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81.
Joshua M. Borin Mary L. Moser Adam G. Hansen David A. Beauchamp Stephen C. Corbett Brett R. Dumbauld Casey Pruitt Jennifer L. Ruesink Cinde Donoghue 《Environmental Biology of Fishes》2017,100(12):1561-1573
Habitat use can be complex, as tradeoffs among physiology, resource abundance, and predator avoidance affect the suitability of different environments for different species. Green sturgeon (Acipenser medirostris), an imperiled species along the west coast of North America, undertake extensive coastal migrations and occupy estuaries during the summer and early fall. Warm water and abundant prey in estuaries may afford a growth opportunity. We applied a bioenergetics model to investigate how variation in estuarine temperature, spawning frequency, and duration of estuarine residence affect consumption and growth potential for individual green sturgeon. We assumed that green sturgeon achieve observed annual growth by feeding solely in conditions represented by Willapa Bay, Washington, an estuary annually frequented by green sturgeon and containing extensive tidal flats that harbor a major prey source (burrowing shrimp, Neotrypaea californiensis). Modeled consumption rates increased little with reproductive investment (<0.4%), but responded strongly (10–50%) to water temperature and duration of residence, as higher temperatures and longer residence required greater consumption to achieve equivalent growth. Accordingly, although green sturgeon occupy Willapa Bay from May through September, acoustically-tagged individuals are observed over much shorter durations (34 d + 41 d SD, N = 89). Simulations of <34 d estuarine residence required unrealistically high consumption rates to achieve observed growth, whereas longer durations required sustained feeding, and therefore higher total intake, to compensate for prolonged exposure to warm temperatures. Model results provide a range of per capita consumption rates by green sturgeon feeding in estuaries to inform management decisions regarding resource and habitat protection for this protected species. 相似文献
82.
Little is known about the composition and function of the mycorrhizal fungal community in riparian areas, or its importance
in competitive interactions between Populus fremontii, a dominant tree in southwestern United States riparian forests which forms arbuscular and ectomycorrhizas, and Tamarix ramosissima, an introduced tree species that has spread into riparian areas. The objectives of this study were to determine the mycorrhizal
status of Tamarixand to evaluate the effect of mycorrhizal fungal inoculation on Tamarix growth and on the coexistence between Tamarix and Populus.Arbuscular mycorrhizal fungal colonization of Tamarix was very low in both field and greenhouse grown roots, but levels of colonization by dark septate endophytes were high. Fungal
inoculation had little effect on Tamarix seedling growth in monoculture. When Populus and Tamarix were grown together in a greenhouse pot experiment, fungal inoculation reduced the height and biomass of Tamarix but had no effect on Populus. Fungal inoculation shifted coexistence ratios. When Tamarix and Populuswere grown together, Tamarixplants averaged 20 of pot biomass in the uninoculated control but only 5 of pot biomass in the inoculated treatment. These
results indicate that Tamarix is non-mycotrophic and that in this greenhouse experiment inoculation altered patterns of coexistence between Populus and Tamarix. 相似文献
83.
In Caenorhabditis elegans, specific Argonaute proteins are dedicated to the RNAi and microRNA pathways. To uncover how the precise Argonaute selection occurs, we designed dsRNA triggers containing both miRNA and siRNA sequences. While dsRNA carrying nucleotides mismatches can only enter the miRNA pathway, a fully complementary dsRNA successfully rescues let-7 miRNA function and initiates silencing by RNAi. We demonstrated that RDE-1 is essential for RNAi induced by the perfectly paired trigger, yet is not required for silencing by the let-7 miRNA. In contrast, ALG-1/ALG-2 are required for the miRNA function, but not for the siRNA-directed gene silencing. Finally, a dsRNA containing a bulged miRNA and a perfectly paired siRNA can enter both pathways suggesting that the sorting of small RNAs occurs after that the dsRNA trigger has been processed by Dicer. Thus, our data suggest that the selection of Argonaute proteins is affected by two molecular features: (1) the structure of the small RNA duplex; and (2) the Argonautes specific characteristics. 相似文献
84.
