bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron microscopy of whole cells in liquid with nanometer resolution
Authors: Jonge N. de , Peckys D. B. , Kremers G. J. , Piston D. W.
Published: January 2009

Single gold-tagged epidermal growth factor (EGF) molecules bound to cellular EGF receptors of fixed fibroblast cells were imaged in liquid with a scanning transmission electron microscope (STEM). The cells were placed in buffer solution in a microfluidic device with electron transparent windows inside the vacuum of the electron microscope. A spatial resolution of 4 nm and a pixel dwell time of 20 μs were obtained. The liquid layer was sufficiently thick to contain the cells with a thickness of 7 ± 1 μm. The experimental findings are consistent with a theoretical calculation. Liquid STEM is a unique approach for imaging single molecules in whole cells with significantly improved resolution and imaging speed over existing methods.
Female promiscuity promotes the evolution of faster sperm in cichlid fishes
Authors: Fitzpatrick John L. , Montgomerie Robert , Desjardins Julie K. , Stiver Kelly A. , Kolm Niclas , Balshine Sigal
Published: January 2009

Sperm competition, the contest among ejaculates from rival males to fertilize ova of a female, is a common and powerful evolutionary force influencing ejaculate traits. During competitive interactions between ejaculates, longer and faster spermatozoa are expected to have an edge; however, to date, there has been mixed support for this key prediction from sperm competition theory. Here, we use the spectacular radiation of cichlid fishes from Lake Tanganyika to examine sperm characteristics in 29 closely related species. We provide phylogenetically robust evidence that species experiencing greater levels of sperm competition have faster-swimming sperm. We also show that sperm competition selects for increases in the number, size, and longevity of spermatozoa in the ejaculate of a male, and, contrary to expectations from theory, we find no evidence of trade-offs among sperm traits in an interspecific analysis. Also, sperm swimming speed is positively correlated with sperm length among, but not within, species. These different responses to sperm competition at intra- and interspecific levels provide a simple, powerful explanation for equivocal results from previous studies. Using phylogenetic analyses, we also reconstructed the probable evolutionary route of trait evolution in this taxon, and show that, in response to increases in the magnitude of sperm competition, the evolution of sperm traits in this clade began with the evolution of faster (thus, more competitive) sperm.
Nicotine activates TRPM5-dependent and independent taste pathways
Authors: Oliveira-Maia Albino J. , Stapleton-Kotloski Jennifer R. , Lyall Vijay , Phan Tam-Hao T. , Mummalaneni Shobha , Melone Pamela , DeSimone John A. , Nicolelis Miguel A. L. , Simon Sidney A.
Published: January 2009

The orosensory responses elicited by nicotine are relevant for the development and maintenance of addiction to tobacco products. However, although nicotine is described as bitter tasting, the molecular and neural substrates encoding the taste of nicotine are unclear. Here, rats and mice were used to determine whether nicotine activates peripheral and central taste pathways via TRPM5-dependent mechanisms, which are essential for responses to other bitter tastants such as quinine, and/or via nicotinic acetylcholine receptors (nAChRs). When compared with wild-type mice,
Trpm5
−/−
mice had reduced, but not abolished, chorda tympani (CT) responses to nicotine. In both genotypes, lingual application of mecamylamine, a nAChR-antagonist, inhibited CT nerve responses to nicotine and reduced behavioral responses of aversion to this stimulus. In accordance with these findings, rats were shown to discriminate between nicotine and quinine presented at intensity-paired concentrations. Moreover, rat gustatory cortex (GC) neural ensemble activity could also discriminate between these two bitter tastants. Mecamylamine reduced both behavioral and GC neural discrimination between nicotine and quinine. In summary, nicotine elicits taste responses through peripheral TRPM5-dependent pathways, common to other bitter tastants, and nAChR-dependent and TRPM5-independent pathways, thus creating a unique sensory representation that contributes to the sensory experience of tobacco products.
RodZ, a component of the bacterial core morphogenic apparatus
Authors: Alyahya S. Anisah , Alexander Roger , Costa Teresa , Henriques Adriano O. , Emonet Thierry , Jacobs-Wagner Christine
Published: January 2009

The molecular basis of bacterial cell morphogenesis remains largely an open question. Here we discover a morphogenic protein, RodZ, which is widely conserved across the bacterial kingdom. In
Caulobacter crescentus
, RodZ is essential for viability and is involved in all aspects of this organism's complex morphology. Depletion or over-production of RodZ results in grossly misshapen cells with stalk defects. RodZ exhibits a localization pattern during the cell cycle corresponding to sites of active peptidoglycan synthesis. The temporal transition of RodZ between patchy/helical and mid-cell localization mimics and depends on the actin-like MreB cytoskeleton. In
Escherichia coli
, an organism with a distinct mode of growth and MreB localization dynamics, RodZ follows MreB and retains its crucial role in cell morphogenesis, demonstrating conservation of function. Genomic analysis shows that RodZ represents an ancient function unique to bacteria. Multiple sequence alignment of 143 RodZ sequences from species across bacterial phyla identifies an N-terminal cytoplasmic domain with a helix-turn-helix motif, a transmembrane sequence, and a previously unidentified, conserved periplasmic or extracellular C-terminal domain. Both the N- and C-terminal domains are important for function, with the N-terminal domain containing localization determinants. This study uncovers a key missing player in the cytoskeleton-based growth machinery enabling heritable and defined cellular forms in bacteria.
Msc1 links dynamic Swi6/HP1 binding to cell fate determination
Authors: Lawrence Richard J. , Volpe Thomas A.
Published: January 2009

