bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein histidine phosphatase 1 negatively regulates CD4 T cells by inhibiting the K
+
channel KCa3.1
Authors: Srivastava Shekhar , Zhdanova Olga , Di Lie , Li Zhai , Albaqumi Mamdouh , Wulff Heike , Skolnik Edward Y.
Published: September 2008

The calcium activated K
+
channel KCa3.1 plays an important role in T lymphocyte Ca
2+
signaling by helping to maintain a negative membrane potential, which provides an electrochemical gradient to drive Ca
2+
influx. We previously showed that nucleoside diphosphate kinase beta (NDPK-B), a mammalian histidine kinase, is required for KCa3.1 channel activation in human CD4 T lymphocytes. We now show that the mammalian protein histidine phosphatase (PHPT-1) directly binds and inhibits KCa3.1 by dephosphorylating histidine 358 on KCa3.1. Overexpression of wild-type, but not a phosphatase dead, PHPT-1 inhibited KCa3.1 channel activity. Decreased expression of PHPT-1 by siRNA in human CD4 T cells resulted in an increase in KCa3.1 channel activity and increased Ca
2+
influx and proliferation after T cell receptor (TCR) activation, indicating that endogenous PHPT-1 functions to negatively regulate CD4 T cells. Our findings provide a previously unrecognized example of a mammalian histidine phosphatase negatively regulating TCR signaling and are one of the few examples of histidine phosphorylation/dephosphorylation influencing a biological process in mammals.
Tuning
Escherichia coli
for membrane protein overexpression
Authors: Wagner Samuel , Klepsch Mirjam M. , Schlegel Susan , Appel Ansgar , Draheim Roger , Tarry Michael , Högbom Martin , van Wijk Klaas J. , Slotboom Dirk J. , Persson Jan O. , de Gier Jan-Willem
Published: September 2008

A simple generic method for optimizing membrane protein overexpression in
Escherichia coli
is still lacking. We have studied the physiological response of the widely used “Walker strains” C41(DE3) and C43(DE3), which are derived from BL21(DE3), to membrane protein overexpression. For unknown reasons, overexpression of many membrane proteins in these strains is hardly toxic, often resulting in high overexpression yields. By using a combination of physiological, proteomic, and genetic techniques we have shown that mutations in the
lac
UV5 promoter governing expression of T7 RNA polymerase are key to the improved membrane protein overexpression characteristics of the Walker strains. Based on this observation, we have engineered a derivative strain of
E. coli
BL21(DE3), termed Lemo21(DE3), in which the activity of the T7 RNA polymerase can be precisely controlled by its natural inhibitor T7 lysozyme (T7Lys). Lemo21(DE3) is tunable for membrane protein overexpression and conveniently allows optimizing overexpression of any given membrane protein by using only a single strain rather than a multitude of different strains. The generality and simplicity of our approach make it ideal for high-throughput applications.
ECDI-fixed allogeneic splenocytes induce donor-specific tolerance for long-term survival of islet transplants via two distinct mechanisms
Authors: Luo Xunrong , Pothoven Kathryn L. , McCarthy Derrick , DeGutes Mathew , Martin Aaron , Getts Daniel R. , Xia Guliang , He Jie , Zhang Xiaomin , Kaufman Dixon B. , Miller Stephen D.
Published: September 2008

A major challenge for human allogeneic islet transplantation is the development of effective methods to induce donor-specific tolerance to obviate the need for life-long immunosuppression that is toxic to the insulin-producing β cells and detrimental to the host. We developed an efficient donor-specific tolerance therapy that utilizes infusions of ethylene carbodiimide (ECDI)-treated donor splenic antigen-presenting cells that results in indefinite survival of allogeneic islet grafts in the absence of immunosuppression. Furthermore, we show that induction of tolerance is critically dependent on synergistic effects between an intact programmed death 1 receptor–programmed death ligand 1 signaling pathway and CD4+CD25+Foxp3+regulatory T cells. This highly efficient antigen-specific therapy with a complete avoidance of immunosuppression has significant therapeutic potential in human islet cell transplantation.
Revealing the catalytic potential of an acyl-ACP desaturase: Tandem selective oxidation of saturated fatty acids
Authors: Whittle Edward J. , Tremblay Amy E. , Buist Peter H. , Shanklin John
Published: September 2008

