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Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools...
November 29, 2016: Nucleic Acids Research
Bushra Saeed, Vinay K Baranwal, Paramjit Khurana
Lectins are a diverse group of ubiquitously present, highly specific sugar-binding proteins. Members of this large gene family have been assigned broad biological functions from defense to acting as storage proteins. Despite possessing several interesting characteristics, their functions remain essentially undefined. Mulberry ( spp.) known for its medicinal benefits is also a rich source of lectins. Using an exhaustive hidden Markov model (HMM)-based search, we identified the lectin gene complement in C.K. Schneid with around 197 members...
July 2016: Plant Genome
Adriana M Fróes, Fábio F da Mota, Rafael R C Cuadrat, Alberto M R Dávila
β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available...
2016: Frontiers in Microbiology
Ahmad Tamimi, Yaqoub Ashhab, Hashem Tamimi
Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases...
2016: PloS One
N-Y Kim, M-C Kim, Y Kim
Epigenetic modifications have been implicated in the development of therapeutic resistance responsible for the poor prognosis of human malignant mesothelioma (HMM). To find a potential way to overcome this therapeutic resistance, this study investigated the anticancer effects of a DNA demethylating agent, 5-Aza-2'-Deoxycytidine (5-aza-dC), on HMM cells. The 5-aza-dC exhibited minimal detrimental effects on cell survival. However, treatment with 5-aza-dC significantly altered the biological characteristics associated with malignancy, such as cell migration and cell interaction, colony-forming capacity, and invasiveness...
November 18, 2016: Cancer Gene Therapy
Yongli Zhang, Junyi Jiao, Aleksander A Rebane
Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise...
November 15, 2016: Biophysical Journal
Pierre Ambrosini, Ihor Smal, Daniel Ruijters, Wiro Niessen, Adriaan Moelker, Theo van Walsum
In minimal invasive image guided catheterization procedures, physicians require information of the catheter position with respect to the patient's vasculature. However, in fluoroscopic images, visualization of the vasculature requires toxic contrast agent. Static vasculature roadmapping, which can reduce the usage of iodine contrast, is hampered by the breathing motion in abdominal catheterization. In this paper, we propose a method to track the catheter tip inside the patient's 3D vessel tree using intra-operative single-plane 2D X-ray image sequences and a peri-operative 3D rotational angiography (3DRA)...
November 7, 2016: IEEE Transactions on Medical Imaging
Bartosz Janaszek, Anna Tyszka-Zawadzka, Paweł Szczepański
The tunability of graphene-based hyperbolic metamaterial structure operating in SCLU telecom bands is investigated. For the first time it has been shown that for the proper design of a graphene/dielectric multilayer stack, the HMM Type I, Epsilon-Near-Zero and Type II regimes are possible by changing the biasing potential. Numerical results reveal the effect of structure parameters such as the thickness of the dielectric layer as well as a number of graphene sheets in a unit cell (i.e., dielectric/graphene bilayer) on the tunability range and shape of the dispersion characteristics (i...
October 17, 2016: Optics Express
Wei Chen, Yong-Mei Zhang, Christopher Davies
Penicillin-binding proteins (PBPs) function as transpeptidases, carboxypeptidases or endopeptidases during peptidoglycan synthesis in bacteria. As the well-known drug targets for β-lactam antibiotics, the physiological functions of PBPs and whether they are essential for growth is of significant interest. The pathogen Pseudomonas aeruginosa (Pa) poses a particular risk to immunocompromised and cystic fibrosis patients, and is difficult to treat due to antibiotic resistance. To identify potential drug targets among the PBPs in Pa, we performed gene knockouts of all the high-molecular mass (HMM) PBPs and determined impacts on cell growth and morphology, susceptibility to β-lactams, peptidoglycan structure, virulence, and pathogenicity...
November 7, 2016: Antimicrobial Agents and Chemotherapy
M G Strillacci, M C Cozzi, E Gorla, F Mosca, F Schiavini, S I Román-Ponce, F J Ruiz López, A Schiavone, M Marzoni, S Cerolini, A Bagnato
Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis...
November 7, 2016: Animal: An International Journal of Animal Bioscience
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
BACKGROUND: Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. RESULTS: In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i...
November 3, 2016: BMC Bioinformatics
C E Rohlman, M R Blanco, N G Walter
The spliceosome is a biomolecular machine that, in all eukaryotes, accomplishes site-specific splicing of introns from precursor messenger RNAs (pre-mRNAs) with high fidelity. Operating at the nanometer scale, where inertia and friction have lost the dominant role they play in the macroscopic realm, the spliceosome is highly dynamic and assembles its active site around each pre-mRNA anew. To understand the structural dynamics underlying the molecular motors, clocks, and ratchets that achieve functional accuracy in the yeast spliceosome (a long-standing model system), we have developed single-molecule fluorescence resonance energy transfer (smFRET) approaches that report changes in intra- and intermolecular interactions in real time...
