bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced carrier confinement in quantum dots by raising wetting layer state energy
Authors: Moehl Sebastian , Maingault Laurent , Kheng Kuntheak , Mariette Henri
Published: July 2005

A quantum dot design is proposed where the wetting layer states are shifted to higher energies. It is realized by including CdTe quantum dots between two thin MgTe layers. As both materials have nearly the same lattice parameter, the first MgTe layer forms a wetting layer with high carrier state energy. Consequently, the radiative regime of the dots is significantly extended to higher temperatures. The unusual temperature-dependence of the decay time is discussed using a model for localized and delocalized states.
Competing Radical- and Anion-Mediated Pathways in the Reduction of Bridgehead Tosylates with Lithium Aluminium Hydride
Authors: Della Ernest W. , Janowski Wit K.
Published: July 2005

Reaction of norborn-1-yl tosylate with lithium aluminium hydride in boiling
tetrahydrofuran affords a mixture of norbornan-1-ol accompanied by the
ring-opened products 4-methylcyclohexanol and 3-ethylcyclopentanol as their
cis/trans isomers, as well as
p-thiocresol and p-tolyl
disulfide. Evidence strongly suggests that the reaction is mediated by the
norborn-1-yloxy radical rather than the norborn-1-yloxy anion. The process is
initiated by very slow acyl oxygen fission of the norbornyl tosylate, followed
by reduction of the derived p-toluenesulfinate ion to
give the p-thiocresoxide anion. Transfer of an electron
from the latter to the substrate and decomposition of the derived norborn-1-yl
tosylate radical anion leads to the norborn-1-yloxy radical which, upon ring
opening, generates the monocyclic alcohols via the corresponding ketones. It
is noteworthy that, when norborn-1-yl mesylate is exposed to lithium aluminium
hydride, it yields norbornan-1-ol exclusively. In the absence of an efficient
electron-transfer agent, the mechanism of reaction of norborn-1-yl mesylate is
suggested to involve acyl oxygen fission only.
Multiple Metal Coordination by Calixarenes: A Structure Determination of Relevance to the Use of Calixarenes as Solvent Extraction Agents
Authors: Asfari Zouhair , Harrowfield Jack M. , Thuéry Pierre , Nierlich Martine , Vicens Jacques E.
Published: July 2005

An insoluble material formed in attempts to extract the copper(II) complex of
(R,S)-5,5,7,12,12,14-
hexamethyl-1,4,8,11-tetraazacyclotetradecane with the tetraanion of
tetrakis(carboxymethyl) p-t-butylcalix[4]arene
recrystallizes from pyridine with the composition
[Cu(C16H36N4)]
[Na2(C52H60O12)].2C5H5N.4·5H2O.
The crystals are monoclinic, space group P
21/c
(C52h, No. 14);
a 26·8524(8), b
12·8151(2), c 25·6525(8) Å; β
115·356(1)°. The structure was refined on
F2 (11379 reflections, 955
parameters), giving conventional
R1 0·057
(wR2 0·118). The calixarene
encapsulates two sodium ions and has only tenuous connection to the
copper/macrocycle complex through axial coordination of one carboxylate
oxygen.
Visualizing inducible nitric-oxide synthase in living cells with a heme-binding fluorescent inhibitor
Authors: Panda Koustubh , Chawla-Sarkar Mamta , Santos Cecile , Koeck Thomas , Erzurum Serpil C. , Parkinson John F. , Stuehr Dennis J.
Published: July 2005

The study of nitric-oxide synthase (NOS) physiology is constrained by the lack of suitable probes to detect NOS in living cells or animals. Here, we characterized a fluorescent inducible NOS (iNOS) inhibitor called PIF (pyrimidine imidazole FITC) and examined its utility for microscopic imaging of iNOS in living cells. PIF binding to iNOS displayed high affinity, isoform selectivity, and heme specificity, and was essentially irreversible. PIF was used to successfully image iNOS expressed in RAW264.7 cells, HEK293T cells, human A549 epithelial cells, and freshly obtained human lung epithelium. PIF was used to estimate a half-life for iNOS of 1.8 h in HEK293T cells. Our work reveals that fluorescent probes like PIF will be valuable for studying iNOS cell biology and in understanding the pathophysiology of diseases that involve dysfunctional iNOS expression.
Dynamic pattern evolution on scale-free networks
Authors: Zhou Haijun , Lipowsky Reinhard
Published: July 2005

A general class of dynamic models on scale-free networks is studied by analytical methods and computer simulations. Each network consists of
N
vertices and is characterized by its degree distribution,
P
(
k
), which represents the probability that a randomly chosen vertex is connected to
k
nearest neighbors. Each vertex can attain two internal states described by binary variables or Ising-like spins that evolve in time according to local majority rules. Scale-free networks, for which the degree distribution has a power law tail
P
(
k
) ∼
k
-γ
, are shown to exhibit qualitatively different dynamic behavior for γ < 5/2 and γ > 5/2, shedding light on the empirical observation that many real-world networks are scale-free with 2 < γ < 5/2. For 2 < γ < 5/2, strongly disordered patterns decay within a
finite
decay time even in the limit of
infinite
networks. For γ > 5/2, on the other hand, this decay time diverges as ln(
N
) with the network size
N
. An analogous distinction is found for a variety of more complex models including Hopfield models for associative memory networks. In the latter case, the storage capacity is found, within mean field theory, to be independent of
N
in the limit of large
N
for γ > 5/2 but to grow as
N
α
with α = (5 - 2γ)/(γ - 1) for 2 < γ < 5/2.
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
Authors: Das Payel , Matysiak Silvina , Clementi Cecilia
Published: July 2005

Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic protein geometry (as in the simple on-lattice models). We present a coarse-grained model that “naturally” incorporates sequence details and energetic frustration into an overall minimally frustrated folding landscape. The model is coupled with an optimization procedure to design the parameters of the protein Hamiltonian to fold into a desired native structure. The application to the study of src-Src homology 3 domain shows that this coarse-grained model contains the main physical-chemical ingredients that are responsible for shaping the folding landscape of this protein. The results illustrate the importance of nonnative interactions and energetic heterogeneity for a quantitative characterization of folding mechanisms.
Genomic imprinting recapitulated in the human β-globin locus
Authors: Tanimoto Keiji , Shimotsuma Motoshi , Matsuzaki Hitomi , Omori Akane , Bungert Jörg , Engel James Douglas , Fukamizu Akiyoshi
Published: July 2005

A subset of genes in mammals are subject to genomic imprinting. The mouse
H19
gene, for example, is active only when maternally inherited and the neighboring
Igf2
gene is paternally expressed. This imprinted expression pattern is regulated by the imprinting control region (ICR) upstream of the
H19
gene. A maternally inherited
H19
ICR inhibits
Igf2
gene activation by the downstream enhancer due to its insulator function while it suppresses
H19
gene transcription by promoter DNA methylation when paternally inherited. These parent-of-origin specific functions depend on the allele-specific methylation of the ICR DNA, which is established during gametogenesis. Therefore, the ICR may also function as a landmark for epigenetic modifications. To examine whether the ICR confers these activities autonomously, we introduced a 2.9-kbp ICR-containing DNA fragment into a human β-globin yeast artificial chromosome at the 3′ end of the locus control region and established transgenic mouse lines. Expression of all of the β-like globin genes was higher when the transgene was paternally inherited. In accord with this result, transgenic ICR DNA from nucleated erythrocytes was more heavily methylated when paternally transmitted. Chromatin immunoprecipitation assays confirmed that CCCTC binding factor is preferentially recruited to the maternal transgenic ICR
in vivo
. Surprisingly however, the parent-of-origin specific methylation pattern was not observed in germ cell DNA in testis, demonstrating that methylation was established after fertilization. Thus, the ICR autonomously recapitulated imprinting within the normally nonimprinted transgenic β-globin gene locus, but the temporal establishment of imprinting methylation differs from that at the endogenous
Igf2
/
H19
locus.
Epigenetic differences arise during the lifetime of monozygotic twins
Authors: Fraga Mario F. , Ballestar Esteban , Paz Maria F. , Ropero Santiago , Setien Fernando , Ballestar Maria L. , Heine-Suñer Damia , Cigudosa Juan C. , Urioste Miguel , Benitez Javier , Boix-Chornet Manuel , Sanchez-Aguilera Abel , Ling Charlotte , Carlsson Emma , Poulsen Pernille , Vaag Allan , Stephan Zarko , Spector Tim D. , Wu Yue-Zhong , Plass Christoph , Esteller Manel
Published: July 2005

Monozygous twins share a common genotype. However, most monozygotic twin pairs are not identical; several types of phenotypic discordance may be observed, such as differences in susceptibilities to disease and a wide range of anthropomorphic features. There are several possible explanations for these observations, but one is the existence of epigenetic differences. To address this issue, we examined the global and locus-specific differences in DNA methylation and histone acetylation of a large cohort of monozygotic twins. We found that, although twins are epigenetically indistinguishable during the early years of life, older monozygous twins exhibited remarkable differences in their overall content and genomic distribution of 5-methylcytosine DNA and histone acetylation, affecting their gene-expression portrait. These findings indicate how an appreciation of epigenetics is missing from our understanding of how different phenotypes can be originated from the same genotype.
Synaptic mechanisms of persistent reverberatory activity in neuronal networks
Authors: Lau Pak-Ming , Bi Guo-Qiang
Published: July 2005

For brain functions such as working memory and motor planning, neuronal circuits are able to sustain persistent activity after transient inputs. Theoretical studies have suggested that persistent activity can exist in recurrently connected networks as active reverberation. However, the actual cellular processes underlying such reverberation are not well understood. In this study, we investigated the basic synaptic mechanisms responsible for reverberatory activity in small networks of rat hippocampal neurons
in vitro
. We found that brief stimulation of one neuron in a network could evoke, in an all-or-none fashion, reverberatory activity lasting for seconds. The reverberation was likely to arise from recurrent excitation because it was eliminated by partial inhibition of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors (but not by blockade of NMDA receptors). In contrast, blocking inhibitory transmission with bicuculline enhanced the reverberation. Furthermore, paired-pulse stimuli with interpulse intervals of 200–400 ms were more effective than single pulses in triggering reverberation, apparently by eliciting higher levels of asynchronous transmitter release. Suppressing asynchronous release by EGTA-AM abolished reverberation, whereas elevating asynchronous release by strontium substantially enhanced reverberation. Finally, manipulating calcium uptake into or release from intracellular stores also modulated the level of reverberation. Thus, the oft-overlooked asynchronous phase of synaptic transmission plays a central role in the emergent phenomenon of network reverberation.
Rational design of aggregation-resistant bioactive peptides: Reengineering human calcitonin
Authors: Fowler Susan B. , Poon Stephen , Muff Roman , Chiti Fabrizio , Dobson Christopher M. , Zurdo Jesús
Published: July 2005

