bluuebunny/crossref_metadata_2025 huggingface dataset:
Can rodent models of diabetic kidney disease clarify the significance of early hyperfiltration?: recognizing clinical and experimental uncertainties
Authors: Levine David Z.
Published: December 2007

In the past, hyperfiltration and increased glomerular capillary pressure have been identified as important determinants of the development of DN (diabetic nephropathy). Recently, some basic research and clinical reviews on DN have omitted identifying hyperfiltration as an important risk factor. At the same time, different rodent models of DN have been described without and with documented hyperfiltration. In the present review, the importance of hyperfiltration is reassessed, reviewing key clinical and research studies, including the first single nephron studies in a mouse model of DN. From clinical studies of Type 1 and Type 2 diabetes mellitus, it is clear that many patients do not have early hyperfiltration and, even when present, its contribution to subsequent DN remains uncertain. Key mechanisms underlying hyperfiltration in rodent models are reviewed. Findings on intrarenal NO metabolism and the control of single-nephron GFR (glomerular filtration rate) in rodent models of DN are also presented. Characterization of valid experimental models of DN should include a careful delineation of the absence or presence of early hyperfiltration, with special efforts made to establish the specific role hyperfiltration may play in the emergence of DN.
Heightened α1A-adrenergic receptor activity suppresses ischaemia/reperfusion-induced Ins(1,4,5)P3 generation in the mouse heart: a comparison with ischaemic preconditioning
Authors: Amirahmadi Fatemeh , Turnbull Lynne , Du Xiao-Jun , Graham Robert M. , Woodcock Elizabeth A.
Published: December 2007

Reperfusion of ischaemic rat or mouse hearts causes NE [noradrenaline (‘norepinephrine’)] release, stimulation of α1-ARs (α1-adrenergic receptors), PLC (phospholipase C) activation, Ins(1,4,5)P3 generation and the development of arrhythmias. In the present study, we examined the effect of increased α1A-AR drive on these responses. In hearts from non-transgenic mice (α1A-WT), Ins(1,4,5)P3 generation was observed after 2 min of reperfusion following 30 min of zero-flow ischaemia. No Ins(1,4,5)P3 response was observed in hearts from transgenic mice with 66-fold overexpression of α1A-AR (α1A-TG). This was despite the fact that α1A-TG hearts had 8–10-fold higher PLC responses to NE than α1A-WT under normoxic conditions. The immediate phospholipid precursor of Ins(1,4,5)P3, PtdIns(4,5)P2, responded to ischaemia and reperfusion similarly in α1A-WT and α1A-TG mice. Thus the lack of Ins(1,4,5)P3 generation in α1A-TG mice is not caused by limited availability of PtdIns(4,5)P2. Overall, α1-AR-mediated PLC activity was markedly enhanced in α1A-WT mice under reperfusion conditions, but responses in α1A-TG mice were not significantly different in normoxia and post-ischaemic reperfusion. Ischaemic preconditioning prevented Ins(1,4,5)P3 generation after 30 min of ischaemic insult in α1A-WT mice. However, the precursor lipid PtdIns(4,5)P2 was also reduced by preconditioning, whereas heightened α1A-AR activity did not influence PtdIns(4,5)P2 responses in reperfusion. Thus preconditioning and α1A-AR overexpression have different effects on early signalling responses, even though both prevented Ins(1,4,5)P3 generation. These studies demonstrate a selective inhibitory action of heightened α1A-AR activity on immediate post-receptor signalling responses in early post-ischaemic reperfusion.
Does compensatory nitric oxide and angiotensin II receptor activity reduce arterial stiffness in early-stage insulin resistance?
Authors: Woodman Richard J.
Published: December 2007

Increased arterial stiffness is influenced by both functional and structural properties of the vessel wall, including changes in content of smooth muscle, elastin and collagen, reduced endothelial production of NO and increased release of endothelin-1 or AngII (angiotensin II). The RAS (renin–angiotensin) system is likely to be central to increases in arterial stiffness, since the changes in arterial structure observed with enhanced AngII activity are similar to the same pathophysiological changes that contribute to arterial stiffness. The role of AT1R and AT2R (AngII type 1 and type 2 receptors respectively) in the development of arterial stiffening, particularly in the early stages of insulin resistance, is however unclear. In this issue of Clinical Science, Brillante and co-workers have observed that in insulin-resistant subjects exhibiting reduced arterial stiffness, wave reflection from small-to-medium-sized, but not large, arteries was increased following separate intravenous infusions of AngII, the selective AT2R inhibitor PD123319 and the NO inhibitor L-NMMA (NG-monomethyl-L-arginine) in comparison with normal healthy age- and sex-matched controls. These increases probably reflect increased AT1R and AT2R expression/activity in addition to up-regulation of basal NO release in the small-to-medium-sized arteries. These changes may be compensatory mechanisms related to early vascular damage and may have clinical implications for treatment in hypertensive patients with evidence of the metabolic syndrome.
Conductance of Si nanowires formed by breaking Si-Si junctions
Authors: Iwanari Tomoki , Sakata Toyo , Miyatake Yutaka , Kurokawa Shu , Sakai Akira
Published: December 2007

