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1.
Thomas R. Raffel James O. Lloyd-Smith Stanley K. Sessions Peter J. Hudson Jason R. Rohr 《Oecologia》2011,165(4):1031-1042
The manner in which parasite intensity and aggregation varies with host age can provide insights into parasite dynamics and
help identify potential means of controlling infections in humans and wildlife. A significant challenge is to distinguish
among competing mechanistic hypotheses for the relationship between age and parasite intensity or aggregation. Because different
mechanisms can generate similar relationships, testing among competing hypotheses can be difficult, particularly in wildlife
hosts, and often requires a combination of experimental and model fitting approaches. We used field data, experiments, and
model fitting to distinguish among ten plausible drivers of a curvilinear age–intensity relationship and increasing aggregation
with host age for echinostome trematode infections of green frogs. We found little support for most of these proposed drivers
but did find that the parsimonious explanation for the observed age–intensity relationship was seasonal exposure to echinostomes.
The parsimonious explanation for the aggregated distribution of parasites in this host population was heterogeneity in exposure.
A predictive model incorporating seasonal exposure indicated that tadpoles hatching early or late in the breeding season should
have lower trematode burdens at metamorphosis, particularly with simulated warmer climates. Application of this multi-pronged
approach (field surveys, lab experiments, and modeling) to additional parasite–host systems could lead to discovery of general
patterns in the drivers of parasite age–intensity and age–distribution relationships. 相似文献
2.
We demonstrate a novel NMR method for the mapping of protein–protein interaction sites. In our approach protein–protein binding
sites are mapped by competition binding experiments using indirect NMR reporter technology and Ala positional scanning. The
methodology provides high sensitivity, ease of implementation and high-throughput capabilities. The feasibility of the technique
is demonstrated with an application to the β-Catenin/Tcf4 complex. 相似文献
3.
Siemer AB Ritter C Steinmetz MO Ernst M Riek R Meier BH 《Journal of biomolecular NMR》2006,34(2):75-87
The partial 15N and 13C solid-state NMR resonance assignment of the HET-s prion protein fragment 218–289 in its amyloid form is presented. It is
based on experiments measured at MAS frequencies in the range of 20–40 kHz using exclusively adiabatic polarization-transfer
schemes. The resonance assignment within each residue is based on two-dimensional 13C––13C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two-
and three-dimensional 15N––13C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the
78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving
rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances
are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two
fragments of about 20 residues.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
4.
Dabros M Dennewald D Currie DJ Lee MH Todd RW Marison IW von Stockar U 《Bioprocess and biosystems engineering》2009,32(2):161-173
This work evaluates three techniques of calibrating capacitance (dielectric) spectrometers used for on-line monitoring of
biomass: modeling of cell properties using the theoretical Cole–Cole equation, linear regression of dual-frequency capacitance
measurements on biomass concentration, and multivariate (PLS) modeling of scanning dielectric spectra. The performance and
robustness of each technique is assessed during a sequence of validation batches in two experimental settings of differing
signal noise. In more noisy conditions, the Cole–Cole model had significantly higher biomass concentration prediction errors
than the linear and multivariate models. The PLS model was the most robust in handling signal noise. In less noisy conditions,
the three models performed similarly. Estimates of the mean cell size were done additionally using the Cole–Cole and PLS models,
the latter technique giving more satisfactory results. 相似文献
5.
Three field predator exclusion experiments were conducted in 1992 on a lagoonal muddy pan of the Bay of Cádiz to measure the
effects of large epibenthic predators (fish and crustacean decapods) on the benthic macroinvertebrate community at different
periods of the year (May–June, August–September, November–December). At the end of each field experiment (30–31 days), benthic
macrofaunal communities within exclosures and control plots (three replicates for each treatment) were compared. There were
no considerable exclosure artifacts in all three experiments, but a great heterogenity in the spatial macrofaunal distribution
was observed especially in the late autumn experiment. No systematic change in overall faunal characteristics was observed
with the exclusion of epibenthic predators, except significantly greater mean individual sizes (all experiments) and lower
total densities (June and December) within exclosures. For several benthic species, a statistically detectable increased density
and larger mean individual size were also observed within exclosures in May–June and August–September experiments but not
in December, probably related to the higher predatory activity during the warm season. Conversely, the amphipod Microdeutopus gryllotalpa showed lower density but also larger mean size when epibenthic predators were excluded. An algal cover (Ulva) was present at three field experiments and had a mixed effect on the density of benthic macrofauna. Some epifaunal species
(or epifaunal stages) were positively affected by the algal biomass, while some infaunal species were negatively affected. 相似文献
6.
