2024-03-29T06:14:14Z
http://www.jmolbiochem.com/index.php/JmolBiochem/oai
oai:ojs.jmolbiochem.com:article/18
2012-06-19T05:49:22Z
JmolBiochem:REV
"120215 2012 eng "
dc
Modulation of monocyte/macrophage-derived cytokine and chemokine profile by persistent Hepatitis C virus (HCV) infection leads to chronic inflammation
Kochlios, Emmanouil; Hellenic Pasteur Institute
Foka, Pelagia; Hellenic Pasteur Institute
Mavromara, Penelope; Hellenic Pasteur Institute
HCV; monocytes; macrophages; cytokines; chemokines; inflammation; hepatocellular carcinoma; lymphotropism
<p>HCV infection presents a major public health problem, with more than 170 million people infected worldwide. Chronicity and persistence of infection constitute the hallmark of the disease. Although HCV is a hepatotropic virus, subsets of immune cells have been found to be permissive to infection and viral replication. Peripheral blood monocytes, attracted to the site of infection and differentiated into macrophages, and resident hepatic macrophages, known as Kupffer cells, are important mediators of innate immunity, through production of several chemokines and cytokines in addition to their phagocytic activity. HCV proteins have been shown to modulate the cytokine and chemokine production profile of monocytes/macrophages, as it is suggested by both <em>in vitro</em> and clinical studies. This modified expression profile appears crucial for the establishment of aberrant inflammation that leads to liver cirrhosis and hepatocellular carcinoma.</p>
Lorem Ipsum Press
2012-02-15 17:34:13
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/18
Journal of Molecular Biochemistry; Vol 1, No 1 (2012)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/27
2012-06-19T05:50:24Z
JmolBiochem:REV
"120616 2012 eng "
dc
Vertebrate scavenger receptor class B member 2 (SCARB2): comparative studies of a major lysosomal membrane glycoprotein
Holmes, Roger Stephen; Griffith University
Vertebrates; SCARB2; comparative proteomics; comparative genomics; evolution; thrombospondin receptor
<p>Scavenger receptor class B member 2 (SCARB2) (also LIMP-2, CD36L2 or LGP85) is a major lysosomal membrane glycoprotein involved in endosomal and lysosomal biogenesis and maintenance. SCARB2 acts as a receptor for the lysosomal mannose-6-phosphate independent targeting of β-glucuronidase and enterovirus 71 and influences Parkinson’s disease and epilepsy. Genetic deficiency of this protein causes deafness and peripheral neuropathy in mice as well as myoclonic epilepsy and nephrotic syndrome in humans. Comparative SCARB2 amino acid sequences and structures and <em>SCARB2</em> gene locations were examined using data from several vertebrate genome projects. Vertebrate SCARB2 sequences shared 43-100% identity as compared with 30-36% sequence identities with other CD36-like superfamily members, SCARB1 and CD36. At least 10 N-glycosylation sites were conserved among most vertebrate SCARB2 proteins examined. Sequence alignments, key amino acid residues and conserved predicted secondary structures were examined, including cytoplasmic, transmembrane and external lysosomal membrane sequences: cysteine disulfide residues, thrombospondin (THP1) binding sites and 16 proline and 20 glycine conserved residues, which may contribute to short loop formation within the exomembrane SCARB2 sequences. Vertebrate <em>SCARB2 </em>genes contained 12 coding exons. The human <em>SCARB2</em> gene contained a CpG island (CpG100), ten microRNA-binding sites and several transcription factor binding sites (including PPARA) which may contribute to a higher level (2.4 times average) of gene expression. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate <em>SCARB2 </em>gene with vertebrate <em>SCARB1</em> and <em>CD36</em> genes. These suggested that <em>SCARB2</em> originated from duplications of the <em>CD36</em> gene in an ancestral genome forming three vertebrate <em>CD36</em> gene family members: <em>SCARB1</em>, <em>SCARB2</em> and <em>CD36</em>.</p>
Lorem Ipsum Press
2012-06-16 12:06:38
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/27
Journal of Molecular Biochemistry; Vol 1, No 2 (2012)
en
http://www.jmolbiochem.com/index.php/JmolBiochem/article/download/27/201
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/60
