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161.
Oktaviani NA Otten R Dijkstra K Scheek RM Thulin E Akke M Mulder FA 《Biomolecular NMR assignments》2011,5(1):79-84
Here we present the 100% complete assignment chemical shift of non-labile 1H, 15N and 13C nuclei of Calbindin D9k P43G. The assignment includes all non-exchangeable side chain nuclei, including ones that are rarely reported, such as LysNζ
as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge
our assignments for Calbindin D9k extend beyond previous studies reaching near-completeness (Vis et al. in Biochem 33:14858–14870, 1994; Yamazaki et al. in J Am Chem Soc 116:6464–6465, 1994; Yamazaki et al. in Biochem 32:5656–5669, 1993b). 相似文献
162.
We have biochemically and functionally characterized the pseudomurein cell wall-binding (PMB) domain that is present at the C-terminus of the Surface (S)-layer protein MTH719 from Methanothermobacter thermautotrophicus. Chemical denaturation of the protein with guanidinium hydrochloride occurred at 3.8 M. A PMB-GFP fusion protein not only binds to intact pseudomurein of methanogenic archaea, but also to spheroplasts of lysozyme-treated bacterial cells. This binding is pH dependent. At least two of the three motifs that are present in the domain are necessary for binding. Limited proteolysis revealed a possible cleavage site in the spacing sequence between motifs 1 and 2 of the PMB domain, indicating that the motif region itself is protected from proteases. 相似文献
163.
164.
165.
Jennifer A. Dijkstra Kate L. Buckman Darren Ward David W. Evans Michele Dionne Celia Y. Chen 《PloS one》2013,8(3)
Marine food webs are the most important link between the global contaminant, methylmercury (MeHg), and human exposure through consumption of seafood. Warming temperatures may increase human exposure to MeHg, a potent neurotoxin, by increasing MeHg production as well as bioaccumulation and trophic transfer through marine food webs. Studies of the effects of temperature on MeHg bioaccumulation are rare and no study has specifically related temperature to MeHg fate by linking laboratory experiments with natural field manipulations in coastal ecosystems. We performed laboratory and field experiments on MeHg accumulation under varying temperature regimes using the killifish, Fundulus heteroclitus. Temperature treatments were established in salt pools on a coastal salt marsh using a natural temperature gradient where killifish fed on natural food sources. Temperatures were manipulated across a wider range in laboratory experiments with killifish exposed to MeHg enriched food. In both laboratory microcosms and field mesocosms, MeHg concentrations in killifish significantly increased at elevated temperatures. Moreover, in field experiments, other ancillary variables (salinity, MeHg in sediment, etc.) did not relate to MeHg bioaccumulation. Modeling of laboratory experimental results suggested increases in metabolic rate as a driving factor. The elevated temperatures we tested are consistent with predicted trends in climate warming, and indicate that in the absence of confounding factors, warmer sea surface temperatures could result in greater in bioaccumulation of MeHg in fish, and consequently, increased human exposure. 相似文献
166.
Antonie Koetsier Liselotte van Asten Frederika Dijkstra Wim van der Hoek Bianca E. Snijders Cees C. van den Wijngaard Hendriek C. Boshuizen Gé A. Donker Dylan W. de Lange Nicolette F. de Keizer Niels Peek 《PloS one》2013,8(12)
Objectives
Severe influenza can lead to Intensive Care Unit (ICU) admission. We explored whether ICU data reflect influenza like illness (ILI) activity in the general population, and whether ICU respiratory infections can predict influenza epidemics.Methods
We calculated the time lag and correlation between ILI incidence (from ILI sentinel surveillance, based on general practitioners (GP) consultations) and percentages of ICU admissions with a respiratory infection (from the Dutch National Intensive Care Registry) over the years 2003–2011. In addition, ICU data of the first three years was used to build three regression models to predict the start and end of influenza epidemics in the years thereafter, one to three weeks ahead. The predicted start and end of influenza epidemics were compared with observed start and end of such epidemics according to the incidence of ILI.Results
Peaks in respiratory ICU admissions lasted longer than peaks in ILI incidence rates. Increases in ICU admissions occurred on average two days earlier compared to ILI. Predicting influenza epidemics one, two, or three weeks ahead yielded positive predictive values ranging from 0.52 to 0.78, and sensitivities from 0.34 to 0.51.Conclusions
ICU data was associated with ILI activity, with increases in ICU data often occurring earlier and for a longer time period. However, in the Netherlands, predicting influenza epidemics in the general population using ICU data was imprecise, with low positive predictive values and sensitivities. 相似文献167.