We have fabricated Si nanowires (NWs) by breaking Si-Si tip-sample junctions and studied their conductance for both p-n and p-p-type junctions at room temperature. Upon breaking the junction by retracting the Si tip from the Si clean surface, the conductance decreases by orders of magnitude from ∼1G0 to ∼10−6G0, where G0 is the quantum unit of conductance. The conductance histogram plotted against log(G∕G0) reveals peaklike structures for G>10−3G0, but becomes featureless for 10−6G0<G<10−3G0. In this low-conductance region, the histogram shows strong dependence on bias polarity and doping; the p-type-tip-n-type-sample junctions under positive sample biases yield large intensity in the histogram, while the same junctions under the opposite bias polarity and the p-p junctions under both bias polarities show small intensity below 10−4G0. This observation suggests that longer and thinner Si NWs can be preferably formed in the reversely biased p-n Si junctions. We also investigated how the conductance of Si NWs varies with the tip displacement ΔL and found a quadratic dependence of log(G∕G0) on ΔL, suggesting the localization of carriers in disordered Si NWs.
Marangoni instability in ultrathin two-layer films
Authors: Nepomnyashchy A. A. , Simanovskii I. B.
Published: December 2007

The development of instabilities under the joint action of the van der Waals forces and Marangoni stresses in a two-layer film on a heated or cooled substrate, is considered. The problem is solved by means of a linear stability theory and nonlinear simulations. Nontrivial change of the droplet shape in the presence of the Marangoni effect, which manifests itself as the deformation of a “plateau” into an “inkpot,” is observed. The appearance of the threshold oscillations predicted by the linear stability theory is confirmed by nonlinear simulations.
A new emissive-probe method for electron temperature measurement in radio-frequency plasmas
Authors: Kusaba Kouta , Shindo Haruo
Published: December 2007

A new method to measure electron temperature by an emissive probe has been proposed. The method is based on measurement of the functional relationship between the floating potential and the heating voltage of emissive probe. From the measured data of the floating potential change as a function of the heating voltage, the electron temperature could be determined by comparing with the theoretical curve obtained under the assumption of Maxwellian distribution. The overall characteristic of the floating potential change could be explained as a function of the heating voltage. The electron temperatures obtained by the present method were consistent with those measured by the rf-compensated Langmuir probe within the error. These experimental verifications were made in the electron density range of 2.6×1011–2.8×1012cm−3. It was stressed that the present method is advantageous in that the probe is operated in a floating condition, hence applicable to plasmas produced in an insulated container.
Geometry dependence of the charge transfer at YBa2Cu3O7-metal interfaces
Authors: Schuster C. , Schwingenschlögl U.
Published: December 2007

Transport in electronic devices based on high-Tc superconductors depends critically on the charge redistribution at interfaces, since the band structure is modified on a local scale. Using the density functional theory approach for relaxed YBa2Cu3O7-metal contacts, the charge transfer into the superconductor has been studied [U. Schwingenschlögl and C. Schuster, Appl. Phys. Lett. 90, 192502 (2007)]. In the present paper we discuss the systematics inherent in the local electronic structure of the near-contact YBa2Cu3O7 sites, in particular, the dependence on the contact geometry.
Lagrangians galore
Authors: Nucci M. C. , Leach P. G. L.
Published: December 2007

Searching for a Lagrangian may seem either a trivial endeavor or an impossible task. In this paper, we show that the Jacobi last multiplier associated with the Lie symmetries admitted by simple models of classical mechanics produces (too?) many Lagrangians in a simple way. We exemplify the method by such a classic as the simple harmonic oscillator, the harmonic oscillator in disguise [H. Goldstein, Classical Mechanics, 2nd edition (Addison-Wesley, Reading, MA, 1980)], and the damped harmonic oscillator. This is the first paper in a series dedicated to this subject.
Domain size effects in a uniaxial ferroelectric relaxor system: The case of SrxBa1−xNb2O6
Authors: Voelker Uwe , Heine Urs , Gödecker Christoph , Betzler Klaus
Published: December 2007

We present investigations of the domain dynamics and of the evolution of the critical exponent β in a ferroelectric relaxor system, exemplarily in the up-to-date controversial strontium barium niobate (SBN). k-space spectroscopy at the phase-transition and when applying an electric field reveals a size-dependent response of the domains. This is supported by pyroelectric measurements that show, by analysis in terms of criticality, the critical exponent β is not only dependent on the level of poling but also on the manner in which the poling was achieved. It must be concluded that the crystals undergo a phase transition not—as commonly assumed—in a uniform way with homogeneous polarization throughout the crystal. Instead they behave as a set of more or less independent domains with size-dependent stability. Therefore, one should be very careful with critical exponents—especially those derived from experiments that explicitly or implicitly—assume a uniform polarization behavior.
Critical thickness control by deposition rate for epitaxial BaTiO3 thin films grown on SrTiO3(001)
Authors: Kawai M. , Kan D. , Isojima S. , Kurata H. , Isoda S. , Shimakawa Y. , Kimura S. , Sakata O.
Published: December 2007

Ba Ti O 3 ∕ Sr Ti O 3 ( 001 ) epitaxial thin films were prepared at various growth rates by pulsed laser deposition, and their heterostructures were evaluated by synchrotron x-ray diffraction measurements and cross-sectional scanning transmission electron microscopy observations. In a film grown at a low deposition rate (0.01nm∕s), misfit dislocations are found near the interface and a fully relaxed BaTiO3 thin film grows epitaxially on the substrate. On the other hand, a film grown at a high deposition rate (0.04nm∕s) consists of strained and relaxed BaTiO3 lattices. Our results showed that the critical thickness of BaTiO3∕SrTiO3(001) epitaxial thin films can be controlled by the deposition rate and that the critical thickness increases with increasing deposition rate, and by adjusting the deposition rate, we were able to prepare epitaxial thin films consisting of fully strained BaTiO3, partially strained BaTiO3, or fully relaxed BaTiO3.
The importance of middle-range Hartree-Fock-type exchange for hybrid density functionals
Authors: Henderson Thomas M. , Izmaylov Artur F. , Scuseria Gustavo E. , Savin Andreas
Published: December 2007

