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https://www.readbyqxmd.com/read/28088189/mars-improving-multiple-circular-sequence-alignment-using-refined-sequences
#1
Lorraine A K Ayad, Solon P Pissis
BACKGROUND: A fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the linearisation (sequencing) of a circular molecular structure; or inconsistencies introduced into sequence databases due to different linearisation standards. These scenarios are relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087505/2016-update-of-the-asas-eular-management-recommendations-for-axial-spondyloarthritis
#2
Désirée van der Heijde, Sofia Ramiro, Robert Landewé, Xenofon Baraliakos, Filip Van den Bosch, Alexandre Sepriano, Andrea Regel, Adrian Ciurea, Hanne Dagfinrud, Maxime Dougados, Floris van Gaalen, Pál Géher, Irene van der Horst-Bruinsma, Robert D Inman, Merryn Jongkees, Uta Kiltz, Tore K Kvien, Pedro M Machado, Helena Marzo-Ortega, Anna Molto, Victoria Navarro-Compàn, Salih Ozgocmen, Fernando M Pimentel-Santos, John Reveille, Martin Rudwaleit, Jochen Sieper, Percival Sampaio-Barros, Dieter Wiek, Jürgen Braun
To update and integrate the recommendations for ankylosing spondylitis and the recommendations for the use of tumour necrosis factor inhibitors (TNFi) in axial spondyloarthritis (axSpA) into one set applicable to the full spectrum of patients with axSpA. Following the latest version of the European League Against Rheumatism (EULAR) Standardised Operating Procedures, two systematic literature reviews first collected the evidence regarding all treatment options (pharmacological and non-pharmacological) that were published since 2009...
January 13, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28087320/poly-adp-ribose-polymerase-activity-and-inhibition-in-cancer
#3
REVIEW
Caleb Dulaney, Samuel Marcrom, Jennifer Stanley, Eddy S Yang
Genomic instability resultant from defective DNA repair mechanisms is a fundamental hallmark of cancer. The poly(ADP-ribose) polymerase (PARP) proteins 1, 2 and 3 catalyze the polymerization of poly(ADP-ribose) and covalent attachment to proteins in a phylogenetically ancient form of protein modification. PARPs play a role in base excision repair, homologous recombination, and non-homologous end joining. The discovery that loss of PARP activity had cytotoxic effects in cells deficient in homologous recombination has sparked a decade of translational research efforts that culminated in the FDA approval of an oral PARP inhibitor for clinical use in patients with ovarian cancer and defective homologous recombination...
January 10, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28080136/isoniazid-a-review-of-characteristics-properties-and-analytical-methods
#4
Guilherme Felipe Dos Santos Fernandes, Hérida Regina Nunes Salgado, Jean Leandro Dos Santos
Isoniazid is a synthetic antimicrobial and one of the most important first-line drugs used in the treatment of tuberculosis. Since it was introduced in the therapy in 1952, the drug remains at the front line of the antituberculosis treatment mainly due to its potency and high selectivity against Mycobacterium tuberculosis. Pharmaceutical analysis and therapeutic drug monitoring of isoniazid in both, pharmaceuticals and biological samples, plays an important role to comprehend aspects regarding to bioavailability, bioequivalence and therapeutic monitoring during patients following-up...
January 12, 2017: Critical Reviews in Analytical Chemistry
https://www.readbyqxmd.com/read/28079510/a-comparison-of-discontinuation-rates-of-tofacitinib-and-biologic-disease-modifying-antirheumatic-drugs-in-rheumatoid-arthritis-a-systematic-review-and-bayesian-network-meta-analysis
#5
Sun-Kyeong Park, Min-Young Lee, Eun-Jin Jang, Hye-Lin Kim, Dong-Mun Ha, Eui-Kyung Lee
OBJECTIVES: The purpose of this study was to compare the discontinuation rates of tofacitinib and biologics (tumour necrosis factor inhibitors (TNFi), abatacept, rituximab, and tocilizumab) in rheumatoid arthritis (RA) patients considering inadequate responses (IRs) to previous treatment(s). METHODS: Randomised controlled trials of tofacitinib and biologics - reporting at least one total discontinuation, discontinuation due to lack of efficacy (LOE), and discontinuation due to adverse events (AEs) - were identified through systematic review...
January 5, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/28079365/twist-and-shout-single-molecule-mechanochemistry
#6
Hongbin Li, Gilbert C Walker
Chemical reactions can be accelerated by various means, including applied mechanical forces. If the direction of the force does not project well onto the desired reaction coordinate, then only poor acceleration is achieved. Recent developments in single polymer mechanics illustrate how to overcome this limitation, in a simple cis-trans isomerization reaction. Generalizing the approach, synthetic chemistry can be used to attach tethers to different parts of reacting molecular fragments to direct the force usefully...