A high propensity to aggregate into intractable deposits is a common problem limiting the production and use of many peptides and proteins in a wide range of biotechnological and pharmaceutical applications. Many therapeutic polypeptides are frequently abandoned at an early stage in their development because of problems with stability and aggregation. It has been shown recently that parameters describing the physicochemical properties of polypeptides can be used as predictors of protein aggregation. Here we demonstrate that these and similar tools can be applied to the rational redesign of bioactive molecules with a significantly reduced aggregation propensity without loss of physiological activity. This strategy has been exemplified by designing variants of the hormone calcitonin that show a significantly reduced aggregation propensity, yet maintain, or even increase, their potency when compared to the current therapeutic forms. The results suggest that this approach could be used successfully to enhance the solubility and efficacy of a wide range of other peptide and protein therapeutics.
Hepatic to pancreatic switch defines a role for hemostatic factors in cellular plasticity in mice
Authors: Shanmukhappa Kumar , Mourya Reena , Sabla Gregg E. , Degen Jay L. , Bezerra Jorge A.
Published: July 2005

In multiple systems, impaired proteolysis associated with the loss of the hemostatic factor plasminogen (Plg) results in fibrin-dependent defects in tissue repair. However, repair within the liver is known to be defective in Plg-deficient (Plg
o
) mice independent of fibrin clearance and appears to be compromised in part by the poor clearance of necrotic cells. Based on these findings, we examined the hepatic transcriptome after injury in search of transcriptional programs that are sensitive to the Plg/fibrinogen system. To this end, we generated biotinylated cRNA pools from livers of Plg
o
mice and controls before and after a single dose of the hepatotoxin carbon tetrachloride and hybridized them against high-density oligonucleotide arrays. Analysis of the gene expression platform identified an unexpected transcriptional signature within challenged livers of Plg
o
mice for pancreatic gene products, including trypsinogen-2, amylase-2, elastase-1, elastase-2, and cholesteryl-ester lipase. Validation studies found that this transcriptional program also contained products of the endocrine pancreas (Reg-1 and insulin genes) and the expression of the pancreatic transcription factors p48 and PDX-1. By using a
LacZ
transgene to trace the cellular source of pancreatic gene expression, we found that PDX-1 was expressed in albumin-positive cells that were morphologically indistinguishable from hepatocytes, and in albumin-negative epithelioid cells within zones of pericentral injury. More detailed studies revealed that the mechanisms of heterotopic gene expression in Plg
o
mice required fibrin(ogen). Collectively, these data reveal a regulatory role for the hemostatic factors plasmin(ogen) and fibrin(ogen) in cellular plasticity within adult tissues of the digestive system.
Prediction of water and metal binding sites and their affinities by using the Fold-X force field
Authors: Schymkowitz Joost W. H. , Rousseau Frederic , Martins Ivo C. , Ferkinghoff-Borg Jesper , Stricher Francois , Serrano Luis
Published: July 2005

The empirical force field Fold-X was developed previously to allow rapid free energy calculations in proteins. Here, we present an enhanced version of the force field allowing prediction of the position of structural water molecules and metal ions, together called single atom ligands. Fold-X picks up 76% of water molecules found to interact with two or more polar atoms of proteins in high-resolution crystal structures and predicts their position to within 0.8 Å on average. The prediction of metal ion-binding sites have success rates between 90% and 97% depending on the metal, with an overall standard deviation on the position of binding of 0.3-0.6 Å. The following metals were included in the force field: Mg2+, Ca2+, Zn2+, Mn2+, and Cu2+. As a result, the current version of Fold-X can accurately decorate a protein structure with biologically important ions and water molecules. Additionally, the free energy of binding of Ca2+and Zn2+(i.e., the natural logarithm of the dissociation constant) and its dependence on ionic strength correlate reasonably well with the experimental data available in the literature, allowing one to discriminate between high- and low-affinity binding sites. Importantly, the accuracy of the energy prediction presented here is sufficient to efficiently discriminate between Mg2+, Ca2+, and Zn2+binding.
Modifying specific cysteines of the electrophile-sensing human Keap1 protein is insufficient to disrupt binding to the Nrf2 domain Neh2
Authors: Eggler Aimee L. , Liu Guowen , Pezzuto John M. , van Breemen Richard B. , Mesecar Andrew D.
Published: July 2005

The risks of cancer and other degenerative diseases caused by reactive oxygen species and electrophiles can be reduced by the up-regulation of detoxifying enzymes. A major mechanism whereby these protective enzymes are induced occurs through activation of the antioxidant response element (ARE) by the oxidative-stress sensor protein Kelch-like ECH-associated protein 1 (Keap1) and the transcription factor NF-E2-related factor 2 (Nrf2). Under basal conditions, Keap1 sequesters Nrf2 in the cytoplasm by binding to its Neh2 domain. Chemical inducers such as sulforaphane are known to react with Keap1 cysteine residues, thereby promoting Nrf2 nuclear accumulation and hence ARE activation. A widely accepted model for Nrf2 nuclear accumulation is that modification of Keap1 cysteines leads directly to dissociation of the Keap1-Nrf2 complex. This model is based on studies with mouse proteins and has served as the experimental basis and hypothesis for numerous investigations. Through a combination of chemical, mass spectrometry, and isothermal titration calorimetry methods, we have tested the direct-dissociation model using a series of ARE inducers: sulforaphane, isoliquiritigenin, 15-deoxy-Δ12,14-prostaglandin-J2, menadione, 1-Cl-2,4-dinitrobenzene, and biotinylated iodoacetamide. Surprisingly, these data suggest that the direct disruption model for Keap1-Nrf2 is incorrect. The relative reactivity of human Keap1 cysteines was determined. In addition to the same five cysteines identified for mouse Keap1, two highly reactive and previously unobserved cysteines were identified. Based on these results, a model is proposed that should aid in the understanding of Keap1-Nrf2 signaling mechanisms.
Autoinhibition of
Escherichia coli
Rep monomer helicase activity by its 2B subdomain
Authors: Brendza Katherine M. , Cheng Wei , Fischer Christopher J. , Chesnik Marla A. , Niedziela-Majka Anita , Lohman Timothy M.
Published: July 2005

