bluuebunny/crossref_metadata_2025 huggingface dataset:
A protein microarray-based analysis of
S
-nitrosylation
Authors: Foster Matthew W. , Forrester Michael T. , Stamler Jonathan S.
Published: October 2009

The ubiquitous cellular influence of nitric oxide (NO) is exerted substantially through protein
S
-nitrosylation. Whereas NO is highly promiscuous, physiological
S
-nitrosylation is typically restricted to one or very few Cys residue(s) in target proteins. The molecular basis for this specificity may derive from properties of the target protein, the
S
-nitrosylating species, or both. Here, we describe a protein microarray-based approach to investigate determinants of
S
-nitrosylation by biologically relevant low-mass
S
-nitrosothiols (SNOs). We identify large sets of yeast and human target proteins, among which those with active-site Cys thiols residing at N termini of α-helices or within catalytic loops were particularly prominent. However,
S
-nitrosylation varied substantially even within these families of proteins (e.g., papain-related Cys-dependent hydrolases and rhodanese/Cdc25 phosphatases), suggesting that neither secondary structure nor intrinsic nucleophilicity of Cys thiols was sufficient to explain specificity. Further analyses revealed a substantial influence of NO-donor stereochemistry and structure on efficiency of
S
-nitrosylation as well as an unanticipated and important role for allosteric effectors. Thus, high-throughput screening and unbiased proteome coverage reveal multifactorial determinants of
S
-nitrosylation (which may be overlooked in alternative proteomic analyses), and support the idea that target specificity can be achieved through rational design of
S
-nitrosothiols.
Emergent gene order in a model of modular polyketide synthases
Authors: Callahan Benjamin , Thattai Mukund , Shraiman Boris I.
Published: October 2009

Polyketides are a class of biologically active heteropolymers produced by assembly line-like multiprotein complexes of modular polyketide synthases (PKS). The polyketide product is encoded in the order of the PKS proteins in the assembly line, suggesting that polyketide diversity derives from combinatorial rearrangement of these PKS complexes. Remarkably, the order of PKS genes on the chromosome follows the order of PKS proteins in the assembly line: This fact is commonly referred to as “collinearity”. Here we propose an evolutionary origin for collinearity and demonstrate the mechanism by using a computational model of PKS evolution in a population. Assuming continuous evolutionary pressure for novel polyketides, and that new polyketide pathways are formed by horizontal transfer/recombination of PKS-encoding DNA, we demonstrate the existence of a broad range of parameters for which collinearity emerges spontaneously. Collinearity confers no fitness advantage in our model; it is established and maintained through a “secondary selection” mechanism, as a trait which increases the probability of forming long, novel PKS complexes through recombination. Consequently, collinearity hitchhikes on the successful genotypes which periodically sweep through the evolving population. In addition to computer simulation of a simplified model of PKS evolution, we provide a mathematical framework describing the secondary selection mechanism, which generalizes beyond the context of the present model.
Simultaneous prediction of protein folding and docking at high resolution
Authors: Das Rhiju , André Ingemar , Shen Yang , Wu Yibing , Lemak Alexander , Bansal Sonal , Arrowsmith Cheryl H. , Szyperski Thomas , Baker David
Published: October 2009

Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be stabilized largely by interactions with other monomers and hence not the lowest energy state of a single chain. Building on the Rosetta framework, we present a general method to simultaneously model the folding and docking of multiple-chain interleaved homo-oligomers. For more than a third of the cases in a benchmark set of interleaved homo-oligomers, the method generates near-native models of large α-helical bundles, interlocking β sandwiches, and interleaved α/β motifs with an accuracy high enough for molecular replacement based phasing. With the incorporation of NMR chemical shift information, accurate models can be obtained consistently for symmetric complexes with as many as 192 total amino acids; a blind prediction was within 1 Å rmsd of the traditionally determined NMR structure, and fit independently collected RDC data equally well. Together, these results show that the Rosetta “fold-and-dock” protocol can produce models of homo-oligomeric complexes with near-atomic-level accuracy and should be useful for crystallographic phasing and the rapid determination of the structures of multimers with limited NMR information.
Simian immunodeficiency virus envelope glycoprotein counteracts tetherin/BST-2/CD317 by intracellular sequestration
Authors: Gupta Ravindra K. , Mlcochova Petra , Pelchen-Matthews Annegret , Petit Sarah J. , Mattiuzzo Giada , Pillay Deenan , Takeuchi Yasuhiro , Marsh Mark , Towers Greg J.
Published: October 2009