Hybrid functionals are responsible for much of the utility of modern Kohn-Sham density functional theory. When rigorously applied to solid-state metallic and small band gap systems, however, the slow decay of their nonlocal Hartree-Fock-type exchange makes hybrids computationally challenging and introduces unphysical effects. This can be remedied by using a range-separated hybrid which only keeps short-range nonlocal exchange, as in the functional of Heyd et al. [J. Chem. Phys. 118, 8207 (2003)]. On the other hand, many molecular properties require full long-range nonlocal exchange, which can also be included by means of a range-separated hybrid such as the recently introduced LC-ωPBE functional [O. A. Vydrov and G. E. Scuseria, J. Chem. Phys. 125, 234109 (2006)]. In this paper, we show that a three-range hybrid which mainly includes middle-range Hartree-Fock-type exchange and neglects long- and short-range Hartree-Fock-type exchange yields excellent accuracy for thermochemistry, barrier heights, and band gaps, emphasizing that the middle-range part of the 1∕r potential seems crucial to accurately model these properties.
Effects of a thin (In)GaAs layer on the structural and optical properties of InAs∕InAlGaAs quantum dots
Authors: Kim Jin Soo , Yang Youngsin , Lee Cheul-Ro , Lee In Hwan , Yu Yeon Tae , Ahn Haeng Keun , Seol Kyeong Won , Kim Jong Su , Leem Jae-Young , Ryu Mee-Yi
Published: December 2007

The introduction of a thin (In)GaAs layer between an InAs quantum dot (QD) layer and an InAlGaAs layer altered the structural and optical properties of self-assembled InAs∕InAlGaAs QDs grown on InP (001) substrates. The emission peak of the InAs QDs on a thin In0.32Ga0.68As layer grown on InAlGaAs was redshifted with increasing thickness of the In0.32Ga0.68As layer. However, the photoluminescence (PL) peak of the InAs QDs on a thin GaAs layer grown on InAlGaAs was blueshifted with increasing thickness of the GaAs layer, and the PL yield was also drastically decreased. Although the lattice constants of both In0.32Ga0.68As and GaAs are smaller than that of InAlGaAs, which would be expected to have a similar type of strain modulation, the structural and optical properties of the InAs QDs were significantly different because of the different nucleation characteristics of QDs.
Coupling of surface waves in highly defined one-dimensional porous silicon photonic crystals for gas sensing applications
Authors: Descrovi Emiliano , Frascella Francesca , Sciacca Beniamino , Geobaldo Francesco , Dominici Lorenzo , Michelotti Francesco
Published: December 2007

We describe the use of one-dimensional porous silicon (p-Si) photonic crystals for guiding TE-polarized surface electromagnetic waves (SEWs). Although bulk and interface roughnesses might deteriorate the optical response of photonic structures, we observed reflection spectra presenting narrow (≲6nm) reflectivity anomalies associated with SEWs. In analogy with surface plasmons, SEWs are strongly sensitive to surface modifications. As a proof of principle for a sensor, we provide a direct real-time monitoring of the reversible interactions of organic vapors with the p-Si multilayer. We highlight the higher sensitivity of the SEW-based detection scheme as compared to a method exploiting perturbations of waveguide modes.
Interannual variations in cephalopod consumption by albatrosses at South Georgia: implications for future commercial exploitation of cephalopods
Authors: Xavier J. C. , Wood A. G. , Rodhouse P. G. , Croxall J. P.
Published: December 2007

Assessing the consumption of prey by predators in the marine environment is key to fisheries assessment and management. Although environmental and ecological variations can affect the consumption of certain prey by albatrosses interannually, this issue has not been addressed to date. In the present study, the interannual consumption of cephalopods by grey-headed and black-browed albatrosses was assessed while breeding at South Georgia between 1996 and 2000, by comparing consumption estimates from a reparameterised version of the South Georgia Seabird Impact Assessment (SGSIA) model. The reparameterised model showed that there are considerable interannual variations in cephalopod consumption in both albatross species, with the highest consumption occurring in 1996 (5787 tonnes; for black-browed albatrosses) and 1997 (11 627 tonnes; for grey-headed albatrosses), and the lowest in 2000 (2309 tonnes and 772 tonnes for grey-headed and black-browed albatrosses respectively). These interannual variations were linked to oceanographic conditions and changes in cephalopod abundance/availability to predators. The cephalopod species with the most commercial potential (Martialia hyadesi, Kondakovia longimana, Moroteuthis knipovitchi and Gonatus antarcticus) also showed considerable differences in their consumption by predators. Owing to the importance of these squid species in the diet of albatrosses, precautionary measures for future commercial exploitation are suggested.
Flood and drought impacts on the opening regime of a wave-dominated estuary
Authors: Rustomji Paul
Published: December 2007

