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Mol Biosyst 2017 Nov;13(12):2715-2728

The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, Gansu 730000, China.

Hypothalamic dysfunction is a key factor in depression; increasing evidence highlights neuroinflammation abnormalities as well as imbalances in neurotransmitters and the purinergic system in the pathophysiology of depression. However, little is known about the metabolomic changes in the hypothalamus of depressed patients with neuroinflammation. Herein, taking advantage of the well-established lipopolysaccharide (LPS)-induced depression mouse model, we measured metabolic changes in the hypothalamus using gas chromatography-mass spectrometry (GC-MS). Read More

Mol Biosyst 2017 11;13(12):2729-2730

Division of Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.

Correction for 'Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity - a computational study' by M. Tomin et al., Mol. Read More

Mol Biosyst 2017 Nov;13(12):2531-2544

Department of Physics, Indian Institute of Science, Bengaluru 560012, India.

A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of 'flexible disorder' and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA) and (PAKKA), represent the tails of several bacterial DNA-binding proteins. Read More

Mol Biosyst 2017 Nov;13(12):2697-2703

Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.

In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA-ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Read More

Mol Biosyst 2017 Nov;13(12):2704-2714

School of Life Science, Ulsan National Institute of Science and Technology, Ulsan, South Korea.

The prevalence of Staphylococcus aureus worldwide as a nosocomial infectious agent is recognized but the reason behind the spread of this bacterium has remained elusive. Here, we hypothesized that the communication of S. aureus might benefit from it blocking other bacteria from establishing themselves on the surface. Read More

Mol Biosyst 2017 Nov;13(12):2509-2520

Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.

The protein arginine methyltransferase (PRMT) family of enzymes comprises nine family members in mammals. They catalyze arginine methylation, either monomethylation or symmetric/asymmetric dimethylation of histone and non-histone proteins. PRMT methylation of its substrate proteins modulates cellular processes such as signal transduction, transcription, and mRNA splicing. Read More

Mol Biosyst 2017 Nov;13(12):2498-2508

School of Biological Sciences, Nanyang Technological University, 637551, Singapore.

Host immune evasion is a key strategy for the continual survival of many microbial pathogens including Apicomplexan protozoan: Plasmodium spp., the causative agent of Malaria. The malaria parasite has evolved a variety of mechanisms to evade the host immune responses within its two hosts: the female Anopheles mosquito vector and vertebrate host. Read More

Mol Biosyst 2017 Nov;13(12):2453-2465

Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Australia.

Cone snails are predatory gastropods whose neurotoxic venom peptides (conotoxins) have been extensively studied for pharmacological probes, venom evolution mechanisms and potential therapeutics. Conotoxins have a wide range of structural and functional classes that continue to undergo accelerated evolution that underlies the rapid expansion of the genus over their short evolutionary history. A number of pharmacological classes, driven by separately evolved defensive and predatory venoms, have been hypothesised to facilitate shifts in prey that exemplify the adaptability of cone snails. Read More

Mol Biosyst 2017 Nov;13(12):2489-2497

Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India.

Infectious diseases caused by bacterial pathogens pose a major concern to public health and, thus, greater attention must be given to providing insightful knowledge on host-pathogen interactions. There are several theories addressing the dynamics of complex mechanisms of host-pathogen interactions. The availability of an ample number of universally accepted model systems, including vertebrates, invertebrates, and mammalian cells, provides in-depth transcriptomics data to evaluate these complex mechanisms during host-pathogen interactions. Read More

Mol Biosyst 2017 Nov;13(12):2687-2696

Epidemiology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy.

Endocrine disrupting chemicals (EDCs) are natural or synthetic exogenous substances affecting human health. Although present at low concentrations in the environment, they can cause a broad range of negative effects on the endocrine functions by mimicking the action of steroid hormones due to their structural similarity. Hormonal unbalance can play an important role in carcinogenesis at any stage of disease. Read More

Mol Biosyst 2017 Nov;13(12):2672-2686

Department of Physics, University of Trento, via Sommarive 14, Trento, Italy.

