bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE
Authors: Xia Ke , Manning Marta , Hesham Helai , Lin Qishan , Bystroff Christopher , Colón Wilfredo
Published: October 2007

Most proteins are in equilibrium with partially and globally unfolded conformations. In contrast, kinetically stable proteins (KSPs) are trapped by an energy barrier in a specific state, unable to transiently sample other conformations. Among many potential roles, it appears that kinetic stability (KS) is a feature used by nature to allow proteins to maintain activity under harsh conditions and to preserve the structure of proteins that are prone to misfolding. The biological and pathological significance of KS remains poorly understood because of the lack of simple experimental methods to identify this property and its infrequent occurrence in proteins. Based on our previous correlation between KS and a protein's resistance to the denaturing detergent SDS, we show here the application of a diagonal 2D (D2D) SDS/PAGE assay to identify KSPs in complex mixtures. We applied this method to the lysate of
Escherichia coli
and upon proteomics analysis have identified 50 nonredundant proteins that were SDS-resistant (i.e., kinetically stable). Structural and functional analyses of a subset (44) of these proteins with known 3D structure revealed some potential structural and functional biases toward and against KS. This simple D2D SDS/PAGE assay will allow the widespread investigation of KS, including the proteomics-level identification of KSPs in different systems, potentially leading to a better understanding of the biological and pathological significance of this intriguing property of proteins.
Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases
Authors: Lahm A. , Paolini C. , Pallaoro M. , Nardi M. C. , Jones P. , Neddermann P. , Sambucini S. , Bottomley M. J. , Lo Surdo P. , Carfı́ A. , Koch U. , De Francesco R. , Steinkühler C. , Gallinari P.
Published: October 2007

Previous findings have suggested that class IIa histone deacetylases (HDACs) (HDAC4, -5, -7, and -9) are inactive on acetylated substrates, thus differing from class I and IIb enzymes. Here, we present evidence supporting this view and demonstrate that class IIa HDACs are very inefficient enzymes on standard substrates. We identified HDAC inhibitors unable to bind recombinant human HDAC4 while showing inhibition in a typical HDAC4 enzymatic assay, suggesting that the observed activity rather reflects the involvement of endogenous copurified class I HDACs. Moreover, an HDAC4 catalytic domain purified from bacteria was 1,000-fold less active than class I HDACs on standard substrates. A catalytic Tyr is conserved in all HDACs except for vertebrate class IIa enzymes where it is replaced by His. Given the high structural conservation of HDAC active sites, we predicted the class IIa His-Nε2 to be too far away to functionally substitute the class I Tyr-OH in catalysis. Consistently, a Tyr-to-His mutation in class I HDACs severely reduced their activity. More importantly, a His-976-Tyr mutation in HDAC4 produced an enzyme with a catalytic efficiency 1,000-fold higher than WT, and this “gain of function phenotype” could be extended to HDAC5 and -7. We also identified trifluoroacetyl-lysine as a class IIa-specific substrate
in vitro
. Hence, vertebrate class IIa HDACs may have evolved to maintain low basal activities on acetyl-lysines and to efficiently process restricted sets of specific, still undiscovered natural substrates.
Loss of Bardet–Biedl syndrome proteins causes defects in peripheral sensory innervation and function
Authors: Tan Perciliz L. , Barr Travis , Inglis Peter N. , Mitsuma Norimasa , Huang Susan M. , Garcia-Gonzalez Miguel A. , Bradley Brian A. , Coforio Stephanie , Albrecht Phillip J. , Watnick Terry , Germino Gregory G. , Beales Philip L. , Caterina Michael J. , Leroux Michel R. , Rice Frank L. , Katsanis Nicholas
Published: October 2007

Reception and interpretation of environmental stimuli is critical for the survival of all organisms. Here, we show that the ablation of
BBS1
and
BBS4
, two genes mutated in Bardet–Biedl syndrome and that encode proteins that localize near the centrioles of sensory neurons, leads to alterations of s.c. sensory innervation and trafficking of the thermosensory channel TRPV1 and the mechanosensory channel STOML3, with concomitant defects in peripheral thermosensation and mechanosensation. The thermosensory phenotype is recapitulated in
Caenorhabditis elegans
, because BBS mutants manifest deficient thermosensory responses at both physiological and nociceptive temperatures and defective trafficking of OSM-9, a polymodal sensory channel protein and a functional homolog of TRPV1 or TRPV4. Our findings suggest a hitherto unrecognized, but essential, role for mammalian basal body proteins in the acquisition of mechano- and thermosensory stimuli and highlight potentially clinical features of ciliopathies in humans.
The prokaryotic Cys
2
His
2
zinc-finger adopts a novel fold as revealed by the NMR structure of
Agrobacterium tumefaciens
Ros DNA-binding domain
Authors: Malgieri Gaetano , Russo Luigi , Esposito Sabrina , Baglivo Ilaria , Zaccaro Laura , Pedone Emilia M. , Di Blasio Benedetto , Isernia Carla , Pedone Paolo V. , Fattorusso Roberto
Published: October 2007