Wave-dominated estuaries are affected by floods generated in their hinterland catchments as well as marine tide and wave processes. The interaction of these terrestrial and marine influences controls the opening regime of the estuary. Despite the well documented environmental pressures on estuaries including elevated nutrient loadings and abstraction of river flows, little research concerning the variability and controls on estuary mouth opening regimes exists. From water level observations of Tuross Lake estuary in south-eastern Australia, the estuary’s recent opening regime is reconstructed and shown to vary significantly over time. Floodwaters fill the estuary and scour the estuary mouth, enhancing the exchange of marine water between the estuary and the ocean, which manifests as an increased tidal range within the estuary. Between floods, tide and wave activity caused aggradation of the estuary mouth such that the tidal range within the estuary declined by 0.5–0.7 mm per day as the mouth became more constricted. Under conditions of low river flow, high evaporative losses and seasonal reductions in ocean wave height, the estuary mouth can close completely. Using twentieth century streamflow estimates, it is shown that hydrologic variability is likely to have resulted in large variations in the estuary’s opening regime. Since 2000, there have been relatively few flood-driven scour events and this explains the relatively congested state of the current estuary mouth. Predicted hydrologic changes under enhanced atmospheric carbon dioxide concentrations are also likely to enhance the variability in the estuary’s opening regime.
Refinement of the x-ray structure of the RC–LH1 core complex from
Rhodopseudomonas palustris
by single-molecule spectroscopy
Authors: Richter Martin F. , Baier Jürgen , Southall June , Cogdell Richard J. , Oellerich Silke , Köhler Jörgen
Published: December 2007

A unique combination of single-molecule spectroscopy with numerical simulations has allowed us to achieve a refined structural model for the bacteriochlorophyll
a
(BChl
a
) pigment arrangement in reaction center–light-harvesting 1 core complexes of
Rhodopseudomonas palustris
. Details in the optical spectra, such as spectral separation and mutual polarizations of spectral bands, are compared with results from numerical simulations for various models of the BChl
a
arrangement that were all well within the 4.8-Å limit of the accuracy of the available x-ray structure. The experimental data are consistent with a geometry where 15 BChl
a
dimers, each taken homologous to those from light-harvesting 2 complex from
Rhodopseudomonas acidophila
, are arranged in an overall elliptical structure featuring a gap on the long side of the ellipse.
Mutations of HNF-1β inhibit epithelial morphogenesis through dysregulation of SOCS-3
Authors: Ma Zhendong , Gong Yimei , Patel Vishal , Karner Courtney M. , Fischer Evelyne , Hiesberger Thomas , Carroll Thomas J. , Pontoglio Marco , Igarashi Peter
Published: December 2007

Hepatocyte nuclear factor-1β (HNF-1β) is a Pit-1, Oct-1/2, Unc-86 (POU) homeodomain-containing transcription factor expressed in the kidney, liver, pancreas, and other epithelial organs. Mutations of HNF-1β cause maturity-onset diabetes of the young, type 5 (MODY5), which is characterized by early-onset diabetes mellitus and congenital malformations of the kidney, pancreas, and genital tract. Knockout of HNF-1β in the mouse kidney results in cyst formation. However, the signaling pathways and transcriptional programs controlled by HNF-1β are poorly understood. Using genome-wide chromatin immunoprecipitation and DNA microarray (ChIP-chip) and microarray analysis of mRNA expression, we identified
SOCS3
(suppressor of cytokine signaling-3) as a previously unrecognized target gene of HNF-1β in the kidney. HNF-1β binds to the
SOCS3
promoter and represses
SOCS3
transcription. The expression of
SOCS3
is increased in HNF-1β knockout mice and in renal epithelial cells expressing dominant-negative mutant HNF-1β. Increased levels of SOCS-3 inhibit HGF-induced tubulogenesis by decreasing phosphorylation of Erk and STAT-3. Conversely, knockdown of SOCS-3 in renal epithelial cells expressing dominant-negative mutant HNF-1β rescues the defect in HGF-induced tubulogenesis by restoring phosphorylation of Erk and STAT-3. Thus, HNF-1β regulates tubulogenesis by controlling the levels of SOCS-3 expression. Manipulating the levels of SOCS-3 may be a useful therapeutic approach for human diseases induced by HNF-1β mutations.
Reconstruction of ancestral protein interaction networks for the bZIP transcription factors
Authors: Pinney John W. , Amoutzias Grigoris D. , Rattray Magnus , Robertson David L.
Published: December 2007

As whole-genome protein–protein interaction datasets become available for a wide range of species, evolutionary biologists have the opportunity to address some of the unanswered questions surrounding the evolution of these complex systems. Protein interaction networks from divergent organisms may be compared to investigate how gene duplication, deletion, and rewiring processes have shaped the evolution of their contemporary structures. However, current approaches for comparing observed networks from multiple species lack the phylogenetic context necessary to reconstruct the evolutionary history of a network. Here we show how probabilistic modeling can provide a platform for the quantitative analysis of multiple protein interaction networks. We apply this technique to the reconstruction of ancestral networks for the bZIP family of transcription factors and find that excellent agreement is obtained with an alternative sequence-based method for the prediction of leucine zipper interactions. Further analysis shows our probabilistic method to be significantly more robust to the presence of noise in the observed network data than a simple parsimony-based approach. In addition, the integration of evidence over multiple species means that the same method may be used to improve the quality of noisy interaction data for extant species. The ancestral states of a protein interaction network have been reconstructed here by using an explicit probabilistic model of network evolution. We anticipate that this model will form the basis of more general methods for probing the evolutionary history of biochemical networks.
Deficient ryanodine receptor
S
-nitrosylation increases sarcoplasmic reticulum calcium leak and arrhythmogenesis in cardiomyocytes
Authors: Gonzalez Daniel R. , Beigi Farideh , Treuer Adriana V. , Hare Joshua M.
Published: December 2007