It is estimated that plants contain thousands of fatty acid structures, many of which arise by the action of membrane-bound desaturases and desaturase-like enzymes. The details of “unusual” e.g., hydroxyl or conjugated, fatty acid formation remain elusive, because these enzymes await structural characterization. However, soluble plant acyl-ACP (acyl carrier protein) desaturases have been studied in far greater detail but typically only catalyze desaturation (dehydrogenation) reactions. We describe a mutant of the castor acyl-ACP desaturase (T117R/G188L/D280K) that converts stearoyl-ACP into the allylic alcohol
trans
-isomer (
E
)-10-18:1-9-OH via a cis isomer (
Z
)-9-18:1 intermediate. The use of regiospecifically deuterated substrates shows that the conversion of (
Z
)-9-18:1 substrate to (
E
)-10-18:1-9-OH product proceeds via hydrogen abstraction at C-11 and highly regioselective hydroxylation (>97%) at C-9.
18
O-labeling studies show that the hydroxyl oxygen in the reaction product is exclusively derived from molecular oxygen. The mutant enzyme converts (
E
)-9-18:1-ACP into two major products, (
Z
)-10-18:1-9-OH and the conjugated linolenic acid isomer, (
E
)-9-(
Z
)-11-18:2. The observed product profiles can be rationalized by differences in substrate binding as dictated by the curvature of substrate channel at the active site. That three amino acid substitutions, remote from the diiron active site, expand the range of reaction outcomes to mimic some of those associated with the membrane-bound desaturase family underscores the latent potential of O
2
-dependent nonheme diiron enzymes to mediate a diversity of functionalization chemistry. In summary, this study contributes detailed mechanistic insights into factors that govern the highly selective production of unusual fatty acids.
NMR structures of two designed proteins with high sequence identity but different fold and function
Authors: He Yanan , Chen Yihong , Alexander Patrick , Bryan Philip N. , Orban John
Published: September 2008

How protein sequence codes for 3D structure remains a fundamental question in biology. One approach to understanding the folding code is to design a pair of proteins with maximal sequence identity but retaining different folds. Therefore, the nonidentities must be responsible for determining which fold topology prevails and constitute a fold-specific folding code. We recently designed two proteins, GA88 and GB88, with 88% sequence identity but different folds and functions [Alexanderet al.(2007)Proc Natl Acad Sci USA104:11963–11968]. Here, we describe the detailed 3D structures of these proteins determined in solution by NMR spectroscopy. Despite a large number of mutations taking the sequence identity level from 16 to 88%, GA88 and GB88 maintain their distinct wild-type 3-α and α/β folds, respectively. To our knowledge, the 3D-structure determination of twomonomericproteins with such high sequence identity but different fold topology is unprecedented. The geometries of the seven nonidentical residues (of 56 total) provide insights into the structural basis for switching between 3-α and α/β conformations. Further mutation of a subset of these nonidentities, guided by the GA88 and GB88 structures, leads to proteins with even higher levels of sequence identity (95%) and different folds. Thus, conformational switching to an alternative monomeric fold of comparable stability can be effected with just a handful of mutations in a small protein. This result has implications for understanding not only the folding code but also the evolution of new folds.
Functional genetic screening reveals the role of mitochondrial cytochrome
b
as a mediator of FAS-induced apoptosis
Authors: Komarov Andrei P. , Rokhlin Oskar W. , Yu Chang-An , Gudkov Andrei V.
Published: September 2008

Functional selection of genetic suppressor elements (GSEs), engineered gene fragments that interfere with the function of a particular gene product, was used to identify regulators of FAS-induced apoptosis. Chicken DF-1 cells expressing human FAS receptor and susceptible to FAS-induced apoptosis were infected with a GSE library consisting of randomly fragmented normalized chicken cDNAs in a replication-competent avian retroviral vector. Virus-producing cells were subjected to several rounds of selection using FAS agonistic antibodies, resulting in isolation of a set of GSEs conferring resistance to FAS-induced apoptosis. Surprisingly, one of the isolated GSEs encoded a 42 amino acid-long polypeptide derived from the C-terminal half of cytochrome
b
(Cyt b) encoded by the mitochondrial genome. Subsequent experiments showed that caspase 8-dependent cleavage of mitochondrial Cyt b and translocation of its C-terminal half into the cytoplasm occurred during FAS-induced apoptosis in both chicken and human cells. Ectopic cytoplasmic expression of either full-length Cyt b or its C-terminal half in several human cell lines induced apoptosis, which could be suppressed by the isolated GSE, but not by Bcl2 over-expression or Apaf-1 or cytochrome
c
knock-down. These results reveal a cytochrome
c
-independent branch of FAS-induced apoptosis involving cleavage and cytoplasmic release of mitochondrial Cyt b.
Stimulated emission depletion (STED) nanoscopy of a fluorescent protein-labeled organelle inside a living cell
Authors: Hein Birka , Willig Katrin I. , Hell Stefan W.
Published: September 2008