The first putative prokaryotic Cys
2
His
2
zinc-finger domain has been identified in the transcriptional regulator Ros from
Agrobacterium tumefaciens
, indicating that the Cys
2
His
2
zinc-finger domain, originally thought to be confined to the eukaryotic kingdom, could be widespread throughout the living kingdom from eukaryotic, both animal and plant, to prokaryotic. In this article we report the NMR solution structure of Ros DNA-binding domain (Ros87), providing 79 structural characterization of a prokaryotic Cys
2
His
2
zinc-finger domain. The NMR structure of Ros87 shows that the putative prokaryotic Cys
2
His
2
zinc-finger sequence is indeed part of a significantly larger zinc-binding globular domain that possesses a novel protein fold very different from the classical fold reported for the eukaryotic classical zinc-finger. The Ros87 globular domain consists of 58 aa (residues 9–66), is arranged in a βββαα topology, and is stabilized by an extensive 15-residue hydrophobic core. A backbone dynamics study of Ros87, based on
15
N R
1
,
15
N R
2
, and heteronuclear
15
N-{
1
H}-NOE measurements, has further confirmed that the globular domain is uniformly rigid and flanked by two flexible tails. Mapping of the amino acids necessary for the DNA binding onto Ros87 structure reveals the protein surface involved in the DNA recognition mechanism of this new zinc-binding protein domain.
Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories
Authors: Hess Samuel T. , Gould Travis J. , Gudheti Manasa V. , Maas Sarah A. , Mills Kevin D. , Zimmerberg Joshua
Published: October 2007

Organization in biological membranes spans many orders of magnitude in length scale, but limited resolution in far-field light microscopy has impeded distinction between numerous biomembrane models. One canonical example of a heterogeneously distributed membrane protein is hemagglutinin (HA) from influenza virus, which is associated with controversial cholesterol-rich lipid rafts. Using fluorescence photoactivation localization microscopy, we are able to image distributions of tens of thousands of HA molecules with subdiffraction resolution (≈40 nm) in live and fixed fibroblasts. HA molecules form irregular clusters on length scales from ≈40 nm up to many micrometers, consistent with results from electron microscopy. In live cells, the dynamics of HA molecules within clusters is observed and quantified to determine an effective diffusion coefficient. The results are interpreted in terms of several established models of biological membranes.
Nonstationary increments, scaling distributions, and variable diffusion processes in financial markets
Authors: Bassler Kevin E. , McCauley Joseph L. , Gunaratne Gemunu H.
Published: October 2007

Fat-tailed distributions have been reported in fluctuations of financial markets for more than a decade. Sliding interval techniques used in these studies implicitly assume that the underlying stochastic process has stationary increments. Through an analysis of intraday increments, we explicitly show that this assumption is invalid for the Euro–Dollar exchange rate. We find several time intervals during the day where the standard deviation of increments exhibits power law behavior in time. Stochastic dynamics during these intervals is shown to be given by diffusion processes with a diffusion coefficient that depends on time and the exchange rate. We introduce methods to evaluate the dynamical scaling index and the scaling function empirically. In general, the scaling index is significantly smaller than previously reported values close to 0.5. We show how the latter as well as apparent fat-tailed distributions can occur only as artifacts of the sliding interval analysis.
Confocal light absorption and scattering spectroscopic microscopy monitors organelles in live cells with no exogenous labels
Authors: Itzkan Irving , Qiu Le , Fang Hui , Zaman Munir M. , Vitkin Edward , Ghiran Ionita C. , Salahuddin Saira , Modell Mark , Andersson Charlotte , Kimerer Lauren M. , Cipolloni Patsy B. , Lim Kee-Hak , Freedman Steven D. , Bigio Irving , Sachs Benjamin P. , Hanlon Eugene B. , Perelman Lev T.
Published: October 2007

This article reports the development of an optical imaging technique, confocal light absorption and scattering spectroscopic (CLASS) microscopy, capable of noninvasively determining the dimensions and other physical properties of single subcellular organelles. CLASS microscopy combines the principles of light-scattering spectroscopy (LSS) with confocal microscopy. LSS is an optical technique that relates the spectroscopic properties of light elastically scattered by small particles to their size, refractive index, and shape. The multispectral nature of LSS enables it to measure internal cell structures much smaller than the diffraction limit without damaging the cell or requiring exogenous markers, which could affect cell function. Scanning the confocal volume across the sample creates an image. CLASS microscopy approaches the accuracy of electron microscopy but is nondestructive and does not require the contrast agents common to optical microscopy. It provides unique capabilities to study functions of viable cells, which are beyond the capabilities of other techniques.
Sulforaphane mobilizes cellular defenses that protect skin against damage by UV radiation
Authors: Talalay Paul , Fahey Jed W. , Healy Zachary R. , Wehage Scott L. , Benedict Andrea L. , Min Christine , Dinkova-Kostova Albena T.
Published: October 2007

