bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and enzymatic characterization of a glycoside hydrolase family 31 α-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification
Authors: Larsbrink Johan , Izumi Atsushi , Ibatullin Farid M. , Nakhai Azadeh , Gilbert Harry J. , Davies Gideon J. , Brumer Harry
Published: March 2011

The desire for improved methods of biomass conversion into fuels and feedstocks has re-awakened interest in the enzymology of plant cell wall degradation. The complex polysaccharide xyloglucan is abundant in plant matter, where it may account for up to 20% of the total primary cell wall carbohydrates. Despite this, few studies have focused on xyloglucan saccharification, which requires a consortium of enzymes including endo-xyloglucanases, α-xylosidases, β-galactosidases and α-L-fucosidases, among others. In the present paper, we show the characterization of Xyl31A, a key α-xylosidase in xyloglucan utilization by the model Gram-negative soil saprophyte Cellvibrio japonicus. CjXyl31A exhibits high regiospecificity for the hydrolysis of XGOs (xylogluco-oligosaccharides), with a particular preference for longer substrates. Crystallographic structures of both the apo enzyme and the trapped covalent 5-fluoro-β-xylosyl-enzyme intermediate, together with docking studies with the XXXG heptasaccharide, revealed, for the first time in GH31 (glycoside hydrolase family 31), the importance of a PA14 domain insert in the recognition of longer oligosaccharides by extension of the active-site pocket. The observation that CjXyl31A was localized to the outer membrane provided support for a biological model of xyloglucan utilization by C. japonicus, in which XGOs generated by the action of a secreted endo-xyloglucanase are ultimately degraded in close proximity to the cell surface. Moreover, the present study diversifies the toolbox of glycosidases for the specific modification and saccharification of cell wall polymers for biotechnological applications.
Superfamily I helicases as modular components of DNA-processing machines
Authors: Dillingham Mark S.
Published: March 2011

Helicases are a ubiquitous and abundant group of motor proteins that couple NTP binding and hydrolysis to processive unwinding of nucleic acids. By targeting this activity to a wide range of specific substrates, and by coupling it with other catalytic functionality, helicases fulfil diverse roles in virtually all aspects of nucleic acid metabolism. The present review takes a look back at our efforts to elucidate the molecular mechanisms of UvrD-like DNA helicases. Using these well-studied enzymes as examples, we also discuss how helicases are programmed by interactions with partner proteins to participate in specific cellular functions.
Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases
Authors: Szczelkun Mark D.
Published: March 2011

To cleave DNA, the Type III RM (restriction–modification) enzymes must communicate the relative orientation of two recognition sequences, which may be separated by many thousands of base pairs. This long-range interaction requires ATP hydrolysis by a helicase domain, and both active (DNA translocation) and passive (DNA sliding) modes of motion along DNA have been proposed. Potential roles for ATP binding and hydrolysis by the helicase domains are discussed, with a focus on bipartite ATPases that act as molecular switches.
The emerging role of FK506-binding proteins as cancer biomarkers: a focus on FKBPL
Authors: McKeen Hayley D. , Brennan Donal J. , Hegarty Shauna , Lanigan Fiona , Jirstrom Karin , Byrne Christopher , Yakkundi Anita , McCarthy Helen O. , Gallagher William M. , Robson Tracy
Published: March 2011

FKBPs (FK506-binding proteins) have long been recognized as key regulators of the response to immunosuppressant drugs and as co-chaperones of steroid receptor complexes. More recently, evidence has emerged suggesting that this diverse protein family may also represent cancer biomarkers owing to their roles in cancer progression and response to treatment. FKBPL (FKBP-like) is a novel FKBP with roles in GR (glucocorticoid receptor), AR (androgen receptor) and ER (oestrogen receptor) signalling. FKBPL binds Hsp90 (heat-shock protein 90) and modulates translocation, transcriptional activation and phosphorylation of these steroid receptors. It has been proposed as a novel prognostic and predictive biomarker, where high levels predict for increased recurrence-free survival in breast cancer patients and enhanced sensitivity to endocrine therapy. Since this protein family has roles in a plethora of signalling pathways, its members represent novel prognostic markers and therapeutic targets for cancer diagnosis and treatment.
Ferritin heavy chain‐mediated iron homoeostasis regulates expression of IL‐10 in Chlamydia trachomatis‐infected HeLa cells
Authors: Vardhan Harsh , Gupta Rishein , Jha Rajneesh , Bhengraj Apurb Rashmi , Mittal Aruna
Published: March 2011