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Read More

Mol Biosyst 2017 Nov;13(12):2660-2671

Department of Biochemistry and Molecular Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

ADP-ribosylation is a protein post-translational modification catalyzed by ADP-ribose transferases (ARTs). ART activity is critical in mediating many cellular processes, and is required for DNA damage repair. All five histone proteins are extensively ADP-ribosylated by ARTs upon induction of DNA damage. Read More

Mol Biosyst 2017 Nov;13(12):2650-2659

College of Information Engineering, Changsha Medical University, Changsha, 410219, China.

An increasing amount of evidence indicates that microRNAs (miRNAs) are closely related to many important biological processes and play a significant role in various human diseases. More and more researchers have begun to seek effective methods to predict potential miRNA-disease associations. However, reliable computational methods to predict potential disease-related miRNAs are lacking. Read More

Mol Biosyst 2017 Nov;13(12):2521-2530

Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, West Bengal, India.

Expression level provides important clues about gene function. Previously, various efforts have been undertaken to profile human genes according to their expression level. Intrinsically disordered proteins (IDPs) do not adopt any rigid conformation under physiological conditions, however, are considered as an important functional class in all domains of life. Read More

Mol Biosyst 2017 Nov;13(12):2638-2649

Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.

In all organisms, DNA glycosylases initiate base excision repair pathways resulting in removal of aberrant bases from DNA. Human SMUG1 belongs to the superfamily of uracil-DNA glycosylases catalyzing the hydrolysis of the N-glycosidic bond of uridine and uridine lesions bearing oxidized groups at C5: 5-hydroxymethyluridine (5hmU), 5-formyluridine (5fU), and 5-hydroxyuridine (5hoU). An apurinic/apyrimidinic (AP) site formed as the product of an N-glycosylase reaction is tightly bound to hSMUG1, thus inhibiting the downstream action of AP-endonuclease APE1. Read More

Mol Biosyst 2017 Nov;13(12):2477-2488

Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, UK.

Regulation of protein translation constitutes a crucial step in control of gene expression. In comparison to transcriptional regulation, however, translational control has remained a significantly under-studied layer of gene expression. This trend is now beginning to shift thanks to recent advances in next-generation sequencing, proteomics, and microscopy based methodologies which allow accurate monitoring of protein translation rates, from single target messenger RNA molecules to genome-wide scale studies. Read More

Mol Biosyst 2017 Nov;13(12):2625-2637

Dipartimento di Area Medica, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy.

Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Read More

Mol Biosyst 2017 Nov;13(12):2615-2624

Department of Industrial Engineering, University of Puerto Rico Mayagüez, Mayagüez, Puerto Rico.

Hedgehog signaling (Hh) has been shown to be hyper-activated in several cancers. However, active Hh signaling can promote or inhibit tumor growth; thus identification of markers beyond main canonical Hh target genes is needed to improve patient selection and clinical outcome in response to Hh inhibitors. Cancer-associated fibroblasts (CAFs) have been linked with tumor progression and beneficial response to Hh inhibitors. Read More

Mol Biosyst 2017 Nov;13(12):2603-2614

Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata 700108, India.

Toxic cyanobacteria blooms populate water bodies by consuming external nutrients and releasing cyanotoxins that are detrimental for other aquatic species, producing a significant impact on the plankton ecosystem and food web. To exercise population-level control of toxin production, understanding the biochemical mechanisms that explain cyanotoxin regulation within a bacterial cell is of utmost importance. In this study, we explore the mechanistic events to investigate the dependence of toxin microcystin on external nitrogen, a known regulator of the toxin, and for the first time, propose a kinetic model that analyzes the intracellular conditions required to ensure nitrogen dependence on microcystin. Read More

Mol Biosyst 2017 Nov;13(12):2592-2602

Department of Computer Science, FAST National University of Computer & Emerging Sciences, Peshawar, Pakistan.