UV radiation (UVR) is a complete carcinogen that elicits a constellation of pathological events, including direct DNA damage, generation of reactive oxidants that peroxidize lipids and damage other cellular components, initiation of inflammation, and suppression of the immune response. Recent dramatic increases in the incidence of nonmelanoma skin cancers are largely attributable to higher exposure of an aging population to UVR. Therefore, the development of cellular strategies for intrinsic protection of the skin against the deleterious effects of UVR is imperative. Here we show that erythema resulting from UVR is a comprehensive and noninvasive biomarker for assessing UVR damage and can be precisely and easily quantified in human skin. Topical application of sulforaphane-rich extracts of 3-day-old broccoli sprouts up-regulated phase 2 enzymes in the mouse and human skin, protected against UVR-induced inflammation and edema in mice, and reduced susceptibility to erythema arising from narrow-band 311-nm UVR in humans. In six human subjects (three males and three females, 28–53 years of age), the mean reduction in erythema across six doses of UVR (300–800 mJ/cm
2
in 100 mJ/cm
2
increments) was 37.7% (range 8.37–78.1%;
P
= 0.025). This protection against a carcinogen in humans is catalytic and long lasting.
Mechanical control of the directional stepping dynamics of the kinesin motor
Authors: Hyeon Changbong , Onuchic José N.
Published: October 2007

Among the multiple steps constituting the kinesin mechanochemical cycle, one of the most interesting events is observed when kinesins move an 8-nm step from one microtubule (MT)-binding site to another. The stepping motion that occurs within a relatively short time scale (≈100 μs) is, however, beyond the resolution of current experiments. Therefore, a basic understanding to the real-time dynamics within the 8-nm step is still lacking. For instance, the rate of power stroke (or conformational change) that leads to the undocked-to-docked transition of neck-linker is not known, and the existence of a substep during the 8-nm step still remains a controversial issue in the kinesin community. By using explicit structures of the kinesin dimer and the MT consisting of 13 protofilaments, we study the stepping dynamics with varying rates of power stroke (
k

p

). We estimate that
k

p

−1
≲ 20 μs to avoid a substep in an averaged time trace. For a slow power stroke with
k

p

−1
> 20 μs, the averaged time trace shows a substep that implies the existence of a transient intermediate, which is reminiscent of a recent single-molecule experiment at high resolution. We identify the intermediate as a conformation in which the tethered head is trapped in the sideway binding site of the neighboring protofilament. We also find a partial unfolding (cracking) of the binding motifs occurring at the transition state ensemble along the pathways before binding between the kinesin and MT.
On SCH and the approachability property
Authors: Gitik Moti , Sharon Assaf
Published: October 2007

We construct a model of¬SCH+¬AP+{}^\neg SCH +^\neg AP +(Very Good Scale). This answers questions of Cummings, Foreman, Magidor and Woodin.
Blaschke representation of functions on the circle
Authors: Wegert Elias , von Wolfersdorf Lothar
Published: October 2007

We prove that every unimodularly bounded measurable function on the complex unit circle admits a representation
\[

f
=

f
+

+

f
−

1
+

f
¯

−

f
+

,

f=\frac {f_++f_-}{1+\overline {f}_-f_+},

\]
where

f
+

f_+

and

f
−

f_-

extend holomorphically into the interior and the exterior of the circle, respectively,

f
−

f_-

vanishes at infinity, and both functions are unimodularly bounded. The representation is unique if

‖
f

‖
∞

>
1

\|f\|_\infty >1

.
Gorenstein rings and irreducible parameter ideals
Authors: Marley Thomas , Rogers Mark , Sakurai Hideto
Published: October 2007

Given a Noetherian local ring

(
R
,
m
)

(R,m)

it is shown that there exists an integer

ℓ
\ell

such that

R
R

is Gorenstein if and only if some system of parameters contained in

m

ℓ

m^{\ell }

generates an irreducible ideal. We obtain as a corollary that

R
R

is Gorenstein if and only if every power of the maximal ideal contains an irreducible parameter ideal.
A new construction of the unstable manifold for the measure-preserving H{é}non map
Authors: Jensen Erik
Published: October 2007

Let

H
H

denote the measure-preserving Hénon map with the parameter

a
>
0

a > 0

. The map

H
H

has a hyperbolic fixed point

p
\boldsymbol {p}

. The main result of this paper is that the unstable mainfold of

p
\boldsymbol {p}

is the iterated limit of a very simple set. Informally,
\[

W
u

(
p
)
=

lim

n
→
∞

H
n

(

L

)

W^u(\boldsymbol {p}) = \lim _{n\to \infty } H^n(\mathcal L)

\]
where

L

\mathcal L

is the line

y
=
−
x

y=-x

and

W
u

(
p
)

W^u(\boldsymbol {p})

denotes the unstable manifold of

p
\boldsymbol {p}

.
Rademacher bounded families of operators on 𝐿₁
Authors: Kalton N. , Kucherenko T.
Published: October 2007

We give a characterization of R-bounded families of operators on

L
1

.

L_1.