Tetherin is an IFN-inducible restriction factor that inhibits HIV-1 particle release in the absence of the HIV-1 countermeasure, viral protein U (Vpu). Although ubiquitous in HIV-1 and simian immunodeficiency viruses from chimpanzees, greater spot nosed monkeys, mustached monkeys, and Mona monkeys, other primate lentiviruses do not encode a Vpu protein. Here we demonstrate that SIV from Tantalus monkeys (SIVtan) encodes an envelope glycoprotein (SIVtan Env) able to counteract tetherin from Tantalus monkeys, rhesus monkeys, sooty mangabeys, and humans, but not from pigs. We show that sensitivity to Vpu but not SIVtan Env can be transferred with the human tetherin transmembrane region. We also identify a mutation in the tetherin extracellular domain, which almost completely abolishes sensitivity of human tetherin to SIVtan Env without compromising antiviral activity or sensitivity to Vpu. SIVtan Env expression results in a reduction of surface tetherin, as well as reduction in tetherin co-localization with mature surface-associated virus. Immuno-electron microscopy reveals co-localization of SIVtan Env with tetherin in intracellular tubulo-vesicular structures, suggesting that tetherin is sequestered away from budding virions at the cell surface. Along with HIV-1 Vpu and SIV Nef, envelope glycoprotein is the third and most broadly active lentiviral-encoded tetherin countermeasure to be described. Our observations emphasize the importance of tetherin in protecting mammals against viral infection and suggest that HIV-1 Vpu inhibitors may select active envelope mutants.
Molecular basis for insulin fibril assembly
Authors: Ivanova Magdalena I. , Sievers Stuart A. , Sawaya Michael R. , Wall Joseph S. , Eisenberg David
Published: October 2009

In the rare medical condition termed injection amyloidosis, extracellular fibrils of insulin are observed. We found that the segment of the insulin B-chain with sequence LVEALYL is the smallest segment that both nucleates and inhibits the fibrillation of full-length insulin in a molar ratio–dependent manner, suggesting that this segment is central to the cross-β spine of the insulin fibril. In isolation from the rest of the protein, LVEALYL forms microcrystalline aggregates with fibrillar morphology, the structure of which we determined to 1 Å resolution. The LVEALYL segments are stacked into pairs of tightly interdigitated β-sheets, each pair displaying the dry steric zipper interface typical of amyloid-like fibrils. This structure leads to a model for fibrils of human insulin consistent with electron microscopic, x-ray fiber diffraction, and biochemical studies.
A [Cu
2
O]
2+
core in Cu-ZSM-5, the active site in the oxidation of methane to methanol
Authors: Woertink Julia S. , Smeets Pieter J. , Groothaert Marijke H. , Vance Michael A. , Sels Bert F. , Schoonheydt Robert A. , Solomon Edward I.
Published: October 2009

Driven by the depletion of crude oil, the direct oxidation of methane to methanol has been of considerable interest. Promising low-temperature activity of an oxygen-activated zeolite, Cu-ZSM-5, has recently been reported in this selective oxidation and the active site in this reaction correlates with an absorption feature at 22,700 cm
−1
. In the present study, this absorption band is used to selectively resonance enhance Raman vibrations of this active site.
18
O
2
labeling experiments allow definitive assignment of the observed vibrations and exclude all previously characterized copper-oxygen species for the active site. In combination with DFT and normal coordinate analysis calculations, the oxygen activated Cu core is uniquely defined as a bent mono-(μ-oxo)dicupric site. Spectroscopically validated electronic structure calculations show polarization of the low-lying singly-occupied molecular orbital of the [Cu
2
O]
2+
core, which is directed into the zeolite channel, upon approach of CH
4
. This induces significant oxyl character into the bridging O atom leading to a low transition state energy consistent with experiment and explains why the bent mono-(μ-oxo)dicupric core is highly activated for H atom abstraction from CH
4
. The oxygen intermediate of Cu-ZSM-5 is now the most well defined species active in the methane monooxygenase reaction.
Foundations, lessons, and insider tips for MSR research
Authors: Fornaciari Charles J. , Lund Dean Kathy
Published: October 2009

Any new field of inquiry struggles with issues such as domain uniqueness, research methodologies, construct definition and operationalization, and foundational literature identification. Following Hambrick's (1990) seminal study of strategic management, we similarly examine the management,
spirituality, and religion (MSR) field. Using Hambrick's methodology for citation analysis and a dataset of the founding decade of MSR empirical articles, we offer a guide for those doing MSR research. Study outcomes include the 50 most cited MSR works, the 50 most cited journals that MSR
scholars use as the foundation of their research, and a theme analysis of the 50 foundational works. Our goals are threefold: to list the seminal works that should inform the framing of future work, to list a variety of possible MSR journal scholarship inspirations and outlets, and to empirically
demonstrate current and past MSR research topics so new and experienced MSR scholars can move beyond extant work.
Spiritual behaviour in the workplace as a topic for research
Authors: Hernández López Lidia , Ramos Ramos Rosario , Ramos Ramos Sergio
Published: October 2009

Spirituality at work is a fascinating and complex variable. It is linked to findings for business management such that it makes organizations grow faster, increases efficiency, enhances organizational performance, improves communication and a greater sense of team and community, and
is related positively to employee's attitudes towards their work. Consequently, more employers are encouraging the expression of spirituality in the workplace as a way to boost loyalty and increase morale. However, there is empirical evidence that runs contrary to the common assertion of employees
that they desire or expect organizational and supervisory involvement in their spirituality in the workplace. With the aim of specifying the construct of spirituality at work, the article proposes a theoretical approach that assumes that spirituality in the workplace is not independent of
environmental influence. It investigates the various processes and elements that interact at individual, organizational, and societal levels.
Circumstantial development and athletic excellence: The role of date of birth and birthplace
Authors: Baker Joe , Schorer Jörg , Cobley Stephen , Schimmer Gabriele , Wattie Nick
Published: October 2009