Chlamydia trachomatis is the leading cause of sexually transmitted infection worldwide, in which disease outcome is determined by the balance between pro‐ and anti‐inflammatory host immune responses. Iron plays important roles in regulation and enhancement of various pro‐ and anti‐inflammatory cytokines. Earlier studies have established essentiality of iron in C. trachomatis infection; however, there is lack of study wherein modulatory effect of iron regulated protein [FHC (ferritin heavy chain)] in regulation of anti‐inflammatory cytokine IL (interleukin)‐10 has been investigated. In this study, immunoblotting results showed the up‐regulation of FHC in C. trachomatis‐infected HeLa cells in comparison with mock (in vitro control). Further secretory IL‐10 level was significantly increased (P<0.001) or decreased (P<0.001) in response to iron supplementation [FAC (ferric ammonium citrate)] and depletion [DFO (deferoxamine)], respectively. However, in C. trachomatis‐infected HeLa cells, levels of IL‐10 remain higher, irrespective of availability of iron in comparison with their respective control. These results showed that secretion of IL‐10 and expressions of FHC have concordance. Further, to understand interdependence of IL‐10 and iron homoeostasis (regulation), the levels of IL‐10 were compared with iron‐responsive GFP (green fluorescent protein) expression in HeLa‐229 cells. The mean fluorescent intensities of GFP were in accordance with levels of IL‐10 in C. trachomatis‐infected cells. These results showed the association of secreted IL‐10, FHC and iron homoeostasis in C. trachomatis‐infected HeLa‐229 cells. This study provides insight into host–Chlamydia interaction at the crossroad of iron metabolism and immune responses and may help in realizing the potential of iron homoeostasis modulators in treatment of chronic chlamydial infection.
Histamine promotes the expression of receptors TLR2 and TLR4 and amplifies sensitivity to lipopolysaccharide and lipoteichoic acid treatment in human gingival fibroblasts
Authors: Gutiérrez‐Venegas Gloria , Cruz‐Arrieta Sandra , Villeda‐Navarro Mónica , Méndez‐Mejía José Antonio
Published: March 2011

The vasoactive hydrophilic amine histamine is the most important molecule released by mast cells. However, histamine's role in activating intracellular responses in HGFs (human gingival fibroblasts) has not been evaluated to date. In the present study, we investigated the effect of histamine and of Gram‐negative [LPS (lipopolysaccharide)] and Gram‐positive [LTA (lipoteichoic acid)] bacterial components on the modulation of the inflammatory response of HGFs. We incubated HGFs with histamine to determine whether this hydrophilic amine regulates overexpression of TLR2 (Toll‐like receptor 2) and TLR4, which recognize LTA and LPS respectively. Our experiments demonstrated that histamine increases transcription and translation of TLR2 and TLR4. Incubation with LTA or LPS in the presence of histamine markedly increased expression of COX2 (cyclo‐oxygenase 2) and synthesis of prostaglandin E2. These results suggest that histamine plays an important role in modulating the innate immune response, and likewise, that LTA and LPS regulate the adaptive immune response. The present study provides information about the regulation and expression of molecules that promote chronic inflammatory processes leading to the emergence of periodontitis and the consequent loss of the dental organ.
Population ecology of the long-nosed potoroo (Potorous tridactylus) on French Island, Victoria
Authors: Frankham Greta J. , Reed Robert L. , Fletcher Terry P. , Handasyde Kath A.
Published: March 2011

The elusive nature of the long-nosed potoroo (Potorous tridactylus) has hindered the collection of long-term data for this threatened species. Between June 2005 and May 2009, data on the ecology of a wild population of long-nosed potoroos located on French Island, Victoria, were collected during a series of research projects. Over this period, 33 individual potoroos were trapped a total of 251 times. Up to nine individuals were known to be alive at once on the 15-ha study site of mature remnant native forest. Adult potoroos showed high site fidelity and significant sexual size dimorphism, with males heavier and having longer head and pes lengths than females. Congruent with other studies, we found no evidence of seasonality in breeding. Births occurred in every month of the year and the testis volume of males did not vary throughout the year. In contrast to previous studies, however, we did not observe peaks in breeding activity. Our research and review of existing literature suggests that the ecology of the long-nosed potoroo is strongly influenced by local environmental conditions and emphasises the need to consider long-term and site-specific data when developing management strategies to conserve this ecologically important species.
Modelling Early-type Stars in Eclipsing Binaries of Open Clusters: A New Method for Age Determination from the Ratio of Radii
Authors: Yıldız M.
Published: March 2011

Binary systems, in particular eclipsing binaries, are essential sources of knowledge of the fundamental properties of stars. The ages of binaries, members of open clusters, are constrained by their own fundamental properties and by those of the hosting cluster. The ages of eleven open clusters are here found by constructing models for the components of twelve eclipsing binaries. The difference between the ages we find and the ages of the clusters derived from isochrone fitting is up to 40%. For the binary system V497 Cep in NGC 7160, the difference is about 100%. Binary systems whose primary component is about to complete its main-sequence lifetime, such as V453 Cyg and V906 Sco, are the most suitable systems for age determination. Using model results for these stars, we derive an expression for sensitive and uncomplicated relative age determination of binary systems (age divided by the main-sequence lifetime of the primary star). The expression is given as a logarithm of radii ratio divided by a logarithm of mass ratio. Two advantages of this expression are that: (i) it is nearly independent of the assumed chemical composition of the models because of the appearance of the ratio of radii; and (ii) the ratios of radii and masses are observationally much more precise than their absolute values. We also derive another expression using luminosities rather than radii and compare results.
Astrophysical Supercomputing with GPUs: Critical Decisions for Early Adopters
Authors: Fluke Christopher J. , Barnes David G. , Barsdell Benjamin R. , Hassan Amr H.
Published: March 2011