We demonstrate far-field optical imaging with subdiffraction resolution of the endoplasmic reticulum (ER) in the interior of a living mammalian cell. The diffraction barrier is overcome by applying stimulated emission depletion (STED) on a yellow fluorescent protein tag. Imaging individual structural elements of the ER revealed a focal plane (
x
,
y
) resolution of <50 nm inside the living cell, corresponding to a 4-fold improvement over that of a confocal microscope and a 16-fold reduction in the focal-spot cross-sectional area. A similar gain in resolution is realized with both pulsed- and continuous-wave laser illumination. Images of highly convoluted parts of the ER reveal a similar resolution improvement in 3D optical sectioning by a factor of 3 along the optic axis (
z
). Time-lapse STED recordings document morphological changes of the ER over time. Thus, nanoscale 3D imaging of organelles in the interior of living cells greatly expands the scope of light microscopy in cell biology.
Word classes in sign languages
Authors: Schwager Waldemar , Zeshan Ulrike
Published: September 2008

The topic of word classes remains curiously under-represented in the sign language literature due to many theoretical and methodological problems in sign linguistics. This article focuses on language-specific classifications of signs into word classes in two different sign languages: German Sign Language and Kata Kolok, the sign language of a village community in Bali.

The article discusses semantic and structural criteria for identifying word classes in the target sign languages. On the basis of a data set of signs, these criteria are systematically tested out as a first step towards an inductive classification of signs. Approaches and analyses relating to the problem of word classes in linguistic typology are used for shedding new light on the issue of word class distinctions in sign languages.
Roots, stems and word classes
Authors: Lehmann Christian
Published: September 2008

The assignment of a linguistic sign to a word class is an operation that must be seen as part of the overall transformation of extralinguistic substance into linguistic form. In this, it is comparable to such processes as the transitivization of a verbal base, which further specifies a relatively rough categorization. Languages differ both in the extent to which they structure the material by purely grammatical criteria and in the level at which they do this. The root and the stem are the lowest levels at which a linguistic sign can be categorized in terms of language-specific structure. Further categorization is then achieved at the level of the syntagm.

An empirical investigation comparing the categorization of roots and stems in a sample of six languages (English, German, Latin, Spanish, Yucatec Maya, Mandarin Chinese) turns up far-reaching differences. These differences in the amount of categorization that languages apply to linguistic signs at the most basic levels throw into doubt any thesis claiming universal categoriality or acategoriality for roots. Such a static view must be replaced by a dynamic one which asks for the role of categorization in linguistic activity. At the same time, these differences raise the issue of the amount of structure — or of grammar — that is necessary for a human language.1
Precategoriality and syntax-based parts of speech
Authors: Bisang Walter
Published: September 2008

Late Archaic Chinese is a precategorial language, i.e., a language whose lexical items are not preclassified in the lexicon for the syntactic functions of N and V. This will be shown on the basis of structural-conceptual criteria as those developed by Croft (2000) and Sasse (1993b) as well as on the basis of methodological criteria as those suggested by Evans & Osada (2005). As is claimed in Construction Grammar (Goldberg 1995, 2005), the meaning of lexical items is derived by integrating their own lexical meaning with the meaning contributed by the construction. The construction analysed in this paper is the argument structure construction. Linking between lexicon and syntax is subject to stereotypical pragmatic implicatures (Levinson 2000) that follow a version of the animacy hierarchy. As it will turn out, Late Archaic Chinese does not strictly lack parts of speech. In fact, without the distinction of nouns and verbs at the level of syntax it would not be possible to analyse utterances in Late Archaic Chinese. The only thing that Late Archaic Chinese can do without is noun/verb distinction in the lexicon. This typologically remarkable property is due to a process of morphological change. If such a historical process can take place irrespective of parts-of-speech distinctions, precategoriality in the lexicon cannot be a robust universal feature even if most theoretical approaches take it for granted.
Covert word classes
Authors: Donohue Mark
Published: September 2008

Examining syntactic categories in Tukang Besi, an Austronesian language of Indonesia, we find that there are additions to the traditional fixed categories. In addition to the firmly definable categories of nouns and verbs, there are many lexical items that are precategorial: they may be used, without derivation, with either nominal morphosyntax or verbal morphosyntax. Additionally, there is a class of ‘adjectives’ that display odd behaviour in terms of morphological markedness reversals and functional use, and which, under closer examination, turn out to have a variable categorial status, dependent on the structural position in which they are used, obligatorily appearing as part of the head of their phrase, V in a VP and N in an NP. Morphosyntactic tests for the different claims are given and discussed.
The acquisition of syntactic categories in Jakarta Indonesian
Authors: Gil David
Published: September 2008