Eukaryotic genomes can be organized into distinct domains of heterochromatin or euchromatin. In the fission yeast
Schizosaccharomyces pombe
, assembly of heterochromatin at the silent mating-type region is critical for cell fate determination in the form of mating-type switching. Here, we report that the ubiquitin ligase, Msc1, is a critical factor required for proper cell fate determination in
S. pombe
. In the absence of Msc1, the in vivo mobility of Swi6 at heterochromatic foci is compromised, and centromere heterochromatin becomes hyperenriched with the heterochromatin binding protein Swi6/HP1. However, at the mating-type locus, Swi6 recruitment is defective in the absence of Msc1. Therefore, Msc1 links maintaining dynamic heterochromatin with proper heterochromatin assembly and cell fate determination. These findings have implications for understanding mechanisms of differentiation in other organisms.
Induction of TLR4-target genes entails calcium/calmodulin-dependent regulation of chromatin remodeling
Authors: Lai Dazhi , Wan Mimi , Wu Jie , Preston-Hurlburt Paula , Kushwaha Ritu , Grundström Thomas , Imbalzano Anthony N. , Chi Tian
Published: January 2009

Upon toll-like receptor 4 (TLR4) signaling in macrophages, the mammalian Swi/Snf-like BAF chromatin remodeling complex is recruited to many TLR4 target genes where it remodels their chromatin to promote transcription. Here, we show that, surprisingly, recruitment is not sufficient for chromatin remodeling; a second event, dependent on calcium/calmodulin (CaM), is additionally required. Calcium/CaM directly binds the HMG domain of the BAF57 subunit within the BAF complex. Calcium/CaM antagonists, including a CaM-binding peptide derived from BAF57, abolish BAF-dependent remodeling and gene expression without compromising BAF recruitment. BAF57 RNAi and BAF57 dominant negative mutants defective in CaM binding similarly impair the induction of BAF target genes. Our data implicate calcium/CaM in TLR4 signaling, and reveal a previously undescribed, recruitment-independent mode of regulation of the BAF complex that is probably achieved through a direct CaM-BAF interaction.
A network biology approach to aging in yeast
Authors: Lorenz David R. , Cantor Charles R. , Collins James J.
Published: January 2009

In this study, a reverse-engineering strategy was used to infer and analyze the structure and function of an aging and glucose repressed gene regulatory network in the budding yeast
Saccharomyces cerevisiae
. The method uses transcriptional perturbations to model the functional interactions between genes as a system of first-order ordinary differential equations. The resulting network model correctly identified the known interactions of key regulators in a 10-gene network from the Snf1 signaling pathway, which is required for expression of glucose-repressed genes upon calorie restriction. The majority of interactions predicted by the network model were confirmed using promoter-reporter gene fusions in gene-deletion mutants and chromatin immunoprecipitation experiments, revealing a more complex network architecture than previously appreciated. The reverse-engineered network model also predicted an unexpected role for transcriptional regulation of the
SNF1
gene by hexose kinase enzyme/transcriptional repressor Hxk2, Mediator subunit Med8, and transcriptional repressor Mig1. These interactions were validated experimentally and used to design new experiments demonstrating Snf1 and its transcriptional regulators Hxk2 and Mig1 as modulators of chronological lifespan. This work demonstrates the value of using network inference methods to identify and characterize the regulators of complex phenotypes, such as aging.
Environmental change and economic development in coastal Peru between 5,800 and 3,600 years ago
Authors: Sandweiss Daniel H. , Solís Ruth Shady , Moseley Michael E. , Keefer David K. , Ortloff Charles R.
Published: January 2009

Between ≈5,800 and 3,600 cal B.P. the biggest architectural monuments and largest settlements in the Western Hemisphere flourished in the Supe Valley and adjacent desert drainages of the arid Peruvian coast. Intensive net fishing, irrigated orchards, and fields of cotton with scant comestibles successfully sustained centuries of increasingly complex societies that did not use ceramics or loom-based weaving. This unique socioeconomic adaptation was abruptly abandoned and gradually replaced by societies more reliant on food crops, pottery, and weaving. Here, we review evidence and arguments for a severe cycle of natural disasters—earthquakes, El Niño flooding, beach ridge formation, and sand dune incursion—at ≈3,800 B.P. and hypothesize that ensuing physical changes to marine and terrestrial environments contributed to the demise of early Supe settlements.
Erythropoietin modulation of astrocyte water permeability as a component of neuroprotection
Authors: Gunnarson Eli , Song Yutong , Kowalewski Jacob M. , Brismar Hjalmar , Brines Michael , Cerami Anthony , Andersson Ulf , Zelenina Marina , Aperia Anita
Published: January 2009

Disturbed brain water homeostasis with swelling of astroglial cells is a common complication in stroke, trauma, and meningitis and is considered to be a major cause of permanent brain damage. Astroglial cells possess the water channel aquaporin 4 (AQP4). Recent studies from our laboratory have shown that glutamate, acting on group I metabotropic glutamate receptors (mGluRs), increases the permeability of astrocyte AQP4, which, in situations of hypoxia-ischemia, will increase astrocyte water uptake. Here we report that erythropoietin (EPO), which in recent years has emerged as a potent neuro-protective agent, antagonizes the effect of a group I mGluR agonist on astrocyte water permeability. Activation of group I mGluRs triggers fast and highly regular intracellular calcium oscillations and we show that EPO interferes with this signaling event by altering the frequency of the oscillations. These effects of EPO are immediate, in contrast to the neuroprotective effects of EPO that are known to depend upon gene activation. Our findings indicate that EPO may directly reduce the risk of astrocyte swelling in stroke and other brain insults. In support of this conclusion we found that EPO reduced the neurological symptoms in a mouse model of primary brain edema known to depend upon AQP4 water transport.
Alternatively splicedSpalaxheparanase inhibits extracellular matrix degradation, tumor growth, and metastasis
Authors: Nasser Nicola J. , Avivi Aaron , Shafat Itay , Edovitsky Evgeny , Zcharia Eyal , Ilan Neta , Vlodavsky Israel , Nevo Eviatar
Published: January 2009