Altered Ca
2+
homeostasis is a salient feature of heart disease, where the calcium release channel ryanodine receptor (RyR) plays a major role. Accumulating data support the notion that neuronal nitric oxide synthase (NOS1) regulates the cardiac RyR via
S
-nitrosylation. We tested the hypothesis that NOS1 deficiency impairs RyR
S
-nitrosylation, leading to altered Ca
2+
homeostasis. Diastolic Ca
2+
levels are elevated in NOS1
−/−
and NOS1/NOS3
−/−
but not NOS3
−/−
myocytes compared with wild-type (WT), suggesting diastolic Ca
2+
leakage. Measured leak was increased in NOS1
−/−
and NOS1/NOS3
−/−
but not in NOS3
−/−
myocytes compared with WT. Importantly, NOS1
−/−
and NOS1/NOS3
−/−
myocytes also exhibited spontaneous calcium waves. Whereas the stoichiometry and binding of FK-binding protein 12.6 to RyR and the degree of RyR phosphorylation were not altered in NOS1
−/−
hearts, RyR2
S
-nitrosylation was substantially decreased, and the level of thiol oxidation increased. Together, these findings demonstrate that NOS1 deficiency causes RyR2 hyponitrosylation, leading to diastolic Ca
2+
leak and a proarrhythmic phenotype. NOS1 dysregulation may be a proximate cause of key phenotypes associated with heart disease.
Rapid dental development in a Middle Paleolithic Belgian Neanderthal
Authors: Smith Tanya M. , Toussaint Michel , Reid Donald J. , Olejniczak Anthony J. , Hublin Jean-Jacques
Published: December 2007

The evolution of life history (pace of growth and reproduction) was crucial to ancient hominin adaptations. The study of dental development facilitates assessment of growth and development in fossil hominins with greater precision than other skeletal analyses. During tooth formation, biological rhythms manifest in enamel and dentine, creating a permanent record of growth rate and duration. Quantification of these internal and external incremental features yields developmental benchmarks, including ages at crown completion, tooth eruption, and root completion. Molar eruption is correlated with other aspects of life history. Recent evidence for developmental differences between modern humans and Neanderthals remains ambiguous. By measuring tooth formation in the entire dentition of a juvenile Neanderthal from Scladina, Belgium, we show that most teeth formed over a shorter time than in modern humans and that dental initiation and eruption were relatively advanced. By registering manifestations of stress across the dentition, we are able to present a precise chronology of Neanderthal dental development that differs from modern humans. At 8 years of age at death, this juvenile displays a degree of development comparable with modern human children who are several years older. We suggest that age at death in juvenile Neanderthals should not be assessed by comparison with modern human standards, particularly those derived from populations of European origin. Moreover, evidence from the Scladina juvenile and other similarly aged hominins suggests that a prolonged childhood and slow life history are unique to
Homo sapiens
.
Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility
Authors: Dass Brinda , Tardif Steve , Park Ji Yeon , Tian Bin , Weitlauf Harry M. , Hess Rex A. , Carnes Kay , Griswold Michael D. , Small Christopher L. , MacDonald Clinton C.
Published: December 2007

Polyadenylation, the process of eukaryotic mRNA 3′ end formation, is essential for gene expression and cell viability. Polyadenylation of male germ cell mRNAs is unusual, exhibiting increased alternative polyadenylation, decreased AAUAAA polyadenylation signal use, and reduced downstream sequence element dependence. CstF-64, the RNA-binding component of the cleavage stimulation factor (CstF), interacts with pre-mRNAs at sequences downstream of the cleavage site. In mammalian testes, meiotic XY-body formation causes suppression of X-linked CstF-64 expression during pachynema. Consequently, an autosomal paralog, τCstF-64 (gene name
Cstf2t
), is expressed during meiosis and subsequent haploid differentiation. Here we show that targeted disruption of
Cstf2t
in mice causes aberrant spermatogenesis, specifically disrupting meiotic and postmeiotic development, resulting in male infertility resembling oligoasthenoteratozoospermia. Furthermore, the
Cstf2t
mutant phenotype displays variable expressivity such that spermatozoa show a broad range of defects. The overall phenotype is consistent with a requirement for τCstF-64 in spermatogenesis as indicated by the significant changes in expression of thousands of genes in testes of
Cstf2t
−/−
mice as measured by microarray. Our results indicate that, although the infertility in
Cstf2t
−/−
males is due to low sperm count, multiple genes controlling many aspects of germ-cell development depend on τCstF-64 for their normal expression. Finally, these transgenic mice provide a model for the study of polyadenylation in an isolated
in vivo
system and highlight the role of a growing family of testis-expressed autosomal retroposed variants of X-linked genes.
Structural elements of the cholesterol-dependent cytolysins that are responsible for their cholesterol-sensitive membrane interactions
Authors: Soltani Casie E. , Hotze Eileen M. , Johnson Arthur E. , Tweten Rodney K.
Published: December 2007