Researchers are only beginning to understand how contextual variables such as date of birth and birthplace affect the development of elite athletes. This article considers the generality of birthplace and date‐of‐birth effects in varying sport contexts. The Study 1 examined how environmental factors associated with an athlete's date‐of‐birth and size of birthplace predict the likelihood of becoming an Olympic athlete in Canada, the United States of America, Germany, and the United Kingdom. Study 2 examined date‐of‐birth and birthplace effects among athletes playing in the first professional league in Germany. Study 2 also examined the validity of birthplace as a proxy for early developmental environment by comparing birthplace with the place of first sports club in four German sports leagues. Results from both studies showed no consistent findings for date of birth. Findings from Study 2 also suggested incongruence between birthplace and location of first sports club as proxies for early developmental environment. Although there was some consistency suggesting elite athletes are less likely to come from very small or excessively large communities, exceptions occurred both within and across sport contexts. These results suggest that any developmental effects of date and place of birth are buffered by broader socio‐cultural factors.
Physical characteristics, physiological attributes, and on‐court performances of handball players: A review
Authors: Ziv Gal , Lidor Ronnie
Published: October 2009

The main purpose of this article was to review a series of studies (n=23) on physical characteristics, physiological attributes, throwing velocity and accuracy, and on‐court performances of male handball players – amateur players, experienced players, professional players, and players on the national team. Five main findings emerged from our review: (1) Elite players are heavier and have higher fat‐free mass than amateur players. (2) The maximal oxygen uptake of male players is between 50 and 60 ml · kg−1 · min−1. (3) Throwing velocity is higher by as much as 9% in elite male players compared with amateur male players. (4) Heart rates can rise above 160 beats · min−1 in male players during a game. (5) On‐court distance covered in a game averaged approximately 4 km and ranged between 2 and 5 km, depending on playing position. Our methodological concerns based on the reviewed studies are: (a) a lack of on‐court physiological data; (b) a lack of experimental/manipulative studies; (c) limited data on throwing accuracy; and (d) a lack of longitudinal studies. The practical implications include: (a) strength and power exercises should be emphasized in conditioning programmes, as they are associated with both sprint performance and throwing velocity; (b) speed and agility drills should also be implemented in conditioning programmes; and (c) specificity of training based upon the position of the player is of great importance when planning strength and conditioning programmes.
Analytic approximation of the Tavis–Cummings ground state via projected states
Authors: Castaños Octavio , Nahmad-Achar Eduardo , López-Peña Ramón , Hirsch Jorge G
Published: October 2009

We show that an excellent approximation to the exact quantum solution of the ground state of the Tavis–Cummings model is obtained by means of a semi-classical projected state. This state has an analytical form in terms of model parameters and, in contrast to the exact quantum state, allows for an analytical calculation of the expectation values of field and matter observables, entanglement entropy between field and matter, squeezing parameter and population probability distributions. The fidelity between this projected state and the exact quantum ground state is very close to 1, except for the region of classical phase transitions. We compare the analytical results with those of the exact solution obtained through direct Hamiltonian diagonalization as a function of atomic separation energy and matter–field coupling.
XAS study of the orientation of oriented carbon nanotube films
Authors: Medjo R Eba , Sendja B Thiodjio , Mane J Mane , Ateba P Owono
Published: October 2009

We report a quantitative x-ray absorption spectroscopy (XAS) study of the orientation of carbon nanotubes (CNTs) grown on plain SiO2(thickness 8 nm)/Si(100) substrates by a catalytically enhanced dc hot filament chemical vapour deposition (CVD) process. The alignment and orientation of CNT films are generally provided in the literature by scanning electron microscope (SEM) and transmission electron microscope (TEM) images qualitatively. A very few other techniques have been used to more deeply study the alignment of CNTs grown by the CVD technique, such as x-ray diffraction (XRD) or grazing-incidence small-angle x-ray scattering (GISAXS). XAS recorded on the C K-edge provides information on the local environment around carbon atoms and helps us study the orientation of CNTs. We find spectral features very similar to those of HOPG, in agreement with the literature. Meanwhile, we do not observe any extinction of the π* band at grazing incidence. CNTs have an averaged direction perpendicular to the surface of the substrate.
Inverse and conventional magnetic entropy change in La0.8Sm0.2Mn2Si2 and La0.775Gd0.225Mn2Si2 compounds
Authors: Emre Baris , Dincer Ilker , Elerman Yalcin , Duman Eyup
Published: October 2009

The magnetic and magnetocaloric properties of La0.8Sm0.2Mn2Si2 and La0.775Gd0.225Mn2Si2 compounds have been studied by temperature- and magnetic field-dependent magnetic measurements. Both compounds crystallize in the ThCr2Si2-type structure with the space group I4/mmm. Both compounds exhibit reentrant magnetic phase transitions and field-induced transitions from antiferromagnetic to ferromagnetic or ferrimagnetic state. The isothermal magnetic entropy change is estimated by using the Maxwell relation and Landau theory. Both compounds show inverse and conventional magnetocaloric effects around transition temperatures. Application of Landau theory on magnetic transitions shows good agreement with the result obtained by Maxwell theory.
Mammalian pre-mRNA 3′ End Processing Factor CF Im68 Functions in mRNA Export
Authors: Ruepp Marc-David , Aringhieri Chiara , Vivarelli Silvia , Cardinale Stefano , Paro Simona , Schümperli Daniel , Barabino Silvia M.L.
Published: October 2009

