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https://www.readbyqxmd.com/read/28212856/probis-tools-algorithm-database-and-web-servers-for-predicting-and-modeling-of-biologically-interesting-proteins
#1
REVIEW
Janez Konc, Dušanka Janežič
ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis...
February 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28212811/polymorphisms-of-blood-forms-and-in-vitro-metacyclogenesis-of-trypanosoma-cruzi-i-ii-and-iv
#2
Camila Piva Abegg, Ana Paula de Abreu, Juliane Lopes da Silva, Silvana Marques de Araújo, Mônica Lúcia Gomes, Érika Cristina Ferreira, Max Jean de Ornelas Toledo
Trypanosoma cruzi is the etiologic agent of American trypanosomiasis has broad biological and genetic diversity. Remaining to be studied are polymorphisms of the blood forms and metacyclogenesis of different T. cruzi discrete typing units (DTUs). Our goal was to evaluate the relationship between T. cruzi DTUs, the morphology of blood trypomastigotes, and in vitro metacyclogenesis. T. cruzi strains that pertained to DTUs TcI, TcII, and TcIV from different Brazilian states were used. Parameters that were related to the morphology of eight strains were assessed in thin blood smears that were obtained from mice that were inoculated with blood or culture forms, depending on strain...
February 14, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#3
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28211906/dynamics-of-male-meiotic-recombination-frequency-during-plant-development-using-fluorescent-tagged-lines-in-arabidopsis-thaliana
#4
Fan Li, Nico De Storme, Danny Geelen
Meiotic homologous recombination plays a central role in creating genetic variability, making it an essential biological process relevant to evolution and crop breeding. In this study, we used pollen-specific fluorescent tagged lines (FTLs) to measure male meiotic recombination frequency during the development of Arabidopsis thaliana. Interestingly, a subset of pollen grains consistently shows loss of fluorescence expression in tested lines. Using nine independent FTL intervals, the spatio-temporal dynamics of male recombination frequency was assessed during plant development, considering both shoot type and plant age as independent parameters...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210797/mathematical-modelling-of-clostridial-acetone-butanol-ethanol-fermentation
#5
REVIEW
Thomas Millat, Klaus Winzer
Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematical models have been employed to elucidate the complex interlinked regulation and conditions that determine these two distinct metabolic states and govern the transition between them. In this review, we discuss these models with a focus on the mechanisms controlling intra- and extracellular changes between acidogenesis and solventogenesis...
February 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28209761/genetic-adaptation-of-the-schizothoracine-fishes-to-the-phased-uplifting-of-qinghai-tibetan-plateau
#6
Dongsheng Zhang, Mengchao Yu, Peng Hu, Sihua Peng, Yimeng Liu, Weiwen Li, Congcong Wang, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen
Many species of Schizothoracine, a sub-family of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion in high-altitudes, we sequenced tissue transcriptomes of two highland and two sub-highland Schizothoracines, and analyzed gene evolution patterns by comparing to lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fishes lived around 32...
February 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28208827/on-the-uniqueness-of-the-standard-genetic-code
#7
Gabriel S Zamudio, Marco V José
In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes...
February 13, 2017: Life
https://www.readbyqxmd.com/read/28208702/the-glutamate-dehydrogenase-pathway-and-its-roles-in-cell-and-tissue-biology-in-health-and-disease
#8
REVIEW
Andreas Plaitakis, Ester Kalef-Ezra, Dimitra Kotzamani, Ioannis Zaganas, Cleanthe Spanaki
Glutamate dehydrogenase (GDH) is a hexameric enzyme that catalyzes the reversible conversion of glutamate to α-ketoglutarate and ammonia while reducing NAD(P)⁺ to NAD(P)H. It is found in all living organisms serving both catabolic and anabolic reactions. In mammalian tissues, oxidative deamination of glutamate via GDH generates α-ketoglutarate, which is metabolized by the Krebs cycle, leading to the synthesis of ATP. In addition, the GDH pathway is linked to diverse cellular processes, including ammonia metabolism, acid-base equilibrium, redox homeostasis (via formation of fumarate), lipid biosynthesis (via oxidative generation of citrate), and lactate production...
February 8, 2017: Biology
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#9
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207531/delayed-effort-induced-swelling-with-myofasciitis-and-systemic-manifestations-a-so-far-unrecognized-type-of-pressure-induced-urticaria
#10
Anne-Claire Bursztejn, Dan Lipsker
Diseases characterized by recurrent symptoms with prolonged intervals without any clinical manifestations can pose diagnostic difficulties. Some diagnoses will be obvious but other situations can be very challenging.To nosologically delineate a new entity characterized by recurrent flares of induration of the forearms and legs with swelling of the extremities accompanied by intense fatigue and variable other symptoms.Retrospective observational study of patients recorded from 2000 to 2015. All patients included were seen during a consultation at the Dermatology Department of the University Hospital of Strasbourg, France...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28205535/phylogenetic-analysis-of-eukaryotic-neet-proteins-uncovers-a-link-between-a-key-gene-duplication-event-and-the-evolution-of-vertebrates
#11
Madhuri A Inupakutika, Soham Sengupta, Rachel Nechushtai, Patricia A Jennings, Jose' N Onuchic, Rajeev K Azad, Pamela Padilla, Ron Mittler
NEET proteins belong to a unique family of iron-sulfur proteins in which the 2Fe-2S cluster is coordinated by a CDGSH domain that is followed by the "NEET" motif. They are involved in the regulation of iron and reactive oxygen metabolism, and have been associated with the progression of diabetes, cancer, aging and neurodegenerative diseases. Despite their important biological functions, the evolution and diversification of eukaryotic NEET proteins are largely unknown. Here we used the three members of the human NEET protein family (CISD1, mitoNEET; CISD2, NAF-1 or Miner 1; and CISD3, Miner2) as our guides to conduct a phylogenetic analysis of eukaryotic NEET proteins and their evolution...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205377/culture-independent-genomics-of-a-novel-chlamydial-pathogen-of-fish-provides-new-insight-into-host-specific-adaptations-utilised-by-these-intracellular-bacteria
#12
Alyce Taylor-Brown, Trestan Pillonel, Andrew Bridle, Weihong Qi, Nathan Bachmann, Terrence L Miller, Gilbert Greub, Barbara Nowak, Helena M B Seth-Smith, Lloyd Vaughan, Adam Polkinghorne
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridisation...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28203112/bone-contusion-progression-from-traumatic-knee-injury-association-of-rate-of-contusion-resolution-with-injury-severity
#13
Douglas R Pedersen, Georges Y El-Khoury, Dan R Thedens, Mothana Saad-Eldine, Phinit Phisitkul, Annunziato Amendola
BACKGROUND: Bone contusions are frequently encountered in magnetic resonance imaging (MRI) evaluation of knee anterior cruciate ligament (ACL) injuries. Their role as indicators of injury severity remains unclear, primarily due to indeterminate levels of joint injury forces and to a lack of preinjury imaging. PURPOSE: The purpose of this study was to 1) quantify bone contusion pathogenesis following traumatic joint injuries using fixed imaging follow-ups, and 2) assess the feasibility of using longitudinal bone contusion volumes as an indicator of knee injury severity...