2012-10-21T03:53:39Z
JmolBiochem:REV
"121018 2012 eng "
dc
Role of Cbl-associated protein/ponsin in receptor tyrosine kinase signaling and cell adhesion
Tomasovic, Ana; Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, D-35392 Giessen, Germany
Kurrle, Nina; Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, D-35392 Giessen, Germany
Banning, Antje; Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, D-35392 Giessen, Germany
Tikkanen, Ritva; Institute of Biochemistry, Medical Faculty, University of Giessen, Friedrichstrasse 24, D-35392 Giessen, Germany
Receptor tyrosine kinase; insulin; diabetes; cell adhesion
<span style="font-family: Times New Roman; font-size: small;"> </span><p>The Cbl-associated protein/ponsin (CAP) is an adaptor protein that contains a so-called Sorbin homology (SoHo) domain and three Src homology 3 (SH3) domains which are engaged in diverse protein-protein interactions. CAP has been shown to function in the regulation of the actin cytoskeleton and cell adhesion and to be involved in the differentiation of muscle cells and adipocytes. In addition, it participates in signaling pathways through several receptor tyrosine kinases such as insulin and neurotrophin receptors. In the last couple of years, several studies have shed light on the details of these processes and identified novel interaction partners of CAP. In this review, we summarize these recent findings and provide an overview on the function of CAP especially in cell adhesion and membrane receptor signaling.</p><span style="font-family: Times New Roman; font-size: small;"> </span>
Lorem Ipsum Press
Deutsche Forschungsgemeinschaft DFG, von Behring Röntgen Foundation, State of Hessen
2012-10-21 03:53:39
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/60
Journal of Molecular Biochemistry; Vol 1, No 3
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/87
2013-02-22T18:18:49Z
JmolBiochem:REV
"130220 2013 eng "
dc
Tumor markers in finding recurrent disease in colorectal cancer: a diagnostic review
Verberne, Charlotte; University Medical Center Groningen
Jong, Helma de; University Medical Center Groningen
Grossmann, Irene; University Medical Center Groningen
Bock, Geertruida de; University Medical Center Groningen
Wiggers, Theo; University Medical Center Groningen
Kema, Ido; University Medical Center Groningen
Muller Kobold, Anneke; University Medical Center Groningen
tumor marker; CEA; clinical biochemistry; colorectal cancer
<p>Aim: In the search for evidence-based follow-up of patients after resection for colorectal cancer, numerous tumor markers have been proposed. This review has evaluated these markers and comments on the diagnostic accuracy in finding recurrent disease in relation to Carcino-Embryonic Antigen (CEA).</p> <p>Methods: A comprehensive literature review (1985-2010) was performed by two independent reviewers. Sensitivity and specificity of markers mentioned in the articles were checked by recalculation. A validated quality score system was used to estimate study quality.</p> <p>Results: Seventeen studies focusing on eight different markers were included. Three markers were shown to have comparable or better accuracy than CEA: TPA, CA 242 and CA 72-4 in at least one study. These three markers, from four independent studies, showed a tumor marker sensitivity of > 60% in combination with an outperformance of CEA in follow-up. These results were not confirmed by six other studies investigating the same markers.</p> <p>Conclusion: This review revealed three tumor markers other than CEA that have been shown to adequately indicate recurrences in colorectal cancer. However, comparability of studies was difficult. Therefore a prospective study of these markers seems necessary to investigate their real value, and to overcome design and inclusion biases.</p>
Lorem Ipsum Press
2013-02-22 18:18:49
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/87
Journal of Molecular Biochemistry; Vol 2, No 1 (2013)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/89
2013-02-22T18:18:49Z
JmolBiochem:REV
"130220 2013 eng "
dc
Metabolism of triacylglycerols in Rhodococcus species: insights from physiology and molecular genetics
Alvarez, Héctor M.; University of Patagonia
Silva, Roxana A.
Herrero, Marisa
Hernández, Martín A.
Villalba, María S.