Heparanase is an endoglycosidase that degrades heparan sulfate (HS) at the cell surface and in the extracellular matrix. Heparanase is expressed mainly by cancer cells, and its expression is correlated with increased tumor aggressiveness, metastasis, and angiogenesis. Here, we report the cloning of a unique splice variant (splice 36) of heparanase from the subterranean blind mole rat (Spalax). This splice variant results from skipping part of exon 3, exons 4 and 5, and part of exon 6 and functions as a dominant negative to the wild-type enzyme. It inhibits HS degradation, suppresses glioma tumor growth, and decreases experimental B16–BL6 lung colonization in a mouse model. Intriguingly,Spalaxsplice variant 7 of heparanase (which results from skipping of exon 7) is devoid of enzymatic activity, but unlike splice 36 it enhances tumor growth. Our results demonstrate that alternative splicing of heparanase regulates its enzymatic activity and might adapt the heparanase function to the fluctuating normoxic–hypoxic subterranean environment thatSpalaxexperiences. Development of anticancer drugs designed to suppress tumor growth, angiogenesis, and metastasis is a major challenge, of which heparanase inhibition is a promising approach. We anticipate that the heparanase splicing model, evolved during 40 million years of Spalacid adaptation to underground life, would pave the way for the development of heparanase-based therapeutic modalities directed against angiogenesis, tumor growth, and metastasis.
FGF-dependent left–right asymmetry patterning in zebrafish is mediated by Ier2 and Fibp1
Authors: Hong Sung-Kook , Dawid Igor B.
Published: January 2009

Establishment of left–right asymmetry in vertebrates requires nodal, Wnt-PCP and FGF signaling and involves ciliogenesis in a laterality organ. Effector genes through which FGF signaling affects laterality have not been described. We isolated the zebrafish
ier2
and
fibp1
genes as FGF target genes and show that their protein products interact. Knock down of these factors interferes with establishment of organ laterality and causes defective cilia formation in Kupffer's Vesicle, the zebrafish laterality organ. Cilia are also lost after suppression of FGF8, but can be rescued by injection of
ier2
and
fibp1
mRNA. We conclude that Ier2 and Fibp1 mediate FGF signaling in ciliogenesis in Kupffer's Vesicle and in the establishment of laterality in the zebrafish embryo.
Conventionalized as -similes in English
Authors: Moon Rosamund
Published: January 2009

This paper reports on a corpus-based investigation of conventionalized English similes which follow the pattern (as) ADJECTIVE as NOUN GROUP. It begins by describing their formal and semantic characteristics, and then discusses issues of variation, approaches to handling variation, and procedures for establishing the simile lexicon. It reports on the frequencies observed in the Bank of English for as-similes, including their distribution in British English, and compares these to frequencies observed in other corpora. Finally, it speculates on how conventionalized as-similes survive in the lexicon, in spite of their apparent infrequency in (corpus) text; sets out a characterization of as-similes; and suggests some implications for phraseological studies in general.
Collocations and colligations associated with discourse functions of unspecific anaphoric nouns
Authors: Yamasaki Nozomi
Published: January 2009

This paper investigates how particular collocations and colligations are associated with discourse functions of unspecific anaphoric nouns. Unspecific anaphoric nouns such as problem, reason, idea and fault, called labels here, encapsulate and replace a preceding stretch of discourse. Such nouns used as a cohesive device also perform an evaluative function by recategorizing their specific meanings. Labels prefer particular syntactic environments according to the discourse function that is highlighted. Corpus-based research also reveals that unspecific nouns differ in their favoured syntactic pattern and in the favoured premodifiers used in each pattern. Differences between writing and speech in collocations and colligations associated with labels are also attributed to the different discourse functions they realize in each genre. paper argues that discourse dimensions should be brought into collocational and colligational descriptions of words that have discourse-managing functions.
Physical training decreases waist circumference in postmenopausal borderline overweight women
Authors: BERGSTRÖM INGRID , LOMBARDO CIRA , BRINCK JONAS
Published: January 2009