Export of mRNA from the nucleus is linked to proper processing and packaging into ribonucleoprotein complexes. Although several observations indicate a coupling between mRNA 3′ end formation and export, it is not known how these two processes are mechanistically connected. Here, we show that a subunit of the mammalian pre-mRNA 3′ end processing complex, CF Im68, stimulates mRNA export. CF Im68 shuttles between the nucleus and the cytoplasm in a transcription-dependent manner and interacts with the mRNA export receptor NXF1/TAP. Consistent with the idea that CF Im68 may act as a novel adaptor for NXF1/TAP, we show that CF Im68 promotes the export of a reporter mRNA as well as of endogenous mRNAs, whereas silencing by RNAi results in the accumulation of mRNAs in the nucleus. Moreover, CF Im68 associates with 80S ribosomes but not polysomes, suggesting that it is part of the mRNP that is remodeled in the cytoplasm during the initial stages of translation. These results reveal a novel function for the pre-mRNA 3′ end processing factor CF Im68 in mRNA export.
The E3 Ubiquitin Ligases Hrd1 and gp78 Bind to and Promote Cholera Toxin Retro-Translocation
Authors: Bernardi Kaleena M. , Williams Jeffrey M. , Kikkert Marjolein , van Voorden Sjaak , Wiertz Emmanuel J. , Ye Yihong , Tsai Billy
Published: October 2009

To cause disease, cholera toxin (CT) is transported from the cell surface to the endoplasmic reticulum (ER) lumen where the catalytic CTA1 subunit retro-translocates to the cytosol to induce pathological water secretion. Two retro-translocon components are the Derlins and ER-associated multi-spanning E3 ubiquitin ligases including Hrd1 and gp78. We demonstrated previously that Derlin-1 facilitates CTA1 retro-translocation. However, as CTA1 is neither ubiquitinated on lysines nor at its N-terminus, the role of E3 ligases in toxin retro-translocation is unclear. Here, we show that expression of mutant Hrd1 and gp78 and a mutant E2-conjugating enzyme dedicated to retro-translocation (Ube2g2) decrease CTA1 retro-translocation. Hrd1 knockdown also attenuated toxin retro-translocation. Binding studies demonstrate that Hrd1 and gp78 interact with CT and protein disulfide isomerase, an ER chaperone that unfolds CTA1 to initiate translocation. Moreover, we find that the toxin's association with Hrd1 and gp78 is blocked by dominant-negative Derlin-1, suggesting that CT is targeted initially to Derlin-1 and then transferred to Hrd1 and gp78. These data demonstrate a role of the E3 ubiquitin ligases in CTA1 retro-translocation, implicate a sequence of events experienced by the toxin on the ER membrane, and raise the possibility that ubiquitination is involved in the transport process.
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations
Authors: Yu W. , Clyne M. , Khoury M. J. , Gwinn M.
Published: October 2009

Summary: We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continuously updated from PubMed. These applications provide user-friendly interfaces for searching summarized information on human genetic associations, using either genes or diseases as the starting point.

Availability: Phenopedia and Genopedia can be freely accessed at http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do and http://www.hugenavigator.net/HuGENavigator/startPagePedia.do, respectively.

Contact:  wby0@cdc.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Severe cardiomyopathy following treatment with the tumour necrosis factor‐α inhibitor adalimumab for Crohn's disease
Authors: Emmert Maximilian Y. , Salzberg Sacha P. , Emmert Lorenz S. , Behjati Sohil , Plass Andre , Felix Christian , Falk Volkmar , Gruenenfelder Juerg
Published: October 2009

Adalimumab belongs to the group of tumour necrosis factor‐α inhibitors and has been approved for the treatment Crohn's Disease since 2007. Herein we report a severe adverse reaction to adalimumab in a 25‐year‐old female patient. One week after the initial‐dose of adalimumab (160 mg), which was initiated due to an acute exacerbation of Crohn's disease, the patient developed a fulminant cardiomyopathy. In severe cardiogenic shock, the patient required an extracorporeal membrane‐oxygenation system for 8 days until cardiac recovery.
Sleep apnoea induces cardiac electrical instability assessed by T‐wave alternans in patients with congestive heart failure
Authors: Takasugi Nobuhiro , Nishigaki Kazuhiko , Kubota Tomoki , Tsuchiya Kunihiko , Natsuyama Kenji , Takasugi Mieko , Nawa Takahide , Ojio Shinsuke , Aoyama Takuma , Kawasaki Masanori , Takemura Genzou , Minatoguchi Shinya
Published: October 2009

Aims

To assess the involvement of sleep apnoea in nocturnal sudden cardiac death (SCD) by evaluating cardiac electrical instability using T‐wave alternans (TWA), a risk marker for lethal cardiac arrhythmias, and severity of sleep apnoea in congestive heart failure (CHF) patients.

Methods and results

A total of 40 CHF patients simultaneously underwent overnight simplified respiratory polygraphy and 24 h continuous electrocardiography. Peak TWA during both daytime and nighttime were calculated by the modified moving average method. The patients were divided into two groups; 30 patients with daytime predominant TWA (whose peak TWA was higher during daytime than during nighttime) and 10 with nighttime predominant. Apnoea–hypopnoea index (AHI) was significantly higher in patients with nighttime predominant TWA than in those with daytime predominant (35.9 ± 8.1 vs. 23.9 ± 14.4 events/h, P = 0.02), and was an independent predictor of nighttime predominant TWA (odds ratio, 1.08; 95% confidence interval, 1.01–1.16; P = 0.03). Moreover, peak TWA during the night was correlated positively with AHI (P < 0.001), and AHI was an independent determinant of nocturnal TWA value (r2 = 0.27, P = 0.009).