Rhodococcus, triacylglycerols, biosynthesis and degradation genes
<p>Rhodococcus bacteria possess the ability to accumulate variable amounts of triacylglycerols (TAG) during growth on diverse carbon sources. The evolution seems to have selected these microorganisms as specialists in the accumulation of TAG among bacteria, since their biochemistry is efficiently designed for the biosynthesis and mobilization of these lipids. Detailed research of rhodococcal TAG metabolism started only a few years ago; thus, the fundamental understanding of this process and its regulation remains to be clarified. However, some interesting advances in the basic knowledge on TAG metabolism in rhodococci have been made. Most studies have focused on the physiology of TAG biosynthesis and mobilization in rhodococci. Only recently, some advances in molecular biology and genetics on TAG metabolism occurred as a result of the increasing available genomic information and the development of new genetic tools for rhodococci. These studies have been focused principally on some enzymes of TAG biosynthesis, such as the wax esters/diacylglycerolacyltransferases (WS/DGAT) and TAG granule-associated proteins. In this context, the most relevant achievements of basic research in the field have been summarized in this review article.</p>
Lorem Ipsum Press
2013-02-22 18:18:49
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/89
Journal of Molecular Biochemistry; Vol 2, No 1 (2013)
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Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/97
2013-12-06T05:44:31Z
JmolBiochem:REV
"131017 2013 eng "
dc
RETRACTED ARTICLE: The biochemistry of male homosexuality
Kotsi, Ioanna
Vlachaki, Chrisanthy
Tsitsas, George Dimosthenis; Harokopio University of Athens
male homosexuality, fraternal birth order, maternal immune hypothesis, heterosexuality, homosexuality
<p>Homosexuality is a common occurrence in humans and other species. It is a complex, universal phenomenon whose genetic and evolutionary basis is poorly understood. Despite great progress in the sciences, our understanding of the determinants of sexual orientation and, more specifically, of male homosexuality, is incomplete. In this paper, we have reviewed the biological causes of male homosexuality, which may provide clues for further research in this field, as provable biological or genetic differences between heterosexuals and homosexuals that weren't caused by their behaviour haven’t been found.</p><p><span><strong>This article has been retracted due to plagiarism. An erratum will be published in Volume 3, Issue 1 (2014).</strong></span></p>
Lorem Ipsum Press
2013-10-17 00:00:00
http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/97
Journal of Molecular Biochemistry; Vol 2, No 3 (2013)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/103
2013-06-23T06:49:30Z
JmolBiochem:REV
"130622 2013 eng "
dc
Somatostatin and Epidermal Growth Factor Receptors: Implications in Breast Cancer
Kumar, Ujendra; Faculty of Pharmaceutical sciences, University of British Columbia
Kharmate, Geetanjali; Faculty of Pharmaceutical Sciences
Post Doctoral fellow
Breast Cancer, Dimerization, Heterodimerization, Epidermal growth factor, Epidermal growth factor Receptors, Somatostatin, Somatostatin Receptors
<p>Despite several advances, the underlying mechanism of complexity of breast cancer progression still remains elusive. In addition to the genetic predisposition, several growth factor receptors including insulin growth factor receptor (IGF), platelet derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) relaying proliferative signals are accountable for disease progression. Epidermal growth factor receptors (EGFRs, or commonly known as ErbBs), members of the receptor tyrosine kinase family (RTKs), play a central role in tumor growth, progression and metastatic disease. Typically, agonist dependent activation of EGFR results in receptor phosphorylation, homo- and/or heterodimerization and modulation of signaling pathways leading to cell proliferation, survival and metastasis. Targeting one or multiple steps in EGFR-mediated tumor progression may serve as a better approach in drug therapies. Unlike EGFRs, G-protein coupled somatostatin receptors (SSTRs) have been recognized as negative regulators of breast tumors. The activation of SSTRs modulates downstream signaling responsible for tumor growth and consequent cytostatic or cytotoxic effects on tumor proliferation. SSTR subtypes are well characterized to form homo-and/or heterodimers within the same family as well as with other GPCRs. Clinically, the chimeric molecule targeting both SSTR5 and dopamine receptors (specifically dopamine receptor 2) is in use for the treatment of pituitary tumors. This review describes the interplay between SSTRs and EGFR and the potential role of such cross talk in attenuation of EGFR-mediated signaling pathways involved in tumorigenesis. Furthermore, recent findings supporting the role of SSTR in EGFR-mediated signaling in tumor biology are discussed in detail.</p>