General-purpose computing on graphics processing units (GPGPU) is dramatically changing the landscape of high performance computing in astronomy. In this paper, we identify and investigate several key decision areas, with a goal of simplifying the early adoption of GPGPU in astronomy. We consider the merits of OpenCL as an open standard in order to reduce risks associated with coding in a native, vendor-specific programming environment, and present a GPU programming philosophy based on using brute force solutions. We assert that effective use of new GPU-based supercomputing facilities will require a change in approach from astronomers. This will likely include improved programming training, an increased need for software development best practice through the use of profiling and related optimisation tools, and a greater reliance on third-party code libraries. As with any new technology, those willing to take the risks and make the investment of time and effort to become early adopters of GPGPU in astronomy, stand to reap great benefits.
Nucleosynthesis in the Stellar Systems ω Centauri and M22
Authors: Da Costa G. S. , Marino A. F.
Published: March 2011

The stellar system ω Centauri (ω Cen) is well known for the large range in elemental abundances among its member stars. Recent work has indicated that the globular cluster M22 (NGC 6656) also possesses an internal abundance range, albeit substantially smallerthan that in ω Cen. Here we compare, as a function of [Fe/H], element-to-iron ratios in the two systems for a number of different elements using data from abundance analyses of red giant branch stars. It appears that the nucleosynthetic enrichment processes were very similar in these two systems despite the substantial difference in total mass.
What Is a Galaxy? Cast Your Vote Here
Authors: Forbes Duncan A. , Kroupa Pavel
Published: March 2011

Although originally classified as galaxies, Ultra-Compact Dwarfs (UCDs) have many properties in common with globular star clusters. The debate on the origin and nature of UCDs, and the recently discovered ultra-faint dwarf spheroidal (dSph) galaxies which contain very few stars, has motivated us to as the question ‘What is a galaxy?’ Our aim here is to promote further discussion of how to define a galaxy and, in particular, what separates it from a star cluster. Like most previous definitions, we adopt the requirement of gravitationally bound stellar system as a minimum. In order to distinguish a dwarf galaxy from a globular cluster, we discuss other possible requirements, such as a minimum size, a long two-body relaxation time a satellite system, the presence of complex stellar populations and non-baryonic dark matter. We briefly mention the implications of the adoption of each of these definitions. Some special cases of objects with a ambiguous nature are also discussed. Finally, we give our favoured criteria, and in the spirit of ‘collective wisdom’, invite readers to vote on their prefered definition of a galaxy via a dedicated website.
Eastern Equatorial Pacific productivity and related-CO
2
changes since the last glacial period
Authors: Calvo Eva , Pelejero Carles , Pena Leopoldo D. , Cacho Isabel , Logan Graham A.
Published: March 2011

Understanding oceanic processes, both physical and biological, that control atmospheric CO
2
is vital for predicting their influence during the past and into the future. The Eastern Equatorial Pacific (EEP) is thought to have exerted a strong control over glacial/interglacial CO
2
variations through its link to circulation and nutrient-related changes in the Southern Ocean, the primary region of the world oceans where CO
2
-enriched deep water is upwelled to the surface ocean and comes into contact with the atmosphere. Here we present a multiproxy record of surface ocean productivity, dust inputs, and thermocline conditions for the EEP over the last 40,000 y. This allows us to detect changes in phytoplankton productivity and composition associated with increases in equatorial upwelling intensity and influence of Si-rich waters of sub-Antarctic origin. Our evidence indicates that diatoms outcompeted coccolithophores at times when the influence of Si-rich Southern Ocean intermediate waters was greatest. This shift from calcareous to noncalcareous phytoplankton would cause a lowering in atmospheric CO
2
through a reduced carbonate pump, as hypothesized by the Silicic Acid Leakage Hypothesis. However, this change does not seem to have been crucial in controlling atmospheric CO
2
, as it took place during the deglaciation, when atmospheric CO
2
concentrations had already started to rise. Instead, the concomitant intensification of Antarctic upwelling brought large quantities of deep CO
2
-rich waters to the ocean surface. This process very likely dominated any biologically mediated CO
2
sequestration and probably accounts for most of the deglacial rise in atmospheric CO
2
.
Global growth and stability of agricultural yield decrease with pollinator dependence
Authors: Garibaldi Lucas A. , Aizen Marcelo A. , Klein Alexandra M. , Cunningham Saul A. , Harder Lawrence D.
Published: March 2011