Objective. To examine if healthy borderline overweight postmenopausal women with osteoporosis can improve their waist circumference and lipid profile with a moderate physical training program. Design. Randomized controlled trial. Setting. One hundred and twelve postmenopausal women were randomized to normal sedentary life or one year of physical training consisting of three brisk walks and 1–2 aerobic exercises/week. Main Outcome Measures. Waist circumference reduction, waist circumference reduction in relation to observed level of participation in physical intervention and changes in cholesterol, triglycerides, apolipoproteins B and A1 and high‐sensitivity C‐reactive protein (hs‐CRP). Results. At start the mean (SD) waist circumference was 83.6 (7.7) and 81.8 (7.5) cm in the control and training groups, respectively. In relation to baseline, the 12 months intervention led to a waist reduction of 0.3 cm (2.7) (p = 0.36) and 1.6 cm (4.7) (p = 0.02) in the respective groups but the inter‐group comparison was not significant in an intention‐to‐treat analysis (p = 0.09). The ninety‐two women completing the study intervention were analyzed per protocol. A tendency for better waist reduction in relation to the women's observed physical intensity level was observed (p = 0.07, ANOVA for linear trend across training intensity levels). Training women improved their waist circumference 1.7 cm (p = 0.01) compared to baseline and was borderline significantly better than controls (p = 0.059). No significant changes in response to the intervention were observed for blood pressure, cholesterol, triglycerides, apolipoproteins and hs‐CRP. Conclusions. A moderate physical exercise program for healthy postmenopausal women during one year reduced the waist circumference in a training intensity dependent manner.
First‐trimester maternal plasma cytokine levels, pre‐pregnancy body mass index, and spontaneous preterm delivery
Authors: CURRY ALLISON ELIZABETH , THORSEN POUL , DREWS CAROLYN , SCHENDEL DIANA , SKOGSTRAND KRISTIN , FLANDERS WILLIAM DANA , HOUGAARD DAVID , OLSEN JØRN , VOGEL IDA
Published: January 2009

Objective. To examine associations between first‐trimester plasma cytokines and spontaneous preterm delivery (sPTD). Design. A case‐control study was nested within the Danish National Birth Cohort, a cohort of women with 101,042 pregnancies from 1997 to 2002 who were recruited during pregnancy and followed prospectively. Sample. Subjects included 107 women delivering singleton infants at 24–29 weeks, 353 at 30–33 weeks, 422 at 34–36 weeks, and 1,372 at ≥37 weeks. Methods. Maternal plasma interleukin (IL)‐2, IL‐6, tumor necrosis factor (TNF)‐α, interferon (IFN)‐γ, and granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) were measured at a median of eight weeks gestation using multiplex flow cytometry. Adjusted odds ratios (ORs) were obtained using polytomous logistic regression. Main outcome measures. sPTD categorized as: 24–29 weeks, 30–33 weeks, 34–36 weeks, and ≥37 weeks (controls). Results. Elevated TNF‐α and GM‐CSF were associated with an increased risk of delivery at 34–36 weeks. In underweight women, sPTD <34 weeks was associated with elevated (>75th percentile) IL‐6 (OR = 5.62, 95% confidence interval (CI): 1.73, 18.26) and TNF‐α (OR = 3.02, CI: 1.02, 8.91) compared with term delivery. Conversely, among obese women, elevated IL‐2 (OR = 0.30, CI: 0.11, 0.78) and TNF‐α (OR = 0.15, CI: 0.05, 0.47) were associated with a reduced risk of delivering at <34 weeks. Cytokines were not related to delivery at <34 weeks in normal‐weight and overweight women. Conclusions. These findings suggest that the association between first‐trimester plasma cytokine levels and sPTD may depend on pre‐pregnancy body mass index.
Corps de nombres peu ramifiés et formes automorphes autoduales
Authors: Chenevier G. , Clozel L.
Published: January 2009

Let

S
S

be a finite set of primes,

p
p

in

S
S

, and

Q

S

\mathbb {Q}_S

a maximal algebraic extension of

Q

\mathbb {Q}

unramified outside

S
S

and

∞
\infty

. Assume that

|

S

|

≥
2

|S|\geq 2

. We show that the natural maps
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper G a l left-parenthesis double-struck upper Q Subscript p Baseline overbar slash double-struck upper Q Subscript p Baseline right-parenthesis right-arrow upper G a l left-parenthesis double-struck upper Q Subscript upper S Baseline slash double-struck upper Q right-parenthesis">

Gal
⁡
(

Q

p

¯

/

Q

p

)
→
Gal
⁡
(

Q

S

/

Q

)

\operatorname {Gal}(\overline {\mathbb {Q}_p}/\mathbb {Q}_p) \rightarrow \operatorname {Gal}(\mathbb {Q}_S/\mathbb {Q})

\]
are injective. Much of the paper is devoted to the problem of constructing self-dual automorphic cuspidal representations of

GL
⁡
(
2
n
,

A

Q

)

\operatorname {GL}(2n,\mathbb {A}_{\mathbb {Q}})

with prescribed properties at all places, which we study via Arthur’s twisted trace formula. The techniques we develop also shed some light on the orthogonal/symplectic alternative for self-dual representations of

GL
⁡
(
2
n
)

\operatorname {GL}(2n)

.
Negative dependence and the geometry of polynomials
Authors: Borcea Julius , Brändén Petter , Liggett Thomas
Published: January 2009

We introduce the class ofstrongly Rayleighprobability measures by means of geometric properties of their generating polynomials that amount to the stability of the latter. This class covers important models such as determinantal measures (e.g. product measures and uniform random spanning tree measures) and distributions for symmetric exclusion processes. We show that strongly Rayleigh measures enjoy all virtues of negative dependence, and we also prove a series of conjectures due to Liggett, Pemantle, and Wagner, respectively. Moreover, we extend Lyons’ recent results on determinantal measures, and we construct counterexamples to several conjectures of Pemantle and Wagner on negative dependence and ultra log-concave rank sequences.
Uniform energy distribution for an isoperimetric problem with long-range interactions
Authors: Alberti Giovanni , Choksi Rustum , Otto Felix
Published: January 2009

We study minimizers of a nonlocal variational problem. The problem is a mathematical paradigm for the ubiquitous phenomenon of energy-driven pattern formation induced by competing short- and long-range interactions. The short-range interaction is attractive and comes from an interfacial energy, and the long-range interaction is repulsive and comes from a nonlocal energy contribution. In particular, the problem is the sharp interface version of a problem used to model microphase separation of diblock copolymers. A natural conjecture is that in all space dimensions, minimizers are essentially periodic on an intrinsic scale. However, proving any periodicity result turns out to be a formidable task in dimensions larger than one.