Conclusion

In CHF patients, sleep apnoea induces cardiac electrical instability manifested as TWA, reflecting increased risk of nocturnal SCD. Moreover, some CHF patients with sleep apnoea exhibit nighttime predominant TWA. Therefore, TWA should also be evaluated during the night.
Decreased soluble TWEAK levels predict an adverse prognosis in patients with chronic stable heart failure
Authors: Chorianopoulos Emmanuel , Rosenberg Mark , Zugck Christian , Wolf Johanna , Katus Hugo A. , Frey Norbert
Published: October 2009

Aims

Tumour necrosis factor (TNF)‐like weak inducer of apoptosis (sTWEAK) is a multifunctional cytokine that has recently been implicated in cardiovascular disease. The aim of this study was to define the plasma levels of sTWEAK in patients with stable chronic heart failure and evaluate the possibility of a prognostic impact of sTWEAK.

Methods and results

sTWEAK levels in plasma samples from 364 patients with systolic heart failure were compared with 36 control patients. The median levels of sTWEAK in heart failure patients were significantly lower than those of the control group (217 pg/mL, interquartile range 136–311 vs. 325 pg/mL, interquartile range 250–394 pg/mL). Moreover, sTWEAK levels were lower in patients with ischaemic cardiomyopathy vs. dilated cardiomyopathy and correlated significantly with functional NYHA class. Patients with plasma levels below a ROC‐derived cut‐off value of 227 pg/mL had a significantly higher mortality rate after 4 years. Upon univariate and multivariate analyses, sTWEAK levels below 227 pg/mL emerged as an independent predictor of subsequent death.

Conclusion

In contrast to other cytokines shown to be increased in heart failure patients, plasma levels of sTWEAK are significantly reduced in chronic stable heart failure. In addition, lower plasma levels of sTWEAK predict an adverse prognosis independent of established risk markers such as NT‐proBNP.
Individual quotas, fishing effort allocation, and over-quota discarding in mixed fisheries
Authors: Poos J. J. , Bogaards J. A. , Quirijns F. J. , Gillis D. M. , Rijnsdorp A. D.
Published: October 2009

Poos, J. J., Bogaards, J. A., Quirijns, F. J., Gillis, D. M., and Rijnsdorp, A. D. 2010. Individual quotas, fishing effort allocation, and over-quota discarding in mixed fisheries. – ICES Journal of Marine Science, 67: 323–333. Many fisheries are managed by total allowable catches (TACs) and a substantial part by individual quotas. Such output management has not been successful in mixed fisheries when fishers continue to fish while discarding marketable fish. We analyse the effects of individual quotas on spatial and temporal effort allocation and over-quota discarding in a multispecies fishery. Using a spatially explicit dynamic-state variable model, the optimal fishing strategy of fishers constrained by annual individual quotas, facing uncertainty in catch rates, is studied. Individual fishers will move away from areas with high catches of the restricted quota species and, depending on the cost of fishing, will stop fishing in certain periods of the year. Individual vessels will discard marketable fish, but only after their individual quota for the species under consideration has been reached. These results are in line with observations on effort allocation and discarding of marketable fish, both over-quota discarding and highgrading, by the Dutch beam-trawl fleet. The models we present can be used to predict the outcomes of management and are therefore a useful tool for fisheries scientists and managers.
Tropical warming and the dynamics of endangered primates
Authors: Wiederholt Ruscena , Post Eric
Published: October 2009

Many primate species are severely threatened, but little is known about the effects of global warming and the associated intensification of El Niño events on primate populations. Here, we document the influences of the El Niño southern oscillation (ENSO) and hemispheric climatic variability on the population dynamics of four genera of ateline (neotropical, large-bodied) primates. All ateline genera experienced either an immediate or a lagged negative effect of El Niño events. ENSO events were also found to influence primate resource levels through neotropical arboreal phenology. Furthermore, frugivorous primates showed a high degree of interspecific population synchrony over large scales across Central and South America attributable to the recent trends in large-scale climate. These results highlight the role of large-scale climatic variation and trends in ateline primate population dynamics, and emphasize that global warming could pose additional threats to the persistence of multiple species of endangered primates.
With his memory magnetically erased, a monkey knows he is uncertain
Authors: Washburn David A. , Gulledge Jonathan P. , Beran Michael J. , Smith J. David
Published: October 2009

Although intelligence is associated with what one knows, it is also important to recognize and to respond adaptively when one is uncertain. This competency has been examined developmentally and comparatively, but it is difficult to distinguish between objective versus subjective cues to which organisms may respond. In this study, transcranial magnetic stimulation was used to disrupt cognitive processing by a rhesus monkey (
Macaca mulatta
) in a computerized divided visual field memory task. When magnetic stimulation disrupted neural activity in the cerebral hemisphere that initially processed the visual images, recognition accuracy declined and use of the uncertain response significantly increased, relative to control conditions. Thus, the monkey tended to respond adaptively when he did not know the answer—where uncertainty was produced by targeted disruption of the neural processing of a stimulus—even in the absence of external, objective cues to corroborate his subjective, metacognitive assessment of uncertainty.
Individual consistency in flight initiation distances in burrowing owls: a new hypothesis on disturbance-induced habitat selection
Authors: Carrete Martina , Tella José L.
Published: October 2009

