Prognostic value of neutrophil-to-lymphocyte ratio in breast cancer
Publication date: Available online 12 May 2015 Source:FEBS Open Bio Author(s): Jie Chen , Qiwen Deng , Yuqin Pan , Bangshun He , Houqun Ying , Huiling Sun , Xian Liu , Shukui Wang Inflammation is an essential component of pathogenesis and progression of cancer. A high neutrophil-to-lymphocyte ratio (NLR) is considered as a prognostic indicator for breast cancer. This meta-analysis was conducted to establish the overall accuracy of the NLR test in the diagnosis of breast cancer. A comprehensive search of the literature was conducted by using PubMed, Web of Science and China National Knowledge Infrastructure (CNK...
Source: FEBS Open Bio - May 17, 2015 Category: Molecular Biology Source Type: research
Substrate specificity of mitochondrial intermediate peptidase analysed by a support-bound peptide library
Publication date: Available online 16 May 2015 Source:FEBS Open Bio Author(s): M.F.M. Marcondes , F.M. Alves , D.M. Assis , I.Y. Hirata , L. Juliano , V. Oliveira , M.A. Juliano The substrate specificity of recombinant human mitochondrial intermediate peptidase (hMIP) using a synthetic support-bound FRET peptide library is presented. The collected fluorescent beads, which contained the hydrolysed peptides generated by hMIP, were sequenced by Edman degradation. The results showed that this peptidase presents a remarkable preference for polar uncharged residues at P1 and P1́ substrate positions: Ser=Gln>Th...
Source: FEBS Open Bio - May 17, 2015 Category: Molecular Biology Source Type: research
HIV-1 matrix domain removal ameliorates virus assembly and processing defects incurred by positive nucleocapsid charge elimination
Publication date: Available online 9 April 2015 Source:FEBS Open Bio Author(s): Li-Jung Ko , Fu-Hsien Yu , Kuo-Jung Huang , Chin-Tien Wang Human immunodeficiency virus type 1 nucleocapsid (NC) basic residues presumably contribute to virus assembly via RNA, which serves as a scaffold for Gag-Gag interaction during particle assembly. To determine whether NC basic residues play a role in Gag cleavage (thereby impacting virus assembly), Gag processing efficiency and virus particle production were analyzed for an HIV-1 mutant NC15A, with alanine serving as a substitute for all NC basic resides. Results indicate that NC1...
Source: FEBS Open Bio - April 9, 2015 Category: Molecular Biology Source Type: research
Expression of nephronectin is inhibited by oncostatin M via both JAK/STAT and MAPK pathways
Publication date: Available online 8 April 2015 Source:FEBS Open Bio Author(s): Tamaki Kurosawa , Atsushi Yamada , Masamichi Takami , Dai Suzuki , Yoshiro Saito , Katsuhiro Hiranuma , Takuya Enomoto , Naoko Morimura , Matsuo Yamamoto , Takehiko Iijima , Tatsuo Shirota , Hiroyuki Itabe , Ryutaro Kamijo Nephronectin (Npnt), also called POEM, is an extracellular matrix protein considered to play critical roles as an adhesion molecule in the development and functions of various tissues, such as the kidneys, liver, and bones. In the present study, we examined the molecular mechanism of Npnt gene expression and ...
Source: FEBS Open Bio - April 8, 2015 Category: Molecular Biology Source Type: research
The AhR agonist VAF347 augments retinoic acid-induced differentiation in leukemia cells
Publication date: Available online 8 April 2015 Source:FEBS Open Bio Author(s): Christopher N. Ibabao , Rodica P. Bunaciu , Deanna M.W. Schaefer , Andrew Yen In binary cell-fate decisions, driving one lineage and suppressing the other are conjoined. We have previously reported that aryl hydrocarbon receptor (AhR) promotes retinoic acid (RA)-induced granulocytic differentiation of lineage bipotent HL-60 myeloblastic leukemia cells. VAF347, an AhR agonist, impairs the development of CD14+CD11b+ monocytes from granulo-monocytic (GM) stage precursors. We thus hypothesized that VAF347 propels RA-induced granulocytic dif...