Accurate elucidation of genome wide protein-protein interactions is crucial for understanding the regulatory processes of the cell. High-throughput techniques, such as the yeast-2-hybrid (Y2H) assay, co-immunoprecipitation (co-IP), mass spectrometric (MS) protein complex identification, affinity purification (AP) etc., are generally relied upon to determine protein interactions. Read More

Mol Biosyst 2017 Nov;13(12):2466-2476

Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.

Voltage-dependent anion channels (VDACs) are a family of three mitochondrial porins and the most abundant integral membrane proteins of the mitochondrial outer membrane (MOM). VDACs are known to be involved in metabolite/ion transport across the MOM and in many cellular processes ranging from mitochondria-mediated apoptosis to the control of energy metabolism, by interacting with cytosolic, mitochondrial and cytoskeletal proteins and other membrane channels. Despite redundancy and compensatory mechanisms among VDAC isoforms, they display not only different channel properties and protein expression levels, but also distinct protein partners. Read More

Mol Biosyst 2017 Nov;13(12):2583-2591

Shanghai Key Laboratory of Multidimensional Information Processing, East China Normal University, Shanghai 200262, China.

Prediction of new associations between drugs and targeting pathways can provide valuable clues for drug discovery & development. However, information integration and a class-imbalance problem are important challenges for available prediction methods. This paper proposes a prediction of potential associations between drugs and pathways based on a disease-related LSA-PU-KNN method. Read More

Mol Biosyst 2017 Nov;13(12):2564-2573

Department of Urology, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an 223200, China.

Renal cell carcinoma (RCC) is the leading cause of death in renal malignancies. MicroRNA-590-5p (miR-590-5p) is of great importance in the processes of many cancers regarding regulation of cancer cell invasion and proliferation. In our study, alternation of miR-590-5p expression in RCC cell lines through transfection with pre-miR-590-5p (up-regulation) or anti-miR-590-5p (down-regulation) was performed. Read More

Mol Biosyst 2017 Nov;13(12):2574-2582

School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.

Mass spectrometry (MS) has become an increasingly important technique to analyze proteins. In popular bottom-up MS-based proteomics, reduction and alkylation are routine steps to facilitate peptide identification. However, incomplete reactions and side reactions may occur, which compromise the experimental results. Read More

Mol Biosyst 2017 Nov;13(12):2551-2563

Analiza Inc, 3516 Superior Ave, Suite 4407B, Cleveland, OH, USA.

Solvent properties of water in aqueous solutions of polyethylene glycols of various molecular weights, l-proline, betaine, and a series of chlorides of varied concentrations are assayed using three solvatochromic dyes. The properties include solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity. These properties are also evaluated in mixtures of two polymers, polymer and osmolyte, and two osmolytes. Read More

Mol Biosyst 2017 Nov;13(12):2545-2550

Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.

Cysteine S-sulfenylation is a major type of posttranslational modification that contributes to protein structure and function regulation in many cellular processes. Experimental identification of S-sulfenylation sites is challenging, due to the low abundance of proteins and the inefficient experimental methods. Computational identification of S-sulfenylation sites is an alternative strategy to annotate the S-sulfenylated proteome. Read More

Mol Biosyst 2017 Oct;13(11):2428-2439

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China.

Genome sequencing technology has generated a vast amount of genomic and epigenomic data, and has provided us a great opportunity to study gene functions on a global scale from an epigenomic view. In the last decade, network-based studies, such as those based on PPI networks and co-expression networks, have shown good performance in capturing functional relationships between genes. However, the functions of a gene and the mechanism of interaction of genes with each other to elucidate their functions are still not entirely clear. Read More

Mol Biosyst 2017 Oct;13(11):2195-2201

Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, People's Republic of China.