This paper presents empirical evidence for a theory of syntactic categories in the tradition of categorial grammar, in which more complex categories are derived from simpler ones by means of category formation operators. In Jakarta Indonesian, almost all words and larger expressions belong to a single open syntactic category, S(entence), while a small residue of semantically heterogeneous items belong to a single closed syntactic category S/S. The theory predicts that in first-language acquisition, simpler categories are acquired before more complex ones. Thus, for Jakarta Indonesian, it predicts that the category S is be acquired before the category S/S. Examination of a naturalistic corpus of almost one million utterances provides support for this prediction, deriving from errors of overgeneralization, in which members of S/S exhibit the distributional properties of members of S.
Possible phonological cues in categorial acquisition
Authors: Don Jan , Erkelens Marian
Published: September 2008

This paper reports an experiment in which adult native speakers of Dutch were asked to categorize nonce stems. These were presented without any morphological or other information about their potential class-membership. We expected that subjects would be able to categorize these words solely on the basis of phonological information. Nouns in Dutch have a richer possible syllable-structure than verbs (Trommelen 1989) and therefore, we expected that stimuli with a ‘nominal’ syllable make-up could be identified by the subjects as nouns where the other stimuli were ambiguous between nouns and verbs. The results show that this is indeed the case, adding to the evidence that native speakers of a language are able to use phonological information to categorize the words of their language.
Lexical semantic constraints on noun roots and noun borrowability
Authors: Nichols Lynn
Published: September 2008

While nouns are thought to be more easily borrowed than verbs, this investigation demonstrates that there may be limitations on noun borrowing into certain languages. The case of Zuni is examined, in which conditions of contact similar to that of neighboring languages nevertheless result in a different treatment of the noun lexicon. The possibility of borrowing natural kind nouns into Zuni exists alongside a tendency against borrowing nouns of the artifact type. It is argued that the source of this tendency against artifact noun borrowing in Zuni is the grammatical complexity of the lexical semantic representation for these nouns: grammatical complexity in Zuni noun roots appears to be dispreferred. These findings belie the claim of Thomason and Kaufman (1988) that “any linguistic feature can be transferred to any other language” given an appropriate degree of contact.
Degree words, intensification, and word class distinctions in Romance languages
Authors: Salazar-García Ventura
Published: September 2008

This paper emphasises the explanatory possibilities of a parts-of-speech theory in which the notions of differentiation, flexibility, and rigidity are not perceived as mutually exclusive typological paths, but as potentially compatible grammatical strategies. The type of analysis such a theory makes possible is first applied to Spanish quantifiers and subsequently extended to degree words expressing intensification in modern Romance languages. The paper also pays attention to the formal mechanisms associated with the expression of degree words. One of the most significant conclusions is that degree words classified as differentiated adverbs tend to function as modifiers of modifiers. The modification of predicates and that of terms (especially, mass nouns) are roles usually played by flexible modifiers.
On flexible and rigid nouns
Authors: Rijkhoff Jan
Published: September 2008

This article argues that in addition to the major flexible lexical categories in Hengeveld’s classification of parts-of-speech systems (Contentive, Non-Verb, Modifier), there are also flexible word classes within the rigid lexical category Noun (Set Noun, Sort Noun, General Noun). Members of flexible word classes are characterized by their vague semantics, which in the case of nouns means that values for the semantic features Shape and Homogeneity are either left undetermined or they are specified in such a way that they do not quite match the properties of the kind of entity denoted by the flexible item in the external world. I will then argue that flexible word classes constitute a proper category (i.e. they are not the result of a merger of some rigid word classes) in that members of flexible word categories display the same properties regarding category membership as members of rigid word classes. Finally this article wants to claim that the distinction between rigid and flexible noun categories (a) adds a new dimension to current classifications of parts-of-speech systems, (b) correlates with certain grammatical phenomena (e.g. so-called number discord), and (c) helps to explain the parts-of-speech hierarchy.
Parts of speech and dependent clauses in Functional Discourse Grammar
Authors: Hengeveld Kees , van Lier Eva
Published: September 2008

In this paper we use the Theory of Functional Discourse Grammar to show that parts-of-speech (PoS) and dependent clauses (DCs) can both be defined in terms of the functions they may express. On the basis of this parallel treatment, we predict that the functional possibilities of PoS and DCs in languages are comparable. This hypothesis is tested using a sample of 23 languages. The results do show similarities between the functional patterns of the two types of constructions.
Keeping the fires burning: militarisation and the politics of gender in South Africa
Authors: Cock Jacklyn
Published: September 2008