Source: FEBS Open Bio - April 8, 2015 Category: Molecular Biology Source Type: research
Imaging and force measurement of LDL and HDL by AFM in air and liquid
Publication date: Available online 7 April 2015 Source:FEBS Open Bio Author(s): Chaoye Gan , Meiying Ao , Zhanghua Liu , Yong Chen The size and biomechanical properties of lipoproteins are tightly correlated with their structures/functions. While atomic force microscopy (AFM) has been used to image lipoproteins the force measurement of these nano-sized particles is missing. We detected that the sizes of LDL and HDL in liquid are close to the commonly known values. The Young’s modulus of LDL or HDL is ∼0.4 GPa which is similar to that of some viral capsids or nanovesicles but greatly larger than that of various ...
Source: FEBS Open Bio - April 7, 2015 Category: Molecular Biology Source Type: research
Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site
Publication date: Available online 2 April 2015 Source:FEBS Open Bio Author(s): Shalini Iyer , Penelope J. La-Borde , Karl A.P. Payne , Mark R. Parsons , Anthony J. Turner , R. Elwyn Isaac , K. Ravi Acharya Eukaryotic aminopeptidase P1 (APP1), also known as X-prolyl aminopeptidase (XPNPEP1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the N-terminus of peptides possessing a penultimate N-terminal proline residue. The enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cl...
Source: FEBS Open Bio - April 2, 2015 Category: Molecular Biology Source Type: research
Cloning and expressing a highly functional and substrate specific farnesoic acid o-methyltransferase from the Asian citrus psyllid (Diaphorina citri Kuwayama)
Publication date: Available online 28 March 2015 Source:FEBS Open Bio Author(s): Evelien Van Ekert , Robert G. Shatters Jr. , Pierre Rougé , Charles A. Powell , Guy Smagghe , Dov Borovsky The Asian citrus psyllid, Diaphorina citri, transmits a phloem-limited bacterium, Candidatus ‘Liberibacter’ asiaticus that causes citrus greening disease. Because juvenile hormone (JH) plays an important role in adult and nymphal development, we studied the final steps in JH biosynthesis in D. citri. A putative JH acid methyltransferase ortholog gene (jmtD) and its cognate cDNA were identified by searching D. citri genome d...
Source: FEBS Open Bio - March 29, 2015 Category: Molecular Biology Source Type: research
Novel Cosic resonance (standing wave) solutions for components of the JAK–STAT cellular signaling pathway: A convergence of spectral density profiles
Publication date: Available online 25 March 2015 Source:FEBS Open Bio Author(s): Lukasz M. Karbowski , Nirosha J. Murugan , Michael A. Persinger Cosic discovered that spectral analyses of a protein sequence after each constituent amino acid had been transformed into an appropriate pseudopotential predicted a resonant energy between interacting molecules. Several experimental studies have verified the predicted peak wavelength of photons within the visible or near-visible light band for specific molecules. Here, this concept has been applied to a classic signaling pathway, JAK–STAT, traditionally composed of nine s...
Source: FEBS Open Bio - March 28, 2015 Category: Molecular Biology Source Type: research
Evaluation of the diagnostic value of alpha-L-fucosidase, alpha-fetoprotein and thymidine kinase 1 with ROC and logistic regression for hepatocellular carcinoma
Publication date: Available online 26 March 2015 Source:FEBS Open Bio Author(s): Shi-Yan Zhang , Bi-Ding Lin , Bu-Ren Li The purpose of this study was to evaluate the diagnostic efficiency for hepatocellular carcinoma (HCC) with the combined analysis of alpha-L-fucosidase (AFU), alpha-fetoprotein (AFP) and thymidine kinase 1 (TK1). Serum levels of AFU, AFP and TK1 were measured in: 116 patients with HCC, 109 patients with benign hepatic diseases, and 104 normal subjects. The diagnostic value was analyzed using the logistic regression equation and receiver operating characteristic curves (ROC). Statistical distributi...