Long non-coding RNAs (lncRNAs), non-protein-coding RNAs that are more than 200 nucleotides in length, have been demonstrated to play a vital role in the pathophysiology of human diseases, particularly in tumorigenesis and progression of cancers. Dysregulation of lncRNAs, which serve as either oncogenes or tumor suppressor genes, is involved in diverse cellular processes, such as proliferation, dedifferentiation, migration, invasion and anti-apoptosis. Promoter of CDKN1A antisense DNA damage-activated RNA (PANDAR), which was recently found to manifest aberrant expression in various malignancies including non-small cell lung cancer, hepatocellular carcinoma, colorectal cancer and gastric cancer, is a novel cancer-related lncRNA. Read More

Mol Biosyst 2017 Oct;13(11):2254-2267

Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, avenue de Luminy, Case 932, 13288 Marseille Cedex 09, Marseille, France.

Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V protein which shares with P its N-terminal, intrinsically disordered region (PNT) and possesses a unique C-terminal domain predicted to be folded and to bind zinc (ZnFD). Henipavirus V proteins antagonize IFN signaling through PNT-mediated binding to STAT1, and several paramyxoviral V proteins promote STAT1 degradation through binding to DDB1. Read More

Mol Biosyst 2017 Oct;13(11):2418-2427

School of Computer Science and Technology, University of Science and Technology of China, Hefei, People's Republic of China.

Altered metabolism is often identified as a cause or an effect of physiology and pathogenesis. But it is difficult to predict the metabolic flux distributions of multicellular organisms due to the lack of an explicit metabolic objective function. Here we present a computational method which can successfully describe the differences in metabolism between two different conditions on a large scale. Read More

Mol Biosyst 2017 Oct;13(11):2407-2417

Division of Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.

Dipeptidyl peptidase III (DPP III) from the human gut symbiont Bacteroides thetaiotaomicron (Bt) is the first identified prokaryotic DPP III orthologue. It has low sequence similarity to the thoroughly studied human DPP III, and differently from eukaryotic orthologues it has a cysteine (Cys450) residue in the zinc-binding motif HEXXGH (HECLGH). The recently determined crystal structure of BtDPP III showed that its 3D structure, similar to the structure of the human DPP III, consists of two domains with a wide cleft in between. Read More

Mol Biosyst 2017 Oct;13(11):2222-2225

Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259-B40, Midori-ku, Yokohama 226-8501, Japan.

Mannose-modified lectin-binding peptides were obtained from an α-helical-designed peptide phage library. Concanavalin A (ConA) was used as a representative target protein for the lectin family. The identified glycopeptides could selectively bind to ConA with micromolar affinity. Read More

Mol Biosyst 2017 Oct;13(11):2401-2406

ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP 13083-970 Campinas - SP, Brazil.

Particular lipid profiles have been found in two different protozoa of the Leishmania genus. Leishmania infantum, a visceral leishmaniasis causative agent and Leishmania amazonensis, a cutaneous leishmaniasis, reveal distinctive lipid contents of phosphatidylethanolamine and phosphatidylserine plasmalogens, sphingolipids, phosphatidylinositols, phosphatidylcholine, and phosphatidylethanolamine, which have been shown to be related to species, life-cycle of the parasite, and macrophage infection. L. Read More

Mol Biosyst 2017 Oct;13(11):2392-2400

Kidney Research Institute, Division of Nephrology, West China Hospital of Sichuan University, Chengdu, China.

Diabetic kidney disease (DKD) is the leading cause of ESRD; however, early intervention can greatly prevent the progression of DKD; thus, sensitive biomarkers for DKD are still required. This study was aimed at the identification of potential biomarkers and revelation of underlying pathways in DKD patients by non-targeted metabolomics. Gas chromatography-mass spectrometry was used to analyze urine obtained from the control and type 2 diabetes mellitus (T2DM) and DKD patients, and the renal histological changes in DKD patients were assessed. Read More

Mol Biosyst 2017 Oct;13(11):2379-2391

Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium.

Extracellular microRNAs (miRNAs) carried by exosomes can play a key role in cell-to-cell communication. Deregulation of miRNA expression and exosome secretion have been related to pathological conditions such as cancer. While it is known that circulating miRNAs can alter gene expression in recipient cells, it remains unclear how significant the dynamical impact of these extracellular miRNAs is. Read More

Mol Biosyst 2017 Oct;13(11):2370-2378

Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.