This article focuses on the connection between women and militarisation. It is a connection which is obscured by analyses which conceptualise war as a male affair and the military as a patriarchal institution from which women are excluded and by whom they are often victimised. White women contribute to the militarisation of South African society in both material and ideological terms. At the same time a minority of white women are a source of resistance to the system of apartheid which militarism defends. The ‘politics of gender’, the power relations between men and women which are structured around opposing notions of ‘masculinity’ and ‘femininity’, shape both these processes of incorporation and challenge.
The politics of religion in Nigeria: the parameters of the 1987 crisis in Kaduna State
Authors: Ibrahim Jibrin
Published: September 2008

This article analyses the immediate and long term causes of the outbreak of religious violence between Muslims and Christians in Kaduna State, Nigeria, in 1987. The author argues that the crisis arose from the politicisation of religion in the regional contest for power. On the one hand is the issue of the rise of fundamentalist Christianity and Islam. On the other is the struggle for political power by the ‘northern Oligarchy’ within the north and against the south in which religion has become a means for forging new coalitions.
GOSLING: a rule-based protein annotator using BLAST and GO
Authors: Jones Craig E. , Schwerdt Julian , Bretag Tessa Arwen , Baumann Ute , Brown Alfred L.
Published: September 2008

Summary: GOSLING is a web-based protein function annotator that uses a decision tree-derived rule set to quickly predict Gene Ontology terms for a protein. A score is assigned to each term prediction that is indicative of the accuracy of the prediction. Due to its speed and accuracy GOSLING is ideally suited for high-throughput annotation tasks.

Availability:  https://www.sapac.edu.au/gosling

Contact:  craig@cs.adelaide.edu.au
TESE: generating specific protein structure test set ensembles
Authors: Sirocco Francesco , Tosatto Silvio C. E.
Published: September 2008

Summary: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of α-helical repeat proteins with more than 120 residues and resolution <2.0 Å. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported.

Availability: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/.

Contact:  silvio.tosatto@unipd.it
tCal: transcriptional probability calculator using thermodynamic model
Authors: Zhou Xin , Su Zhen
Published: September 2008

Summary: Thermodynamic model has been proposed as a realistic model of gene transcriptional regulation in bacteria, in which transcription probability calculation is based on physical interpretation of biological knowledge. We extend the published results in this area, and derive a relatively new model which could serve as a generalized form of previous results. To facilitate the application in gene network modeling studies, we implement our model in a Python module, ‘tCal’. With minimum programming efforts, user can use tCal to build transcription units, and either compute the transcription probabilities, or construct SBML models of regulatory networks.

Availability: tCal module and its online version can be found at: http://bioinformatics.cau.edu.cn/tCal.

Contact:  zhensu@cau.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Specific alignment of structured RNA: stochastic grammars and sequence annealing
Authors: Bradley Robert K. , Pachter Lior , Holmes Ian
Published: September 2008

Motivation: Whole-genome screens suggest that eukaryotic genomes are dense with non-coding RNAs (ncRNAs). We introduce a novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple alignments. This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences.

Results: When tested on the benchmark datasets BRalibase II and BRalibase 2.1, Stemloc-AMA has comparable sensitivity to and better specificity than the best competing methods. We use a large-scale random sequence experiment to show that while most alignment programs maximize sensitivity at the expense of specificity, even to the point of giving complete alignments of non-homologous sequences, Stemloc-AMA aligns only sequences with detectable homology and leaves unrelated sequences largely unaligned. Such accurate and specific alignments are crucial for comparative-genomics analysis, from inferring phylogeny to estimating substitution rates across different lineages.

Availability:  Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis.

Contact:  lpachter@math.berkeley.edu; ihh@berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hitting the buffers: conspecific aggression undermines benefits of colonial breeding under adverse conditions
Authors: Ashbrook Kate , Wanless Sarah , Harris Mike P , C. Hamer Keith
Published: September 2008

Colonial breeding in birds is widely considered to benefit individuals through enhanced protection against predators or transfer of information about foraging sites. This view, however, is largely based on studies of seabirds carried out under favourable conditions. Recent breeding failures at many seabird colonies in the UK provide an opportunity to re-examine costs and benefits of coloniality under adverse conditions. Common guillemots
Uria aalge
are highly colonial cliff-nesting seabirds with very flexible parental care. Although the single chick is normally never left alone, more than 50 per cent of offspring were left unattended at a North Sea colony in 2007, apparently because poor conditions forced both parents to forage simultaneously. Contrary to expectation, unattended chicks were not killed by avian predators. Rather, although non-breeders and failed breeders sometimes provided alloparental care, unattended chicks were frequently attacked by breeding guillemots at neighbouring sites, often with fatal consequences. These results highlight a previously unsuspected trade-off between provisioning chicks and avoiding conspecific attacks, and indicate that understanding how environmental conditions affect social dynamics is crucial to interpreting costs and benefits of colonial breeding.
We know that the wasps ‘know’: cryptic successors to the queen inRopalidia marginata
Authors: Bhadra Anindita , Gadagkar Raghavendra
Published: September 2008