In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.
Figure The location of the ligands (complex B – blue; complex E – red; and complex F –
green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4
– purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC
and IC loops are not shown
Electronic Supplementary Material Supplementary material is available at 相似文献
7.
V. V. Moiseenko R. N. Hamm A. J. Waker W. V. Prestwich 《Radiation and environmental biophysics》1998,37(3):167-172
Radiation-induced DNA single- and double-strand breaks were modeled for 660 keV photon radiation and scavenger capacity mimicking
the cellular environment. Atomistic representation of DNA in B form with a first hydration shell was utilized to model direct
and indirect damage. Monte Carlo generated electron tracks were used to model energy deposition in matter and to derive initial
spatial distributions of species which appear in the medium following radiolysis. Diffusion of species was followed with time,
and their reactions with DNA and each other were modeled in an encounter-controlled manner. Three methods to account for hydroxyl
radical diffusion in a cellular environment were tested: assumed exponential survival, time-limited modeling and modeling
of reactions between hydroxyl radicals and scavengers in an encounter-controlled manner. Although the method based on modeling
scavenging in an encounter-controlled manner is more precise, it requires substantially more computer resources than either
the exponential or time-limiting method. Scavenger concentrations of 0.5 and 0.15 M were considered using exponential and
encounter-controlled methods with reaction rate set at 3×109 dm3 mol–1 s–1. Diffusion length and strand break yields, predicted by these two methods for the same scavenger molarity, were different
by 20%–30%. The method based on limiting time of chemistry follow-up to 10–9 s leads to DNA damage and radical diffusion estimates similar to 0.5 M scavenger concentration in the other two methods.
The difference observed in predictions made by the methods considered could be tolerated in computer simulations of DNA damage.
Received: 3 June 1998 / Accepted in revised form: 16 July 1998 相似文献
8.
Jehle S Hiller M Rehbein K Diehl A Oschkinat H van Rossum BJ 《Journal of biomolecular NMR》2006,36(3):169-177
A simple spectroscopic filtering technique is presented that may aid the assignment of 13C and 15N resonances of methyl-containing amino-acids in solid-state magic-angle spinning (MAS) NMR. A filtering block that selects methyl resonances is introduced in two-dimensional (2D) 13C-homonuclear and 15N–13C heteronuclear correlation experiments. The 2D 13C–13C correlation spectra are recorded with the methyl filter implemented prior to a 13C–13C mixing step. It is shown that these methyl-filtered 13C-homonuclear correlation spectra are instrumental in the assignment of Cδ resonances of leucines by suppression of Cγ–Cδ cross peaks. Further, a methyl filter is implemented prior to a 15N–13C transferred-echo double resonance (TEDOR) exchange scheme to obtain 2D 15N–13C heteronuclear correlation spectra. These experiments provide correlations between methyl groups and backbone amides. Some of the observed sequential 15N–13C correlations form the basis for initial sequence-specific assignments of backbone signals of the outer-membrane protein G. 相似文献
9.
Peng QP Cao SF Lyu QF Xue SG Jin W Liu XY Zhang WJ Nielsen HI Kuang YP 《In vitro cellular & developmental biology. Animal》2011,47(8):565-572
The purpose of this study is to develop a novel method for the cryopreservation and efficient post-thaw recovery of individual
or small numbers of human spermatozoa. Spermatozoa equilibrated in cryoprotectant buffer were injected with an intracytoplasmic
sperm injection (ICSI) needle into a droplet of cryoprotectant on a homemade cryoleaf. The droplet was of cryoprotectant and
seminal plasma at a ratio of 1:1. The sperm-loaded cryoleaf was slowly lowered over and stored in liquid nitrogen. Spermatozoa
were thawed in a 37°C oil bath without dilution and centrifugation. To test the fertilizing ability of these spermatozoa,
the recovered spermatozoa were injected by ICSI into 1-d-old or in vitro-matured human oocytes. Fresh spermatozoa from the
same semen samples served as controls. The trials were performed in two separate experiments. In the first set of experiments,
92 spermatozoa were thawed and carefully investigated. The spermatozoa from percutaneous epididymal sperm aspiration had a
motility recovery of 92.9% (13/14); ejaculated spermatozoa had a motility recovery of 61.5% (48/78), and only 1.3% (1/78)
was lost. Together in the first and second set of experiments, the fertilization rates for the fresh and frozen–thawed spermatozoa
were 67.6% (25/37) and 60.6% (40/66), respectively (P = 0.052). The mean embryo cleavage rates in the fresh and frozen–thawed groups were 88% (22/25) and 85% (34/40), respectively
(P = 0.990). This cryopreservation method for individual or small numbers of human spermatozoa was efficient and simple. These
findings make this method a promising technique for the clinical application of ejaculated sperm from oligozoospermic patients. 相似文献
10.