The pore-forming mechanism of the cholesterol-dependent cytolysins (CDCs) exhibits an absolute requirement for membrane cholesterol. The structural elements of the CDCs that mediate this interaction are not well understood. Three short hydrophobic loops (L1–L3) and a highly conserved undecapeptide sequence at the tip of domain 4 of the CDC structure are known to anchor the CDC to the membrane. It has been thought that the undecapeptide directly mediates the interaction of the CDCs with a cholesterol-rich cell surface. Herein we show that the L1–L3 loops, not the undecapeptide, are responsible for mediating the specific interaction of the CDCs with cholesterol-rich membranes. The membrane insertion of the undecapeptide was uncoupled from membrane binding by the covalent modification of the undecapeptide cysteine thiol. Modification of the cysteine prevented prepore to pore conversion, but did not affect membrane binding, thus demonstrating that undecapeptide membrane insertion follows that of the L1–L3 loops. These studies provide an example of a structural motif that specifically mediates the interaction of a bacterial toxin with a cholesterol-rich membrane.
Intrinsic single-domain switching in ferroelectric materials on a nearly ideal surface
Authors: Kalinin S. V. , Rodriguez B. J. , Jesse S. , Chu Y. H. , Zhao T. , Ramesh R. , Choudhury S. , Chen L. Q. , Eliseev E. A. , Morozovska A. N.
Published: December 2007

Ferroelectric domain nucleation and growth in multiferroic BiFeO
3
is studied on a single-domain level by using piezoresponse force spectroscopy. Variation of local electromechanical response with dc tip bias is used to determine the size of the domain formed below the conductive scanning probe tip. The domain parameters are calculated self-consistently from the decoupled Green function theory by using tip geometry determined from the domain wall profile. The critical parameters of the nucleating domain and the activation energy for nucleation are determined. The switching mechanism is modeled by using the phase-field method, and comparison with experimental results shows that the nucleation biases are within a factor of ≈2 of the intrinsic thermodynamic limit. The role of atomic-scale defects and long-range elastic fields on nucleation bias lowering is discussed. These measurements open a pathway for quantitative studies of the role of a single defect on kinetics and thermodynamics of first order bias-induced phase transitions and electrochemical reactions.
Diet-induced obesity in mice causes changes in immune responses and bone loss manifested by bacterial challenge
Authors: Amar Salomon , Zhou Qingde , Shaik-Dasthagirisaheb Yazdani , Leeman Susan
Published: December 2007

Obesity has been suggested to be associated with an increased susceptibility to bacterial infection. However, few studies have examined the effect of obesity on the immune response to bacterial infections. In the present study, we investigated the effect of obesity on innate immune responses to
Porphyromonas gingivalis
infection, an infection strongly associated with periodontitis. Mice with diet-induced obesity (DIO) and lean control C57BL/6 mice were infected orally or systemically with
P. gingivalis
, and periodontal pathology and systemic immune responses were examined postinfection. After oral infection with
P. gingivalis
, mice with DIO had a significantly higher level of alveolar bone loss than the lean controls. Oral microbial sampling disclosed higher levels of
P. gingivalis
in mice with DIO vs. lean mice during and after infection. Furthermore, animals with DIO exposed to oral infection or systemic inoculation of live
P. gingivalis
developed a blunted inflammatory response with reduced expression of TNF-α, IL-6, and serum amyloid A (SAA) at all time points compared with lean mice. Finally, peritoneal macrophages harvested from mice with DIO and exposed to
P. gingivalis
exhibited reduced levels of proinflammatory cytokines compared with lean mice and when exposed to
P. gingivalis
LPS treatment had a significantly reduced recruitment of NF-κB to both TNF-α and IL-10 promoters 30 min after exposure. These data indicate that obesity interferes with the ability of the immune system to appropriately respond to
P. gingivalis
infection and suggest that this immune dysregulation participates in the increased alveolar bone loss after bacterial infection observed in mice with DIO.
Enhanced sensitivity to IGF-II signaling links loss of imprinting ofIGF2to increased cell proliferation and tumor risk
Authors: Kaneda Atsushi , Wang Chiaochun J. , Cheong Raymond , Timp Winston , Onyango Patrick , Wen Bo , Iacobuzio-Donahue Christine A. , Ohlsson Rolf , Andraos Rita , Pearson Mark A. , Sharov Alexei A. , Longo Dan L. , Ko Minoru S. H. , Levchenko Andre , Feinberg Andrew P.
Published: December 2007

Loss of imprinting (LOI) of the insulin-like growth factor-II gene (IGF2), leading to abnormal activation of the normally silent maternal allele, is a common human epigenetic population variant associated with a 5-fold increased frequency of colorectal neoplasia. Here, we show first that LOI leads specifically to increased expression of proliferation-related genes in mouse intestinal crypts. Surprisingly, LOI(+) mice also have enhanced sensitivity to IGF-II signaling, not simply increased IGF-II levels, becausein vivoblockade with NVP-AEW541, a specific inhibitor of the IGF-II signaling receptor, showed reduction of proliferation-related gene expression to levels half that seen in LOI(−) mice. Signal transduction assays in microfluidic chips confirmed this enhanced sensitivity with marked augmentation of Akt/PKB signaling in LOI(+) cells at low doses of IGF-II, which was reduced in the presence of the inhibitor to levels below those found in LOI(−) cells, and was associated with increased expression of the IGF1 and insulin receptor genes. We exploited this increased IGF-II sensitivity to develop anin vivochemopreventive strategy using the azoxymethane (AOM) mutagenesis model. LOI(+) mice treated with AOM showed a 60% increase in premalignant aberrant crypt foci (ACF) formation over LOI(−) mice.In vivoIGF-II blockade with NVP-AEW541 abrogated this effect, reducing ACF to a level 30% lower even than found in exposed LOI(−) mice. Thus, LOI increases cancer risk in a counterintuitive way, by increasing the sensitivity of the IGF-II signaling pathway itself, providing a previously undescribed epigenetic chemoprevention strategy in which cells with LOI are “IGF-II addicted” and undergo reduced tumorigenesis in the colon upon IGF-II pathway blockade.
Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes
Authors: Shroff Hari , Galbraith Catherine G. , Galbraith James A. , White Helen , Gillette Jennifer , Olenych Scott , Davidson Michael W. , Betzig Eric
Published: December 2007