DNA helicases catalyze separation of double-helical DNA into its complementary single strands, a process essential for DNA replication, recombination, and repair. The
Escherichia coli
Rep protein, a superfamily 1 DNA helicase, functions in DNA replication restart and is required for replication of several bacteriophages. Monomers of Rep do not display helicase activity
in vitro
; in fact, DNA unwinding requires Rep dimerization. Here we show that removal of the 2B subdomain of Rep to form RepΔ2B activates monomer helicase activity, albeit with limited processivity. Although both full length Rep and RepΔ2B monomers can translocate with 3′ to 5′ directionality along single-stranded DNA, the 2B subdomain inhibits the helicase activity of full length Rep. This suggests an autoregulatory mechanism for Rep helicase, which may apply to other nonhexameric helicases, whereby helicase activity is regulated by the rotational conformational state of the 2B subdomain; formation of a Rep dimer may relieve autoinhibition by altering the 2B subdomain orientation.
Human-induced dwarfing of Himalayan snow lotus,
Saussurea laniceps
(Asteraceae)
Authors: Law Wayne , Salick Jan
Published: July 2005

Because evolutionary processes such as genetic drift and natural selection play a crucial role in determining the response that species will have to human-induced disturbances, there is increasing interest in the evolutionary aspects of conservation biology. Harvesting select individuals in natural plant populations can bring about unforeseen impacts that may negatively affect fitness. We analyzed how human harvesting affects two congeners known as snow lotus. Over a period of 100 years, there was a negative trend in plant height (
r
2
= 0.4361,
P
< 0.001) for the intensely collected and rare species,
Saussurea laniceps
, but not in the less intensely collected species,
Saussurea medusa
. Additionally,
S. laniceps
were significantly smaller in areas of high harvest than in areas with low harvest (
Z
= 4.91,
P
< 0.0001), but this was not so for
S. medusa
. Humans can unconsciously drive evolution and must be considered when managing threatened species.
ELL-associated factors 1 and 2 are positive regulators of RNA polymerase II elongation factor ELL
Authors: Kong Stephanie E. , Banks Charles A. S. , Shilatifard Ali , Conaway Joan Weliky , Conaway Ronald C.
Published: July 2005

In human cells, the ELL family of transcription factors includes at least three members, which are all capable of stimulating the overall rate of elongation by RNA polymerase II by suppressing transient pausing by the enzyme at many sites along DNA. In this report, we identify the ELL-associated factors (EAF)1 and EAF2 as strong positive regulators of ELL elongation activity. Our findings provide insights into the structure and function of ELL family transcription factors, and they bring to light direct roles for the EAF proteins in regulation of RNA polymerase II transcription.
LUX ARRHYTHMO
encodes a Myb domain protein essential for circadian rhythms
Authors: Hazen Samuel P. , Schultz Thomas F. , Pruneda-Paz Jose L. , Borevitz Justin O. , Ecker Joseph R. , Kay Steve A.
Published: July 2005

In higher plants, the circadian clock orchestrates fundamental processes such as light signaling and the transition to flowering. We isolated mutants of the circadian clock from an
Arabidopsis thaliana
mutagenized reporter line by screening for seedlings with long hypocotyl phenotypes and subsequently assaying for abnormal clock-regulated
CAB2
::
LUC
expression. This screen identified five mutant alleles of a clock gene,
LUX ARRHYTHMO
(
LUX
), that significantly affect amplitude and robustness of rhythms in both constant white light and dark conditions. In addition, the transition from vegetative to floral development is accelerated and hypocotyl elongation is accentuated in these mutants under light:dark cycles. We genetically mapped the mutations by bulk segregant analysis with high-density oligonucleotide array genotyping to a small putative Myb transcription factor related to other clock components and response regulators in
Arabidopsis
. The negative arm of the
Arabidopsis
circadian clock,
CIRCADIAN CLOCK ASSOCIATED
(
CCA1
) and
LATE ELONGATED HYPOCOTYL
(
LHY
), is repressed in the
lux
mutants, whereas
TIMING OF CAB2 EXPRESSION
(
TOC1
) is activated. We demonstrate that CCA1 and LHY bind to the evening element motif in the
LUX
promoter, which strongly suggests that these proteins repress
LUX
expression, as they do
TOC1
. The data are also consistent with LUX being necessary for activation of
CCA1
and
LHY
expression.
The C-terminal lysines fine-tune P53 stress responses in a mouse model but are not required for stability control or transactivation
Authors: Krummel Kurt A. , Lee Crystal J. , Toledo Franck , Wahl Geoffrey M.
Published: July 2005

