bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian design of synthetic biological systems
Authors: Barnes Chris P. , Silk Daniel , Sheng Xia , Stumpf Michael P. H.
Published: August 2011

Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system that has given rise to the data that we observe, whereas in the latter, we seek to construct the system that produces the data that we would like to observe, i.e., the desired behavior. Our approach allows us to exploit methods from Bayesian statistics, including efficient exploration of models spaces and high-dimensional parameter spaces, and the ability to rank models with respect to their ability to generate certain types of data. Bayesian model selection furthermore automatically strikes a balance between complexity and (predictive or explanatory) performance of mathematical models. To deal with the complexities of molecular systems we employ an approximate Bayesian computation scheme which only requires us to simulate from different competing models to arrive at rational criteria for choosing between them. We illustrate the advantages resulting from combining the design and modeling (or
in silico
prototyping) stages currently seen as separate in synthetic biology by reference to deterministic and stochastic model systems exhibiting adaptive and switch-like behavior, as well as bacterial two-component signaling systems.
Connective tissue growth factor acts within both endothelial cells and β cells to promote proliferation of developing β cells
Authors: Guney Michelle A. , Petersen Christine P. , Boustani Andre , Duncan Matthew R. , Gunasekaran Uma , Menon Renuka , Warfield Courtney , Grotendorst Gary R. , Means Anna L. , Economides Aris N. , Gannon Maureen
Published: August 2011

Type 1 and type 2 diabetes result from an absolute or relative reduction in functional β-cell mass. One approach to replacing lost β-cell mass is transplantation of cadaveric islets; however, this approach is limited by lack of adequate donor tissue. Therefore, there is much interest in identifying factors that enhance β-cell differentiation and proliferation in vivo or in vitro. Connective tissue growth factor (CTGF) is a secreted molecule expressed in endothelial cells, pancreatic ducts, and embryonic β cells that we previously showed is required for β-cell proliferation, differentiation, and islet morphogenesis during development. The current study investigated the tissue interactions by which CTGF promotes normal pancreatic islet development. We found that loss of CTGF from either endothelial cells or β cells results in decreased embryonic β-cell proliferation, making CTGF unique as an identified β cell-derived factor that regulates embryonic β-cell proliferation. Endothelial CTGF inactivation was associated with decreased islet vascularity, highlighting the proposed role of endothelial cells in β-cell proliferation. Furthermore, CTGF overexpression in β cells during embryogenesis using an inducible transgenic system increased islet mass at birth by promoting proliferation of immature β cells, in the absence of changes in islet vascularity. Together, these findings demonstrate that CTGF acts in an autocrine manner during pancreas development and suggest that CTGF has the potential to enhance expansion of immature β cells in directed differentiation or regeneration protocols.
Reconstruction of a 1,910-y-long locust series reveals consistent associations with climate fluctuations in China
Authors: Tian Huidong , Stige Leif C. , Cazelles Bernard , Kausrud Kyrre Linne , Svarverud Rune , Stenseth Nils C. , Zhang Zhibin
Published: August 2011

It is becoming increasingly clear that global warming is taking place; however, its long-term effects on biological populations are largely unknown due to lack of long-term data. Here, we reconstructed a 1,910-y-long time series of outbreaks of Oriental migratory locusts (
Locusta migratoria manilensis
) in China, on the basis of information extracted from >8,000 historical documents. First by analyzing the most recent period with the best data quality using generalized additive models, we found statistically significant associations between the reconstructed locust abundance and indexes of precipitation and temperature at both annual (A.D. 1512–1911) and decadal (A.D. 1000–1900) scales: There were more locusts under dry and cold conditions and when locust abundance was high in the preceding year or decade. Second, by exploring locust–environment correlations using a 200-y moving window, we tested whether these associations also hold further back in time. The locust–precipitation correlation was found to hold at least as far back as to A.D. 500, supporting the robustness of this link as well as the quality of both reconstructions. The locust–temperature correlation was weaker and less consistent, which may reflect this link being indirect and thus more easily moderated by other factors. We anticipate that further analysis of this unique time series now available to the scientific community will continue to provide insights into biological consequences of climate change in the years to come.
A widespread class of reverse transcriptase-related cellular genes
Authors: Gladyshev Eugene A. , Arkhipova Irina R.
Published: August 2011