Promoter binding specificity is one of the important characteristics of transcription by Mycobacterium tuberculosis (Mtb) sigma (σ) factors, which remains unexplored due to limited structural evidence. Our previous study on the structural features of Mtb-SigH, consisting of three alpha helices, and its interaction with core RNA polymerase has been extended herein to determine the little known DNA sequence recognition pattern involving its cognate promoters. Herein, high resolution X-ray crystallographic structures of the protein-DNA complexes were inspected to determine the tentative DNA-binding helix of the σ factor. Read More

Mol Biosyst 2017 Oct;13(11):2362-2369

Department of Mathematics, Dalian Maritime University, No. 1 Linghai Road, Dalian, 116026, China.

Protein carbonylation is one of the most important biomarkers of oxidative protein damage and such protein damage is linked to various diseases and aging. It is thus vital that carbonylation sites are identified accurately. In this study, CarSite, a novel bioinformatics tool, was established to identify carbonylation sites in human proteins. Read More

Mol Biosyst 2017 Oct;13(11):2350-2361

The Second Clinical Medical College of Nanjing Medical University, Nanjing, 210000, Jiangsu, People's Republic of China.

Recently, substantial evidence has demonstrated that long non-coding RNAs (lncRNAs) play critical roles in multiple cancers including colorectal cancer (CRC). Utilizing publicly available lncRNA-expression-profiling data from the Gene Expression Omnibus (GEO) dataset GSE21510, we screened SNHG17 as a new candidate lncRNA associated with CRC development and progression. We further demonstrated that SNHG17 was upregulated in CRC tissues, and that its overexpression was significantly correlated with tumor size, TNM stage, and lymph node metastasis in CRC patients. Read More

Mol Biosyst 2017 Oct;13(11):2218-2221

Department of Physical Chemistry II, Ruhr University Bochum, Universitättstr. 150, 44801 Bochum, Germany.

Changes of the extracellular milieu could affect cellular crowding. To prevent detrimental effects, cells use adaptation mechanisms to react to such conditions. Using fluorescent crowding sensors, we show that the initial response to osmotic stress is fast but imperfect, while the slow response renders cells more tolerant to stress, particularly in the presence of osmolytes. Read More

Mol Biosyst 2017 Oct;13(11):2338-2349

CSIR-National Chemical Laboratory, Pune-411008, India.

Methylglyoxal (MG) is a highly reactive dicarbonyl known to be elevated under the hyperglycemic conditions of diabetes and is implicated in the development of diabetic complications. Therefore, the current study investigates the role of MG in exacerbating insulin resistance at the insulin signaling level, as well as its effect on the global proteomic level. By using insulin sensitive rat muscle cells (L6) and Chinese hamster ovary (CHO) cells stably expressing the insulin receptor (IR) and a glucose transporter fused with green fluorescent protein (GLUT4-GFP), we have observed that MG impairs insulin signaling, inhibits GLUT4 translocation and reduces glucose uptake. Read More

Mol Biosyst 2017 Oct;13(11):2235-2253

Graduate Program in Computational and Data Sciences, Department of Computational Biosciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.

The overarching goal of delineating molecular principles underlying differentiation of the activation mechanisms in cyclin-dependent kinases (CDKs) is important for understanding regulatory divergences among closely related kinases which can be exploited in drug discovery of targeted and allosteric inhibitors. To systematically characterize dynamic, energetic and network signatures of the activation mechanisms, we combined atomistic simulations and elastic network modeling with the analysis of the residue interaction networks and rigidity decomposition of the CDK2-cyclin A and CDK4-cyclin D1/D3 complexes. The results of this study show that divergences in the activation mechanisms of CDK2 and CDK4 may be determined by differences in stabilization and allosteric cooperativity of the regulatory regions. Read More

Mol Biosyst 2017 Oct;13(11):2328-2337

School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, People's Republic of China.