Human welfare depends on the amount and stability of agricultural production, as determined by crop yield and cultivated area. Yield increases asymptotically with the resources provided by farmers’ inputs and environmentally sensitive ecosystem services. Declining yield growth with increased inputs prompts conversion of more land to cultivation, but at the risk of eroding ecosystem services. To explore the interdependence of agricultural production and its stability on ecosystem services, we present and test a general graphical model, based on Jensen's inequality, of yield–resource relations and consider implications for land conversion. For the case of animal pollination as a resource influencing crop yield, this model predicts that incomplete and variable pollen delivery reduces yield mean and stability (inverse of variability) more for crops with greater dependence on pollinators. Data collected by the Food and Agriculture Organization of the United Nations during 1961–2008 support these predictions. Specifically, crops with greater pollinator dependence had lower mean and stability in relative yield and yield growth, despite global yield increases for most crops. Lower yield growth was compensated by increased land cultivation to enhance production of pollinator-dependent crops. Area stability also decreased with pollinator dependence, as it correlated positively with yield stability among crops. These results reveal that pollen limitation hinders yield growth of pollinator-dependent crops, decreasing temporal stability of global agricultural production, while promoting compensatory land conversion to agriculture. Although we examined crop pollination, our model applies to other ecosystem services for which the benefits to human welfare decelerate as the maximum is approached.
Impaired NMDA receptor transmission alters striatal synapses and DISC1 protein in an age-dependent manner
Authors: Ramsey Amy J. , Milenkovic Marija , Oliveira Ana F. , Escobedo-Lozoya Yasmin , Seshadri Saurav , Salahpour Ali , Sawa Akira , Yasuda Ryohei , Caron Marc G.
Published: March 2011

NMDA receptors are key regulators of synaptic plasticity, and their hypofunction is thought to contribute to the pathophysiology of CNS disorders. Furthermore, NMDA receptors participate in the formation, maintenance, and elimination of synapses. The consequences of NMDA receptor hypofunction on synapse biology were explored in a genetic mouse model, in which the levels of NMDA receptors are reduced to 10% of normal levels (i.e., NR1-knockdown mice). In these mice, synapse number is reduced in an age-dependent manner; reductions are observed at the postpubertal age of 6 wk, but normal at 2 wk of age. Efforts to uncover the biochemical underpinnings of this phenomenon reveal synapse-specific reductions in 14–3-3ε protein and in Disrupted in Schizophrenia-1 (DISC1), two schizophrenia susceptibility factors that have been implicated in the regulation of spine density. Subchronic administration of MK-801, an NMDA receptor antagonist, produces similar synaptic reductions in both spine density and DISC1, indicating that synaptic levels of DISC1 are regulated by NMDA receptor function. The synaptic reduction of DISC1 and 14–3-3ε is developmentally correlated with the age-dependent decrease in striatal spine density.
Quantification of developmental birdsong learning from the subsyllabic scale to cultural evolution
Authors: Lipkind Dina , Tchernichovski Ofer
Published: March 2011

Quantitative analysis of behavior plays an important role in birdsong neuroethology, serving as a common denominator in studies spanning molecular to system-level investigation of sensory-motor conversion, developmental learning, and pattern generation in the brain. In this review, we describe the role of behavioral analysis in facilitating cross-level integration. Modern sound analysis approaches allow investigation of developmental song learning across multiple time scales. Combined with novel methods that allow experimental control of vocal changes, it is now possible to test hypotheses about mechanisms of vocal learning. Further, song analysis can be done at the population level across generations to track cultural evolution and multigenerational behavioral processes. Complementing the investigation of song development with noninvasive brain imaging technology makes it now possible to study behavioral dynamics at multiple levels side by side with developmental changes in brain connectivity and in auditory responses.
Natural immune boosting in pertussis dynamics and the potential for long-term vaccine failure
Authors: Lavine Jennie S. , King Aaron A. , Bjørnstad Ottar N.
Published: March 2011

Incidence of whooping cough, unlike many other childhood diseases for which there is an efficacious vaccine, has been increasing over the past twenty years despite high levels of vaccine coverage. Its reemergence has been particularly noticeable among teenagers and adults. Many hypotheses have been put forward to explain these two patterns, but parsimonious reconciliation of clinical data on the limited duration of immunity with both pre- and postvaccine era age-specific incidence remains a challenge. We consider the immunologically relevant, yet epidemiologically largely neglected, possibility that a primed immune system can respond to a lower dose of antigen than a naive one. We hypothesize that during the prevaccine era teenagers’ and adults’ primed immunity was frequently boosted by reexposure, so maintaining herd immunity in the face of potentially eroding individual immunity. In contrast, low pathogen circulation in the current era, except during epidemic outbreaks, allows immunity to be lost before reexposure occurs. We develop and analyze an age-structured model that encapsulates this hypothesis. We find that immune boosting must be more easily triggered than primary infection to account for age-incidence data. We make age-specific and dynamical predictions through bifurcation analysis and simulation. The boosting model proposed here parsimoniously captures four key features of pertussis data from highly vaccinated countries: (
i
) the shift in age-specific incidence, (
ii
) reemergence with high vaccine coverage, (
iii
) the possibility for cyclic dynamics in the pre- and postvaccine eras, and (
iv
) the apparent shift from susceptible-infectious-recovered (SIR)-like to susceptible-infectious-recovered-susceptible (SIRS)-like phenomenology of infection and immunity to
Bordetella pertussis
.
Histone deacetylase inhibitor treatment dramatically reduces cholesterol accumulation in Niemann-Pick type C1 mutant human fibroblasts
Authors: Pipalia Nina H. , Cosner Casey C. , Huang Amy , Chatterjee Anamitra , Bourbon Pauline , Farley Nathan , Helquist Paul , Wiest Olaf , Maxfield Frederick R.
Published: March 2011