Unlike other primitively eusocial wasps,Ropalidia marginatacolonies are usually headed by remarkably docile and behaviourally non-dominant queens who are nevertheless completely successful in maintaining reproductive monopoly. As in other species, loss of the queen results in one of the workers taking over as the next queen. But unlike in other species, here, the queen's successor cannot be predicted on the basis of dominance rank, other behaviours, age, body size or even ovarian development, in the presence of the former queen. But the swiftness with which one and only one individual becomes evident as the potential queen led us to suspect that there might be a designated successor to the queen known to the wasps, even though we cannot identify her in the queen's presence. Here, we present the results of experiments that support such a ‘cryptic successor’ hypothesis, and thereby lend credence to the idea that queen (and potential queen) pheromones act as honest signals of their fertility, inR. marginata.
Distributed robustness in cellular networks: insights from synthetic evolved circuits
Authors: Macia Javier , Solé Ricard V
Published: September 2008

Evolved natural systems are known to display some sort of distributed robustness against the loss of individual components. Such type of robustness is not just the result of redundancy. Instead, it seems to be based on degeneracy, i.e. the ability of elements that are structurally different to perform the same function or yield the same output. Here, we explore the problem of how relevant is degeneracy in a class of evolved digital systems formed by NAND gates, and what types of network structures underlie the resilience of evolved designs to the removal or loss of a given unit. It is shown that our fault tolerant circuits are obtained only if robustness arises in a distributed manner. No such reliable systems were reached just by means of redundancy, thus suggesting that reliable designs are necessarily tied to degeneracy.
Surface wrinkling of a channelized flow
Authors: Slim A.C , Balmforth N.J , Craster R.V , Miller J.C
Published: September 2008

We consider an inclined rectangular duct of constant cross-section conveying viscous fluid and covered by an elastic plate. The fluid is described by the Stokes equations and the plate by the Föppl–von Kármán equations. The equations admit an equilibrium solution in which the plate is flat and fluid flows underneath due to gravity. This base flow induces a varying traction across the plate, which can lead to out-of-plane buckling due to the associated in-plane shear. Linear stability analysis demonstrates that buckling occurs for sufficiently thin plates on steep slopes and deep channels. The most unstable modes take the form of either symmetric or antisymmetric downslope-directed chevron patterns that travel downstream at a fraction of the average speed of the base flow. An analogous analysis shows that similar buckling also occurs if the elastic plate is replaced by a thin skin of very viscous fluid. Our description provides a simple model for the formation of ropy pahoehoe lava.
A note on the unsteady motion under gravity of a corner point on a free surface: a generalization of Stokes' theory
Authors: Needham D.J , Billingham J
Published: September 2008

In this paper, we develop a theory based on local asymptotic coordinate expansions for the unsteady propagation of a corner point on the constant-pressure free surface bounding an incompressible inviscid fluid in irrotational motion under the action of gravity. This generalizes the result of Stokes and Michell relating to the horizontal propagation of a corner at constant speed.
Time dependence of groundwater pumping from a well near a river
Authors: Llewellyn Smith Stefan G , Davis Anthony M.J
Published: September 2008

The time-dependent flow of groundwater through an aquifer, generated from rest by pumping from a well close to a river, is calculated without making Dupuit's approximation. The governing equations reduce to the diffusion equation for the pressure head with mixed boundary conditions at the surface of the aquifer and at the base of the river. Using transform techniques, the problem is reduced to an infinite set of linear equations. The steady-state solution provides a guide to the numerical solution of the time-dependent problem. Results are presented for the flux from the river into the aquifer as well as for the flux from the aquifer into the river and out again. Explicit expressions for these fluxes are obtained in the case of rivers that are narrow compared with the aquifer depth. The steady-state flux is then much smaller than the transient flux. Results are significantly different from those obtained using the Dupuit approximation.
The interactions between shear bands and rigid lamellar inclusions in a ductile metal matrix
Authors: Dal Corso Francesco , Bigoni Davide
Published: September 2008

A ductile metal matrix (modelled as a nonlinear elastic material) containing a dilute suspension of an iso-oriented lamellar stiff phase (modelled as stiffeners, i.e. zero thickness, rigid inclusions) is subject to a simple shear of finite amount, parallel to the inclusion orientation, and subsequently perturbed through an incremental Mode I loading, uniform at infinity. Solution to this problem permits analytical investigations of the emergence of shear bands and their interaction with a rigid inclusion (involving a stress square-root singularity at its tip) and discloses the mechanisms of ductile failure in reinforced materials (explaining for instance the experimental evidence that shear bands tend to nucleate and grow parallel to thin hard inclusions). Finally, investigated beyond the elliptic range, the obtained solution becomes non-unique and reveals non-decay and singularity of the fields, facts that provide analytical justification for the difficulties associated with numerical treatment of shear bands.
Are ecosystem services stabilized by differences among species? A test using crop pollination
Authors: Winfree Rachael , Kremen Claire
Published: September 2008