P53 is an unstable transcription factor that is mutated in a majority of human cancers. With a significant role in initiating cell elimination programs, a network has evolved to fine-tune P53 transcriptional output and prevent errant activation. Modifications of the C terminus have long been viewed as critical binary determinants of P53 stability or activation. However, these conclusions are based on
in vitro
transfection or biochemical analyses where the stoichiometries between P53 and its regulators are perturbed. Therefore, we tested the importance of the C-terminal regulatory region for P53 control in mice where the seven C-terminal lysines were changed to arginine (
Trp-53
7KR
). Surprisingly, the homozygous mutant mice are viable and phenotypically normal. We have functionally characterized the mutant protein in both MEFs and thymocytes, revealing the unexpected result that Trp-53
7KR
exhibits a normal half-life and functions like WT P53 in cell cycle arrest and apoptosis, and in an E1A-ras xenograft tumor suppression assay. However, a significant difference is that P53
7KR
is activated more easily by DNA damage in thymus than WT P53. Importantly, although MEFs encoding WT P53 spontaneously emerge from crisis to become immortal in a 3T3 growth protocol, we do not observe any such escape with the P53
7KR
cells. We propose that the C-terminal modifications believed to be critical for proper P53 regulation are not essential, but contribute to a fine-tuning mechanism of homeostatic control
in vivo
.
A reversible molecular valve
Authors: Nguyen Thoi D. , Tseng Hsian-Rong , Celestre Paul C. , Flood Amar H. , Liu Yi , Stoddart J. Fraser , Zink Jeffrey I.
Published: July 2005

In everyday life, a macroscopic valve is a device with a movable control element that regulates the flow of gases or liquids by blocking and opening passageways. Construction of such a device on the nanoscale level requires (
i
) suitably proportioned movable control elements, (
ii
) a method for operating them on demand, and (
iii
) appropriately sized passageways. These three conditions can be fulfilled by attaching organic, mechanically interlocked, linear motor molecules that can be operated under chemical, electrical, or optical stimuli to stable inorganic porous frameworks (i.e., by self-assembling organic machinery on top of an inorganic chassis). In this article, we demonstrate a reversibly operating nanovalve that can be turned on and off by redox chemistry. It traps and releases molecules from a maze of nanoscopic passageways in silica by controlling the operation of redox-activated bistable [2]rotaxane molecules tethered to the openings of nanopores leading out of a nanoscale reservoir.
Numerical simulation of a laboratory-scale turbulent V-flame
Authors: Bell J. B. , Day M. S. , Shepherd I. G. , Johnson M. R. , Cheng R. K. , Grcar J. F. , Beckner V. E. , Lijewski M. J.
Published: July 2005

We present a three-dimensional, time-dependent simulation of a laboratory-scale rod-stabilized premixed turbulent V-flame. The experimental parameters correspond to a turbulent Reynolds number, Re

t

= 40, and to a Damköhler number,

D
a

= 6. The simulations are performed using an adaptive time-dependent low-Mach-number model with detailed chemical kinetics and a mixture model for differential species diffusion. The algorithm is based on a second-order projection formulation and does not require an explicit subgrid model for turbulence or turbulence/chemistry interaction. Adaptive mesh refinement is used to dynamically resolve the flame and turbulent structures. Here, we briefly discuss the numerical procedure and present detailed comparisons with experimental measurements showing that the computation is able to accurately capture the basic flame morphology and associated mean velocity field. Finally, we discuss key issues that arise in performing these types of simulations and the implications of these issues for using computation to form a bridge between turbulent flame experiments and basic combustion chemistry.
Identification of mast cell progenitors in adult mice
Authors: Chen Ching-Cheng , Grimbaldeston Michele A. , Tsai Mindy , Weissman Irving L. , Galli Stephen J.
Published: July 2005

It is well known that mast cells are derived from hematopoietic stem cells. However, in adult hematopoiesis, a committed mast cell progenitor has not yet been identified in any species, nor is it clear at what point during adult hematopoiesis commitment to the mast cell lineage occurs. We identified a cell population in adult mouse bone marrow, characterized as Lin-c-Kit+Sca-1--Ly6c-FcεRIα-CD27-β7+T1/ST2+, that gives rise only to mast cells in culture and that can reconstitute the mast cell compartment when transferred into c-kitmutant mast cell-deficient mice. In addition, our experiments strongly suggest that these adult mast cell progenitors are derived directly from multipotential progenitors instead of, as previously proposed, common myeloid progenitors or granulocyte/macrophage progenitors.
Valproate activates bovine leukemia virus gene expression, triggers apoptosis, and induces leukemia/lymphoma regression
in vivo
Authors: Achachi Amine , Florins Arnaud , Gillet Nicolas , Debacq Christophe , Urbain Patrice , Foutsop Germain Manfouo , Vandermeers Fabian , Jasik Agnieszka , Reichert Michal , Kerkhofs Pierre , Lagneaux Laurence , Burny Arsène , Kettmann Richard , Willems Luc
Published: July 2005

