
European journal of cancer (Oxford, England : 1990). 30-Jul-2015
The CCP score is an independent prognostic marker in early stage lung adenocarcinoma. The prognostic score provides superior risk estimates than stage alone. The threefold higher risk in the high-risk group defines a subset of patients that should consider therapeutic choices to improve outcome.
JNK is required for maintaining the tumor-initiating cell-like properties of acquired chemoresistant human cancer cells.Monday, August 03, 2015
Liu Y, Zhang X, Wang J, Yang J, Tan WF,
Acta pharmacologica Sinica. 3-Aug-2015
JNK maintains the tumor-initiating cell-like properties of acquired chemoresistant K562/A02 and KB/VCR cells potentially through activating the Hedgehog pathway. Thus, disruption of tumor-initiating cell-like properties by targeting JNK may be a new approach to combating acquired chemoresistance.
Synergistic suppression of human breast cancer cells by combination of plumbagin and zoledronic acid In vitro.Monday, August 03, 2015
Qiao H, Wang TY, Yan W, Qin A, Fan QM, Han XG, Wang YG, Tang TT,
Acta pharmacologica Sinica. 3-Aug-2015
Combination of ZA and PL synergistically suppresses human breast cancer MDA-MB-231SArfp cells in vitro. PL can inhibit ZA-induced activation of the Notch-1 signaling pathway and subsequently reduce the expression of Bcl-2, thus potentiating cancer cell apoptosis.
Biosynthesis-Assisted Structural Elucidation of the Bartolosides, Chlorinated Aromatic Glycolipids from Cyanobacteria.Monday, August 03, 2015
Leão PN, Nakamura H, Costa M, Pereira AR, Martins R, Vasconcelos V, Gerwick WH, Balskus EP,
Angewandte Chemie (International ed. in English). 31-Jul-2015
The isolation of the bartolosides, unprecedented cyanobacterial glycolipids featuring aliphatic chains with chlorine substituents and C-glycosyl moieties, is reported. Their chlorinated dialkylresorcinol (DAR) core presented a major structural-elucidation challenge. To overcome this, we discovered the bartoloside (brt) biosynthetic gene cluster and linked it to the natural products through in vitro characterization of the DAR-forming ketosynthase and aromatase. Bioinformatic analysis also revealed a novel potential halogenase. Knowledge of the bartoloside biosynthesis constrained the DAR core structure by defining key pathway intermediates, ultimately allowing us to determine the full structures of the bartolosides. This work illustrates the power of genomics to enable the use of biosynthetic information for structure elucidation.
[Association between intracellular zinc levels and nutritional status in HIV-infected and uninfected children exposed to the virus].Monday, August 03, 2015
G EM, C ME, L MR, J GP,
Revista chilena de pediatría. 31-7-2015
The deterioration of nutritional status and growth retardation in children were associated with HIV, but not with the levels of intracellular zinc. The dietary intake of this nutrient was not associated with levels of zinc in monocytes or CD4 + and CD4- lymphocytes.
Source: NCBI - Disclaimer and Copyright notice
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