Biological diversity could enhance ecosystem service provision by increasing the mean level of services provided, and/or by providing more consistent (stable) services over space and time. Ecological theory predicts that when an ecosystem service is provided by many species, it will be stabilized against disturbance by a variety of ‘stabilizing mechanisms.’ However, few studies have investigated whether stabilizing mechanisms occur in real landscapes affected by human disturbance. We used two datasets on crop pollination by wild native bees to screen for and differentiate among three stabilizing mechanisms: density compensation (negative co-variance among species' abundances); response diversity (differential response to environmental variables among species); and cross-scale resilience (response to the same environmental variable at different scales by different species). In both datasets, we found response diversity and cross-scale resilience, but not density compensation. We conclude that stabilizing mechanisms may contribute to the stability of pollination services in our study areas, emphasizing the insurance value of seemingly ‘redundant’ species. Furthermore, the absence of density compensation that we found at the landscape scale contrasts with findings of previous small-scale experimental and modelling work, suggesting that we should not assume that density compensation will stabilize ecosystem services in real landscapes.
A serial founder effect model for human settlement out of Africa
Authors: Deshpande Omkar , Batzoglou Serafim , Feldman Marcus W , Luca Cavalli-Sforza L
Published: September 2008

The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50–60 Kyr ago and archaeo–ethno–demographic information. In addition to a colonization rate of 0.09–0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.
Carotenoid-based colour of acanthocephalan cystacanths plays no role in host manipulation
Authors: Kaldonski Nicolas , Perrot-Minnot Marie-Jeanne , Dodet Raphaël , Martinaud Guillaume , Cézilly Frank
Published: September 2008

Manipulation by parasites is a catchy concept that has been applied to a large range of phenotypic alterations brought about by parasites in their hosts. It has, for instance, been suggested that the carotenoid-based colour of acanthocephalan cystacanths is adaptive through increasing the conspicuousness of infected intermediate hosts and, hence, their vulnerability to appropriate final hosts such as fish predators. We revisited the evidence in favour of adaptive coloration of acanthocephalan parasites in relation to increased trophic transmission using the crustacean amphipodGammarus pulexand two species of acanthocephalans,Pomphorhynchus laevisandPolymorphus minutus. Both species show carotenoid-based colorations, but rely, respectively, on freshwater fish and aquatic bird species as final hosts. In addition, the two parasites differ in the type of behavioural alteration brought to their common intermediate host.Pomphorhynchus laevisreverses negative phototaxis inG. pulex, whereasP. minutusreverses positive geotaxis. In aquaria, trout showed selective predation forP. laevis-infected gammarids, whereasP. minutus-infected ones did not differ from uninfected controls in their vulnerability to predation. We tested for an effect of parasite coloration on increased trophic transmission by painting a yellow–orange spot on the cuticle of uninfected gammarids and by masking the yellow–orange spot of infected individuals with inconspicuous brown paint. To enhance realism, match of colour between painted mimics and true parasite was carefully checked using a spectrometer. We found no evidence for a role of parasite coloration in the increased vulnerability of gammarids to predation by trout. Painted mimics did not differ from control uninfected gammarids in their vulnerability to predation by trout. In addition, covering the place through which the parasite was visible did not reduce the vulnerability of infected gammarids to predation by trout. We discuss alternative evolutionary explanations for the origin and maintenance of carotenoid-based colorations in acanthocephalan parasites.
Social fishes and single mothers: brain evolution in African cichlids
Authors: Gonzalez-Voyer Alejandro , Winberg Svante , Kolm Niclas
Published: September 2008

As with any organ, differences in brain size—after adequate control of allometry—are assumed to be a response to selection. With over 200 species and an astonishing diversity in niche preferences and social organization, Tanganyikan cichlids present an excellent opportunity to study brain evolution. We used phylogenetic comparative analyses of sexed adults from 39 Tanganyikan cichlid species in a multiple regression framework to investigate the influence of ecology, sexual selection and parental care patterns on whole brain size, as well as to analyse sex-specific effects. First, using species-specific measures, we analysed the influence of diet, habitat, form of care (mouthbrooding or substrate guarding), care type (biparental or female only) and intensity of sexual selection on brain size, while controlling for body size. Then, we repeated the analyses for male and female brain size separately. Type of diet and care type were significantly correlated with whole brain size. Sex-specific analyses showed that female brain size correlated significantly with care type while male brain size was uncorrelated with care type. Our results suggest that more complex social interactions associated with diet select for larger brains and further that the burden of uniparental care exerts high cognitive demands on females.
Testosterone responses to competition in men are related to facial masculinity
Authors: Pound Nicholas , Penton-Voak Ian S , Surridge Alison K
Published: September 2008