MicroRNAs (miRNAs), as a kind of important small endogenous single-stranded non-coding RNA, play critical roles in a large number of human diseases. However, the currently known experimental verifications of the disease-miRNA associations are still rare and experimental identification is time-consuming and labor-intensive. Accordingly, identifying potential disease-related miRNAs to help people understand the pathogenesis of complex diseases has become a hot topic. Read More

Mol Biosyst 2017 Oct;13(11):2202-2217

Human Metabolomics, North-West University, Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa.

Chronic human immunodeficiency virus (HIV) infection, separately and in combination with highly active antiretroviral therapy (HAART) is closely associated with oxidative stress (OS). Most studies demonstrating redox imbalances in HIV-infected individuals have done so using conventional biochemical methodologies. The limited simultaneous detection of multiple OS markers within one sample is a major drawback of these methodologies and can be addressed through the use of metabonomics. Read More

Mol Biosyst 2017 Oct;13(11):2323-2327

Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Lab, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China.

The emergence of antibiotic resistance caused by β-lactamases, including serine β-lactamases (SβLs) and metallo-β-lactamases (MβLs), is a global public health threat. L1, a B3 subclass MβL, hydrolyzes almost all of known β-lactam antibiotics. We report a simple and straightforward UV-Vis approach for real-time activity assays of β-lactamases inside living bacterial cells, and this method has been exemplified by choosing antibiotics, L1 enzyme, Escherichia coli expressing L1 (L1 E. Read More

Mol Biosyst 2017 Oct;13(11):2226-2234

Laboratory for Computational Biochemistry & Molecular Design, Department of Phytomedicine, Qingdao Agricultural University, Qingdao 266109, China.

Chirality is a ubiquitous basic attribute of nature, which inseparably relates to the life activity of living organisms. However, enantiomeric differences have still failed to arouse enough attention during the biological evaluation and practical application of chiral substances, and this poses a large threat to human health. In the current study, we explore the enantioselective biorecognition of a chiral compound by an asymmetric biomolecule, and then decipher the molecular basis of such a biological phenomenon on the static and, in particular, the dynamic scale. Read More

Mol Biosyst 2017 09;13(10):2181

Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.

Correction for 'An integrated anti-arrhythmic target network of a Chinese medicine compound, Wenxin Keli, revealed by combined machine learning and molecular pathway analysis' by Taiyi Wang et al., Mol. BioSyst. Read More

Mol Biosyst 2017 Oct;13(11):2310-2322

Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.

Immune therapy is generally seen as the future of cancer treatment. The discovery of tumor-associated antigens and cytotoxic T lymphocyte epitope peptides spurned intensive research into effective peptide-based cancer vaccines. One of the major obstacles hindering the development of peptide-based cancer vaccines is the lack of humoral response induction. Read More

Mol Biosyst 2017 Oct;13(11):2303-2309

Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai 410210, India.

Adhesive interactions between molecules on tumor cells and those on target organs play a key role in organ specific metastasis. Poly-N-acetyl-lactosamine (polyLacNAc) substituted N-oligosaccharides on melanoma cell surface glycoproteins promote lung specific metastasis via galectin-3 by facilitating their arrest and extravasation. This study reports the identification and characterization of galectin-3 interacting proteins using a combination of galectin-3 sepharose affinity and leucoagglutinating phytohemagglutinin (L-PHA) columns. Read More

Mol Biosyst 2017 Oct;13(11):2289-2302

Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran.

MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. miRNA profiles of rice (Oryza sativa L. cv. Read More

Mol Biosyst 2017 Oct;13(11):2277-2288

Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

According to GLOBOCAN 2012, the incidence and the mortality rate of colorectal, stomach and liver cancers are the highest among the total gastrointestinal (GI) cancers. Here we aimed to find the common genes and pathways that are simultaneously deregulated in these three malignancies using systems biology approaches. Here we conducted a differential expression analysis on high-quality gene expression datasets of gastric cancer (GC), colorectal cancer (CRC) and hepatocellular carcinoma (HCC). Read More