Niemann-Pick type C (NPC) disease is predominantly caused by mutations in the NPC1 protein that affect intracellular cholesterol trafficking and cause accumulation of unesterified cholesterol and other lipids in lysosomal storage organelles. We report the use of a series of small molecule histone deacetylase (HDAC) inhibitors in tissue culture models of NPC human fibroblasts. Some HDAC inhibitors lead to a dramatic correction in the NPC phenotype in cells with either one or two copies of the

NPC1
I1061T

mutation, and for several of the inhibitors, correction is associated with increased expression of NPC1 protein. Increased NPC1
I1061T
protein levels may partially account for the correction of the phenotype, because this mutant can promote cholesterol efflux if it is delivered to late endosomes and lysosomes. The HDAC inhibitor treatment is ineffective in an NPC2 mutant human fibroblast line. Analysis of the isoform selectivity of the compounds used implicates HDAC1 and/or HDAC2 as likely targets for the observed correction, although other HDACs may also play a role. LBH589 (panobinostat) is an orally available HDAC inhibitor that crosses the blood–brain barrier and is currently in phase III clinical trials for several types of cancer. It restores cholesterol homeostasis in cultured NPC1 mutant fibroblasts to almost normal levels within 72 h when used at 40 nM. The findings that HDAC inhibitors can correct cholesterol storage defects in human NPC1 mutant cells provide the potential basis for treatment options for NPC disease.
Cell cycle restriction by histone H2AX limits proliferation of adult neural stem cells
Authors: Fernando Ruani N. , Eleuteri Boris , Abdelhady Shaimaa , Nussenzweig Andre , Andäng Michael , Ernfors Patrik
Published: March 2011

Adult neural stem cell proliferation is dynamic and has the potential for massive self-renewal yet undergoes limited cell division in vivo. Here, we report an epigenetic mechanism regulating proliferation and self-renewal. The recruitment of the PI3K-related kinase signaling pathway and histone H2AX phosphorylation following GABA
A
receptor activation limits subventricular zone proliferation. As a result, NSC self-renewal and niche size is dynamic and can be directly modulated in both directions pharmacologically or by genetically targeting H2AX activation. Surprisingly, changes in proliferation have long-lasting consequences on stem cell numbers, niche size, and neuronal output. These results establish a mechanism that continuously limits proliferation and demonstrates its impact on adult neurogenesis. Such homeostatic suppression of NSC proliferation may contribute to the limited self-repair capacity of the damaged brain.
Rv3615c is a highly immunodominant RD1 (Region of Difference 1)-dependent secreted antigen specific for
Mycobacterium tuberculosis
infection
Authors: Millington Kerry A. , Fortune Sarah M. , Low Jeffrey , Garces Alejandra , Hingley-Wilson Suzanne M. , Wickremasinghe Melissa , Kon Onn M. , Lalvani Ajit
Published: March 2011

The 6-kDa early secretory antigenic target of
Mycobacterium tuberculosis
(ESAT-6) and the 10-kDa culture filtrate antigen (CFP-10), encoded in region of difference 1 (RD1) and secreted by the ESAT-6 system 1 (Esx-1) secretion system, are the most immunodominant and highly
M. tuberculosis
(MTB)-specific antigens. These attributes are responsible for their primary importance in tuberculosis (TB) immunodiagnosis and vaccine development. Rv3615c [Esx-1 substrate protein C (EspC)], encoded outside RD1, is similar in size and sequence homology to CFP-10 and ESAT-6, suggesting it might be a target of cellular immunity in TB. Using ex vivo enzyme-linked immunospot- and flow cytometry-based cytokine-secretion assay, we comprehensively assessed cellular immune responses to EspC in patients with active TB, latently infected persons, and uninfected bacillus Calmette–Guérin (BCG)-vaccinated controls. EspC was at least as immunodominant as ESAT-6 and CFP-10 in both active and latent TB infection. EspC contained broadly recognized CD4
+
and CD8
+
epitopes, inducing a predominantly CD4
+
T-cell response that comprised functional T-cell subsets secreting both IFN-γ and IL-2 as well as functional T-cell subsets secreting only IFN-γ. Surprisingly, T-cell responses to EspC were as highly specific (93%) for MTB infection as responses to ESAT-6 and CFP-10, with only 2 of 27 BCG-vaccinated controls responding to each antigen. Using quantitative proteomics and metabolically labeled mutant and genetically complemented MTB strains, we identified the mechanism of the specificity of anti-EspC immunity as the Esx-1 dependence of EspC secretion. The high immunodominance of EspC, equivalent to that of ESAT-6 and CFP-10, makes it a TB vaccine candidate, and its high specificity confers strong potential for T-cell–based immunodiagnosis.
Timescale-dependent shaping of correlation by olfactory bulb lateral inhibition
Authors: Giridhar Sonya , Doiron Brent , Urban Nathaniel N.
Published: March 2011