Daniel Warner Luis M. M. Ferreira Michel J. H. Breuer Jan Dijkstra Wilbert F. Pellikaan 《PloS one》2013,8(10)
We describe the use of carbon stable isotope (13C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically 13C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha−1) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the δ13C (i.e. the ratio 13C:12C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C27–C36) and passage kinetics were determined for the most abundant C29, C31 and C33
n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K
1) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p≤0.002) increase with carbon chain length. K
1 estimates were comparable to those of the 13C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to 0.71; p≤0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of 13C versus 12C. Our results suggest that 13C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the δ13C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics. 相似文献
168.
Mingkwan Nipitwattanaphon John Wang Michiel B. Dijkstra Laurent Keller 《Molecular ecology》2013,22(14):3797-3813
A remarkable social polymorphism is controlled by a single Mendelian factor in the fire ant Solenopsis invicta. A genomic element marked by the gene Gp‐9 determines whether workers tolerate one or many fertile queens in their colony. Gp‐9 was recently shown to be part of a supergene with two nonrecombining variants, SB and Sb. SB/SB and SB/Sb queens differ in how they initiate new colonies, and in many physiological traits, for example odour and maturation rate. To understand how a single genetic element can affect all these traits, we used a microarray to compare gene expression patterns between SB/SB and SB/Sb queens of three different age classes: 1‐day‐old unmated queens, 11‐day‐old unmated queens and mated, fully reproductive queens collected from mature field colonies. The number of genes that were differentially expressed between SB/SB and SB/Sb queens of the same age class was smallest in 1‐day‐old queens, maximal in 11‐day‐old queens and intermediate in reproductive queens. Gene ontology analysis showed that SB/SB queens upregulate reproductive genes faster than SB/Sb queens. For all age classes, genes inside the supergene were overrepresented among the differentially expressed genes. Consistent with the hypothesized greater number of transposons in the Sb supergene, 13 transposon genes were upregulated in SB/Sb queens. Viral genes were also upregulated in SB/Sb mature queens, consistent with the known greater parasite load in colonies headed by SB/Sb queens compared with colonies headed by SB/SB queens. Eighteen differentially expressed genes between reproductive queens were involved in chemical signalling. Our results suggest that many genes in the supergene are involved in regulating social organization and queen phenotypes in fire ants. 相似文献
169.
Hook SE Steele MA Northwood KS Dijkstra J France J Wright AD McBride BW 《FEMS microbiology ecology》2011,78(2):275-284
Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet, transitioned to a 65% grain diet for 3 weeks, and returned to the hay diet for 3 weeks. Rumen fluid, rumen solids, and feces were sampled during weeks 0 (hay), 1 and 3 (high grain), and 4 and 6 (hay). SARA was diagnosed during week 1, with a pH below 5.6 for 4.6±1.4 h. Bacterial density was significantly lower in the rumen solids with high grain (P=0.047). Rumen fluid clone libraries from weeks 0, 3, and 6 were assessed at the 98% level and 154 operational taxonomic units were resolved. Week 3 diversity significantly differed from week 0, and community structure differed from weeks 0 and 6 (P<0.0001). Clones belonging to the phylum Firmicutes predominated. Compared with the hay diet, the high-grain diet contained clones from Selenomonas ruminantium and Succiniclasticum ruminis, but lacked Eubacterium spp. SARA adaptation was found to significantly alter bacterial density, diversity, and community structure, warranting further investigation into the role bacteria play in SARA adaptation. 相似文献
170.
Palomo M Pijning T Booiman T Dobruchowska JM van der Vlist J Kralj S Planas A Loos K Kamerling JP Dijkstra BW van der Maarel MJ Dijkhuizen L Leemhuis H 《The Journal of biological chemistry》2011,286(5):3520-3530
Branching enzyme (EC 2.4.1.18; glycogen branching enzyme; GBE) catalyzes the formation of α1,6-branching points in glycogen. Until recently it was believed that all GBEs belong to glycoside hydrolase family 13 (GH13). Here we describe the cloning and expression of the Thermus thermophilus family GH57-type GBE and report its biochemical properties and crystal structure at 1.35-Å resolution. The enzyme has a central (β/α)7-fold catalytic domain A with an inserted domain B between β2 and α5 and an α-helix-rich C-terminal domain, which is shown to be essential for substrate binding and catalysis. A maltotriose was modeled in the active site of the enzyme which suggests that there is insufficient space for simultaneously binding of donor and acceptor substrates, and that the donor substrate must be cleaved before acceptor substrate can bind. The biochemical assessment showed that the GH57 GBE possesses about 4% hydrolytic activity with amylose and in vitro forms a glucan product with a novel fine structure, demonstrating that the GH57 GBE is clearly different from the GH13 GBEs characterized to date. 相似文献