Lorem Ipsum Press
2013-06-23 06:49:30
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/103
Journal of Molecular Biochemistry; Vol 2, No 2 (2013)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/122
2014-06-30T12:38:35Z
JmolBiochem:REV
"140630 2014 eng "
dc
Molecular dynamics simulations through GPU video games technologies
Loukatou, Styliani
Papageorgiou, Louis
Fakourelis, Paraskevas
Filntisi, Arianna
Polychronidou, Eleftheria
Bassis, Ioannis
Megalooikonomou, Vasileios
Makałowski, Wojciech
Vlachakis, Dimitrios
Kossida, Sophia
Molecular Dynamics; GPGPU; CUDA;
<p>Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD).</p> <p>MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU).</p> <p>A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.</p>
Lorem Ipsum Press
2014-06-30 00:00:00
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/122
Journal of Molecular Biochemistry; Vol 3, No 2 (2014)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/130
2014-11-03T23:20:15Z
JmolBiochem:REV
"141031 2014 eng "
dc
SOCS, inflammation, and metabolism
Inagaki-Ohara, Kyoko; Research Institute, National Center for Global Health and Medicine (NCGM)
Yoshimura, Akihiko; Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku, Tokyo, 160-8582, Japan
SOCS; obesity; cancer; leptin; insulin
<p>Obesity is characterized by the development of low-grade chronic inflammation, which is a contributing factor in defective energy metabolism. A hallmark of metabolic dysregulation, obesity is a life-style disease that contributes to diabetes, hypertension, and dyslipidemia. Further, recent studies warn that obesity can be a risk factor for certain cancers and exacerbates infectious diseases. This association is called the “metabolic domino”. Suppressor of cytokine signaling (SOCS) proteins are negative feedback regulators of cytokine and hormone signaling mediated by the JAK-STAT signaling pathway. SOCS proteins regulate cell-cell communication through JAK-STAT-dependent cytokines and signaling by Toll-like receptors (TLRs) and they may be influenced by dietary factors such as fatty acids and glucose. In this review, we focus on the role of the JAK-STAT-SOCS signaling cascade in metabolic disorder and obesity-related diseases.</p>
Lorem Ipsum Press
Kyoko Inagaki-Ohara, Research Institute, National Center for Global Health and Medicine (NCGM), Akihiko Yoshimura, Department of Microbiology and Immunology, Keio University School of Medicine
2014-11-03 23:20:15
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/130
Journal of Molecular Biochemistry; Vol 3, No 3
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/145
2015-07-20T10:59:17Z
JmolBiochem:REV
"150719 2015 eng "
dc
Protein phosphorylation prediction: limitations, merits and pitfalls
Vlachakis, Dimitrios; Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527
Bencurova, Elena; Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04181, Kosice
Papageorgiou, Louis; Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527
Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, University Campus, Athens, 15784
Bhide, Mangesh; Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 04181
Institute of Neuroimmunology, Slovak Academy of Sciences, 84245 Bratislava
Kossida, Sophia; Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
IMGT®, the international ImMunoGeneTics information system®, Institute of Human Genetics, Montpellier, France
Bioinformatics; Protein Phosphorylation; Post-Translational Modifications; Benchmark; Phosphorylation Prediction; GPS; NetPhos; Phospho.ELM; PPSP; SMALI; ScanSite; Musite; NetPhos
<p>Protein phosphorylation is a major protein post-translational modification process that plays a pivotal role in numerous cellular processes, such as recognition, signaling or degradation. It can be studied experimentally by various methodologies, including western blot analysis, site-directed mutagenesis, 2D gel electrophoresis, mass spectrometry etc. A number of in silico tools have also been developed in order to predict plausible phosphorylation sites in a given protein. In this review, we conducted a benchmark study including the leading protein phosphorylation prediction software, in an effort to determine which performs best. The first place was taken by GPS 2.2, having predicted all phosphorylation sites with a 83% fidelity while in second place came NetPhos 2.0 with 69%.</p> <p> </p><p> </p>
Lorem Ipsum Press
2015-07-20 10:59:17
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/145
Journal of Molecular Biochemistry; Vol 4, No 2 (2015)
en
http://www.jmolbiochem.com/index.php/JmolBiochem/article/download/145/503
http://www.jmolbiochem.com/index.php/JmolBiochem/article/download/145/504
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/150
2015-11-27T19:50:59Z
JmolBiochem:REV
"151127 2015 eng "
dc
Biochemical and cytogenetic changes in postovulatory and in vitro aged mammalian oocytes: a predisposition to aneuploidy
Mailhes, John B.