Source: FEBS Open Bio - March 27, 2015 Category: Molecular Biology Source Type: research
Mining disease genes using integrated protein–protein interaction and gene–gene co-regulation information
In this study, we constructed an eQTL-based gene–gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining. (Source: FEBS Open Bio)
Source: FEBS Open Bio - March 27, 2015 Category: Molecular Biology Source Type: research
Novel Cosic resonance (standing wave) solutions for components of the JAK-STAT cellular signaling pathway: a convergence of spectral density profiles
Publication date: Available online 25 March 2015 Source:FEBS Open Bio Author(s): Lukasz M. Karbowski , Nirosha J. Murugan , Michael A. Persinger Cosic discovered that spectral analyses of a protein sequence after each constituent amino acid had been transformed into an appropriate pseudopotential predicted a resonant energy between interacting molecules. Several experimental studies have verified the predicted peak wavelength of photons within the visible or near-visible light band for specific molecules. Here, this concept has been applied to a classic signaling pathway, JAK-STAT, traditionally composed of nine seq...
Source: FEBS Open Bio - March 25, 2015 Category: Molecular Biology Source Type: research
ABCC6 deficiency is associated with activation of BMP signaling in liver and kidney
Publication date: Available online 23 March 2015 Source:FEBS Open Bio Author(s): Ana M. Blazquez-Medela , Pierre J. Guihard , Jiayi Yao , Medet Jumabay , Aldons J. Lusis , Kristina I. Boström , Yucheng Yao Mutations in ABCC6 (ATP-binding cassette, subfamily C, member 6), an orphan transporter expressed in the liver, are the cause of pseudoxanthoma elasticum. Since ABCC6 was reported to affect matrix Gla protein (MGP), an inhibitor of bone morphogenetic proteins (BMPs), we studied BMP signaling and expression in various tissues of mice with and without functional ABCC. Enhanced BMP signaling was found in all exa...
Source: FEBS Open Bio - March 23, 2015 Category: Molecular Biology Source Type: research
Impaired respiratory function in MELAS-induced pluripotent stem cells with high heteroplasmy levels
Publication date: Available online 20 March 2015 Source:FEBS Open Bio Author(s): Masaki Kodaira , Hideyuki Hatakeyama , Shinsuke Yuasa , Tomohisa Seki , Toru Egashira , Shugo Tohyama , Yusuke Kuroda , Atsushi Tanaka , Shinichiro Okata , Hisayuki Hashimoto , Dai Kusumoto , Akira Kunitomi , Makoto Takei , Shin Kashimura , Tomoyuki Suzuki , Gakuto Yozu , Masaya Shimojima , Chikaaki Motoda , Nozomi Hayashiji , Yuki Saito , Yu-ichi Goto , Keiichi Fukuda Mitochondrial diseases are heterogeneous disorders, caused by mitochondrial dysfunction. Mitochondria are not regulated solely by nuclear genomic DNA b...
Source: FEBS Open Bio - March 20, 2015 Category: Molecular Biology Source Type: research
Study of circulating IgG antibodies to peptide antigens derived from BIRC5 and MYC in cervical cancer
Publication date: Available online 17 March 2015 Source:FEBS Open Bio Author(s): Yangchun Xu , Yonglong Jin , Linlin Liu , Xuan Zhang , Yubing Chen , Jun Wei The present study was undertaken to detect circulating IgG antibodies to peptide antigens derived from baculoviral IAP repeat-containing protein 5 isoform 2 (BIRC5) and myc proto-oncogene protein (MYC) in cervical cancer. A total of 107 female patients with cervical cancer of stages I and II, and 130 healthy female subjects were recruited for analysis of circulating IgG antibodies to BIRC5 and MYC. Student’s t-test showed significant differences in circula...
Source: FEBS Open Bio - March 17, 2015 Category: Molecular Biology Source Type: research