Leukemogenic viruses like human T-lymphotropic virus and bovine leukemia virus (BLV) presumably persist in the host partly by latent integration of the provirus in a fraction of infected cells, leading to accumulative increase in the outgrowth of transformed cells. Furthermore, viral infection also correlates with a blockade of the apoptotic mechanisms concomitant with an apparent latency of the host cell. Conceptually, induction of viral or cellular gene expression could thus also be used as a therapeutic strategy against retroviral-associated leukemia. Here, we provide evidence that valproate, an inhibitor of deacetylases, activates BLV gene expression in transient transfection experiments and in short-term cultures of primary B-lymphocytes.
In vivo
, valproate injection into newly BLV-inoculated sheep did not abrogate primary infection. However, valproate treatment, in the absence of any other cytotoxic drug, was efficient for leukemia/lymphoma therapy in the sheep model leading to decreased lymphocyte numbers (respectively from 25.6, 35.7, and 46.5 × 10
3
cells per mm
3
to 1.0, 10.6, and 24.3 × 10
3
cells per mm
3
in three leukemic sheep) and tumor regression (from >700 cm
3
to undetectable). The concept of a therapy that targets the expression of viral and cellular genes might be a promising treatment of adult T cell leukemia or tropical spastic paraparesis/human T-lymphotropic virus-associated myelopathy, diseases for which no satisfactory treatment exists so far.
SrSymRK, a plant receptor essential for symbiosome formation
Authors: Capoen Ward , Goormachtig Sofie , De Rycke Riet , Schroeyers Katrien , Holsters Marcelle
Published: July 2005

The symbiosis between legumes and rhizobia is essential for the nitrogen input into the life cycle on our planet. New root organs, the nodules, are established, which house N
2
-fixing bacteria internalized into the host cell cytoplasm as horizontally acquired organelles, the symbiosomes. The interaction is initiated by bacterial invasion via epidermal root hair curling and cell division in the cortex, both triggered by bacterial nodulation factors. Of the several genes involved in nodule initiation that have been identified, one encodes the leucine-rich repeat-type receptor kinase SymRK. In
SymRK
mutants of
Lotus japonicus
or its orthologs in
Medicago
sp. and
Pisum sativum
, nodule initiation is arrested at the level of the root hair interaction. Because of the epidermal block, the role of SymRK at later stages of nodule development remained enigmatic. To analyze the role of SymRK downstream of the epidermis, the water-tolerant legume
Sesbania rostrata
was used that has developed a nodulation strategy to circumvent root hair responses for bacterial invasion. Evidence is provided that SymRK plays an essential role during endosymbiotic uptake in plant cells.
Formation of organelle-like N
2
-fixing symbiosomes in legume root nodules is controlled by
DMI2
Authors: Limpens Erik , Mirabella Rossana , Fedorova Elena , Franken Carolien , Franssen Henk , Bisseling Ton , Geurts René
Published: July 2005

In most legume nodules, the N
2
-fixing rhizobia are present as organelle-like structures inside their host cells. These structures, named symbiosomes, contain one or a few rhizobia surrounded by a plant membrane. Symbiosome formation requires the release of bacteria from cell-wall-bound infection threads. In primitive legumes, rhizobia are hosted in intracellular infection threads that, in contrast to symbiosomes, are bound by a cell wall. The formation of symbiosomes is presumed to represent a major step in the evolution of legume–nodule symbiosis, because symbiosomes facilitate the exchange of metabolites between the two symbionts. Here, we show that the genes, which are essential for initiating nodule formation, are also actively transcribed in mature
Medicago truncatula
nodules in the region where symbiosome formation occurs. At least one of these genes, encoding the receptor kinase DOES NOT MAKE INFECTIONS 2 (DMI2) is essential for symbiosome formation. The protein locates to the host cell plasma membrane and to the membrane surrounding the infection threads. A partial reduction of
DMI2
expression causes a phenotype that resembles the infection structures found in primitive legume nodules, because infected cells are occupied by large intracellular infection threads instead of by organelle-like symbiosomes.
Physical limits to biochemical signaling
Authors: Bialek William , Setayeshgar Sima
Published: July 2005

Many crucial biological processes operate with surprisingly small numbers of molecules, and there is renewed interest in analyzing the impact of noise associated with these small numbers. Twenty-five years ago, Berg and Purcell showed that bacterial chemotaxis, where a single-celled organism must respond to small changes in concentration of chemicals outside the cell, is limited directly by molecule counting noise and that aspects of the bacteria"s behavioral and computational strategies must be chosen to minimize the effects of this noise. Here, we revisit and generalize their arguments to estimate the physical limits to signaling processes within the cell and argue that recent experiments are consistent with performance approaching these limits.
Modulation of epithelial neoplasia and lymphoid hyperplasia in PTEN
+/-
mice by the p85 regulatory subunits of phosphoinositide 3-kinase
Authors: Luo Ji , Sobkiw Cassandra L. , Logsdon Nicole M. , Watt John M. , Signoretti Sabina , O'Connell Fionnuala , Shin Eyoung , Shim Youngju , Pao Lily , Neel Benjamin G. , DePinho Ronald A. , Loda Massimo , Cantley Lewis C.
Published: July 2005

Mice with heterozygous deletion of the
PTEN
tumor suppressor gene develop a range of epithelial neoplasia as well as lymphoid hyperplasia. Previous studies suggest that PTEN suppresses tumor formation by acting as a phosphoinositide phosphatase to limit signaling by phosphoinositide 3-kinase (PI3K). Here, we examined the effect of deleting various regulatory subunits of PI3K (p85α and p85β) on epithelial neoplasia and lymphoid hyperplasia in PTEN
+/-
mice. Interestingly, we found the loss of one p85α allele with or without the loss of p85β led to increased incidence of intestinal polyps. Signaling downstream of PI3K was enhanced in the PTEN
+/-
p85α
+/-
p85β
-/-
polyps, as judged by an increased fraction of both cells with cytoplasmic staining of the transcription factor FKHR and cells with positive staining for the proliferation marker Ki-67. In contrast, the incidence of prostate intraepithelial neoplasia was not significantly altered in PTEN
+/-
mice heterozygous for p85α or null for p85β, whereas the fraction of proliferating cells in prostate intraepithelial neoplasia was reduced in mice lacking p85β. Finally, there was no significant change in T lymphocyte hyperplasia in the PTEN
+/-
mice with various p85 deletions, although anti-CD3-stimulated AKT activation was somewhat reduced in the p85α
+/-
background. These results indicate that decreasing the levels of different p85 regulatory subunits can result in enhanced PI3K signaling in some tissues and decreased PI3K signaling in others, supporting the model that, although p85 proteins are essential for class I
A
PI3K signaling, they can function as inhibitors of PI3K signaling in some tissues and thus suppress tumor formation.
Selective thyroid receptor modulation by GC-1 reduces serum lipids and stimulates steps of reverse cholesterol transport in euthyroid mice
Authors: Johansson Lisen , Rudling Mats , Scanlan Thomas S. , Lundåsen Thomas , Webb Paul , Baxter John , Angelin Bo , Parini Paolo
Published: July 2005