Relationships between androgens and the size of sexually dimorphic male traits have been demonstrated in several non-human species. It is often assumed that a similar relationship exists for human male faces, but clear evidence of an association between circulating testosterone levels and the size of masculine facial traits in adulthood is absent. Here we demonstrate that, after experimentally determined success in a competitive task, men with more a masculine facial structure show higher levels of circulating testosterone than men with less masculine faces. In participants randomly allocated to a ‘winning’ condition, testosterone was elevated relative to pre-task levels at 5 and 20 min post-task. In a control group of participants allocated to a ‘losing’ condition there were no significant differences between pre- and post-task testosterone. An index of facial masculinity based on the measurement of sexually dimorphic facial traits was not associated with pre-task (baseline) testosterone levels, but was associated with testosterone levels 5 and 20 min after success in the competitive task. These findings indicate that a man's facial structure may afford important information about the functioning of his endocrine system.
Do New Caledonian crows solve physical problems through causal reasoning?
Authors: Taylor A.H , Hunt G.R , Medina F.S , Gray R.D
Published: September 2008

The extent to which animals other than humans can reason about physical problems is contentious. The benchmark test for this ability has been the trap-tube task. We presented New Caledonian crows with a series of two-trap versions of this problem. Three out of six crows solved the initial trap-tube. These crows continued to avoid the trap when the arbitrary features that had previously been associated with successful performances were removed. However, they did not avoid the trap when a hole and a functional trap were in the tube. In contrast to a recent primate study, the three crows then solved a causally equivalent but visually distinct problem—the trap-table task. The performance of the three crows across the four transfers made explanations based on chance, associative learning, visual and tactile generalization, and previous dispositions unlikely. Our findings suggest that New Caledonian crows can solve complex physical problems by reasoning both causally and analogically about causal relations. Causal and analogical reasoning may form the basis of the New Caledonian crow's exceptional tool skills.
Strain-specific priming of resistance in the red flour beetle,
Tribolium castaneum
Authors: Roth Olivia , Sadd Ben M , Schmid-Hempel Paul , Kurtz Joachim
Published: September 2008

As invertebrates lack the molecular machinery employed by the vertebrate adaptive immune system, it was thought that they consequently lack the ability to produce lasting and specific immunity. However, in recent years, it has been demonstrated that the immune defence of invertebrates is by far more complicated and specific than previously envisioned. Lasting immunity following an initial exposure that proves protection on a secondary exposure has been shown in several species of invertebrates. This phenomenon has become known as immune priming. In the cases where it is explicitly tested, this priming can also be highly specific. In this study, we used survival assays to test for specific priming of resistance in the red flour beetle,
Tribolium castaneum
, using bacteria of different degrees of relatedness. Our results suggest an unexpected degree of specificity that even allows for differentiation between different strains of the same bacterium. However, our findings also demonstrate that specific priming of resistance in insects may not be ubiquitous across all bacteria.
Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification
Authors: Wen Bo , Wu Hao , Bjornsson Hans , Green Roland D. , Irizarry Rafael , Feinberg Andrew P.
Published: September 2008

Most genome-level analysis treats the two parental alleles equivalently, yet diploid genomes contain two parental genomes that are often epigenetically distinct. While single nucleotide polymorphisms (SNPs) can be used to distinguish these genomes, it would be useful to develop a generalized strategy for identifying candidate genes or regions showing allele-specific differences, independent of SNPs. We have explored this problem by looking for overlapping marks in the genome related to both euchromatin (histone H3 dimethyl lysine-4 [H3K4Me2]) and heterochromatin (DNA methylation [DNAm]). “Double hits” were defined by the intersection of H3K4Me2 and DNAm. For the top 5% of marks, defined by a sliding window, imprinted gene regions were enriched for double hits 5.4-fold. When the location information of CTCF binding sites were integrated, the “triple hits” were enriched 76-fold for known imprinted genes in the regions studied. The double hits in imprinted genes were found to occur usually at the site of alternative or antisense transcripts. In addition, four of four imprinted genes tested showing double hits also showed allele-specific methylation. We suggest that overlapping euchromatin/heterochromatin marks are common and are enriched for epigenetically distinct parental chromosome regions. Furthermore, we developed a novel approach to identifying allele-specific marks that is SNP independent, by fractionating using H3K4Me2 antibodies followed by DNA methylation analysis.