We then use this result to study sectorial operators on

L
1

L_1

. We show that if

A
A

is an R-sectorial operator on

L
1

L_1

, then, for any

ϵ
>
0
,

\epsilon >0,

there is an invertible operator

U
:

L
1

→

L
1

U:L_1\to L_1

with

‖
U
−
I
‖
>
ϵ

\|U-I\|>\epsilon

such that for some strictly positive Borel function

w
w

,

U
(

D

(
A
)
)

U(\mathcal {D}(A))

contains the weighted

L
1

L_1

-space

L
1

(
w
)
.

L_1(w).
Common hypercyclic vectors for families of operators
Authors: Gallardo-Gutierrez Eva , Partington Jonathan
Published: October 2007

We provide a criterion for the existence of a residual set of common hypercyclic vectors for an uncountable family of hypercyclic operators which is based on a previous one given by Costakis and Sambarino. As an application, we get common hypercyclic vectors for a particular family of hypercyclic scalar multiples of the adjoint of a multiplier in the Hardy space, generalizing recent results by Abakumov and Gordon and also Bayart. The criterion is applied to other specific families of operators.
Bifurcation of homoclinics
Authors: Pejsachowicz Jacobo
Published: October 2007

We show that homoclinic trajectories of nonautonomous vector fields parametrized by a circle bifurcate from the stationary solution when the asymptotic stable bundles of the linearization at plus and minus infinity are “twisted” in different ways.
Computable analysis and Blaschke products
Authors: Matheson Alec , McNicholl Timothy
Published: October 2007

We show that if a Blaschke product defines a computable function, then it has a computable sequence of zeros in which the number of times each zero is repeated is its multiplicity. We then show that the converse is not true. We finally show that every computable, radial, interpolating sequence yields a computable Blaschke product.
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Authors: Brauer Matthew J. , Huttenhower Curtis , Airoldi Edoardo M. , Rosenstein Rachel , Matese John C. , Gresham David , Boer Viktor M. , Troyanskaya Olga G. , Botstein David
Published: October 2007

We studied the relationship between growth rate and genome-wide gene expression, cell cycle progression, and glucose metabolism in 36 steady-state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil, or leucine). The expression of more than one quarter of all yeast genes is linearly correlated with growth rate, independent of the limiting nutrient. The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions. Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling. We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient. Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate, or ammonia did not; this phenomenon (reminiscent of the “Warburg effect” in cancer cells) was confirmed in batch cultures. Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an “instantaneous growth rate.” This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle.
On the hierarchical classification of G protein-coupled receptors
Authors: Davies Matthew N. , Secker Andrew , Freitas Alex A. , Mendao Miguel , Timmis Jon , Flower Darren R.
Published: October 2007

Motivation: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs.

Results: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases.

Contact:  m.davies@mail.cryst.bbk.ac.uk
NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols
Authors: López-Pérez José Luis , Therón Roberto , del Olmo Esther , Díaz David
Published: October 2007

Motivation: Although natural products represent a reservoir of molecular diversity, the process of isolating and identifying active compounds is a bottleneck in drug discovery programs. The rapid isolation and identification of the bioactive component(s) of natural product mixtures during the bioassay-guided fractionation have become crucial factors in the competition with chemical compound libraries and combinatorial synthetic efforts. In this respect, the use of spectral databases in identification processes is indispensable.

Results: We have developed a database containing 13C spectral information of over 6000 natural compounds, which allows for fast identifications of known compounds present in the crude extracts and provides insight into the structural elucidation of unknown compounds.

Availability:  http://c13.usal.es

Contact:  theron@usal.es
Assessment of Antimalarial Activity against Plasmodium falciparum and Phytochemical Screening of Some Yemeni Medicinal Plants
Authors: Alshawsh Mohammed A. , Mothana Ramzi A. , Al-shamahy Hassan A. , Alsllami Salah F. , Lindequist Ulrike
Published: October 2007

Developing countries, where malaria is one of the most prevalent diseases, still rely on traditional medicine as a source for the treatment of this disease. In the present study, six selected plants (Acalypha fruticosa, Azadirachta indica, Cissus rotundifolia, Echium rauwalfii, Dendrosicyos socotrana and Boswellia elongata) commonly used in Yemen by traditional healers for the treatment of malaria as well as other diseases, were collected from different localities of Yemen, dried and extracted with methanol and water successfully. The antiplasmodial activity of the extracts was evaluated against fresh clinical isolates of Plasmodium falciparum. The selectivity parameters to evaluate the efficacy of these medicinal plants were measured by in vitro micro test (Mark III) according to World Health Organization (WHO) 1996 & WHO 2001 protocols of antimalarial drug tests. Among the investigated 12 extracts, three were found to have significant antiplasmodial activity with IC50 values less than 4 µg/ml, namely the water extracts of A. fruticosa, A. indica and D. socotrana. Six extracts showed moderate activity with IC50 values ranging from 10 to 30 µg/ml and three appeared to be inactive with IC50 values more than 30 µg/ml. In addition, preliminary phytochemical screening of the methanolic and aqueous extracts indicated the presence of saponins, tannins, flavonoids, terpenoids, polysaccharides and peptides.
10‐Hydroxy‐2‐decenoic Acid, a Major Fatty Acid from Royal Jelly, Inhibits VEGF‐Induced Angiogenesis in Human Umbilical Vein Endothelial Cells
Authors: Izuta Hiroshi , Chikaraishi Yuichi , Shimazawa Masamitsu , Mishima Satoshi , Hara Hideaki
Published: October 2007