Thyroid hormones [predominantly 3,5,3′-triiodo-
l
-thyronine (T
3
)] regulate cholesterol and lipoprotein metabolism, but cardiac effects restrict their use as hypolipidemic drugs. T
3
binds to thyroid hormone receptors (TRs) α and β. TRβ is the predominant isoform in liver, whereas T
3
effects on heart rate are mediated mostly by TRα. Drugs that target TRβ or exhibit tissue-selective uptake may improve plasma lipid levels while sparing the heart. Here, we asked how the TRβ- and liver uptake-selective agonist GC-1 influences cholesterol and triglyceride metabolism in euthyroid mice. GC-1 treatment reduced serum cholesterol levels by 25% and serum triglycerides by 75% in chow-fed mice and also attenuated diet-induced hypercholesterolemia. GC-1 reduced plasma high-density lipoprotein cholesterol levels; increased expression of the hepatic high-density lipoprotein receptor, SR-BI; stimulated activity of cholesterol 7α-hydroxylase; and increased fecal excretion of bile acids. Collectively, these results suggest that GC-1 stimulates important steps in reverse cholesterol transport. Use of TRβ and uptake selective agonists such as GC-1 should be further explored as a strategy to improve lipid metabolism in dyslipoproteinemia.
WNK1 activates SGK1 to regulate the epithelial sodium channel
Authors: Xu Bing-e , Stippec Steve , Chu Po-Yin , Lazrak Ahmed , Li Xin-Ji , Lee Byung-Hoon , English Jessie M. , Ortega Bernardo , Huang Chou-Long , Cobb Melanie H.
Published: July 2005

WNK (with no lysine [K]) kinases are serine-threonine protein kinases with an atypical placement of the catalytic lysine. Intronic deletions increase the expression of WNK1 in humans and cause pseudohypoaldosteronism type II, a form of hypertension. WNKs have been linked to ion carriers, but the underlying regulatory mechanisms are unknown. Here, we report a mechanism for the control of ion permeability by WNK1. We show that WNK1 activates the serum- and glucocorticoid-inducible protein kinase SGK1, leading to activation of the epithelial sodium channel. Increased channel activity induced by WNK1 depends on SGK1 and the E3 ubiquitin ligase Nedd4-2. This finding provides compelling evidence that this molecular mechanism contributes to the pathogenesis of hypertension in pseudohypoaldosteronism type II caused by WNK1 and, possibly, in other forms of hypertension.
MicroRNA-binding viral protein interferes with
Arabidopsis
development
Authors: Chellappan Padmanabhan , Vanitharani Ramachandran , Fauquet Claude M.
Published: July 2005

MicroRNAs (miRNAs) are small (≈21 nt), noncoding RNAs that negatively regulate target mRNAs at the posttranscriptional level that are involved in development. In plants, virus-induced disease symptoms often result in developmental abnormalities resembling perturbation of miRNA-mediated function. Here, we report that expression in transgenic plants of a geminivirus-encoded AC4 protein from African cassava mosaic virus Cameroon Strain (ACMV), a suppressor of posttranscriptional gene silencing, was correlated with decreased accumulation of host miRNAs and increased development abnormalities in
Arabidopsis
. Down-regulation of miRNA correlated with an up-regulation of target mRNA level.
In vitro
binding assays revealed the ability of AC4 of ACMV (A-AC4) but not East African cassava mosaic Cameroon virus AC2 to bind single-stranded forms of miRNAs and short interfering RNAs but not double-stranded RNA forms. Normally, a labile intermediate during the miRNA biogenesis/RNA-induced silencing complex assembly, miRNA
*
, was below the level of detection, indicating that AC4 might interfere at a point downstream of the miRNA duplex unwinding process. The association of AC4 with miRNA was demonstrated by the association of A-AC4–GFP fusion protein, extracted from
Arabidopsis
protoplasts, with 2′-
O
-methyloligonucleotide complementary to miR159 (miR159
*
) and by the presence of miRNA with the A-AC4–GFP fusion protein after immunoprecipitation with antibody against GFP. In both assays, A-AC4 protein and miRNA complexes were copurified. These results provide direct evidence that AC4 is a unique virus-encoded posttranscriptional gene-silencing suppressor protein that binds to and presumably inactivates mature miRNAs and thus blocks the normal miRNA-mediated regulation of target mRNAs, resulting in developmental defects in
Arabidopsis
.
Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition
Authors: Chang Chung-I , Ihara Kentaro , Chelliah Yogarany , Mengin-Lecreulx Dominique , Wakatsuki Soichi , Deisenhofer Johann
Published: July 2005

