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91.
Stephan Zindel Vera Ehret Marina Ehret Madeleine Hentschel Samantha Witt Andreas Kr?mer David Fiebig Norbert Jüttner Sabrina Fr?ls Felicitas Pfeifer Hans-Lothar Fuchsbauer 《PloS one》2016,11(2)
Streptomyces mobaraensis DSM 40847 secretes transglutaminase that cross-links proteins via γ-glutamyl-ε-lysine isopeptide bonds. Characterized substrates are inhibitory proteins acting against various serine, cysteine and metalloproteases. In the present study, the bacterial secretome was examined to uncover additional transglutaminase substrates. Fractional ethanol precipitation of the exported proteins at various times of culture growth, electrophoresis of the precipitated proteins, and sequencing of a 39 kDa protein by mass spectrometry revealed the novel beta-lactamase Sml-1. As indicated by biotinylated probes, Sml-1, produced in E. coli, exhibits glutamine and lysine residues accessible for transglutaminase. The chromogenic cephalosporin analogue, nitrocefin, was hydrolyzed by Sml-1 with low velocity. The obtained Km and kcat values of the recombinant enzyme were 94.3±1.8 μM and 0.39±0.03 s-1, respectively. Penicillin G and ampicillin proved to be weak inhibitors of nitrocefin hydrolysis (Ki of 0.1 mM and 0.18 mM). Negligible influence of metals on β-lactamase activity ruled out that Sml-1 is a Zn2+-dependent class B beta-lactamase. Rather, sequence motifs such as SITK, YSN, and HDG forming the active core in a hypothetical structure may be typical for class C beta-lactamases. Based on the results, we assume that the novel transglutaminase substrate ensures undisturbed growth of aerial hyphae in Streptomyces mobaraensis by trapping and inactivating hostile beta-lactam antibiotics. 相似文献
92.
Cassandra S. James Stephen J. Mackay Angela H. Arthington Samantha J. Capon Anna Barnes Ben Pearson 《Ecology and evolution》2016,6(16):5950-5963
The primary objective of this study was to test the relevance of hydrological classification and class differences to the characteristics of woody riparian vegetation in a subtropical landscape in Queensland, Australia. We followed classification procedures of the environmental flow framework ELOHA – Ecological Limits of Hydrologic Alteration. Riparian surveys at 44 sites distributed across five flow classes recorded 191 woody riparian species and 15, 500 individuals. There were differences among flow classes for riparian species richness, total abundance, and abundance of regenerating native trees and shrubs. There were also significant class differences in the occurrence of three common tree species, and 21 indicator species (mostly native taxa) further distinguished the vegetation characteristics of each flow class. We investigated the influence of key drivers of riparian vegetation structure (climate, depth to water table, stream‐specific power, substrate type, degree of hydrologic alteration, and land use) on riparian vegetation. Patterns were explained largely by climate, particularly annual rainfall and temperature. Strong covarying drivers (hydrology and climate) prevented us from isolating the independent influences of these drivers on riparian assemblage structure. The prevalence of species considered typically rheophytic in some flow classes implies a more substantial role for flow in these classes but needs further testing. No relationships were found between land use and riparian vegetation composition and structure. This study demonstrates the relevance of flow classification to the structure of riparian vegetation in a subtropical landscape, and the influence of covarying drivers on riparian patterns. Management of environmental flows to influence riparian vegetation assemblages would likely have most potential in sites dominated by rheophytic species where hydrological influences override other controls. In contrast, where vegetation assemblages are dominated by a diverse array of typical rainforest species, and other factors including broad‐scale climatic gradients and topographic variables have greater influence than hydrology, riparian vegetation is likely to be less responsive to environmental flow management. 相似文献
93.
Genetic mutation analysis at early stages of cell line development using next generation sequencing
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Chapman Wright Joost Groot Samantha Swahn Helen McLaughlin Mei Liu Chongfeng Xu Chao Sun Eric Zheng Scott Estes 《Biotechnology progress》2016,32(3):813-817
A central goal for most biopharmaceutical companies is to reduce the development timeline to reach clinical proof of concept. This objective requires the development of tools that ensure the quality of biotherapeutic material destined for the clinic. Recent advances in high throughput protein analytics provide confidence in our ability to assess productivity and product quality attributes at early stages of cell line development. However, one quality attribute has, until recently, been absent from the standard battery of analytical tests facilitating informed choices early in cell line selection: genetic sequence confirmation. Techniques historically used for mutation analysis, such as detailed mass spectrometry, have limitations on the sample number and turnaround times making it less attractive at early stages. Thus, we explored the utility of Next‐Generation Sequencing (NGS) as a solution to address these limitations. Amplicon sequencing is one such NGS technique that is robust, rapid, sensitive, and amenable to multiplexing, all of which are essential attributes for our purposes. Here we report a NGS method based upon amplicon sequencing that has been successfully incorporated into our cell line development workflow alongside other high‐throughput protein analytical assays. The NGS method has demonstrated its value by identifying at least one Chinese hamster ovary (CHO) clone expressing a variant form of the biotherapeutic in each of the four clinical programs in which it has been utilized. We believe this sequence confirmation method is essential to safely accelerating the time to clinical proof of concept of biotherapeutics, and guard against delays related to sequence mutations. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:813–817, 2016 相似文献
94.