2016: Methods in Enzymology
Ho Chit Siu, Julie A Shah, Leia A Stirling
Surface electromyography (sEMG) is a technique for recording natural muscle activation signals, which can serve as control inputs for exoskeletons and prosthetic devices. Previous experiments have incorporated these signals using both classical and pattern-recognition control methods in order to actuate such devices. We used the results of an experiment incorporating grasp and release actions with object contact to develop an intent-recognition system based on Gaussian mixture models (GMM) and continuous-emission hidden Markov models (HMM) of sEMG data...
October 25, 2016: Sensors
Ana Laura Grazziotin, Eugene V Koonin, David M Kristensen
Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more...
October 26, 2016: Nucleic Acids Research
Yang Xu, Shuang Zhang, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Yu Xue
In this work, we developed a database WERAM ( for histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases and acetyl- or methyl-binding proteins, which catalyze, remove and recognize histone acetylation and methylation sites as 'writers', 'erasers' and 'readers', and synergistically determine the 'histone code'. From the scientific literature, we totally collected over 580 experimentally identified histone regulators from eight model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Schizosaccharomyces pombe and Saccharomyces cerevisiae We also collected ∼900 site-specific regulator-histone relations from the eight species...
October 26, 2016: Nucleic Acids Research
R Finotello, J M Monné Rodriguez, M Vilafranca, J Altimira, G A Ramirez, A Haines, L Ressel
Canine melanoma (CMM) more commonly affects the oral mucosa and the cutis. CMM shares several features with human melanomas (HMM), included resistance to a broad variety of antineoplastic chemotherapy agents. P-glycoprotein 1 (Pgp) expression is a well-recognized feature of multi-drug resistance and the purpose of this study was to investigate its expression in treatment naïve CMM. We also investigated Pgp association with tumour location and histological features. Histology records of CMM were retrieved, including patients from 2012-2014...
October 25, 2016: Veterinary and Comparative Oncology
Jin Woo Huh, Dong Kyu Lee, Hwan-Jin Jeon, Chi Won Ahn
In this study, hybrid-structured metal mesh (HMM) films as potential flexible transparent electrodes, composed of aligned micro-sized metal fibers integrated into random network of metal nanofibers, were fabricated by the combination of electrospinning and metal deposition. These naturally fiber-bridged HMMs, with a gold layer thickness of 85 nm, exhibited a high transmittance of around 90% and a sheet resistance of approximately 10 Ω sq(-1), as well as favorable mechanical stability under bending stress. These results demonstrate that the approach employed herein is a simple, highly efficient, and facile process for fabricating, uniform, interconnected fiber networks with potential for producing high-performance flexible transparent electrodes...
November 25, 2016: Nanotechnology
Fuming Fang, Takahiro Shinozaki, Yasuo Horiuchi, Shingo Kuroiwa, Sadaoki Furui, Toshimitsu Musha
Eye motion-based human-machine interfaces are used to provide a means of communication for those who can move nothing but their eyes because of injury or disease. To detect eye motions, electrooculography (EOG) is used. For efficient communication, the input speed is critical. However, it is difficult for conventional EOG recognition methods to accurately recognize fast, sequentially input eye motions because adjacent eye motions influence each other. In this paper, we propose a context-dependent hidden Markov model- (HMM-) based EOG modeling approach that uses separate models for identical eye motions with different contexts...
2016: Computational Intelligence and Neuroscience
Ishita Mukherjee, Abhijit Chakraborty, Saikat Chakrabarti
BACKGROUND: An active immune surveillance and a range of barriers to infection allow the host to effectively eliminate microbial pathogens. However, pathogens may use diverse strategies to subdue such host defences. For instance, one such mechanism is the use of leucine-rich repeat (LRR) proteins by pathogens (microbial) to cause infection. In this study, we aimed at identifying novel virulence factor(s) in Leishmania donovani, based on the possibility of lateral gene transfers of bacterial virulence factor(s) to L...
October 21, 2016: Parasites & Vectors
Kien Xuan Ngo, Nobuhisa Umeki, Saku T Kijima, Noriyuki Kodera, Hiroaki Ueno, Nozomi Furutani-Umezu, Jun Nakajima, Taro Q P Noguchi, Akira Nagasaki, Kiyotaka Tokuraku, Taro Q P Uyeda
Heavy meromyosin (HMM) of myosin II and cofilin each binds to actin filaments cooperatively and forms clusters along the filaments, but it is unknown whether the two cooperative bindings are correlated and what physiological roles they have. Fluorescence microscopy demonstrated that HMM-GFP and cofilin-mCherry each bound cooperatively to different parts of actin filaments when they were added simultaneously in 0.2 μM ATP, indicating that the two cooperative bindings are mutually exclusive. In 0.1 mM ATP, the motor domain of myosin (S1) strongly inhibited the formation of cofilin clusters along actin filaments...
October 20, 2016: Scientific Reports
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