postovulatory ageing; oocyte; aneuploidy; premature centromere separation
<p>Aneuploidy represents the most prevalent genetic disorder of man. Its association with spontaneous abortions, mental and physical retardation, and numerous malignant cells is well-known. Unfortunately, little is known about the causes and even less about the underlying molecular mechanisms of aneuploidy, especially in mammalian germ cells. Although several etiologies have been proposed for describing human aneuploidy, the only consistent finding remains its positive correlation with maternal age. At the outset, it is essential to point out that there exist numerous potential causes and mechanisms for the etiology of aneuploidy. Nevertheless, information about the molecular mechanisms of chromosome segregation in various species is providing a foundation for research designed to investigate the causes and mechanisms of aneuploidy. The intent of this review is to propose that the biochemical reactions and cellular organelles responsible for accurate chromosome segregation become compromised during postovulatory and in vitro oocyte aging; thus, increasing the probability of faulty chromosome segregation. Recent data have shown that the efficacies of the spindle assembly checkpoint and the chromosome cohesion proteins diminish as oocytes age postovulation and during in vitro culture. Such changes represent potential models for studying aneuploidy. Prior to describing the biochemical and cellular organelle changes found in aged oocytes and their effect on chromosome segregation, an overview of the molecular details surrounding chromosome segregation is presented.</p> <p> </p><p> </p>
Lorem Ipsum Press
2015-11-27 19:50:59
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http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/150
Journal of Molecular Biochemistry; Vol 4, No 3 (2015)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/206
2017-12-08T10:34:20Z
JmolBiochem:REV
"171210 2017 eng "
dc
Zika virus infection: a review of available techniques towards early detection
Glover, Kathleen KM; University of Manitoba
Coombs, Kevin; University of Manitoba
zika virus; zika virus diagnosis; pandemic
<p>Zika virus belongs to the family Flaviviridae as do other viruses like Dengue, West Nile and Yellow Fever. They are arboviruses transmitted by the Aedes species of mosquito. Zika virus was first isolated in rhesus monkeys in Uganda in 1947. Human infections of the virus were found between the 1960s and 1980s in Africa, the Americas, Asia and the Pacific. The similarity in clinical presentation in Zika-infected patients compared with Dengue caused infections to be previously misdiagnosed as Dengue infection. The Zika virus pandemic in 2015 created a lot of concern globally because of little information about available techniques, samples as well as no available antiviral and vaccines for treatment and vaccination against infection. In addition, the vectors identified for transmission, Aedes aegypti and Aedes albopictus, were of great concern due to their ability to survive both temperate and tropical climatic conditions, hence indicating the possible global spread of Zika virus infection. Almost two years after the report of infection in pregnant women in Brazil resulting in microcephalic babies, Zika virus was identified as a public health problem. Thus, a lot of research into early detection and prevention has been conducted to control the spread of the virus. This review paper highlights available information on techniques currently available for diagnosis of infection caused by Zika virus.</p> <p> </p> <p> </p>
Lorem Ipsum Press
2017-12-08 10:34:20
application/pdf
http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/206
Journal of Molecular Biochemistry; Vol 6, No 2 (2017)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/212
2017-12-08T10:34:20Z
JmolBiochem:REV
"171210 2017 eng "
dc
HCV genetics and genotypes dictate future antiviral strategies
Papageorgiou, Louis; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, University Campus, Athens 15784, Greece.
Vlachakis, Chrisanthy; Clinical Dietitian-Nutritionist, PhD, Harokopio University, Kallithea, Attica, Greece.