Vascular endothelial growth factor (VEGF) is reported to be a potent pro‐angiogenic factor that plays a pivotal role in both physiological and pathological angiogenesis. Royal jelly (RJ) is a honeybee product containing various proteins, sugars, lipids, vitamins and free amino acids. 10‐Hydroxy‐2‐decenoic acid (10HDA), a major fatty acid component of RJ, is known to have various pharmacological effects; its antitumor activity being especially noteworthy. However, the mechanism underlying this effect is unclear. We examined the effect of 10HDA on VEGF‐induced proliferation, migration and tube formation in human umbilical vein endothelial cells (HUVECs). Our findings showed that, 10HDA at 20 µM or more significantly inhibited such proliferation, migration and tube formation. Similarly, 10 µM GM6001, a matrix metalloprotease inhibitor, prevented VEGF‐induced migration and tube formation. These findings indicate that 10HDA exerts an inhibitory effect on VEGF‐induced angiogenesis, partly by inhibiting both cell proliferation and migration. Further experiments will be needed to clarify the detailed mechanism.
Native Great Lakes wolves were not restored
Authors: Leonard Jennifer A , Wayne Robert K
Published: October 2007

Wolves from the Great Lakes area were historically decimated due to habitat loss and predator control programmes. Under the protection of the US Endangered Species Act, the population has rebounded to approximately 3000 individuals. We show that the pre-recovery population was dominated by mitochondrial DNA haplotypes from an endemic American wolf referred to here as the Great Lakes wolf. In contrast, the recent population is admixed, and probably derives also from the grey wolf (Canis lupus) of Old World origin and the coyote (Canis latrans). Consequently, the pre-recovery population has not been restored, casting doubt on delisting actions.
Rapid loss of genetic variation in an endangered possum
Authors: Mitrovski P , Hoffmann A.A , Heinze D.A , Weeks A.R
Published: October 2007

The endangered mountain pygmy possum is the only Australian marsupial that hibernates under snow cover. Most of its alpine habitat was burnt by a rare fire in 2003, and habitat loss and disturbance have also occurred owing to ski resort development. Here we show that there has been a rapid loss of genetic variation following habitat loss associated with resort development, but no detectable loss of alleles or decrease in heterozygosity following the fire.
Modelling interactions in fungi
Authors: Falconer Ruth E , Bown James L , White Nia A , Crawford John W
Published: October 2007

Indeterminate organisms have received comparatively little attention in theoretical ecology and still there is much to be understood about the origins and consequences of community structure. The fungi comprise an entire kingdom of life and epitomize the indeterminate growth form. While interactions play a significant role in shaping the community structure of indeterminate organisms, to date most of our knowledge relating to fungi comes from observing interaction outcomes between two species in two-dimensional arena experiments. Interactions in the natural environment are more complex and further insight will benefit from a closer integration of theory and experiment. This requires a modelling framework capable of linking genotype and environment to community structure and function. Towards this, we present a theoretical model that replicates observed interaction outcomes between fungal colonies. The hypotheses underlying the model propose that interaction outcome is an emergent consequence of simple and highly localized processes governing rates of uptake and remobilization of resources, the metabolic cost of production of antagonistic compounds and non-localized transport of internal resources. The model may be used to study systems of many interacting colonies and so provides a platform upon which the links between individual-scale behaviour and community-scale function in complex environments can be built.
Self-focusing of thin liquid jets
Authors: Duchemin Laurent
Published: October 2007

The nonlinear evolution of an initially perturbed free surface perpendicularly accelerated, or of an initially flat free surface subject to a perturbed velocity profile, gives rise to the emergence of thin spikes of fluid. We are investigating the long-time evolution of a thin inviscid jet of this kind, subject or not to a body force acting in the direction of the jet itself. A fully nonlinear theory for the long-time evolution of the jet is given. In two dimensions, the curvature of the tip scales like
t
3
, where
t
is time, and the peak undergoes an overshoot in acceleration which evolves like
t
−5
. In three dimensions, the jet evolves towards an axisymmetric shape, and the curvature and the overshoot in acceleration obey asymptotic laws in
t
2
and
t
−4
, respectively. The asymptotic self-similar shape of the spike is found to be a hyperbola in two dimensions, a hyperboloid in three dimensions. Scaling laws and self-similarity are confronted with two-dimensional computations of the Richtmyer–Meshkov instability.
Pathogen evolution and disease emergence in carnivores
Authors: McCarthy Alex J , Shaw Marie-Anne , Goodman Simon J
Published: October 2007