January 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/28078770/synthetic-plant-virology-for-nanobiotechnology-and-nanomedicine
#7
REVIEW
John F C Steele, Hadrien Peyret, Keith Saunders, Roger Castells-Graells, Johanna Marsian, Yulia Meshcheriakova, George P Lomonossoff
Nanotechnology is a rapidly expanding field seeking to utilize nano-scale structures for a wide range of applications. Biologically derived nanostructures, such as viruses and virus-like particles (VLPs), provide excellent platforms for functionalization due to their physical and chemical properties. Plant viruses, and VLPs derived from them, have been used extensively in biotechnology. They have been characterized in detail over several decades and have desirable properties including high yields, robustness, and ease of purification...
January 11, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28077925/artificial-cells-from-basic-science-to-applications
#8
Can Xu, Shuo Hu, Xiaoyuan Chen
Artificial cells have attracted much attention as substitutes for natural cells. There are many different forms of artificial cells with many different definitions. They can be integral biological cell imitators with cell-like structures and exhibit some of the key characteristics of living cells. Alternatively, they can be engineered materials that only mimic some of the properties of cells, such as surface characteristics, shapes, morphology, or a few specific functions. These artificial cells can have applications in many fields from medicine to environment, and may be useful in constructing the theory of the origin of life...
November 2016: Materials Today
https://www.readbyqxmd.com/read/28076956/sbolme-a-repository-of-sbol-parts-for-metabolic-engineering
#9
Hiroyuki Kuwahara, Xuefeng Cui, Ramzan Umarov, Raik Gruenberg, Chris J Myers, Xin Gao
The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2.0-compliant biochemical parts for a wide range of metabolic engineering applications. The URL of our repository is http://www.cbrc.kaust.edu.sa/sbolme.
January 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28076683/modulation-of-cytotoxicity-by-transcription-coupled-nucleotide-excision-repair-is-independent-of-the-requirement-for-bioactivation-of-acylfulvene
#10
Claudia Otto, Graciela Spivak, Claudia Marie Nathalie Aloisi, Mirco Menigatti, Hanspeter Nägeli, Philip C Hanawalt, Marina Tanasova, Shana J Sturla
Bioactivation as well as DNA repair affect the susceptibility of cancer cells to the action of DNA-alkylating chemotherapeutic drugs. However, information is limited with regard to the relative contributions of these processes to the biological outcome of metabolically activated DNA alkylating agents. We evaluated the influence of cellular bioactivation capacity and DNA repair on cytotoxicity of the DNA alkylating agent, acylfulvene (AF). We compared cytotoxicity and RNA synthesis inhibition by AF and its synthetic activated analog iso-M0 in a panel of fibroblast cell lines with deficiencies in transcription-coupled (TC-NER) or global genome nucleotide excision repair (GG-NER)...
January 11, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28075593/formation-of-nickel-clusters-wrapped-in-carbon-cages-towards-new-endohedral-metallofullerene-synthesis
#11
Alexander S Sinitsa, Thomas W Chamberlain, Thilo Zoberbier, Irina V Lebedeva, Andrey M Popov, Andrey A Knizhnik, Robert L McSweeney, Johannes Biskupek, Ute Kaiser, Andrei N Khlobystov
In spite of the high potential of endohedral metallofullerenes (EMFs) for application in biology, medicine and molecular electronics and recent efforts in EMF synthesis, the variety of EMFs accessible by conventional synthetic methods remains limited and does not include, for example, EMFs of late transition metals. We propose a method in which EMF formation is initiated by electron irradiation in aberration-corrected high-resolution transmission electron spectroscopy (AC-HRTEM) of a metal cluster surrounded by amorphous carbon inside a carbon nanotube serving as a nano-reactor and apply this method for synthesis of nickel EMFs...
January 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28075125/multifunctional-nanoparticles-by-coordinative-self-assembly-of-his-tagged-units-with-metal-organic-frameworks
#12
Ruth Röder, Tobias Preiß, Patrick Hirschle, Benjamin Steinborn, Andreas Zimpel, Miriam Hoehn, Joachim O Rädler, Thomas Bein, Ernst Wagner, Stefan Wuttke, Ulrich Lächelt
Self-assembly of individual units into multicomponent complexes is a powerful approach for the generation of functional super-structures. We present the coordinative interaction of oligohistidine-tags (His-tags) with metal-organic framework nanoparticles (MOF NPs). By this novel concept, different molecular units can be anchored on the outer surface of MOF NPs in a self-assembly process generating multifunctional nanosystems. The article focuses on two main objectives: first, the detailed investigation of the assembly process and fundamental establishment of the novel functionalization concept; and second, its subsequent use for the development of biomacromolecule (e...
January 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28074955/total-synthesis-and-biological-activity-of-dolastatin-16
#13
Loida O Casalme, Arisa Yamauchi, Akinori Sato, Julie G Petitbois, Yasuyuki Nogata, Erina Yoshimura, Tatsufumi Okino, Taiki Umezawa, Fuyuhiko Matsuda
The total synthesis of dolastatin 16, a macrocyclic depsipeptide first isolated from the sea hare Dolabella auricularia as a potential antineoplastic metabolite by Pettit et al., was achieved in a convergent manner. Dolastatin 16 was reported by Tan to exhibit strong antifouling activity, and thus shows promise for inhibiting the attachment of marine benthic organisms such as Amphibalanus amphitrite to ships and submerged artificial structures. Therefore, dolastatin 16 is a potential compound for a new, environmentally friendly antifouling material to replace banned tributyltin-based antifouling paints...