2017: Open Access Journal of Sports Medicine
https://www.readbyqxmd.com/read/28203100/from-amino-acids-polymers-antimicrobial-peptides-and-histones-to-their-possible-role-in-the-pathogenesis-of-septic-shock-a-historical-perspective
#14
Isaac Ginsburg, Peter Vernon van Heerden, Erez Koren
This paper describes the evolution of our understanding of the biological role played by synthetic and natural antimicrobial cationic peptides and by the highly basic nuclear histones as modulators of infection, postinfectious sequelae, trauma, and coagulation phenomena. The authors discuss the effects of the synthetic polymers of basic poly α amino acids, poly l-lysine, and poly l-arginine on blood coagulation, fibrinolysis, bacterial killing, and blood vessels; the properties of natural and synthetic antimicrobial cationic peptides as potential replacements or adjuncts to antibiotics; polycations as opsonizing agents promoting endocytosis/phagocytosis; polycations and muramidases as activators of autolytic wall enzymes in bacteria, causing bacteriolysis and tissue damage; and polycations and nuclear histones as potential virulence factors and as markers of sepsis, septic shock, disseminated intravasclar coagulopathy, acute lung injury, pancreatitis, trauma, and other additional clinical disorders...
2017: Journal of Inflammation Research
https://www.readbyqxmd.com/read/28202809/mammal-body-size-evolution-in-north-america-and-europe-over-20-myr-similar-trends-generated-by-different-processes
#15
Shan Huang, Jussi T Eronen, Christine M Janis, Juha J Saarinen, Daniele Silvestro, Susanne A Fritz
Because body size interacts with many fundamental biological properties of a species, body size evolution can be an essential component of the generation and maintenance of biodiversity. Here we investigate how body size evolution can be linked to the clade-specific diversification dynamics in different geographical regions. We analyse an extensive body size dataset of Neogene large herbivores (covering approx. 50% of the 970 species in the orders Artiodactyla and Perissodactyla) in Europe and North America in a Bayesian framework...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28202655/constraints-in-cancer-evolution
#16
REVIEW
Subramanian Venkatesan, Nicolai J Birkbak, Charles Swanton
Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202600/neoteny-prolongation-of-youth-from-naked-mole-rats-to-naked-apes-humans
#17
REVIEW
Vladimir P Skulachev, Susanne Holtze, Mikhail Y Vyssokikh, Lora E Bakeeva, Maxim V Skulachev, Alexander V Markov, Thomas B Hildebrandt, Viktor A Sadovnichii
It has been suggested that highly social mammals, such as naked mole rats and humans, are long-lived due to neoteny (the prolongation of youth). In both species, aging cannot operate as a mechanism facilitating natural selection because the pressure of this selection is strongly reduced due to 1) a specific social structure where only the "queen" and her "husband(s)" are involved in reproduction (naked mole rats) or 2) substituting fast technological progress for slow biological evolution (humans). Lists of numerous traits of youth that do not disappear with age in naked mole rats and humans are presented and discussed...
April 2017: Physiological Reviews
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#18
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198107/fluorescent-supramolecular-polymeric-materials
#19
REVIEW
Hu Wang, Xiaofan Ji, Zhengtao Li, Feihe Huang
Fluorescent supramolecular polymeric materials are rising stars in the field of fluorescent materials not only because of the inherent optoelectronic properties originating from their chromophores, but also due to the fascinating stimuli-responsiveness and reversibility coming from their noncovalent connections. Especially, these noncovalent connections influence the fluorescence properties of the chromophores because their state of aggregation and energy transfer can be regulated by the assembly-disassembly process...
February 15, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28197917/sumo-in-drosophila-development
#20
Joseph Cao, Albert J Courey
The ubiquitin -like protein SUMO is conjugated covalently to hundreds of target proteins in organisms throughout the eukaryotic domain. Genetic and biochemical studies using the model organism Drosophila melanogaster are beginning to reveal many essential functions for SUMO in cell biology and development. For example, SUMO regulates multiple signaling pathways such as the Ras/MAPK, Dpp, and JNK pathways. In addition, SUMO regulates transcription through conjugation to many transcriptional regulatory proteins, including Bicoid, Spalt , Scm, and Groucho...
2017: Advances in Experimental Medicine and Biology
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