David Morgan Crickette Sanz Jean Robert Onononga Samantha Strindberg 《International journal of primatology》2016,37(6):718-737
Accurate and precise surveys of primate abundance provide the basis for understanding species ecology and essential information for conservation assessments. Owing to the elusive nature of wild apes and the vast region of dense forest they inhabit, population estimates of central chimpanzees (Pan troglodytes troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) have largely relied on surveys of their nests. Specific information about the nesting behavior of apes permits the estimation of the number of nests built (nest creation rate). Similarly, information on nest characteristics and environmental factors can be used to estimate the time it takes nests to decay (nest decay rate). Nest creation and decay rates are then used to convert nest density estimates to absolute ape densities. Population estimates that use site-specific estimates of nest creation and decay rates are more accurate and precise. However, it is common practice to generalize these conversion factors across sites because of the additional cost of studies required to gather the information to estimate them. Over a 9-mo study period, we detected and monitored the time to decay of gorilla nests (N = 514) and chimpanzee nests (N = 521) in northern Republic of Congo. We investigated the influence of nest characteristics and environmental factors on nest survivorship and estimated the mean time to nest decay (or equivalently survival) using MARK. Key factors influencing nest decay rate included ape species, forest type, nest height, mean rainfall, nest structure, nest type, and primary aspects of nest construction. Our findings highlight the synergistic effect of behavior and environment on great ape nest degradation, as well as providing practical insights for improving measures to monitor remaining populations of these endangered species. 相似文献
95.
96.
Badgers prefer cattle pasture but avoid cattle: implications for bovine tuberculosis control
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Rosie Woodroffe Christl A. Donnelly Cally Ham Seth Y. B. Jackson Kelly Moyes Kayna Chapman Naomi G. Stratton Samantha J. Cartwright 《Ecology letters》2016,19(10):1201-1208
Effective management of infectious disease relies upon understanding mechanisms of pathogen transmission. In particular, while models of disease dynamics usually assume transmission through direct contact, transmission through environmental contamination can cause different dynamics. We used Global Positioning System (GPS) collars and proximity‐sensing contact‐collars to explore opportunities for transmission of Mycobacterium bovis [causal agent of bovine tuberculosis] between cattle and badgers (Meles meles). Cattle pasture was badgers’ most preferred habitat. Nevertheless, although collared cattle spent 2914 collar‐nights in the home ranges of contact‐collared badgers, and 5380 collar‐nights in the home ranges of GPS‐collared badgers, we detected no direct contacts between the two species. Simultaneous GPS‐tracking revealed that badgers preferred land > 50 m from cattle. Very infrequent direct contact indicates that badger‐to‐cattle and cattle‐to‐badger M. bovis transmission may typically occur through contamination of the two species’ shared environment. This information should help to inform tuberculosis control by guiding both modelling and farm management. 相似文献
97.
Jang Hoon Kim Abubaker M. A. Morgan Bui Huu Tai Doan Thi Van Nguyen Manh Cuong 《Journal of enzyme inhibition and medicinal chemistry》2016,31(4):640-644
The aim of this study is to search for soluble epoxide hydrolase (sEH) inhibitors from natural plants, bioassay-guided fractionation of lipophilic n-hexane and chloroform layers of an extract of the aerial parts of Glycosmis stenocarpa led to the isolation of 12 compounds (1–12) including murrayafoline-A (1), isomahanine (2), bisisomahanine (3), saropeptate (4), (24?S)-ergost-4-en-3,6-dione (5), stigmasta-4-en-3,6-dion (6), stigmast-4-en-3-one (7), β-sitosterol (8), 24-methylpollinastanol (9), trans-phytol (10), neosarmentol III (11) and (+)-epiloliolide (12). Their structures were elucidated on the basis of spectroscopic data. Among them, neosarmentol III (11) was isolated from nature for the first time. All the isolated compounds were evaluated for their inhibitory activity against sEH. Among isolated carbazole-type compounds, isomahanine (2) and bisisomahanine (3) were identified as a potent inhibitor of sEH, with IC50 values of 22.5?±?1.7 and 7.7?±?1.2?µM, respectively. Moreover, the inhibitory action of 2 and 3 represented mixed-type enzyme inhibition. 相似文献
98.