Accurate determination of the relative positions of proteins within localized regions of the cell is essential for understanding their biological function. Although fluorescent fusion proteins are targeted with molecular precision, the position of these genetically expressed reporters is usually known only to the resolution of conventional optics (≈200 nm). Here, we report the use of two-color photoactivated localization microscopy (PALM) to determine the ultrastructural relationship between different proteins fused to spectrally distinct photoactivatable fluorescent proteins (PA-FPs). The nonperturbative incorporation of these endogenous tags facilitates an imaging resolution in whole, fixed cells of ≈20–30 nm at acquisition times of 5–30 min. We apply the technique to image different pairs of proteins assembled in adhesion complexes, the central attachment points between the cytoskeleton and the substrate in migrating cells. For several pairs, we find that proteins that seem colocalized when viewed by conventional optics are resolved as distinct interlocking nano-aggregates when imaged via PALM. The simplicity, minimal invasiveness, resolution, and speed of the technique all suggest its potential to directly visualize molecular interactions within cellular structures at the nanometer scale.
Modulation of Proteasome Activity by Vitamin E in THP‐1 Monocytes
Authors: Munteanu Adelina , Ricciarelli Roberta , Massone Sara , Zingg Jean‐Marc
Published: December 2007

In THP‐1 monocytes, cellular proteasome inhibition by ritonavir or ALLN is associated with increased production of oxidative stress. Both compounds produced comparable amounts of oxidative stress; however, normalization by α‐tocopherol occurred solely after inhibition by ritonavir, and not by ALLN. Similar to that, α‐tocopherol could normalize the reduced formation of 3‐nitrotyrosine‐modified proteins only after ritonavir treatment. In the absence of any proteasome inhibitor, intrinsic cellular proteasome activity was not modulated by α‐, β‐, and γ‐tocopherols; however, δ‐tocopherol, α‐tocotrienol, and α‐tocopheryl phosphate could significantly inhibit cellular proteasome activity and increased the level of p27Kip1 and p53. Since oxidative stress was reduced by α‐tocopherol only after proteasome inhibition by ritonavir and not by ALLN, it is concluded that, in this experimental system, α‐tocopherol does not act as an antioxidant but interferes with the inhibitory effect of ritonavir.
Tipping the Scales ‐ Specifier Proteins in Glucosinolate Hydrolysis
Authors: Wittstock Ute , Burow Meike
Published: December 2007

Glucosinolates are a group of secondary plant metabolites found in the Brassicales order that are beneficial components of our diet, determine the flavor of a number of vegetables and spices and have been implicated in pest management strategies. These properties, most of the biological activities and the pungent odor and taste associated with glucosinolate‐containing plants are due to the products formed from glucosinolates by their hydrolytic enzymes, myrosinases, upon tissue disruption. Specifier proteins impact the outcome of glucosinolate hydrolysis without having hydrolytic activity on glucosinolates themselves. In the presence of specifier proteins, glucosinolate hydrolysis results in nitriles, epithionitriles and organic thiocyanates whose biological functions are currently unknown. In contrast, isothiocyanates formed in the absence of specifier proteins have been demonstrated to possess a variety of biological activities and are thought to protect plants from herbivore and pathogen attack. This review discusses the current knowledge on plant and insect specifier proteins with special emphasis on their biochemical properties and possible mechanisms of action.
Divergent Regulation of Protein Synthesis in the Cytosol and Endoplasmic Reticulum Compartments of Mammalian Cells
Authors: Stephens Samuel B. , Nicchitta Christopher V.
Published: December 2007

In eukaryotic cells, mRNAs encoding signal sequence-bearing proteins undergo translation-dependent trafficking to the endoplasmic reticulum (ER), thereby restricting secretory and integral membrane protein synthesis to the ER compartment. However, recent studies demonstrating that mRNAs encoding cytosolic/nucleoplasmic proteins are represented on ER-bound polyribosomes suggest a global role for the ER in cellular protein synthesis. Here, we examined the steady-state protein synthesis rates and compartmental distribution of newly synthesized proteins in the cytosol and ER compartments. We report that ER protein synthesis rates exceed cytosolic protein synthesis rates by 2.5- to 4-fold; yet, completed proteins accumulate to similar levels in the two compartments. These data suggest that a significant fraction of cytosolic proteins undergo synthesis on ER-bound ribosomes. The compartmental differences in steady-state protein synthesis rates correlated with a divergent regulation of the tRNA aminoacylation/deacylation cycle. In the cytosol, two pathways were observed to compete for aminoacyl-tRNAs—protein synthesis and aminoacyl-tRNA hydrolysis—whereas on the ER tRNA deacylation is tightly coupled to protein synthesis. These findings identify a role for the ER in global protein synthesis, and they suggest models where compartmentalization of the tRNA acylation/deacylation cycle contributes to the regulation of global protein synthesis rates.
Maintenance of Hormone-sensitive Phosphoinositide Pools in the Plasma Membrane Requires Phosphatidylinositol 4-Kinase IIIα
Authors: Balla Andras , Kim Yeun Ju , Varnai Peter , Szentpetery Zsofia , Knight Zachary , Shokat Kevan M. , Balla Tamas
Published: December 2007