Neurons respond to sensory stimuli by altering the rate and temporal pattern of action potentials. These spike trains both encode and propagate information that guides behavior. Local inhibitory networks can affect the information encoded and propagated by neurons by altering correlations between different spike trains. Correlations introduce redundancy that can reduce encoding but also facilitate propagation of activity to downstream targets. Given this trade-off, how can networks maximize both encoding and propagation efficacy? Here, we examine this problem by measuring the effects of olfactory bulb inhibition on the pairwise statistics of mitral cell spiking. We evoked spiking activity in the olfactory bulb in vitro and measured how lateral inhibition shapes correlations across timescales. We show that inhibitory circuits
simultaneously
increase fast correlation (i.e., synchrony increases) and decrease slow correlation (i.e., firing rates become less similar). Further, we use computational models to show the benefits of fast correlation/slow decorrelation in the context of odor coding. Olfactory bulb inhibition enhances population-level discrimination of similar inputs, while improving propagation of mitral cell activity to cortex. Our findings represent a targeted strategy by which a network can optimize the correlation structure of its output in a dynamic, activity-dependent manner. This trade-off is not specific to the olfactory system, but rather our work highlights mechanisms by which neurons can simultaneously accomplish multiple, and sometimes competing, aspects of sensory processing.
Polymorphic family of injected pseudokinases is paramount in
Toxoplasma
virulence
Authors: Reese Michael L. , Zeiner Gusti M. , Saeij Jeroen P. J. , Boothroyd John C. , Boyle Jon P.
Published: March 2011

Toxoplasma gondii
, an obligate intracellular parasite of the phylum Apicomplexa, has the unusual ability to infect virtually any warm-blooded animal. It is an extraordinarily successful parasite, infecting an estimated 30% of humans worldwide. The outcome of
Toxoplasma
infection is highly dependent on allelic differences in the large number of effectors that the parasite secretes into the host cell. Here, we show that the largest determinant of the virulence difference between two of the most common strains of
Toxoplasma
is the
ROP5
locus. This is an unusual segment of the
Toxoplasma
genome consisting of a family of 4–10 tandem, highly divergent genes encoding pseudokinases that are injected directly into host cells. Given their hypothesized catalytic inactivity, it is striking that deletion of the
ROP5
cluster in a highly virulent strain caused a complete loss of virulence, showing that ROP5 proteins are, in fact, indispensable for
Toxoplasma
to cause disease in mice. We find that copy number at this locus varies among the three major
Toxoplasma
lineages and that extensive polymorphism is clustered into hotspots within the ROP5 pseudokinase domain. We propose that the
ROP5
locus represents an unusual evolutionary strategy for sampling of sequence space in which the gene encoding an important enzyme has been (
i
) catalytically inactivated, (
ii
) expanded in number, and (
iii
) subject to strong positive selection. Such a strategy likely contributes to
Toxoplasma
’s successful adaptation to a wide host range and has resulted in dramatic differences in virulence.
Adaptive evolution of threonine deaminase in plant defense against insect herbivores
Authors: Gonzales-Vigil Eliana , Bianchetti Christopher M. , Phillips George N. , Howe Gregg A.
Published: March 2011

Gene duplication is a major source of plant chemical diversity that mediates plant–herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to α-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related
Solanum
species contain a duplicated
TD
paralog (
TD2
) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gut of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.
Calmodulin protects against alcohol-induced pancreatic trypsinogen activation elicited via Ca
2+
release through IP
3
receptors
Authors: Gerasimenko Julia V. , Lur György , Ferdek Pawel , Sherwood Mark W. , Ebisui Etsuko , Tepikin Alexei V. , Mikoshiba Katsuhiko , Petersen Ole H. , Gerasimenko Oleg V.
Published: March 2011

Alcohol abuse is a major global health problem, but there is still much uncertainty about the mechanisms of action. So far, the effects of ethanol on ion channels in the plasma membrane have received the most attention. We have now investigated actions on intracellular calcium channels in pancreatic acinar cells. Our aim was to discover the mechanism by which alcohol influences calcium homeostasis and thereby understand how alcohol can trigger premature intracellular trypsinogen activation, which is the initiating step for alcohol-induced pancreatitis. We used intact or two-photon permeabilized acinar cells isolated from wild-type mice or mice in which inositol trisphosphate receptors of type 2 or types 2 and 3 were knocked out. In permeabilized pancreatic acinar cells even a relatively low ethanol concentration elicited calcium release from intracellular stores and intracellular trypsinogen activation. The calcium sensor calmodulin (at a normal intracellular concentration) markedly reduced ethanol-induced calcium release and trypsinogen activation in permeabilized cells, effects prevented by the calmodulin inhibitor peptide. A calmodulin activator virtually abolished the modest ethanol effects in intact cells. Both ethanol-elicited calcium liberation and trypsinogen activation were significantly reduced in cells from type 2 inositol trisphosphate receptor knockout mice. More profound reductions were seen in cells from double inositol trisphosphate receptor (types 2 and 3) knockout mice. The inositol trisphosphate receptors, required for normal pancreatic stimulus–secretion coupling, are also responsible for the toxic ethanol action. Calmodulin protects by reducing calcium release sensitivity.
Fidelity of neural reactivation reveals competition between memories
Authors: Kuhl Brice A. , Rissman Jesse , Chun Marvin M. , Wagner Anthony D.
Published: March 2011