The peptidoglycan-recognition protein LCa (PGRP-LCa) is a transmembrane receptor required for activation of the
Drosophila
immune deficiency pathway by monomeric Gram-negative peptidoglycan. We have determined the crystal structure of the ectodomain of PGRP-LCa at 2.5-Å resolution and found two unique helical insertions in the LCa ectodomain that disrupt an otherwise L-shaped peptidoglycan-docking groove present in all other known PGRP structures. The deficient binding of PGRP-LCa to monomeric peptidoglycan was confirmed by biochemical pull-down assays. Recognition of monomeric peptidoglycan involves both PGRP-LCa and -LCx. We showed that association of the LCa and LCx ectodomains
in vitro
depends on monomeric peptidoglycan. The presence of a defective peptidoglycan-docking groove, while preserving a unique role in mediating monomeric peptidoglycan induction of immune response, suggests that PGRP-LCa recognizes the exposed structural features of a monomeric muropeptide when the latter is bound to and presented by the ectodomain of PGRP-LCx. Such features include
N
-acetyl glucosamine and the anhydro bond in the glycan of the muropeptide, which have been demonstrated to be critical for immune stimulatory activity.
Molecular architecture and assembly mechanism of
Drosophila
tripeptidyl peptidase II
Authors: Rockel Beate , Peters Jürgen , Müller Shirley A. , Seyit Gönül , Ringler Philippe , Hegerl Reiner , Glaeser Robert M. , Baumeister Wolfgang
Published: July 2005

In eukaryotes, tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. The 150-kDa subunits of
Drosophila
TPPII assemble into a giant proteolytic complex of 6 MDa with a remarkable architecture consisting of two segmented and twisted strands that form a spindle-shaped structure. A refined 3D model has been obtained by cryoelectron microscopy, which reveals details of the molecular architecture and, in conjunction with biochemical data, provides insight into the assembly mechanism. The building blocks of this complex are apparently dimers, within which the 150-kDa monomers are oriented head to head. Stacking of these dimers leads to the formation of twisted single strands, two of which comprise the fully assembled spindle. This spindle also forms when TPPII is heterologously expressed in
Escherichia coli
, demonstrating that no scaffolding protein is required for complex formation and length determination. Reciprocal interactions of the N-terminal part of subunits from neighboring strands are probably involved in the formation of the native quaternary structure, lending the TPPII spindle a stability higher than that of single strands.
One-dimensional hole gas in germanium/silicon nanowire heterostructures
Authors: Lu Wei , Xiang Jie , Timko Brian P. , Wu Yue , Lieber Charles M.
Published: July 2005

Two-dimensional electron and hole gas systems, enabled through band structure design and epitaxial growth on planar substrates, have served as key platforms for fundamental condensed matter research and high-performance devices. The analogous development of one-dimensional (1D) electron or hole gas systems through controlled growth on 1D nanostructure substrates, which could open up opportunities beyond existing carbon nanotube and nanowire systems, has not been realized. Here, we report the synthesis and transport studies of a 1D hole gas system based on a free-standing germanium/silicon (Ge/Si) core/shell nanowire heterostructure. Room temperature electrical transport measurements clearly show hole accumulation in undoped Ge/Si nanowire heterostructures, in contrast to control experiments on single-component nanowires. Low-temperature studies show well-controlled Coulomb blockade oscillations when the Si shell serves as a tunnel barrier to the hole gas in the Ge channel. Transparent contacts to the hole gas also have been reproducibly achieved by thermal annealing. In such devices, we observe conductance quantization at low temperatures, corresponding to ballistic transport through 1D subbands, where the measured subband energy spacings agree with calculations for a cylindrical confinement potential. In addition, we observe a “0.7 structure,” which has been attributed to spontaneous spin polarization, suggesting the universality of this phenomenon in interacting 1D systems. Lastly, the conductance exhibits little temperature dependence, consistent with our calculation of reduced backscattering in this 1D system, and suggests that transport is ballistic even at room temperature.
Strain-specific morphologies of yeast prion amyloid fibrils
Authors: Diaz-Avalos Ruben , King Chih-Yen , Wall Joseph , Simon Martha , Caspar Donald L. D.
Published: July 2005

Mass per length (mpl) measurements on single amyloid fibrils that specifically propagate the [VH], [VK], and [VL] strains of the yeast prion [PSI] reveal unanticipated differences in their structures. Many fibrils have ≈1.0 prion molecule per 4.7-Å cross-β repeat period, which is consistent with a self-replicating model built by parallel β-sheet hydrogen-bonding of like prion peptide segments, but other fibrils are definitely heavier. The predominantly straight fibrils of the dominant [VH] strain have a bimodal mpl distribution, corresponding to components with ≈1.0 and 1.2 prions per repeat. Fibrils of the weaker [VK] strain, which are almost all wavy, have a monodisperse mpl distribution with a mean of 1.15 prions per repeat. The recessive [VL] strain sample has ≈1.05 prions per repeat in single fibrils and includes ≈10% double fibrils, which are rare in the duplicate [VH] and [VK] samples. All of these samples were assembled from purified recombinant Sup35 prion protein by seeded growth on nuclei extracted from yeast bearing the three [PSI] strains. Infectious and noninfectious spontaneously assembled fibrils of the recombinant prion protein also display different heterogeneous morphologies. The strain-specific morphological differences we have observed directly confirm the structural prediction of the protein-only prion theory but do not have an obvious molecular explanation.