Individuals often consistently differ in personalities and behaviours that allow them to cope with environmental variation. Flight initiation distance (FID) has been measured in a variety of taxa as an estimate of the risk that an individual is willing to take when facing a predator. FID has been used to test life-history trade-offs related to anti-predatory behaviour and for conservation purposes such as to establish buffer zones to minimize human disturbance, given its species-specific consistency. Individual consistency in FID, however, has been largely overlooked. Here we show that, even after controlling for several confounding effects, this behaviour has a strong individual component (repeatability = 0.84–0.92) in a bird species, leaving a small margin for behavioural flexibility. We hypothesize that individuals may distribute themselves among breeding sites depending on their individual susceptibility to human disturbance. This habitat selection hypothesis merits further research, given its implications on both evolutionary and applied ecology research. For example, selection of human-tolerant phenotypes may be promoted through the humanization of habitats occurring worldwide, and when population means instead of individual variability in FID are considered for designing buffer zones to reduce human impacts on wildlife.
Mountain lions prey selectively on prion-infected mule deer
Authors: Krumm Caroline E. , Conner Mary M. , Hobbs N. Thompson , Hunter Don O. , Miller Michael W.
Published: October 2009

The possibility that predators choose prey selectively based on age or condition has been suggested but rarely tested. We examined whether mountain lions (
Puma concolor
) selectively prey upon mule deer (
Odocoileus hemionus
) infected with chronic wasting disease, a prion disease. We located kill sites of mountain lions in the northern Front Range of Colorado, USA, and compared disease prevalence among lion-killed adult (≥2 years old) deer with prevalence among sympatric deer taken by hunters in the vicinity of kill sites. Hunter-killed female deer were less likely to be infected than males (odds ratios (OR) = 0.2, 95% confidence intervals (CI) = 0.1–0.6;
p
= 0.015). However, both female (OR = 8.5, 95% CI = 2.3–30.9) and male deer (OR = 3.2, 95% CI = 1–10) killed by a mountain lion were more likely to be infected than same-sex deer killed in the vicinity by a hunter (
p
< 0.001), suggesting that mountain lions in this area actively selected prion-infected individuals when targeting adult mule deer as prey items.
Visual cues and parental favouritism in a nocturnal bird
Authors: Parejo Deseada , Avilés Jesús M. , Rodríguez Juan
Published: October 2009

Visual signals are crucial for parent–offspring communication, although their functioning has been neglected for nocturnal birds. Here, we investigated parental preference for nestling coloration in nocturnal conditions—a question hitherto unexplored—in a nocturnal raptor, the scops owl (Otus scops). We assessed how parents allocated food during the night in relation to a manipulation of ultraviolet (UV) reflectance of the cere (skin above the beak) of their offspring. Reflectance of the cere shows a marked peak in the UV part of the spectrum, and location of the UV peak is related to nestling body mass (i.e. heavier nestlings have a UV peak at lower wavelengths). We found evidence of parental bias in favour of lighter offspring: UV-reduced nestlings gained more weight during the night than their control siblings. This study provides the first experimental evidence of the use of visual cues for parent–offspring communication in a nocturnal bird.
Giant panda conservation science: how far we have come
Authors: Swaisgood Ronald R. , Wei Fuwen , Wildt David E. , Kouba Andrew J. , Zhang Zejun
Published: October 2009

The giant panda is a conservation icon, but science has been slow to take up its cause in earnest. In the past decade, researchers have been making up for lost time, as reflected in the flurry of activity reported at the symposium
Conservation Science for Giant Pandas and Their Habitat
at the 2009 International Congress for Conservation Biology (ICCB) in Beijing. In reports addressing topics ranging from spatial ecology to molecular censusing, from habitat recovery in newly established reserves to earthquake-induced habitat loss, from new insights into factors limiting carrying capacity to the uncertain effects of climate change, this symposium displayed the vibrant and blossoming application of science to giant panda conservation. Collectively, we find that we have come a long way, but we also reach an all-too-familiar conclusion: the more we know, the more challenges are revealed. While many earlier findings are supported, many of our assumptions are debatable. Here we discuss recent advancements in conservation science for giant pandas and suggest that the way forward is more direct application of emerging science to management and policy.
Correction for Holliday and Flavell, John Robert Stanley Fincham. 11 August 1926 – 9 February 2005
Authors: Holliday Robin , Flavell Richard B.
Published: October 2009

Correction for ‘John Robert Stanley Fincham. 11 August 1926 – 9 February 2005’ by Robin Holliday and Richard B. Flavell (Biogr. Mems Fell. R. Soc.
52
, 83–95.
(doi:
10.1098/rsbm.2006.0007
)).