Human ventral cortex contains at least two visual areas selective for color [1]: a posterior center in the lingual gyrus labeled V4 [2-4], V8 [5], or VO-1 [6] and an anterior center in the medial fusiform that has been labeled V4alpha[3, 4]. We examined the properties of the anterior color center using electrical recording and electrical stimulation in a subject with an electrode implanted over the anterior color center, as determined with BOLD fMRI in the same subject. Presentation of visual stimuli evoked local field potentials from the electrode. Consistent with fMRI, the potentials were larger for chromatic than achromatic stimuli. The potentials differed depending on stimulus color, with blue-purple colors evoking the largest response. The spatial receptive field of the electrode was central/parafoveal with a contralateral bias. In the absence of a visual stimulus, electrical stimulation of the electrode produced an artificial visual percept of a blue-purple color near the center of gaze. These results provide direct evidence of a tight link between selectivity and perception in ventral temporal cortex. Electrical stimulation of the anterior color center is sufficient to produce the conscious percept of a color whose identity is determined by the selectivity of the stimulated neurons. 相似文献
85.
MAVS Dimer Is a Crucial Signaling Component of Innate Immunity and the Target of Hepatitis C Virus NS3/4A Protease 总被引:1,自引:0,他引:1
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Martin Baril Marie-Eve Racine Franois Penin Daniel Lamarre 《Journal of virology》2009,83(3):1299-1311
The mitochondrial antiviral signaling (MAVS) protein plays a central role in innate antiviral immunity. Upon recognition of a virus, intracellular receptors of the RIG-I-like helicase family interact with MAVS to trigger a signaling cascade. In this study, we investigate the requirement of the MAVS structure for enabling its signaling by structure-function analyses and resonance energy transfer approaches in live cells. We now report the essential role of the MAVS oligomer in signal transduction and map the transmembrane domain as the main determinant of dimerization. A combination of mutagenesis and computational methods identified a cluster of residues making favorable van der Waals interactions at the MAVS dimer interface. We also correlated the activation of IRF3 and NF-κB with MAVS oligomerization rather than its mitochondrial localization. Finally, we demonstrated that MAVS oligomerization is disrupted upon expression of HCV NS3/4A protease, suggesting a mechanism for the loss of antiviral signaling. Altogether, our data suggest that the MAVS oligomer is essential in the formation of a multiprotein membrane-associated signaling complex and enables downstream activation of IRF3 and NF-κB in antiviral innate immunity. 相似文献
86.
Ajit K. Satapathy Donald J. Crampton Benjamin B. Beauchamp Charles C. Richardson 《The Journal of biological chemistry》2009,284(21):14286-14295
The multifunctional protein encoded by gene 4 of bacteriophage T7 (gp4)
provides both helicase and primase activity at the replication fork. T7 DNA
helicase preferentially utilizes dTTP to unwind duplex DNA in vitro
but also hydrolyzes other nucleotides, some of which do not support helicase
activity. Very little is known regarding the architecture of the nucleotide
binding site in determining nucleotide specificity. Crystal structures of the
T7 helicase domain with bound dATP or dTTP identified Arg-363 and Arg-504 as
potential determinants of the specificity for dATP and dTTP. Arg-363 is in
close proximity to the sugar of the bound dATP, whereas Arg-504 makes a
hydrogen bridge with the base of bound dTTP. T7 helicase has a serine at
position 319, whereas bacterial helicases that use rATP have a threonine in
the comparable position. Therefore, in the present study we have examined the
role of these residues (Arg-363, Arg-504, and Ser-319) in determining
nucleotide specificity. Our results show that Arg-363 is responsible for dATP,
dCTP, and dGTP hydrolysis, whereas Arg-504 and Ser-319 confer dTTP
specificity. Helicase-R504A hydrolyzes dCTP far better than wild-type
helicase, and the hydrolysis of dCTP fuels unwinding of DNA. Substitution of
threonine for serine 319 reduces the rate of hydrolysis of dTTP without
affecting the rate of dATP hydrolysis. We propose that different nucleotides
bind to the nucleotide binding site of T7 helicase by an induced fit
mechanism. We also present evidence that T7 helicase uses the energy derived
from the hydrolysis of dATP in addition to dTTP for mediating DNA
unwinding.Helicases are molecular machines that translocate unidirectionally along
single-stranded nucleic acids using the energy derived from nucleotide
hydrolysis
(1–3).