The paper presents a set of two-dimensional experiments that utilize direct 13C detection to provide proton–carbon, carbon–carbon and carbon–nitrogen correlations in the bases of nucleic acids. The set
includes a 13C-detected proton–carbon correlation experiment for the measurement of 13C–13C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the 13C–13C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton
with a network of coupled carbons, and a 13C-detected 13C–15N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used
for extracting the carbon–carbon couplings and/or carbon decoupling in the direct dimension, while the S3E procedure is preferred in the indirect dimension of the carbon–nitrogen experiment to obtain the value of the coupling constant.
The experiments supply accurate values of 13C and 15N chemical shifts and carbon–carbon and carbon–nitrogen coupling constants. These values can help to reveal structural features
of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
11.
Ion channels are fundamental molecules in the nervous system that catalyze the flux of ions across the cell membrane. Ion
channel flux activity is comparable to the catalytic activity of enzyme molecules. Saturating concentrations of substrate
induce “dynamic disorder” in the kinetic rate processes of single-enzyme molecules and consequently, develop correlative “memory”
of the previous history of activities. Similarly, binding of ions as substrate alone or in presence of agonists affects the
catalytic turnover of single-ion channels. Here, we investigated the possible existence of dynamic disorder and molecular
memory in the single human-TREK1-channel due to binding of substrate/agonist using the excised inside–out patch-clamp technique.
Our results suggest that the single-hTREK1-channel behaves as a typical Michaelis–Menten enzyme molecule with a high-affinity
binding site for K+ ion as substrate. But, in contrast to enzyme, dynamic disorder in single-hTREK1-channel was not induced by substrate K+ binding, but required allosteric modification of the channel molecule by the agonist, trichloroethanol. In addition, interaction
of trichloroethanol with hTREK1 induced strong correlation in the waiting time and flux intensity, exemplified by distinct
mode-switching between high and low flux activities. This suggested the induction of molecular memory in the channel molecule
by the agonist, which persisted for several decades in time. Our mathematical modeling studies identified the kinetic rate
processes associated with dynamic disorder. It further revealed the presence of multiple populations of distinct conformations
that contributed to the “heterogeneity” and consequently, to the molecular memory phenomenon that we observed. 相似文献
12.
Petri-Jaan Lahtvee Kaspar Valgepea Ranno Nahku Kristo Abner Kaarel Adamberg Raivo Vilu 《Antonie van Leeuwenhoek》2009,96(4):487-496
Growth space of Lactococcus lactis subsp. lactis IL1403 was studied at constant growth rate using D-stat cultivation technique. Starting from steady state conditions in a
chemostat culture (μ = 0.2 h−1), the pH and/or temperature were continuously changed in the range of 5.4–6.4 and 26–34°C, respectively, followed by the
return to the initial environmental conditions. Based on substrate consumption and product formation yields and expression
changes of 1,920 genes, it was shown that changes of physiological state were not dependent on the direction of movement (from
pH 6.3 to 5.4 or from 5.4 to 6.3), showing that quasi steady state values in D-stat corresponded to the steady state values
in chemostats. Relative standard deviation of growth characteristics in triplicate D-stat experiments was below 10%. Continuing
the experiment and reestablishing initial growth conditions revealed in average 7% difference (hysteresis) in growth characteristics
when comparing chemostat steady state cultures prior and after the change of environmental conditions. Similarly, shifts were
also seen at gene expression levels. The large amount of quantitatively reliable data obtained in this study provided a new
insight into dynamic properties of bacterial physiology, and can be used for describing the growth space of microorganisms
by modeling cell metabolism. 相似文献
13.