On page 86, line 30, ‘in that laboratory’ should read ‘at Stanford University’.
Systemic risk: the dynamics of model banking systems
Authors: May Robert M. , Arinaminpathy Nimalan
Published: October 2009

The recent banking crises have made it clear that increasingly complex strategies for managing risk in individual banks have not been matched by corresponding attention to overall systemic risks. We explore some simple mathematical caricatures for ‘banking ecosystems’, with emphasis on the interplay between the characteristics of individual banks (capital reserves in relation to total assets, etc.) and the overall dynamical behaviour of the system. The results are discussed in relation to potential regulations aimed at reducing systemic risk.
Transient virulence of emerging pathogens
Authors: Bolker Benjamin M. , Nanda Arjun , Shah Dharmini
Published: October 2009

Should emerging pathogens be unusually virulent? If so, why? Existing theories of virulence evolution based on a tradeoff between high transmission rates and long infectious periods imply that epidemic growth conditions will select for higher virulence, possibly leading to a transient peak in virulence near the beginning of an epidemic. This transient selection could lead to high virulence in emerging pathogens. Using a simple model of the epidemiological and evolutionary dynamics of emerging pathogens, along with rough estimates of parameters for pathogens such as severe acute respiratory syndrome, West Nile virus and myxomatosis, we estimated the potential magnitude and timing of such transient virulence peaks. Pathogens that are moderately evolvable, highly transmissible, and highly virulent at equilibrium could briefly double their virulence during an epidemic; thus, epidemic-phase selection could contribute significantly to the virulence of emerging pathogens. In order to further assess the potential significance of this mechanism, we bring together data from the literature for the shapes of tradeoff curves for several pathogens (myxomatosis, HIV, and a parasite ofDaphnia) and the level of genetic variation for virulence for one (myxomatosis). We discuss the need for better data on tradeoff curves and genetic variance in order to evaluate the plausibility of various scenarios of virulence evolution.
Correction for Broderick
et al.
, Fidelity and over-wintering of sea turtles
Authors: Broderick Annette C. , Coyne Michael S. , Fuller Wayne J. , Glen Fiona , Godley Brendan J.
Published: October 2009

Correction for ‘Fidelity and over-wintering of sea turtles’ by Annette C. Broderick, Michael S. Coyne, Wayne J. Fuller, Fiona Glen and Brendan J. Godley (Proc. R. Soc. B
274
, 1533–1538.
(doi:
10.1098/rspb.2007.0211
)).

The scale bar in figure 2b was incorrect, and should read as follows: 5 km.
Refugia revisited: individualistic responses of species in space and time
Authors: Stewart John R. , Lister Adrian M. , Barnes Ian , Dalén Love
Published: October 2009

Climate change in the past has led to significant changes in species' distributions. However, how individual species respond to climate change depends largely on their adaptations and environmental tolerances. In the Quaternary, temperate-adapted taxa are in general confined to refugia during glacials while cold-adapted taxa are in refugia during interglacials. In the Northern Hemisphere, evidence appears to be mounting that in addition to traditional southern refugia for temperate species, cryptic refugia existed in the North during glacials. Equivalent cryptic southern refugia, to the south of the more conventional high-latitude polar refugia, exist in montane areas during periods of warm climate, such as the current interglacial. There is also a continental/oceanic longitudinal gradient, which should be included in a more complete consideration of the interaction between species ranges and climates. Overall, it seems clear that there is large variation in both the size of refugia and the duration during which species are confined to them. This has implications for the role of refugia in the evolution of species and their genetic diversity.
The effect of personality on social foraging: shy barnacle geese scrounge more
Authors: Kurvers Ralf H. J. M. , Prins Herbert H. T. , van Wieren Sipke E. , van Oers Kees , Nolet Bart A. , Ydenberg Ronald C.
Published: October 2009

Animals foraging in groups can either search for food themselves (producing) or search for the food discoveries of other individuals (scrounging). Tactic use in producer–scrounger games is partly flexible but individuals tend to show consistency in tactic use under different conditions suggesting that personality might play a role in tactic use in producer–scrounger games. Here we studied the use of producing and scrounging tactics by bold and shy barnacle geese (
Branta leucopsis
), where boldness is a personality trait known to be repeatable over time in this species. We defined individuals as bold, shy or intermediate based on two novel object tests. We scored the frequency of finding food patches (the outcome of investing in producing) and joining patches (the outcome of investing in scrounging) by bold and shy individuals and their feeding time. Shy individuals had a higher frequency of joining than bold individuals, demonstrating for the first time that personality is associated with tactic use in a producer–scrounger game. Bold individuals tended to spend more time feeding than shy individuals. Our results highlight the importance of including individual behavioural variation in models of producer–scrounger games.
Female's courtship threshold allows intruding males to mate with reduced effort
Authors: Stoltz J. A. , Andrade M. C. B.
Published: October 2009

Female decision rules can influence the nature and intensity of sexual selection on males, but empirical demonstrations of rules underlying choice are rare. We hypothesized that female choice is largely based on a courtship duration threshold in the Australian redback spider (
Latrodectus hasselti
) because females kill males before copulation is complete (premature cannibalism) and reduce their paternity if courtship is brief. We used published data to infer that the female's threshold is approximately 100 min of courtship. We support this hypothesis by showing that premature cannibalism is common when the male's courtship duration is below this threshold, but is infrequent and unrelated to duration once courtship exceeds the threshold. We then ask whether females discriminate the source of courtship when rival males compete, as this will determine the effect of the threshold on male competitive tactics. We staged competitions where ‘resident’ males initially courted females in the absence of competition, exceeding the courtship threshold before ‘intruding’ males were introduced. Intruding males mated rapidly but were not prematurely cannibalized by females, in contrast to cases where competition starts before the threshold is surpassed. This suggests females do not distinguish which male satisfies the threshold, allowing intruders to parasitize the courtship efforts of residents. To our knowledge, such exploitation of mating efforts by rival males mediated by a female choice threshold has not been demonstrated elsewhere. Ironically, this female choice threshold and the attendant possibility of courtship parasitism may lead to selection for lower-quality males to recognize and seek out (rather than avoid) webs in which competitors are already present.
Facial cues of dominance modulate the short-term gaze-cuing effect in human observers
Authors: Jones Benedict C. , DeBruine Lisa M. , Main Julie C. , Little Anthony C. , Welling Lisa L. M. , Feinberg David R. , Tiddeman Bernard P.
Published: October 2009