Emerging infectious diseases constitute some of the most pressing problems for both human and domestic animal health, and biodiversity conservation. Currently it is not clear whether the removal of past constraints on geographical distribution and transmission possibilities for pathogens alone are sufficient to give rise to novel host–pathogen combinations, or whether pathogen evolution is also generally required for establishment in novel hosts. Canine distemper virus (CDV) is a morbillivirus that is prevalent in the world dog population and poses an important conservation threat to a diverse range of carnivores. We performed an extensive phylogenetic and molecular evolution analysis on complete sequences of all CDV genes to assess the role of selection and recombination in shaping viral genetic diversity and driving the emergence of CDV in non-dog hosts. We tested the specific hypothesis that molecular adaptation at known receptor-binding sites of the haemagglutinin gene is associated with independent instances of the spread of CDV to novel non-dog hosts in the wild. This hypothesis was upheld, providing compelling evidence that repeated evolution at known functional sites (in this case residues 530 and 549 of the haemagglutinin molecule) is associated with multiple independent occurrences of disease emergence in a range of novel host species.
Epidemiological consequences of an incursion of highly pathogenic H5N1 avian influenza into the British poultry flock
Authors: Sharkey Kieran J , Bowers Roger G , Morgan Kenton L , Robinson Susan E , Christley Robert M
Published: October 2007

Highly pathogenic avian influenza and in particular the H5N1 strain has resulted in the culling of millions of birds and continues to pose a threat to poultry industries worldwide. The recent outbreak of H5N1 in the UK highlights the need for detailed assessment of the consequences of an incursion and of the efficacy of control strategies. Here, we present results from a model of H5N1 propagation within the British poultry industry. We find that although the majority of randomly seeded incursions do not spread beyond the initial infected premises, there is significant potential for widespread infection. The efficacy of the European Union strategy for disease control is evaluated and our simulations emphasize the pivotal role of duck farms in spreading H5N1.
The pace of morphological change: historical transformation of skull shape in St Bernard dogs
Authors: Drake Abby Grace , Klingenberg Christian Peter
Published: October 2007

Owing to the great morphological diversity of domestic dogs (Canis familiaris), the study of historical shape change in dog skulls provides an excellent opportunity for investigating the dynamics of morphological evolution. Breed standards make known which features were selected by breeders. Here we use the methods of geometric morphometrics to study change of skull shape in a series of purebred St Bernard dogs spanning nearly 120 years. A regression of shape on time was highly significant and revealed a consistent trend of shape change that corresponded to the features deemed desirable by the breed standard. Historical shape change in St Bernards involves a broadening of the skull and a tilting of the palate and upper jaw relative to the rest of the skull. This trend appears to be linear throughout the entire period and appears to be continuing. Allometry was ruled out as a contributing factor to this change because there was no consistent trend of historical change in skull size and because neither the patterns of static nor ontogenetic allometry corresponded to the historical shape change. The dramatic modification of the St Bernard skull demonstrates that selection can achieve sustained and substantial change and can completely overcome constraints such as allometry.
The evolution of contact-dependent inhibition in non-growing populations ofEscherichia coli
Authors: Lemonnier Marc , Levin Bruce R , Romeo Tony , Garner Kim , Baquero María-Rosario , Mercante Jeff , Lemichez Emmanuel , Baquero Fernando , Blázquez Jesús
Published: October 2007

In the course of liquid culture, serial passage experiments withEscherichia coliK-12 bearing a mutator gene deletion (ΔmutS) we observed the evolution of strains that appeared to kill or inhibit the growth of the bacteria from where they were derived, their ancestors. We demonstrate that this inhibition occurs after the cells stop growing and requires physical contact between the evolved and ancestral bacteria. Thereby, it is referred to as stationary phase contact-dependent inhibition (SCDI). The evolution of this antagonistic relationship is not anticipated from existing theory and experiments of competition in mass (liquid) culture. Nevertheless, it occurred in the same way (parallel evolution) in the eight independent serial transfer cultures, through different single base substitutions in a gene in the glycogen synthesis pathway,glgC. We demonstrate that the observed mutations inglgC, which codes for ADP-glucose pyrophosphorylase, are responsible for both the ability of the evolved bacteria to inhibit or kill their ancestors and their immunity to that inhibition or killing. We present evidence that without additional evolution, mutator genes, or known mutations inglgC, other strains ofE. coliK-12 are also capable of SCDI or sensitive to this inhibition. We interpret this, in part, as support for the generality of SCDI and also as suggesting that theglgCmutations responsible for the SCDI, which evolved in our experiments, may suppress the action of one or more genes responsible for the sensitivity ofE. colito SCDI. Using numerical solutions to a mathematical model andin vitroexperiments, we explore the population dynamics of SCDI and postulate the conditions responsible for its evolution in mass culture. We conclude with a brief discussion of the potential ecological significance of SCDI and its possible utility for the development of antimicrobial agents, which unlike existing antibiotics, can kill or inhibit the growth of bacteria that are not growing.
Unexpected male choosiness for mates in a spider
Authors: Bel-Venner M.C , Dray S , Allainé D , Menu F , Venner S
Published: October 2007