Dragoumani, Konstantina; Clinical Dietitian-Nutritionist, PhD, Harokopio University, Kallithea, Attica, Greece.
Raftopoulou, Sofia; Sotiria Chest Diseases Hospital,152, Mesogion Av., Athens 11527, Greece.
Brouzas, Dimitrios; 1st Department of Ophthalmology, University of Athens, 154, Mesogion Street, Athens 11527, Greece.
Nicolaides, Nicolas C; Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, “Aghia Sophia” Children’s Hospital, Athens, Greece.
Chrousos, George P; Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, “Aghia Sophia” Children’s Hospital, Athens, Greece.
Saudi Diabetes Study Research Group, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia.
Charmandari, Evangelia; Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, “Aghia Sophia” Children’s Hospital, Athens, Greece.
Megalooikonomou, Vasileios; Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras 26500, Greece.
Vlachakis, Dimitrios; Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras 26500, Greece.
Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece.
HCV; Hepatitis C virus; hepatitis; Genetics; antiviral
<p class="RSCB01ARTAbstract">At the end of the 1980s, the hepatitis C virus (HCV) was cloned and formally identified as the cause of the majority of non-A and non-B hepatitis cases. Today, around 170 million people worldwide are infected with HCV, making it five times more common than infection with the human immunodeficiency virus (HIV). Several methods exist which mediate the spread of infection. One of the most common and efficient is sharing or re-using injecting equipment; studies have indicated that 80-90% of individuals in some populations of intravenous drug users test positive in serum HCV assays. Contracting HCV from infected blood transfusions was also a major cause of infection before screening tests were introduced in the early 1990s. Other possible, but less common, methods of infection transmission include mother-to-child during pregnancy, sexual contact and nosocomial acquisition (for example between surgical or dialysis patients). It appears that concurrent HIV-1 infection increases the risk of HCV transmission via the mother-to-child or sexual routes.</p>
Lorem Ipsum Press
2017-12-08 10:34:20
application/pdf
http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/212
Journal of Molecular Biochemistry; Vol 6, No 2 (2017)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
oai:ojs.jmolbiochem.com:article/269
2021-01-07T15:50:51Z
JmolBiochem:REV
"201230 2020 eng "
dc
Irisin as a Biomarker for Insulin Resistance in Polycystic Ovary Syndrome: a Meta-analysis
Bacopoulou, Flora; Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens, Greece
irisin; biomarker; polycystic ovary syndrome; PCOS; insulin resistance; HOMA-IR
<p>Background: Irisin has attracted growing interest as a potential novel biomarker of polycystic ovary syndrome (PCOS). Aim: A meta-analysis was performed to compare circulating irisin concentrations between PCOS and control women, and to explore the possible relation of irisin and insulin resistance, by associating this hormone with the homeostatic model assessment for insulin resistance (HOMA-IR). Methods: An extended search of the PubMed/Medline, Google Scholar, and Web of Science databases (last updated on 9 March 2019) was performed to identify all articles published in the English language pertaining to circulating irisin in women with PCOS and control women. Results: Eleven studies that involved 1,017 PCOS patients and 669 controls were included. A random effects model revealed a moderate estimate of effect size (SMD: 0.27, 95% CI: -0.13 to 0.67), indicating that circulating irisin concentrations did not differ significantly between PCOS women and controls. Another random effects model (four studies) revealed a moderate estimate of correlation and a statistically significant positive correlation between circulating irisin concentrations and HOMA-IR (Correlation: 0.372, 95% CI: 0.0843 to 0.603, p = 0.012). Irisin may play an important role in PCOS in relation to the inherent insulin resistance of the syndrome. This association requires further clarification in well-designed large-scale studies in women with PCOS.</p>
Lorem Ipsum Press
2021-01-07 15:50:51
application/pdf
http://www.jmolbiochem.com/index.php/JmolBiochem/article/view/269
Journal of Molecular Biochemistry; Vol 9, No 1 (2020)
en
Articles will be published under the terms of the Creative Commons Attribution License allowing unrestricted copying, distribution, transmission and adaptation of the work, under the condition that the original article is properly cited.More specifically, authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).