Remembering an event from the past is often complicated by the fact that our memories are cluttered with similar events. Though competition is a fundamental part of remembering, there is little evidence of how mnemonic competition is neurally represented. Here, we assessed whether competition between visual memories is captured in the relative degree to which target vs. competing memories are reactivated within the ventral occipitotemporal cortex (VOTC). To assess reactivation, we used multivoxel pattern analysis of fMRI data, quantifying the degree to which retrieval events elicited patterns of neural activity that matched those elicited during encoding. Consistent with recent evidence, we found that retrieval of visual memories was associated with robust VOTC reactivation and that the degree of reactivation scaled with behavioral expressions of target memory retrieval. Critically, competitive remembering was associated with more ambiguous patterns of VOTC reactivation, putatively reflecting simultaneous reactivation of target and competing memories. Indeed, the more weakly that target memories were reactivated, the more likely that competing memories were later remembered. Moreover, when VOTC reactivation indicated that conflict between target and competing memories was high, frontoparietal mechanisms were markedly engaged, revealing specific neural mechanisms that tracked competing mnemonic evidence. Together, these findings provide unique evidence that neural reactivation captures competition between individual memories, providing insight into how well target memories are retrieved in the present and how likely competing memories will be remembered in the future.
Usher type 1G protein sans is a critical component of the tip-link complex, a structure controlling actin polymerization in stereocilia
Authors: Caberlotto Elisa , Michel Vincent , Foucher Isabelle , Bahloul Amel , Goodyear Richard J. , Pepermans Elise , Michalski Nicolas , Perfettini Isabelle , Alegria-Prévot Olinda , Chardenoux Sébastien , Do Cruzeiro Marcio , Hardelin Jean-Pierre , Richardson Guy P. , Avan Paul , Weil Dominique , Petit Christine
Published: March 2011

The mechanotransducer channels of auditory hair cells are gated by tip-links, oblique filaments that interconnect the stereocilia of the hair bundle. Tip-links stretch from the tips of stereocilia in the short and middle rows to the sides of neighboring, taller stereocilia. They are made of cadherin-23 and protocadherin-15, products of the Usher syndrome type 1 genes USH1D and USH1F, respectively. In this study we address the role of sans, a putative scaffold protein and product of the USH1G gene. In
Ush1g
−/−
mice, the cohesion of stereocilia is disrupted, and both the amplitude and the sensitivity of the transduction currents are reduced. In
Ush1g
fl/fl
Myo15-cre
+/−
mice, the loss of sans occurs postnatally and the stereocilia remain cohesive. In these mice, there is a decrease in the amplitude of the total transducer current with no loss in sensitivity, and the tips of the stereocilia in the short and middle rows lose their prolate shape, features that can be attributed to the loss of tip-links. Furthermore, stereocilia from these rows undergo a dramatic reduction in length, suggesting that the mechanotransduction machinery has a positive effect on F-actin polymerization. Sans interacts with the cytoplasmic domains of cadherin-23 and protocadherin-15 in vitro and is absent from the hair bundle in mice defective for either of the two cadherins. Because sans localizes mainly to the tips of short- and middle-row stereocilia in vivo, we conclude that it belongs to a molecular complex at the lower end of the tip-link and plays a critical role in the maintenance of this link.
E3 ligase Rad18 promotes monoubiquitination rather than ubiquitin chain formation by E2 enzyme Rad6
Authors: Hibbert Richard G. , Huang Anding , Boelens Rolf , Sixma Titia K.
Published: March 2011

In ubiquitin conjugation, different combinations of E2 and E3 enzymes catalyse either monoubiquitination or ubiquitin chain formation. The E2/E3 complex Rad6/Rad18 exclusively monoubiquitinates the proliferating cell nuclear antigen (PCNA) to signal for “error prone” DNA damage tolerance, whereas a different set of conjugation enzymes is required for ubiquitin chain formation on PCNA. Here we show that human E2 enzyme Rad6b is intrinsically capable of catalyzing ubiquitin chain formation. This activity is prevented during PCNA ubiquitination by the interaction of Rad6 with E3 enzyme Rad18. Using NMR and X-ray crystallography we show that the R6BD of Rad18 inhibits this activity by competing with ubiquitin for a noncovalent “backside” binding site on Rad6. Our findings provide mechanistic insights into how E3 enzymes can regulate the ubiquitin conjugation process.
Agonist activation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site
Authors: Gill JasKiran K. , Savolainen Mari , Young Gareth T. , Zwart Ruud , Sher Emanuele , Millar Neil S.
Published: March 2011