Sexual selection theory traditionally considers choosiness for mates to be negatively related to intra-sexual competition. Males were classically considered to be the competing, but not the choosy, sex. However, evidence of male choosiness is now accumulating. Male choosiness is expected to increase with an individual's competitive ability, and to decrease as intra-sexual competition increases. However, such predictions have never been tested in field conditions. Here, we explore male mate choice in a spider by studying size-assortative pairing in two natural sites that strongly differ in the level of male–male competition. Unexpectedly, our results demonstrate that mate choice shifts from opportunism to high selectivity as competition between males increases. Males experiencing weak competition did not exhibit size-related mating preferences. By contrast, when competition was intense we found strong size-assortative pairing due to male choice: while larger, more competitive males preferentially paired with larger, more fecund females, smaller males chose smaller females. Thus, we show that mating preferences of males vary with their competitive ability. The distinct preferences exhibited by males of different sizes seem to be an adaptive response to the lower reproductive opportunities arising from increased competition between males.
A long-term association between global temperature and biodiversity, origination and extinction in the fossil record
Authors: Mayhew Peter J , Jenkins Gareth B , Benton Timothy G
Published: October 2007

The past relationship between global temperature and levels of biological diversity is of increasing concern due to anthropogenic climate warming. However, no consistent link between these variables has yet been demonstrated. We analysed the fossil record for the last 520 Myr against estimates of low latitude sea surface temperature for the same period. We found that global biodiversity (the richness of families and genera) is related to temperature and has been relatively low during warm ‘greenhouse’ phases, while during the same phases extinction and origination rates of taxonomic lineages have been relatively high. These findings are consistent for terrestrial and marine environments and are robust to a number of alternative assumptions and potential biases. Our results provide the first clear evidence that global climate may explain substantial variation in the fossil record in a simple and consistent manner. Our findings may have implications for extinction and biodiversity change under future climate warming.
Schooling properties of an obligate and a facultative fish species
Authors: Soria M. , Freon P. , Chabanet P.
Published: October 2007

Changes in attraction and repulsion indicators, depending on the species and the group size, were explored under controlled conditions. Two species, displaying different schooling behaviours in the wild were observed: the bigeye scadSelar crumenophthalmusand the barred flagtailKuhlia mugil. In the bigeye scad, the polarity and speed were high and stable, and the nearest neighbour distance (DNN) decreased when the group size increased. In contrast, for the barred flagtail, polarity and speed decreased according to the group size, inducing a loss of cohesion and leading to a disorganized school. TheDNNmean was stable whatever the group size and relatively high. This experiment indicated that the ability to polarize is first a species‐specific trait, rather than a property emerging from the group and led by the circumstances.
The link between migration, the reproductive cycle and condition of Sardinella aurita off Mauritania, north‐west Africa
Authors: Ter Hofstede R. , Dickey‐Collas M. , Mantingh I. T. , Wague A.
Published: October 2007

The annual migration pattern of round sardinella Sardinella aurita up and down the north‐western African coast between 12° N (Senegal) and 22° N (western Sahara) was shown to be associated with spawning activity and a distinct seasonality in fish condition, based on monthly sampling from commercial catches (2000–2003). Some S. aurita were found to spawn throughout the entire year, but a peak in spawning existed during the summer (June to September). The spawning cycle is apparent from seasonality in maturity stages, but is also demonstrated by the increase in gonad mass and fat content of the fish in springtime, the period preceding spawning. During the months after spawning, although feeding is maintained, the physical condition of the fish collapses, and fat content rapidly declines.
Sexual development and reproductive seasonality of hogfish (Labridae: Lachnolaimus maximus), an hermaphroditic reef fish
Authors: McBride R. S. , Johnson M. R.
Published: October 2007

The seasonality, size, age, colour phases and sexual dimorphism of 13 reproductive classes of hogfish Lachnolaimus maximus are described. Analysis of histological sections of gonads (n = 1662) confirmed earlier conclusions that L. maximus is a monandric, protogynous hermaphrodite. Sex change was initiated at the end of the spawning season and over a broad range of sizes and ages. It occurred after a functional female phase (postmaturation) and proceeded more slowly (months) than previously believed. Eventually all individuals changed sex to a terminal male phase. Females were batch spawners, spawning as often as every day during winter and spring. There was no evidence of precocious sperm crypts in active females, sperm competition or other alternative male sexual strategies. Mating has been reported elsewhere to be haremic. The sexual development of L. maximus appears to be adaptive in terms of Ghiselin’s size‐advantage model, which links monandric protogyny and polygyny. The slow rate of sex change, however, poses problems when fishing pressure is high because harvest of a single male has the potential to reduce the reproductive output of an entire harem.
Growth rate and relative otolith size in populations of adult Müller’s pearlside Maurolicus muelleri
Authors: Kristoffersen J. B.
Published: October 2007