Type III phosphatidylinositol (PtdIns) 4-kinases (PI4Ks) have been previously shown to support plasma membrane phosphoinositide synthesis during phospholipase C activation and Ca2+signaling. Here, we use biochemical and imaging tools to monitor phosphoinositide changes in the plasma membrane in combination with pharmacological and genetic approaches to determine which of the type III PI4Ks (α or β) is responsible for supplying phosphoinositides during agonist-induced Ca2+signaling. Using inhibitors that discriminate between the α- and β-isoforms of type III PI4Ks, PI4KIIIα was found indispensable for the production of phosphatidylinositol 4-phosphate (PtdIns4P), phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2], and Ca2+signaling in angiotensin II (AngII)-stimulated cells. Down-regulation of either the type II or type III PI4K enzymes by small interfering RNA (siRNA) had small but significant effects on basal PtdIns4P and PtdIns(4,5)P2levels in32P-labeled cells, but only PI4KIIIα down-regulation caused a slight impairment of PtdIns4P and PtdIns(4,5)P2resynthesis in AngII-stimulated cells. None of the PI4K siRNA treatments had a measurable effect on AngII-induced Ca2+signaling. These results indicate that a small fraction of the cellular PI4K activity is sufficient to maintain plasma membrane phosphoinositide pools, and they demonstrate the value of the pharmacological approach in revealing the pivotal role of PI4KIIIα enzyme in maintaining plasma membrane phosphoinositides.
The Inositol 1,4,5-Trisphosphate Receptor Is Required to Signal Autophagic Cell Death
Authors: Lam David , Kosta Artemis , Luciani Marie-Françoise , Golstein Pierre
Published: December 2007

The signaling pathways governing pathophysiologically important autophagic (ACD) and necrotic (NCD) cell death are not entirely known. In the Dictyostelium eukaryote model, which benefits from both unique analytical and genetic advantages and absence of potentially interfering apoptotic machinery, the differentiation factor DIF leads from starvation-induced autophagy to ACD, or, if atg1 is inactivated, to NCD. Here, through random insertional mutagenesis, we found that inactivation of the iplA gene, the only gene encoding an inositol 1,4,5-trisphosphate receptor (IP3R) in this organism, prevented ACD. The IP3R is a ligand-gated channel governing Ca2+efflux from endoplasmic reticulum stores to the cytosol. Accordingly, Ca2+-related drugs also affected DIF signaling leading to ACD. Thus, in this system, a main pathway signaling ACD requires IP3R and further Ca2+-dependent steps. This is one of the first insights in the molecular understanding of a signaling pathway leading to autophagic cell death.
The Atg1 Kinase Complex Is Involved in the Regulation of Protein Recruitment to Initiate Sequestering Vesicle Formation for Nonspecific Autophagy inSaccharomyces cerevisiae
Authors: Cheong Heesun , Nair Usha , Geng Jiefei , Klionsky Daniel J.
Published: December 2007

Autophagy is the major degradative process for recycling cytoplasmic constituents and eliminating unnecessary organelles in eukaryotic cells. Most autophagy-related (Atg) proteins are recruited to the phagophore assembly site (PAS), a proposed site for vesicle formation during either nonspecific or specific types of autophagy. Therefore, appropriate recruitment of Atg proteins to this site is critical for their function in autophagy. Atg11 facilitates PAS recruitment for the cytoplasm-to-vacuole targeting pathway, which is a specific, autophagy-like process that occurs under vegetative conditions. In contrast, it is not known how Atg proteins are recruited to the PAS, nor which components are involved in PAS formation under nonspecific autophagy-inducing, starvation conditions. Here, we studied PAS assembly during nonspecific autophagy, using an atg11Δ mutant background to eliminate the PAS formation that occurs during vegetative growth. We found that protein complexes containing the Atg1 kinase have two roles for PAS formation during nonspecific autophagy. The Atg1 C terminus mediates an interaction with Atg13 and Atg17, facilitating a structural role of Atg1 that is needed to efficiently organize an initial step of PAS assembly, whereas Atg1 kinase activity affects the dynamics of protein movement at the PAS involved in Atg protein cycling.
Arx1 Is a Nuclear Export Receptor for the 60S Ribosomal Subunit in Yeast
Authors: Hung Nai-Jung , Lo Kai-Yin , Patel Samir S. , Helmke Kara , Johnson Arlen W.
Published: December 2007

We previously showed that nuclear export of the large (60S) ribosomal subunit relies on Nmd3 in a Crm1-dependent manner. Recently the general mRNA export factor, the Mtr2/Mex67 heterodimer, was shown to act as an export receptor in parallel with Crm1. These observations raise the possibility that nuclear export of the 60S subunit in Saccharomyces cerevisiae requires multiple export receptors. Here, we show that the previously characterized 60S subunit biogenesis factor, Arx1, also acts as an export receptor for the 60S subunit. We found that deletion of ARX1 was synthetic lethal with nmd3 and mtr2 mutants and was synthetic sick with several nucleoporin mutants. Deletion of ARX1 led to accumulation of pre-60S particles in the nucleus that were enriched for Nmd3, Crm1, Mex67, and Mtr2, suggesting that in the absence of Arx1, 60S export is impaired even though the subunit is loaded with export receptors. Finally, Arx1 interacted with several nucleoporins in yeast two-hybrid as well as in vitro assays. These results show that Arx1 can directly bridge the interaction between the pre-60S particle and the NPC and thus is a third export receptor for the 60S subunit in yeast.