In this paper, we address a weaker statement concerning the distribution of energy for minimizers. We prove in any space dimension that each component of the energy (interfacial and nonlocal) of any minimizer is uniformly distributed on cubes which are sufficiently large with respect to the intrinsic length scale. Moreover, we also prove an

L
∞

L^\infty

bound on the optimal potential associated with the long-range interactions. This bound allows for an interesting interpretation: Note that the average volume fraction of the optimal pattern in a subsystem of size

R
R

fluctuates around the system average

m
m

. The bound on the potential yields a rate of decay of these fluctuations as

R
R

tends to

+
∞

+\infty

. This rate of decay is stronger than the one for a random checkerboard pattern. In this sense, the optimal pattern has less large-scale variations of the average volume fraction than a pattern with a finite correlation length.
Asymptotic enumeration and limit laws of planar graphs
Authors: Giménez Omer , Noy Marc
Published: January 2009

We present a complete analytic solution to the problem of counting planar graphs. We prove an estimategn∼g⋅n−7/2γnn!g_n \sim g\cdot n^{-7/2} \gamma ^n n!for the numbergng_nof labelled planar graphs onnnvertices, whereγ\gammaandggare explicit computable constants. We show that the number of edges in random planar graphs is asymptotically normal with linear mean and variance and, as a consequence, the number of edges is sharply concentrated around its expected value. Moreover we prove an estimateg(q)⋅n−4γ(q)nn!g(q)\cdot n^{-4}\gamma (q)^n n!for the number of planar graphs withnnvertices and⌊qn⌋\lfloor qn \rflooredges, whereγ(q)\gamma (q)is an analytic function ofqq. We also show that the number of connected components in a random planar graph is distributed asymptotically as a shifted Poisson law1+P(ν)1+P(\nu ), whereν\nuis an explicit constant. Additional Gaussian and Poisson limit laws for random planar graphs are derived. The proofs are based on singularity analysis of generating functions and on perturbation of singularities.
Rotation numbers for quasiperiodically forced circle maps-mode-locking vs. strict monotonicity
Authors: Bjerklöv Kristian , Jäger Tobias
Published: January 2009

We describe the relation between the dynamical properties of a quasiperiodically forced orientation-preserving circle homeomorphism

f
f

and the behaviour of the fibred rotation number with respect to strictly monotone perturbations. Despite the fact that the dynamics in the forced case can be considerably more complicated, the result we obtain is in perfect analogy with the one-dimensional situation. In particular, the fibred rotation number behaves strictly monotonically whenever the rotation vector of

f
f

is irrational, which answers a question posed by Herman (1983). In addition, we obtain the continuous structure of the Arnold tongues in parameter families such as the quasiperiodically forced Arnold circle map.
The Chaperone Activity of GRP94 Toward Insulin-like Growth Factor II Is Necessary for the Stress Response to Serum Deprivation
Authors: Ostrovsky Olga , Ahmed Noreen T. , Argon Yair
Published: January 2009

Insulin-like growth factor (IGF)-II is a hormone with mitogenic activity for many cell types and tissues. We demonstrate that its intracellular processing and secretion strictly depend on the endoplasmic reticulum chaperone glucose-regulated protein (GRP) 94. GRP94 interacts physically and transiently with pro-IGF-II intermediates, and its activity is essential for secretion of active IGF-II, thus establishing IGF-II as a client of GRP94. Embryonic stem (ES) cells that lack GRP94 are hypersensitive to stress conditions such as serum deprivation and die by apoptosis because they cannot respond to the stress by producing active IGF-II. This chaperone–client interaction may explain the previously documented antiapoptotic activity of GRP94 in a number of stress responses.
Fine Tuning the Cell Cycle: Activation of the Cdk1 Inhibitory Phosphorylation Pathway during Mitotic Exit
Authors: Potapova Tamara A. , Daum John R. , Byrd Kendra S. , Gorbsky Gary J.
Published: January 2009

Inactivation of cyclin-dependent kinase (Cdk) 1 promotes exit from mitosis and establishes G1. Proteolysis of cyclin B is the major known mechanism that turns off Cdk1 during mitotic exit. Here, we show that mitotic exit also activates pathways that catalyze inhibitory phosphorylation of Cdk1, a mechanism previously known to repress Cdk1 only during S and G2 phases of the cell cycle. We present evidence that down-regulation of Cdk1 activates Wee1 and Myt1 kinases and inhibits Cdc25 phosphatase during the M to G1 transition. If cyclin B/Cdk1 complex is present in G1, the inhibitory sites on Cdk1 become phosphorylated. Exit from mitosis induced by chemical Cdk inhibition can be reversed if cyclin B is preserved. However, this reversibility decreases with time after mitotic exit despite the continued presence of the cyclin. We show that this G1 block is due to phosphorylation of Cdk1 on inhibitory residues T14 and Y15. Chemical inhibition of Wee1 and Myt1 or expression of Cdk1 phosphorylation site mutants allows reversal to M phase even from late G1. This late Cdk1 reactivation often results in caspase-dependent cell death. Thus, in G1, the Cdk inhibitory phosphorylation pathway is functional and can lock Cdk1 in the inactive state.
TheSaccharomyces cerevisiaeEsc2 and Smc5-6 Proteins Promote Sister Chromatid Junction-mediated Intra-S Repair
Authors: Sollier Julie , Driscoll Robert , Castellucci Federica , Foiani Marco , Jackson Stephen P. , Branzei Dana
Published: January 2009