January 11, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28074641/editorial-methods-and-advances-for-systems-and-synthetic-biology-nanobiotech-and-medicine
#14
EDITORIAL
Jing Zhu, Uta Goebel
Congratulations to the winners of our cover competition. The first prize goes to the cover of the October issue, which was provided by the authors of the article "Chlorella species as hosts for genetic engineering and expression of heterologous proteins: Progress, challenge and perspective" by Bo Yang, Jin Liu, Yue Jiang and Feng Chen (http://dx.doi.org/10.1002/biot.201500617). Very close by only very few votes followed the July issue cover showing a nice illustration of Aspergillus fungi, which was selected by BTJs Production manager Sigi Mehren and Technical editor Bernadette Gmeiner...
January 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28074376/synthetic-biology-genome-editing-and-the-risk-of-bioterrorism
#15
Marko Ahteensuu
The SynBioSecurity argument says that synthetic biology introduces new risks of intentional misuse of synthetic pathogens and that, therefore, there is a need for extra regulations and oversight. This paper provides an analysis of the argument, sets forth a new version of it, and identifies three developments that raise biosecurity risks compared to the situation earlier. The developments include (1) a spread of the required know-how, (2) improved availability of the techniques, instruments and biological parts, and (3) new technical possibilities such as "resurrecting" disappeared pathogens...
January 10, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28073800/relationship-between-exposure-to-tumour-necrosis-factor-inhibitor-therapy-and-incidence-and-severity-of-myocardial-infarction-in-patients-with-rheumatoid-arthritis
#16
Audrey S L Low, Deborah P M Symmons, Mark Lunt, Louise K Mercer, Chris P Gale, Kath D Watson, William G Dixon, Kimme L Hyrich
OBJECTIVES: Patients with rheumatoid arthritis (RA) are at increased risk of myocardial infarction (MI) compared with subjects without RA, with the increased risk driven potentially by inflammation. Tumour necrosis factor inhibitors (TNFi) may modulate the risk and severity of MI. We compared the risk and severity of MI in patients treated with TNFi with that in those receiving synthetic disease-modifying antirheumatic drugs (sDMARDs). METHODS: This analysis included patients with RA recruited from 2001 to 2009 to the British Society for Rheumatology Biologics Register for Rheumatoid Arthritis starting TNFi (etanercept/infliximab/adalimumab) and a biologic-naïve comparator cohort receiving sDMARD...
January 10, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28073262/fluorescence-self-quenching-from-reporter-dyes-informs-on-the-structural-properties-of-amyloid-clusters-formed-in-vitro-and-in-cells
#17
WeiYue Chen, Laurence J Young, Meng Lu, Alessio Zaccone, Florian Ströhl, Na Yu, Gabriele S Kaminski Schierle, Clemens F Kaminski
The characterization of the aggregation kinetics of protein amyloids and the structural properties of the ensuing aggregates are vital in the study of the pathogenesis of many neurodegenerative diseases and the discovery of therapeutic targets. In this article, we show that the fluorescence lifetime of synthetic dyes covalently attached to amyloid proteins informs on the structural properties of amyloid clusters formed both in vitro and in cells. We demonstrate that the mechanism behind such a "lifetime sensor" of protein aggregation is based on fluorescence self-quenching and that it offers a good dynamic range to report on various stages of aggregation without significantly perturbing the process under investigation...
January 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28073246/a-new-era-of-genome-integration-simply-cut-and-paste
#18
Zihe Liu, Youyun Liang, Ee-Lui Ang, Huimin Zhao
Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as non-homologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination...
January 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28073115/pyridazine-based-scaffolds-as-privileged-structures-in-anti-cancer-therapy
#19
M Jaballah, R Serya, K Abouzid
Pyridazines, their oxo derivatives; pyridazinone as well as fused bi- or tricyclic pyridazine containing scaffolds are key structural features of many biologically active compounds with diverse pharmacological applications, including cancer therapy. Since protein kinases play prominent role in tumor biology, the inhibition of its signaling pathway is considered an effective therapeutic option for the treatment of cancer.Based on the various advantages of pyridazines in drug design including modulation of the physico-chemical properties, improving ADME and toxicity profile as well as easy and diverse synthetic methods of access, makes them an invaluable tool for designing compounds as future drugs for targeted cancer treatment...
January 10, 2017: Drug Research
https://www.readbyqxmd.com/read/28071669/use-of-fibonacci-numbers-in-lipidomics-enumerating-various-classes-of-fatty-acids
#20
Stefan Schuster, Maximilian Fichtner, Severin Sasso
In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when cis/trans isomerism is neglected. Since the ratio of two consecutive Fibonacci numbers tends to the Golden section, 1.618, organisms can increase fatty acid variability approximately by that factor per carbon atom invested. Moreover, we show that, under consideration of cis/trans isomerism and/or of modification by hydroxy and/or oxo groups, diversity can be described by generalized Fibonacci numbers (e...
January 10, 2017: Scientific Reports
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