The gene 4 protein encoded by bacteriophage T7 consists of a helicase domain
and a primase domain, located in the C-terminal and N-terminal halves of the
protein, respectively (4). The
T7 helicase functions as a hexamer and has been used as a model to study
ring-shaped replicative helicases. In the presence of dTTP, T7 helicase binds
to single-stranded DNA
(ssDNA)3 as a hexamer
and translocates 5′ to 3′ along the DNA strand using the energy of
hydrolysis of dTTP
(5–7).
T7 helicase hydrolyzes a variety of ribo and deoxyribonucleotides; however,
dTTP hydrolysis is optimally coupled to DNA unwinding
(5).Most hexameric helicases use rATP to fuel translocation and unwind DNA
(3). T7 helicase does hydrolyze
rATP but with a 20-fold higher Km as compared with dTTP
(5,
8). It has been suggested that
T7 helicase actually uses rATP in vivo where the concentration of
rATP is 20-fold that of dTTP in the Escherichia coli cell
(8). However, hydrolysis of
rATP, even at optimal concentrations, is poorly coupled to translocation and
unwinding of DNA (9). Other
ribonucleotides (rCTP, rGTP, and rUTP) are either not hydrolyzed or the poor
hydrolysis observed is not coupled to DNA unwinding
(8). Furthermore, Patel et
al. (10) found that the
form of T7 helicase found in vivo, an equimolar mixture of the
full-length gp4 and a truncated form lacking the zinc binding domain of the
primase, prefers dTTP and dATP. Therefore, in the present study we have
restricted our examination of nucleotides to the deoxyribonucleotides.The nucleotide binding site of the replicative DNA helicases, such as T7
gene 4 protein, bind nucleotides at the subunit interface
(Fig. 1) located between two
RecA-like subdomains that bind ATP
(11,
12). The location of the
nucleotide binding site at the subunit interface provides multiple
interactions of residues with the bound NTP. A number of cis- and
trans-acting amino acids stabilize the bound nucleotide in the
nucleotide binding site and also provide for communication between subunits
(13–15).
Earlier reports revealed that the arginine finger (Arg-522) in T7 helicase is
positioned to interact with the γ-phosphate of the bound nucleotide in
the adjacent subunit (12,
16). However, His-465
(phosphate sensor), Glu-343 (catalytic base), and Asp-424 (Walker motif B)
interacts with the γ-phosphate of the bound nucleotide in the same
subunit (12,
17,
18). The arginine finger and
the phosphate sensor have been proposed to couple NTP hydrolysis to DNA
unwinding. Substitution of Glu-343, the catalytic base, eliminates dTTP
hydrolysis (19), and
substitution of Asp-424 with Asn leads to a severe reduction in dTTP
hydrolysis (20). The conserved
Lys-318 in Walker motif A interacts with the β-phosphate of the bound
nucleotide and plays an important role in dTTP hydrolysis
(21).Open in a separate windowFIGURE 1.Crystal structure of T7 helicase. A, crystal structure of
the hexameric helicase C-terminal domain of gp4
(17). The structure reveals a
ring-shaped molecule with a central core through which ssDNA passes. The
inset shows the interface between two subunits of the helicase with
adenosine 5′-{β,γ-imidol}-triphosphate in the nucleotide
binding site. B, the nucleotide binding site of a monomer of the gp4
with the crucial amino acid residues reported earlier and in the present study
is shown in sticks. The crystal structures of the T7 gene 4 helicase
domain (12) with bound dTTP
(C) and dATP (D). The structures shown are the nucleotide
binding site of T7 helicase as viewed in Pymol by analyzing the PDB files 1cr1
and 1cr2 (12). Arg-504 and
Tyr-535 sandwiches the base of the bound dNTP. Additionally, Arg-504 forms a
hydrogen bridge with dTTP. Arg-363 interacts specifically with the 3-OH group
of bound dATP. AMPPNP, adenosine
5′-(β,γ-imino)triphosphate.Considering the wealth of information on the above residues that are
involved in the hydrolysis of dTTP and the coupling of hydrolysis to
unwinding, it is intriguing that little information is available on nucleotide
specificity. Several crystal structures of T7 helicase in complex with a
nucleotide triphosphate are available. However, most of structures were
crystallized with a non-hydrolyzable analogue of dTTP or the nucleotide was
diffused into the crystal. The crystal structure of the T7 helicase domain
bound with dTTP or dATP was reported by Sawaya et al.
(12). These structures
assisted us in identifying two basic residues (Arg-363 and Arg-504) in close
proximity to the sugar and base of the bound nucleotide whose orientation
suggested that these residues could be involved in nucleotide selection.