Recombination is important for DNA repair, but it can also contribute to genome rearrangements. RecQ helicases, including yeast Sgs1 and human BLM, safeguard genome integrity through their functions in DNA recombination. Sgs1 prevents the accumulation of Rad51-dependent sister chromatid junctions at damaged replication forks, and its functionality seems to be regulated by Ubc9- and Mms21-dependent sumoylation. We show that mutations in Smc5-6 and Esc2 also lead to an accumulation of recombinogenic structures at damaged replication forks. Because Smc5-6 is sumoylated in an Mms21-dependent manner, this finding suggests that Smc5-6 may be a crucial target of Mms21 implicated in this process. Our data reveal that Smc5-6 and Esc2 are required to tolerate DNA damage and that their functionality is critical in genotoxic conditions in the absence of Sgs1. As reported previously for Sgs1 and Smc5-6, we find that Esc2 physically interacts with Ubc9 and SUMO. This interaction is correlated with the ability of Esc2 to promote DNA damage tolerance. Collectively, these data suggest that Esc2 and Smc5-6 act in concert with Sgs1 to prevent the accumulation of recombinogenic structures at damaged replication forks, likely by integrating sumoylation activities to regulate the repair pathways in response to damaged DNA.
The Hydrophobic Cysteine-rich Domain of SNAP25 Couples with Downstream Residues to Mediate Membrane Interactions and Recognition by DHHC Palmitoyl Transferases
Authors: Greaves Jennifer , Prescott Gerald R. , Fukata Yuko , Fukata Masaki , Salaun Christine , Chamberlain Luke H.
Published: January 2009

SNAP25 is synthesized as a soluble protein but must associate with the plasma membrane to function in exocytosis; however, this membrane-targeting pathway is poorly defined. SNAP25 contains a palmitoylated cysteine-rich domain with four cysteines, and we show that coexpression of specific DHHC palmitoyl transferases is sufficient to promote SNAP25 membrane association in HEK293 cells. siRNA-mediated knockdown of its SNARE partner, syntaxin 1A, does not affect membrane interaction of SNAP25 in PC12 cells, whereas specific cysteine-to-alanine mutations perturb membrane binding, which is restored by leucine substitutions. These results suggest a role for cysteine hydrophobicity in initial membrane interactions of SNAP25, and indeed other hydrophobic residues in the cysteine-rich domain are also important for membrane binding. In addition to the cysteine-rich domain, proline-117 is also essential for SNAP25 membrane binding, and experiments in HEK293 cells revealed that mutation of this residue inhibits membrane binding induced by coexpression with DHHC17, but not DHHC3 or DHHC7. These results suggest a model whereby SNAP25 interacts autonomously with membranes via its hydrophobic cysteine-rich domain, requiring only sufficient expression of partner DHHC proteins for stable membrane binding. The role of proline-117 in SNAP25 palmitoylation is one of the first descriptions of elements within substrate proteins that modulate DHHC specificity.
A Primary Role for Golgi Positioning in Directed Secretion, Cell Polarity, and Wound Healing
Authors: Yadav Smita , Puri Sapna , Linstedt Adam D.
Published: January 2009

Peri-centrosomal positioning of the mammalian Golgi apparatus is known to involve microtubule-based motility, but its importance for cellular physiology is a major unanswered question. Here, we identify golgin-160 and GMAP210 as proteins required for centripetal motility of Golgi membranes. In the absence of either golgin, peri-centrosomal positioning of the Golgi apparatus was disrupted while the cytoskeleton remained intact. Although secretion persisted with normal kinetics, it was evenly distributed in response to wounding rather than directed to the wound edge. Strikingly, these cells also completely failed to polarize. Further, directionally persistent cell migration was inhibited such that wound closure was impaired. These findings not only reveal novel roles for golgin-160 and GMAP210 in conferring membrane motility but also indicate that Golgi positioning has an active role in directed secretion, cell polarity, and wound healing.
ADAMs 10 and 17 Represent Differentially Regulated Components of a General Shedding Machinery for Membrane Proteins Such as Transforming Growth Factor α, L-Selectin, and Tumor Necrosis Factor α
Authors: Le Gall Sylvain M. , Bobé Pierre , Reiss Karina , Horiuchi Keisuke , Niu Xiao-Da , Lundell Daniel , Gibb David R. , Conrad Daniel , Saftig Paul , Blobel Carl P.
Published: January 2009

Protein ectodomain shedding is a critical regulator of many membrane proteins, including epidermal growth factor receptor-ligands and tumor necrosis factor (TNF)-α, providing a strong incentive to define the responsible sheddases. Previous studies identified ADAM17 as principal sheddase for transforming growth factor (TGF)-α and heparin-binding epidermal growth factor, but Ca++influx activated an additional sheddase for these epidermal growth factor receptor ligands in Adam17−/− cells. Here, we show that Ca++influx and stimulation of the P2X7R signaling pathway activate ADAM10 as sheddase of many ADAM17 substrates in Adam17−/− fibroblasts and primary B cells. Importantly, although ADAM10 can shed all substrates of ADAM17 tested here in Adam17−/− cells, acute treatment of wild-type cells with a highly selective ADAM17 inhibitor (SP26) showed that ADAM17 is nevertheless the principal sheddase when both ADAMs 10 and 17 are present. However, chronic treatment of wild-type cells with SP26 promoted processing of ADAM17 substrates by ADAM10, thus generating conditions such as in Adam17−/− cells. These results have general implications for understanding the substrate selectivity of two major cellular sheddases, ADAMs 10 and 17.
DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages
Authors: Williams-DeVane ClarLynda R. , Wolf Maritja A. , Richard Ann M.
Published: January 2009

Summary: The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on September 20, 2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare and search the chemical content in each resource, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resources such as PubChem (http://pubchem.ncbi.nlm.nih.gov).