Responding appropriately to gaze cues is essential for fluent social interaction, playing a crucial role in social learning, collaboration, threat assessment and understanding others’ intentions. Previous research has shown that responses to gaze cues can be studied by investigating the gaze-cuing effect (i.e. the tendency for observers to respond more quickly to targets in locations that were cued by others’ gaze than to uncued targets). A recent study demonstrating that macaques demonstrate larger gaze-cuing effects when viewing dominant conspecifics than when viewing subordinate conspecifics suggests that cues of dominance modulate the gaze-cuing effect in at least one primate species. Here, we show a similar effect of facial cues associated with dominance on gaze cuing in human observers: at short viewing times, observers demonstrated a greater cuing effect for gaze cues from masculinized (i.e. dominant) faces than from feminized (i.e. subordinate) faces. Moreover, this effect of facial masculinity on gaze cuing decreased as viewing time was increased, suggesting that the effect is driven by involuntary responses. Our findings suggest that the mechanisms that underpin reflexive gaze cuing evolved to be sensitive to facial cues of others’ dominance, potentially because such differential gaze cuing promoted desirable outcomes from encounters with dominant individuals.
Thermoregulatory behaviour affects prevalence of chytrid fungal infection in a wild population of Panamanian golden frogs
Authors: Richards-Zawacki Corinne L.
Published: October 2009

Predicting how climate change will affect disease dynamics requires an understanding of how the environment affects host–pathogen interactions. For amphibians, global declines and extinctions have been linked to a pathogenic chytrid fungus,Batrachochytrium dendrobatidis. Using a combination of body temperature measurements and disease assays conducted before and after the arrival ofB. dendrobatidis, this study tested the hypothesis that body temperature affects the prevalence of infection in a wild population of Panamanian golden frogs (Atelopus zeteki). The timing of first detection of the fungus was consistent with that of a wave of epidemic infections spreading south and eastward through Central America. During the epidemic, many golden frogs modified their thermoregulatory behaviour, raising body temperatures above their normal set point. Odds of infection decreased with increasing body temperature, demonstrating that even slight environmental or behavioural changes have the potential to affect an individual's vulnerability to infection. The thermal dependency of the relationship betweenB. dendrobatidisand its amphibian hosts demonstrates how the progression of an epidemic can be influenced by complex interactions between host and pathogen phenotypes and the environments in which they are found.
Intensive fish farming and the evolution of pathogen virulence: the case of columnaris disease in Finland
Authors: Pulkkinen K. , Suomalainen L.-R. , Read A. F. , Ebert D. , Rintamäki P. , Valtonen E. T.
Published: October 2009

Ecological changes affect pathogen epidemiology and evolution and may trigger the emergence of novel diseases. Aquaculture radically alters the ecology of fish and their pathogens. Here we show an increase in the occurrence of the bacterial fish diseaseFlavobacterium columnarein salmon fingerlings at a fish farm in northern Finland over 23 years. We hypothesize that this emergence was owing to evolutionary changes in bacterial virulence. We base this argument on several observations. First, the emergence was associated with increased severity of symptoms. Second,F. columnarestrains vary in virulence, with more lethal strains inducing more severe symptoms prior to death. Third, more virulent strains have greater infectivity, higher tissue-degrading capacity and higher growth rates. Fourth, pathogen strains co-occur, so that strains compete. Fifth,F. columnarecan transmit efficiently from dead fish, and maintain infectivity in sterilized water for months, strongly reducing the fitness cost of host death likely experienced by the pathogen in nature. Moreover, this saprophytic infectiousness means that chemotherapy strongly select for strains that rapidly kill their hosts: dead fish remain infectious; treated fish do not. Finally, high stocking densities of homogeneous subsets of fish greatly enhance transmission opportunities. We suggest that fish farms provide an environment that promotes the circulation of more virulent strains ofF. columnare. This effect is intensified by the recent increases in summer water temperature. More generally, we predict that intensive fish farming will lead to the evolution of more virulent pathogens.
Correction for Butlin and Tregenza, Levels of genetic polymorphism: marker loci versus quantitative traits
Authors: Butlin R. K. , Tregenza T.
Published: October 2009

Correction for ‘Levels of genetic polymorphism: marker loci versus quantitative traits’ by R. K. Butlin and T. Tregenza (Phil. Trans. R. Soc. Lond. B
353
, 187–198.
(doi:
10.1098/rstb.1998.0201
)).

Some of the values in table 1 on p. 193 were given incorrectly. The errors do not affect the conclusions drawn in the paper. The corrected table is reproduced below.