Arg-504 together with Tyr-535 sandwich the base of the bound nucleotide at the
subunit interface of the hexameric helicase
(Fig. 1). Arg-504 and Tyr-535
are structurally well conserved in various helicases
(12). However, Arg-504 could
make a hydrogen bridge with the OH group of thymidine, thus suggesting a role
in dTTP specificity. On the other hand, Arg-363 is in close proximity
(∼3.4 Å) to the sugar 3′-OH of bound dATP, whereas in the
dTTP-bound structure this residue is displaced by 7.12 Å
(Fig. 1) from the equivalent
position. Consequently Arg-363 could play a role in dATP binding. The crystal
structures do not provide any information on different interaction of residues
with the phosphates of dATP and dTTP. However, alignment of the residues in
the P-loops of different hexameric helicases reveals that the serine adjacent
to the invariant lysine at position 319 (Ser-319) is conserved in
bacteriophages, whereas bacterial helicases have a conserved threonine in the
equivalent position (supplemental Fig. 1). Bacterial helicases use rATP in the
DNA unwinding reactions. whereas T7 helicase preferentially uses dTTP, and
bacteriophage T4 gene 41 uses rGTP or rATP
(22).Although considerable information is available on the role of residues in
nucleotide binding and dTTP hydrolysis, very little is known on the
determinants of nucleotide specificity. In the present study we made an
attempt to address the role of a few selected residues (Arg-363, Arg-504, and
Ser-319) in determining nucleotide specificity, especially dTTP and dATP, both
of which are hydrolyzed and mediate DNA unwinding. We show that under
physiological conditions T7 helicase uses the energy derived from the
hydrolysis of dATP in addition to dTTP for mediating DNA unwinding. 相似文献
87.
Beauchamp G 《Biology letters》2009,5(1):9-11
Individuals in groups are often thought to scan their surroundings for threats independently of one another. Models, however, suggest that foragers should monitor the vigilance level of their neighbours to prevent cheating, and to gather information about incipient predation risk. Evidence for monitoring of vigilance is scant. Here, I examined changes in vigilance levels in sleeping gulls (Larus sp.) surrounded by neighbours in various states of alertness. Controlling for group size and neighbour density, gulls interrupted sleep more often to scan their surroundings, and were therefore more vigilant, when their neighbours were alert rather than sleeping or preening. The results provide evidence for copying of vigilance within groups of birds, suggesting a complex flow of information about predation risk in groups. 相似文献
88.
Transmission electron microscopy (TEM) is extremely useful for visualizing microglial, oligodendrocytic, astrocytic, and neuronal subcellular compartments (dendrite, dendritic spine, axon, axon terminal, perikaryon), as well as their intracellular organelles and cytoskeleton, in the central nervous system at high spatial resolution. Combined with TEM, pre-embedding immunocytochemistry allows the discrimination of cellular elements with few distinctive features and identification criteria (e.g., microglial perikarya and processes, when using an antibody against the microglia-specific marker Iba1 (ionized calcium binding adaptor molecule 1; as presented here)), identifying the neurotransmitter contents of cellular elements (e.g., serotonergic) and their ultrastructural localization of soluble or membrane-bound proteins (e.g., 5 HT1A and EphA4 receptors). Here, we describe a protocol for transcardiac perfusion of mice with acrolein fixative, removal and sectioning of the brain, as well as immunoperoxidase-diaminobenzidine (DAB) staining, resin embedding, and ultrathin sectioning of the brain sections. Upon completion of these procedures, the immunostained material is ready for examination with TEM. When rigorously performed, this technique provides an excellent compromise between optimal ultrastructural preservation and immunocytochemical detection.Download video file.(101M, mp4) 相似文献
89.
Matthew P. Harrigan Mohammad M. Sultan Carlos X. Hernández Brooke E. Husic Peter Eastman Christian R. Schwantes Kyle A. Beauchamp Robert T. McGibbon Vijay S. Pande 《Biophysical journal》2017,112(1):10-15
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis. MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python application programming interface. MSMBuilder was developed with careful consideration for compatibility with the broader machine learning community by following the design of scikit-learn. The package is used primarily by practitioners of molecular dynamics, but is just as applicable to other computational or experimental time-series measurements. 相似文献
90.