Availability: Data files and documentation may be accessed online at http://epa.gov/ncct/dsstox/.

Contact:  williams.clarlynda@epa.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Levosimendan vs. dobutamine: outcomes for acute heart failure patients on β‐blockers in SURVIVE†
Authors: Mebazaa Alexandre , Nieminen Markku S. , Filippatos Gerasimos S. , Cleland John G. , Salon Jeffrey E. , Thakkar Roopal , Padley Robert J. , Huang Bidan , Cohen‐Solal Alain
Published: January 2009

Aims

Many chronic heart failure (CHF) patients take β‐blockers. When such patients are hospitalized for decompensation, it remains unclear how ongoing β‐blocker treatment will affect outcomes of acute inotrope therapy. We aimed to assess outcomes of SURVIVE patients who were on β‐blocker therapy before receiving a single intravenous infusion of levosimendan or dobutamine.

Methods and results

Cox proportional hazard regression revealed all‐cause mortality benefits of levosimendan treatment over dobutamine when the SURVIVE population was stratified according to baseline presence/absence of CHF history and use/non‐use of β‐blocker treatment at baseline. All‐cause mortality was lower in the CHF/levosimendan group than in the CHF/dobutamine group, showing treatment differences by hazard ratio (HR) at days 5 (3.4 vs. 5.8%; HR, 0.58, CI 0.33–1.01, P = 0.05) and 14 (7.0 vs. 10.3%; HR, 0.67, CI 0.45–0.99, P = 0.045). For patients who used β‐blockers (n = 669), mortality was significantly lower for levosimendan than dobutamine at day 5 (1.5 vs. 5.1% deaths; HR, 0.29; CI 0.11–0.78, P = 0.01).

Conclusion

Levosimendan may be better than dobutamine for treating patients with a history of CHF or those on β‐blocker therapy when they are hospitalized with acute decompensations. These findings are preliminary but important for planning future studies.
Years‐needed‐to‐treat to add 1 year of life: a new metric to estimate treatment effects in randomized trials
Authors: Levy Wayne C. , Mozaffarian Dariush , Linker David T. , Kenyon Kenneth W. , Cleland John G.F. , Komajda Michel , Remme Willem J. , Torp‐Pedersen Christian , Metra Marco , Poole‐Wilson Philip A. ,   on behalf of the COMET Investigators
Published: January 2009

Aims

A standard metric to estimate absolute treatment effects is numbers‐needed‐to‐treat (NNT), which implicitly assumes that all benefits reverse at trial‐end. However, in‐trial survival benefits typically do not reverse until long after trial‐end, so that NNT will substantially underestimate lifetime benefits.

Methods and results

We developed a new concept, years‐needed‐to‐treat (YNT) to add 1 year of life, that quantifies the expected average life expectancy for two treatments including the estimated years of life remaining post‐trial. Numbers‐needed‐to‐treat and YNT were calculated in the COMET trial, in which carvedilol vs. metoprolol tartrate resulted in 17% lower mortality over 4.8 years. A multivariate Cox model was used to predict survival. Remaining years of life were estimated using the mortality‐life‐table method. At trial‐end, survival was 9% higher in the carvedilol arm. Assuming that patients remained on the same therapy post‐trial, the average total years of life for carvedilol vs. metoprolol were 10.63 ± 0.19 vs. 9.48 ± 0.18 (P < 0.0001) or 1.15 (95% confidence interval 0.64–1.66) additional years of life. The YNT was 9.2, indicating that 9.2 person‐years of treatment added 1 person‐year of life, compared with NNT of 59.

Conclusion

Compared with NNT, the YNT method more accurately accounts for potential long‐term benefits of interventions in randomized trials.
Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure
Authors: Shawkey Matthew D , Saranathan Vinodkumar , Pálsdóttir Hildur , Crum John , Ellisman Mark H , Auer Manfred , Prum Richard O
Published: January 2009

Organismal colour can be created by selective absorption of light by pigments or light scattering by photonic nanostructures. Photonic nanostructures may vary in refractive index over one, two or three dimensions and may be periodic over large spatial scales or amorphous with short-range order. Theoretical optical analysis of three-dimensional amorphous nanostructures has been challenging because these structures are difficult to describe accurately from conventional two-dimensional electron microscopy alone. Intermediate voltage electron microscopy (IVEM) with tomographic reconstruction adds three-dimensional data by using a high-power electron beam to penetrate and image sections of material sufficiently thick to contain a significant portion of the structure. Here, we use IVEM tomography to characterize a non-iridescent, three-dimensional biophotonic nanostructure: the spongy medullary layer from eastern bluebirdSialia sialisfeather barbs. Tomography and three-dimensional Fourier analysis reveal that it is an amorphous, interconnected bicontinuous matrix that is appropriately ordered at local spatial scales in all three dimensions to coherently scatter light. The predicted reflectance spectra from the three-dimensional Fourier analysis are more precise than those predicted by previous two-dimensional Fourier analysis of transmission electron microscopy sections. These results highlight the usefulness, and obstacles, of tomography in the description and analysis of three-dimensional photonic structures.
Physical methods for investigating structural colours in biological systems
Authors: Vukusic P , Stavenga D.G
Published: January 2009

Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in technologically engineered systems. However, biological photonic systems are invariably structurally and often compositionally more elaborate than most synthetically fabricated photonic systems. For this reason, an appropriate gamut of physical methods and investigative techniques must be applied correctly so that the systems' photonic behaviour may be appropriately understood. Here, we survey a broad range of the most commonly implemented, successfully used and recently innovated physical methods. We discuss the costs and benefits of various spectrometric methods and instruments, namely scatterometers, microspectrophotometers, fibre-optic-connected photodiode array spectrometers and integrating spheres. We then discuss the role of the materials' refractive index and several of the more commonly used theoretical approaches. Finally, we describe the recent developments in the research field of photonic crystals and the implications for the further study of structural coloration in animals.
Incorporating demographic stochasticity into multi-strain epidemic models: application to influenza A
Authors: Minayev Pavlo , Ferguson Neil
Published: January 2009

We develop mathematical models of the transmission and evolution of multi-strain pathogens that incorporate strain extinction and the stochastic generation of new strains via mutation. The dynamics resulting from these models is then examined with the applied aim of understanding the mechanisms underpinning the evolution and dynamics of rapidly mutating pathogens, such as human influenza viruses. Our approach, while analytically relatively simple, gives results that are qualitatively similar to those obtained from much more complex individually based simulation models. We examine strain dynamics as a function of cross-immunity and key transmission parameters, and show that introducing strain extinction and modelling mutation as a stochastic process significantly changes the model dynamics, leading to lower strain diversity, reduced infection prevalence and shorter strain lifetimes. Finally, we incorporate transient strain-transcending immunity in the model and demonstrate that it reduces strain diversity further, giving patterns of sequential strain replacement similar to that seen in human influenza A viruses.
Passive versus active engulfment: verdict from trajectory simulations of lunge-feeding fin whalesBalaenoptera physalus
Authors: Potvin J. , Goldbogen J. A. , Shadwick R. E.
Published: January 2009

Lunge-feeding in rorqual whales represents the largest biomechanical event on Earth and one of the most extreme feeding methods among aquatic vertebrates. By accelerating to high speeds and by opening their mouth to large gape angles, these whales generate the water pressure required to expand their mouth around a large volume of prey-laden water. Such large influx is facilitated by highly extensible ventral groove blubber (VGB) associated with the walls of the throat (buccal cavity). Based on the mechanical properties of this tissue, previous studies have assumed lunge-feeding to be an entirely passive process, where the flow-induced pressure driving the expansion of the VGB is met with little resistance. Suchcompliant engulfmentwould be facilitated by the compliant properties of the VGB that have been measured on dead specimens. However, adjoining the ventral blubber are several layers of well-developed muscle embedded with mechanoreceptors, thereby suggesting a capability to gauge the magnitude of engulfed water and use eccentric muscle action to control the flux of water into the mouth. An unsteady hydrodynamic model of fin whale lunge-feeding is presented here to test whether engulfment is exclusively passive and compliant or involves muscle action. The model is based on the explicit simulation of the engulfed water as it interacts with the buccal cavity walls of the whale, under different heuristically motivated cavity forces. Our results, together with their comparison with velocity data collected in the field, suggest that adult rorquals actively push engulfed water forward from the very onset of mouth opening in order to successfully complete a lunge. Interestingly, such an action involves arefluxof the engulfed mass rather than the oft-assumedrebound, which would occur mainly at the very end of a lunge sequence dominated by compliant engulfment. Given the great mass of the engulfed water, reflux creation adds a significant source of hydrodynamic drag to the lunge process, but with the benefit of helping to circumvent the problem of removing prey from baleen by enhancing the efficiency of cross-flow filtration after mouth closing. Reflux management for a successful lunge will therefore demand well-coordinated muscular actions of the tail, mouth and ventral cavity.
Recent developments in the understanding of the combined deficiency of FV and FVIII
Authors: Zhang Bin
Published: January 2009

Combined deficiency of factor V (FV) and factor VIII (FVIII) (F5F8D) is a genetic disorder characterized by mild‐to‐moderate bleeding and coordinate reduction in plasma FV and FVIII levels, as well as platelet FV level. Recent studies identified mutations in two genes (LMAN1 and MCFD2) as the cause of F5F8D. Though clinically indistinguishable, MCFD2 mutations generally exhibit lower levels of FV and FVIII than LMAN1 mutations. LMAN1 is a mannose‐specific lectin that cycles between the endoplasmic reticulum (ER) and the ER‐Golgi intermediate compartment. MCFD2 is an EF‐hand domain protein that forms a calcium‐dependent heteromeric complex with LMAN1 in cells. Missense mutations in the EF‐hand domains of MCFD2 abolish the interaction with LMAN1. The LMAN1‐MCFD2 complex may serve as a cargo receptor for the ER‐to‐Golgi transport of FV and FVIII, and perhaps a number of other glycoproteins. The B domain of FVIII may be important in mediating its interaction with the LMAN1‐MCFD2 complex.