Reverse transcriptases (RTs) polymerize DNA on RNA templates. They fall into several structurally related but distinct classes and form an assemblage of RT-like enzymes that, in addition to RTs, also includes certain viral RNA-dependent RNA polymerases (RdRP) synthesizing RNA on RNA templates. It is generally believed that most RT-like enzymes originate from retrotransposons or viruses and have no specific function in the host cell, with telomerases being the only notable exception. Here we report on the discovery and properties of a unique class of RT-related cellular genes collectively named
rvt
. We present evidence that
rvt
s are not components of retrotransposons or viruses, but single-copy genes with a characteristic domain structure that may contain introns in evolutionarily conserved positions, occur in syntenic regions, and evolve under purifying selection. These genes can be found in all major taxonomic groups including protists, fungi, animals, plants, and even bacteria, although they exhibit patchy phylogenetic distribution in each kingdom. We also show that the RVT protein purified from one of its natural hosts,
Neurospora crassa
, exists in a multimeric form and has the ability to polymerize NTPs as well as dNTPs in vitro, with a strong preference for NTPs, using Mn
2+
as a cofactor. The existence of a previously unknown class of single-copy RT-related genes calls for reevaluation of the current views on evolution and functional roles of RNA-dependent polymerases in living cells.
Asymmetric dispersal allows an upstream region to control population structure throughout a species’ range
Authors: Pringle James M. , Blakeslee April M. H. , Byers James E. , Roman Joe
Published: August 2011

In a single well-mixed population, equally abundant neutral alleles are equally likely to persist. However, in spatially complex populations structured by an asymmetric dispersal mechanism, such as a coastal population where larvae are predominantly moved downstream by currents, the eventual frequency of neutral haplotypes will depend on their initial spatial location. In our study of the progression of two spatially separate, genetically distinct introductions of the European green crab (
Carcinus maenas
) along the coast of eastern North America, we captured this process in action. We documented the shift of the genetic cline in this species over 8 y, and here we detail how the upstream haplotypes are beginning to dominate the system. This quantification of an evolving genetic boundary in a coastal system demonstrates that novel genetic alleles or haplotypes that arise or are introduced into upstream retention zones (regions whose export of larvae is not balanced by import from elsewhere) will increase in frequency in the entire system. This phenomenon should be widespread when there is asymmetrical dispersal, in the oceans or on land, suggesting that the upstream edge of a species’ range can influence genetic diversity throughout its distribution. Efforts to protect the upstream edge of an asymmetrically dispersing species’ range are vital to conserving genetic diversity in the species.
Global discovery of small RNAs in
Yersinia pseudotuberculosis
identifies
Yersinia
-specific small, noncoding RNAs required for virulence
Authors: Koo Jovanka T. , Alleyne Trevis M. , Schiano Chelsea A. , Jafari Nadereh , Lathem Wyndham W.
Published: August 2011

A major class of bacterial small, noncoding RNAs (sRNAs) acts by base-pairing with mRNAs to alter the translation from and/or stability of the transcript. Our laboratory has shown that Hfq, the chaperone that mediates the interaction of many sRNAs with their targets, is required for the virulence of the enteropathogen
Yersinia pseudotuberculosis
. This finding suggests that sRNAs play a critical role in the regulation of virulence in this pathogen, but these sRNAs are not known. Using a deep sequencing approach, we identified the global set of sRNAs expressed in vitro by
Y. pseudotuberculosis
. Sequencing of RNA libraries from bacteria grown at 26 °C and 37 °C resulted in the identification of 150 unannotated sRNAs. The majority of these sRNAs are
Yersinia
specific, without orthologs in either
Escherichia coli
or
Salmonella typhimurium
. Six sRNAs are
Y. pseudotuberculosis
specific and are absent from the genome of the closely related species
Yersinia pestis
. We found that the expression of many sRNAs conserved between
Y. pseudotuberculosis
and
Y. pestis
differs in both timing and dependence on Hfq, suggesting evolutionary changes in posttranscriptional regulation between these species. Deletion of multiple sRNAs in
Y. pseudotuberculosis
leads to attenuation of the pathogen in a mouse model of yersiniosis, as does the inactivation in
Y. pestis
of a conserved,
Yersinia
-specific sRNA in a mouse model of pneumonic plague. Finally, we determined the regulon controlled by one of these sRNAs, revealing potential virulence determinants in
Y. pseudotuberculosis
that are regulated in a posttranscriptional manner.
Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation
Authors: Zhu Yiping , Chen Guifang , Lv Fengxiang , Wang Xinlu , Ji Xin , Xu Yihui , Sun Jing , Wu Li , Zheng Yong-Tang , Gao Guangxia
Published: August 2011