We derive models for chemosensitive movement based on Cattaneo's law of heat propagation with finite speed. We apply the
model to pattern formation as observed in experiments with Dictyostelium discoideum, with Salmonella typhimurium and with Escherichia coli. For Salmonella typhimurium we make predictions on pattern formation which can be tested in experiments. We discuss the relations of the Cattaneo models
to classical models and we develop an effective numerical scheme.
Received: 8 October 2001 / Revised version: 2 August 2002 / Published online: 19 November 2002
Key words or phrases: Chemotaxis – Aggregation – Cattaneo model – Numerical schemes
Acknowledgements. We are very grateful for comments of S. Noelle concerning the numerical scheme. We thank K.P. Hadeler and C. Schmeiser for
helpful remarks. The research was supported by the Deutsche Forschungsgemeinschaft, research project ANumE and the Austrian Science Foundation, grant no. W008. 相似文献
14.
15.
Stewart R Song L Carter SM Sigalas C Zaccai NR Kanamarlapudi V Bhat MB Takeshima H Sitsapesan R 《The Journal of membrane biology》2008,222(2):65-77
Ryanodine receptor 2 (RyR2) cDNA has been available for more than 15 years; however, due to the complex nature of ligand gating
in this channel, many aspects of recombinant RyR2 function have been unresearched. We established a stable, inducible HEK
293 cell line expressing full-length rabbit RyR2 cDNA and assessed the single-channel properties of the recombinant RyR2,
with particular reference to ligand regulation with Ca2+ as the permeant ion. We found that the single-channel conductances of recombinant RyR2 and RyR2 isolated from cardiac muscle
are essentially identical, as is irreversible modification by ryanodine. Although it is known that RyR2 expressed in HEK 293
cells is not associated with FKBP12.6, we demonstrate that these channels do not exhibit any discernable disorganized gating
characteristics or subconductance states. We also show that the gating of recombinant RyR2 is indistinguishable from that
of channels isolated from cardiac muscle when activated by cytosolic Ca2+, caffeine or suramin. The mechanisms underlying ATP activation are also similar; however, the experiments highlighted a novel
effect of ATP at physiologically relevant concentrations of 5–10 mM. With Ca2+ as permeant ion, 5–10 mM ATP consistently inactivated recombinant channels (15/16 experiments). Such inactivation was rarely
observed with native RyR2 isolated from cardiac muscle (1 in 16 experiments). However, if the channels were purified, inactivation
by ATP was then revealed in all experiments. This action of ATP may be relevant for inactivation of sarcoplasmic reticulum
Ca2+ release during cardiac excitation–contraction coupling or may represent unnatural behavior that is revealed when RyR2 is
purified or expressed in noncardiac systems.
Richard Stewart and Lele Song—contributed equally to this work. 相似文献
16.
Voziyan PA Johnston M Chao A Bomhoff G Fisher MT 《Journal of structural and functional genomics》2005,6(2-3):183-188
Although GroE chaperonins and osmolytes had been used separately as protein folding aids, combining these two methods provides
a considerable advantage for folding proteins that cannot fold with either osmolytes or chaperonins alone. This technique
rapidly identifies superior folding solution conditions for a broad array of proteins that are difficult or impossible to
fold by other methods. While testing the broad applicability of this technique, we have discovered that osmolytes greatly
simplify the chaperonin reaction by eliminating the requirement for the co-chaperonin GroES which is normally involved in
encapsulating folding proteins within the GroEL–GroES cavity. Therefore, combinations of soluble or immobilized GroEL, osmolytes
and ATP or even ADP are sufficient to refold the test proteins. The first step in the chaperonin/osmolyte process is to form
a stable long-lived chaperonin–substrate protein complex in the absence of nucleotide. In the second step, different osmolyte
solutions are added along with nucleotides, thus forming a ‘folding array’ to identify superior folding conditions. The stable
chaperonin–substrate protein complex can be concentrated or immobilized prior to osmolyte addition. This procedure prevents-off
pathway aggregation during folding/refolding reactions and more importantly allows one to refold proteins at concentrations
(~mg/ml) that are substantially higher than the critical aggregation concentration for given protein. This technique can be
used for successful refolding of proteins from purified inclusion bodies. Recently, other investigators have used our chaperonin/osmolyte
method to demonstrate that a mutant protein that misfolds in human disease can be rescued by GroEL/osmolyte system. Soluble
or immobilized GroEL can be easily removed from the released folded protein using simple separation techniques. The method
allows for isolation of folded monomeric or oligomeric proteins in quantities sufficient for X-ray crystallography or NMR
structural determinations. 相似文献
17.