Eoin N. Leen Frédéric Sorgeloos Samantha Correia Yasmin Chaudhry Fabien Cannac Chiara Pastore Yingqi Xu Stephen C. Graham Stephen J. Matthews Ian G. Goodfellow Stephen Curry 《PLoS pathogens》2016,12(1)
Translation initiation is a critical early step in the replication cycle of the positive-sense, single-stranded RNA genome of noroviruses, a major cause of gastroenteritis in humans. Norovirus RNA, which has neither a 5´ m7G cap nor an internal ribosome entry site (IRES), adopts an unusual mechanism to initiate protein synthesis that relies on interactions between the VPg protein covalently attached to the 5´-end of the viral RNA and eukaryotic initiation factors (eIFs) in the host cell. For murine norovirus (MNV) we previously showed that VPg binds to the middle fragment of eIF4G (4GM; residues 652–1132). Here we have used pull-down assays, fluorescence anisotropy, and isothermal titration calorimetry (ITC) to demonstrate that a stretch of ~20 amino acids at the C terminus of MNV VPg mediates direct and specific binding to the HEAT-1 domain within the 4GM fragment of eIF4G. Our analysis further reveals that the MNV C terminus binds to eIF4G HEAT-1 via a motif that is conserved in all known noroviruses. Fine mutagenic mapping suggests that the MNV VPg C terminus may interact with eIF4G in a helical conformation. NMR spectroscopy was used to define the VPg binding site on eIF4G HEAT-1, which was confirmed by mutagenesis and binding assays. We have found that this site is non-overlapping with the binding site for eIF4A on eIF4G HEAT-1 by demonstrating that norovirus VPg can form ternary VPg-eIF4G-eIF4A complexes. The functional significance of the VPg-eIF4G interaction was shown by the ability of fusion proteins containing the C-terminal peptide of MNV VPg to inhibit in vitro translation of norovirus RNA but not cap- or IRES-dependent translation. These observations define important structural details of a functional interaction between norovirus VPg and eIF4G and reveal a binding interface that might be exploited as a target for antiviral therapy. 相似文献
99.
Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis 总被引:1,自引:0,他引:1
Elisabete Carvalho Pietro Franceschi Antje Feller Lorena Herrera Luisa Palmieri Panagiotis Arapitsas Samantha Riccadonna Stefan Martens 《Metabolomics : Official journal of the Metabolomic Society》2016,12(9):144
Introduction
Raspberries are becoming increasingly popular due to their reported health beneficial properties. Despite the presence of only trace amounts of anthocyanins, yellow varieties seems to show similar or better effects in comparison to conventional raspberries.Objectives
The aim of this work is to characterize the metabolic differences between red and yellow berries, focussing on the compounds showing a higher concentration in yellow varieties.Methods
The metabolomic profile of 13 red and 12 yellow raspberries (of different varieties, locations and collection dates) was determined by UPLC–TOF-MS. A novel approach based on Pearson correlation on the extracted ion chromatograms was implemented to extract the pseudospectra of the most relevant biomarkers from high energy LC–MS runs. The raw data will be made publicly available on MetaboLights (MTBLS333).Results
Among the metabolites showing higher concentration in yellow raspberries it was possible to identify a series of compounds showing a pseudospectrum similar to that of A-type procyanidin polymers. The annotation of this group of compounds was confirmed by specific MS/MS experiments and performing standard injections.Conclusions
In berries lacking anthocyanins the polyphenol metabolism might be shifted to the formation of a novel class of A-type procyanidin polymers.100.
Erica Fleishman Daniel P. Costa John Harwood Scott Kraus David Moretti Leslie F. New Robert S. Schick Lisa K. Schwarz Samantha E. Simmons Len Thomas Randall S. Wells 《Marine Mammal Science》2016,32(3):1004-1021
We provide guidance for monitoring whether human activities affect the physiology or behavior of marine mammals and, if so, whether those effects may lead to changes in survival and reproduction at the population level. We suggest that four elements be included in designing and implementing such a monitoring program. The first is development of a theory of change: a set of mechanistic hypotheses that outline why a given activity might be expected to have one or more measurable effects on individuals and populations, and ideally the magnitude, timing, and duration of the effects. The second element, definition of biologically meaningful effect sizes, ultimately facilitates the development of a monitoring program that can detect those magnitudes of effect with the desired levels of precision. The third element, selection of response variables for monitoring, allows inference to whether observed changes in the status of individuals or populations are attributable to a given activity. Visual observations, passive acoustic and tagging instruments, and direct physical measurements all can provide data that facilitate quantitative hypothesis testing. The fourth element is specification of the temporal sequence of monitoring. These elements also can be used to inform monitoring of the responses of other taxonomic groups to human activities. 相似文献