Within populations of adult Müller’s pearlside Maurolicus muelleri the otolith radius tended to increase with age at a given fish length, which indicated the presence of a growth‐rate effect. Among populations the relative otolith size was negatively correlated to growth‐rate estimates, which again indicated a growth‐rate effect. There were only minor differences in temperature conditions among the locations, and birth‐date differences did not appear to account for variation in otolith radius relative to fish length in older age groups. The presence of a growth‐rate effect may be useful, as the relative otolith size may be used for evaluation of age and growth estimates, although there are several limitations to its usefulness.
Rapid larval growth predisposes sex change and sexual size dimorphism in a protogynous hermaphrodite, Parapercis snyderi Jordan & Starks 1905
Authors: Walker S. P. W. , Ryen C. A. , McCormick M. I.
Published: October 2007

The temporal relationship between growth history, sex‐specific growth divergence and sex change was investigated in the haremic sandperch Parapercis snyderi using otolith microstructure and gonad histology. Parapercis synderi was found to display rapid near‐linear growth with a maximum longevity of 303 days. All individuals matured first as female and later changed sex to become male (monandric protogynous hermaphroditism). Individual age‐based growth histories obtained from otolith increment widths illustrated that males were larger than females at any given age. Males were found to diverge from the female growth trajectory during two ontogenetic periods; during the larval period and during the period that sex change took place. In addition, male otoliths contained a discontinuity, or ‘check mark’, associated with the rapid increase in otolith growth during the sex‐change period. This microstructural feature was absent from all female otoliths. Accelerated growth in male otoliths lasted up to 25 days, following check‐mark formation, after which time otolith growth returned to the pre‐check‐mark rate. Given the isometric relationship between otolith and somatic growth in P. synderi, and the temporal relationship between the time of check‐mark formation and gonad condition, these results strongly suggest that individuals accelerate somatic growth during sex change to become the largest members of the population. Moreover, evidence suggests that the factors that determine the initial growth of larvae influence which individuals will later become males and achieve the highest reproductive success.
Persistent growth effects of temperature and photoperiod in Atlantic cod Gadus morhua
Authors: Imsland A. K. , Foss A. , Koedijk R. , Folkvord A. , Stefansson S. O. , Jonassen T. M.
Published: October 2007

Short‐term environmental manipulations during the early juvenile stage have a large impact on harvesting size of Atlantic cod Gadus morhua nearly 3 years later. A group of juvenile Atlantic cod (initial mass 9·5 g) were reared for 3 months under simulated natural photoperiod or continuous light, and a range of temperatures (7, 10, 13 and 16° C, and a group called T‐step, i.e. with temperature reduced successively from 16 to 13 and 10° C). After termination of the laboratory trial, the fish were moved to sea pens and reared at ambient conditions for 30 months before harvesting in June 2006. Observed growth gain from the 3 month laboratory trial was still persistent following the 30 months of sea‐pen ongrowing. The T‐step group displayed 15, 13, 1 and 10% superior mass gain respectively than the groups initially at 7, 10, 13 and 16° C at harvest in June 2006. Similarly, rearing under continuous light during the initial 3 month period during the early juvenile stage resulted in 1–9% larger size at harvesting compared to fish reared at simulated natural photoperiod. Gonado‐somatic and hepato‐somatic indices were similar in all groups. Contribution to the understanding of the mechanism behind size variation in adult fish can have wide range applications for Atlantic cod fisheries and aquaculture.
Association behaviour of the self‐fertilizing Kryptolebias marmoratus (Poey): the influence of microhabitat use on the potential for a complex mating system
Authors: Martin S. B.
Published: October 2007

Preliminary observations were conducted to identify conspicuous body postures and movements of males and hermaphrodites in the mangrove killifish Kryptolebias marmoratus. These behaviours were used quantitatively to examine the social interactions for experimental pairings of K. marmoratus of different sexual states (i.e. simultaneous hermaphrodite and male) in an aquarium with an open‐water area and simulated crab burrows. This allowed observation of behaviours that could not be observed in the field. Kryptolebias marmoratus, regardless of sexual state and experimental treatment, spent 40% of the time in the burrow. Hermaphrodites exhibited a preference for associating with males rather than other hermaphrodites. The observed complexity of displayed behaviours and interactions between paired conspecifics indicate that K. marmoratus has a rich repertoire of social behaviour not predicted for a strictly selfing species. Also, land crab burrows play an important role in their social interactions.
Swimming capacity and energetics of migrating and non‐migrating morphs of three‐spined sticklebackGasterosteus aculeatusL. and their ecological implications
Authors: Tudorache C. , Blust R. , De Boeck G.
Published: October 2007

The two morphotypes (leiurus and trachurus) of the three‐spined sticklebackGasterosteus aculeatus, caught at the same location and time in the River Scheldt (Belgium), were investigated for physiological differences in swimming capacity and energetics associated with migration. Critical and optimal swimming speeds, maximum speed and gait‐transition speed were significantly higher for the trachurus type. Standard metabolic rate and active metabolic rate were also higher for trachurus, as was scope for activity. Energy stores (protein, lipid and glycogen in liver and white muscle) were mostly similar in the two types, but lipids in trachurus liver tissue were significantly higher.