Conventional nicotinic acetylcholine receptor (nAChR) agonists, such as acetylcholine, act at an extracellular “orthosteric” binding site located at the interface between two adjacent subunits. Here, we present evidence of potent activation of α7 nAChRs via an allosteric transmembrane site. Previous studies have identified a series of nAChR-positive allosteric modulators (PAMs) that lack agonist activity but are able to potentiate responses to orthosteric agonists, such as acetylcholine. It has been shown, for example, that TQS acts as a conventional α7 nAChR PAM. In contrast, we have found that a compound with close chemical similarity to TQS (4BP-TQS) is a potent allosteric agonist of α7 nAChRs. Whereas the α7 nAChR antagonist metyllycaconitine acts competitively with conventional nicotinic agonists, metyllycaconitine is a noncompetitive antagonist of 4BP-TQS. Mutation of an amino acid (M253L), located in a transmembrane cavity that has been proposed as being the binding site for PAMs, completely blocks agonist activation by 4BP-TQS. In contrast, this mutation had no significant effect on agonist activation by acetylcholine. Conversely, mutation of an amino acid located within the known orthosteric binding site (W148F) has a profound effect on agonist potency of acetylcholine (resulting in a shift of ∼200-fold in the acetylcholine dose-response curve), but had little effect on the agonist dose-response curve for 4BP-TQS. Computer docking studies with an α7 homology model provides evidence that both TQS and 4BP-TQS bind within an intrasubunit transmembrane cavity. Taken together, these findings provide evidence that agonist activation of nAChRs can occur via an allosteric transmembrane site.
A Sleeping Beauty transposon-mediated screen identifies murine susceptibility genes for adenomatous polyposis coli (
Apc
)-dependent intestinal tumorigenesis
Authors: Starr Timothy K. , Scott Patricia M. , Marsh Benjamin M. , Zhao Lei , Than Bich L. N. , O'Sullivan M. Gerard , Sarver Aaron L. , Dupuy Adam J. , Largaespada David A. , Cormier Robert T.
Published: March 2011

It is proposed that a progressive series of mutations and epigenetic events leads to human colorectal cancer (CRC) and metastasis. Furthermore, data from resequencing of the coding regions of human CRC suggests that a relatively large number of mutations occur in individual human CRC, most at low frequency. The functional role of these low-frequency mutations in CRC, and specifically how they may cooperate with high-frequency mutations, is not well understood. One of the most common rate-limiting mutations in human CRC occurs in the adenomatous polyposis coli (
APC
) gene. To identify mutations that cooperate with mutant
APC
, we performed a forward genetic screen in mice carrying a mutant allele of
Apc
(

Apc
Min

) using Sleeping Beauty (
SB
) transposon-mediated mutagenesis.

Apc
Min
SB

-mutagenized mice developed three times as many polyps as mice with the

Apc
Min

allele alone. Analysis of transposon common insertion sites (CIS) identified the
Apc
locus as a major target of
SB
-induced mutagenesis, suggesting that
SB
insertions provide an efficient route to biallelic
Apc
inactivation. We also identified an additional 32 CIS genes/loci that may represent modifiers of the

Apc
Min

phenotype. Five CIS genes tested for their role in proliferation caused a significant change in cell viability when message levels were reduced in human CRC cells. These findings demonstrate the utility of using transposon mutagenesis to identify low-frequency and cooperating cancer genes; this approach will aid in the development of combinatorial therapies targeting this deadly disease.
Statistical image analysis reveals features affecting fates of
Myxococcus xanthus
developmental aggregates
Authors: Xie Chunyan , Zhang Haiyang , Shimkets Lawrence J. , Igoshin Oleg A.
Published: March 2011

Starving
Myxococcus xanthus
bacteria use their motility systems to self-organize into multicellular fruiting bodies, large mounds in which cells differentiate into metabolically inert spores. Despite the identification of the genetic pathways required for aggregation and the use of microcinematography to observe aggregation dynamics in WT and mutant strains, a mechanistic understanding of aggregation is still incomplete. For example, it is not clear why some of the initial aggregates mature into fruiting bodies, whereas others disperse, merge, or split into two. Here, we develop high-throughput image quantification and statistical analysis methods to gain insight into
M. xanthus
developmental aggregation dynamics. A quantitative metric of features characterizing each aggregate is used to deduce the properties of the aggregates that are correlated with each fate. The analysis shows that small aggregate size but not neighbor-related parameters correlate with aggregate dispersal. Furthermore, close proximity is necessary but not sufficient for aggregate merging. Finally, splitting occurs for those aggregates that are unusually large and elongated. These observations place severe constraints on the underlying aggregation mechanisms and present strong evidence against the role of long-range morphogenic gradients or biased cell exchange in the dispersal, merging, or splitting of transient aggregates. This approach can be expanded and adapted to study self-organization in other cellular systems.
How frequency and intensity shape diversity–disturbance relationships
Authors: Miller Adam D. , Roxburgh Stephen H. , Shea Katriona
Published: March 2011

Understanding the relationship between disturbance regimes and species diversity has been of central interest to ecologists for decades. For example, the intermediate disturbance hypothesis proposes that diversity will be highest at intermediate levels of disturbance. Although peaked (hump-shaped) diversity–disturbance relationships (DDRs) have been documented in nature, many other DDRs have been reported as well. Here, we begin to theoretically unify these diverse empirical findings by showing how a single simple model can generate several different DDRs, depending on the aspect of disturbance that is considered. Additionally, we elucidate the competition-mediated mechanism underlying our results. Our findings have the potential to reconcile apparently conflicting empirical results on the effects of disturbance on diversity.