Ottesen JT 《Journal of mathematical biology》2003,46(4):309-332
An elastic rubber tube is connected with a stiffer rubber tube forming two halves of a torus and filled with water. Compressing
one of the rubber tubes symmetrically and periodic at a point of asymmetry creates a remarkable unidirectional mean flow in
the system. The size and the direction of the mean flow depend on the frequency of compression, the elasticity of the tubes,
the compression ratio, and the type of compression with respect to time in a complicated manner. The system is modelled using
a one-dimensional theory derived by averaging the Navier-Stokes equations ignoring higher order terms in a certain small quantity.
The one-dimensional model is analysed partly analytically and partly numerically. A series of experiments on a physical realisation
of the system are described. The theoretical findings and experimental results are compared; They show a remarkable agreement
between the experiments and the predictions of the model. Frequencies at which the mean flow change direction are predicted
numerically as well as analytically and the two results are compared.
Received: 21 February 2002 / Revised version: 30 August 2002 / Published online: 17 January 2003
Key words or phrases: Flow – Elastic tubes – Valveless pumping – Navier-Stokes equations – Frequency dependent – One-dimensional model – Experimental
validation 相似文献
18.
Within the framework of the quantum hypothesis of synaptic transmission, the amount of a neurotransmitter released in a unitary
event of calcium-dependent exocytosis corresponds to the content of a synaptic vesicle (SV). The number of these organelles
in the presynaptic terminal is an important index characterizing the functional state of the given synapse. The technique
of estimation of the dimension of the total SV pool, which is based on mathematical modeling and is realized in a computer
experiment, is described. This technique allows one to interpret quantitative estimations obtained in the course of the analysis
of images of random ultrathin sections of presynaptic terminals in the terms of 3D space. The capabilities of this technique
are illustrated using an example of estimation of the size of the total SV pool in asymmetric synapses between neurons of
the radial layer of the murine hippocampal CA1 area.
Neirofiziologiya/Neurophysiology, Vol. 38, No. 3, pp. 219–223, May–June, 2006. 相似文献
19.
A conventional study design among medical and biological experimentalists involves collecting multiple measurements from a study subject. For example, experiments utilizing mouse models in neuroscience often involve collecting multiple neuron measurements per mouse to increase the number of observations without requiring a large number of mice. This leads to a form of statistical dependence referred to as clustering. Inappropriate analyses of clustered data have resulted in several recent critiques of neuroscience research that suggest the bar for statistical analyses within the field is set too low. We compare naïve analytical approaches to marginal, fixed-effect, and mixed-effect models and provide guidelines for when each of these models is most appropriate based on study design. We demonstrate the influence of clustering on a between-mouse treatment effect, a within-mouse treatment effect, and an interaction effect between the two. Our analyses demonstrate that these statistical approaches can give substantially different results, primarily when the analyses include a between-mouse treatment effect. In a novel analysis from a neuroscience perspective, we also refine the mixed-effect approach through the inclusion of an aggregate mouse-level counterpart to a within-mouse (neuron level) treatment as an additional predictor by adapting an advanced modeling technique that has been used in social science research and show that this yields more informative results. Based on these findings, we emphasize the importance of appropriate analyses of clustered data, and we aim for this work to serve as a resource for when one is deciding which approach will work best for a given study. 相似文献
20.
Hope E. Stansfield Bethany P. Kulczewski Kyle E. Lybrand Elizabeth R. Jamieson 《Journal of biological inorganic chemistry》2009,14(2):193-199
Protein microarrays have been used extensively to identify protein–protein interactions; however, this technology has not
been widely applied to protein–DNA interactions. In particular, this work demonstrates the utility of this technique for rapidly
identifying interactions of proteins with metal-modified DNA. Protein macroarray experiments were carried out with high mobility
group protein 1 (HMG-1) and cisplatin- and chromium-modified 50-mer oligonucleotides to demonstrate “proof of principle.”
Commercially available protein microarrays containing many different classes of human proteins were then employed to search
for additional interactions with cisplatin-modified DNA. The results of the microarray experiments confirmed some known interactions
and, more importantly, identified many novel protein interactions, demonstrating the utility of this method as a rapid, high-throughput
technique to discover proteins that interact with metal-modified DNA.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献