The zinc-finger antiviral protein (ZAP) was originally identified as a host factor that inhibits the replication of Moloney murine leukemia virus. Here we report that ZAP inhibits HIV-1 infection by promoting the degradation of specific viral mRNAs. Overexpression of ZAP rendered cells resistant to HIV-1 infection in a ZAP expression level-dependent manner, whereas depletion of endogenous ZAP enhanced HIV-1 infection. Both human and rat ZAP inhibited the propagation of replication-competent HIV-1. ZAP specifically targeted the multiply spliced but not unspliced or singly spliced HIV-1 mRNAs for degradation. We provide evidence indicating that ZAP selectively recruits cellular poly(A)-specific ribonuclease (PARN) to shorten the poly(A) tail of target viral mRNA and recruits the RNA exosome to degrade the RNA body from the 3′ end. In addition, ZAP recruits cellular decapping complex through its cofactor RNA helicase p72 to initiate degradation of the target viral mRNA from the 5′ end. Depletion of each of these mRNA degradation enzymes reduced ZAP's activity. Our results indicate that ZAP inhibits HIV-1 by recruiting both the 5′ and 3′ mRNA degradation machinery to specifically promote the degradation of multiply spliced HIV-1 mRNAs.
Mechanistic basis of bell-shaped dependence of inositol 1,4,5-trisphosphate receptor gating on cytosolic calcium
Authors: Shinohara Tadashi , Michikawa Takayuki , Enomoto Masahiro , Goto Jun-Ichi , Iwai Miwako , Matsu-ura Toru , Yamazaki Haruka , Miyamoto Akitoshi , Suzuki Akio , Mikoshiba Katsuhiko
Published: August 2011

The inositol 1,4,5-trisphosphate (IP
3
) receptor (IP
3
R) is an intracellular Ca
2+
release channel, and its opening is controlled by IP
3
and Ca
2+
. A single IP
3
binding site and multiple Ca
2+
binding sites exist on single subunits, but the precise nature of the interplay between these two ligands in regulating biphasic dependence of channel activity on cytosolic Ca
2+
is unknown. In this study, we visualized conformational changes in IP
3
R evoked by various concentrations of ligands by using the FRET between two fluorescent proteins fused to the N terminus of individual subunits. IP
3
and Ca
2+
have opposite effects on the FRET signal change, but the combined effect of these ligands is not a simple summative response. The bell-shaped Ca
2+
dependence of FRET efficiency was observed after the subtraction of the component corresponding to the FRET change evoked by Ca
2+
alone from the FRET changes evoked by both ligands together. A mutant IP
3
R containing a single amino acid substitution at K508, which is critical for IP
3
binding, did not exhibit this bell-shaped Ca
2+
dependence of the subtracted FRET efficiency. Mutation at E2100, which is known as a Ca
2+
sensor, resulted in ∼10-fold reduction in the Ca
2+
dependence of the subtracted signal. These results suggest that the subtracted FRET signal reflects IP
3
R activity. We propose a five-state model, which implements a dual-ligand competition response without complex allosteric regulation of Ca
2+
binding affinity, as the mechanism underlying the IP
3
-dependent regulation of the bell-shaped relationship between the IP
3
R activity and cytosolic Ca
2+
.
Cross-modal responses in the primary visual cortex encode complex objects and correlate with tactile discrimination
Authors: Vasconcelos Nivaldo , Pantoja Janaina , Belchior Hindiael , Caixeta Fábio Viegas , Faber Jean , Freire Marco Aurelio M. , Cota Vinícius Rosa , Anibal de Macedo Edson , Laplagne Diego A. , Gomes Herman Martins , Ribeiro Sidarta
Published: August 2011

Cortical areas that directly receive sensory inputs from the thalamus were long thought to be exclusively dedicated to a single modality, originating separate labeled lines. In the past decade, however, several independent lines of research have demonstrated cross-modal responses in primary sensory areas. To investigate whether these responses represent behaviorally relevant information, we carried out neuronal recordings in the primary somatosensory cortex (S1) and primary visual cortex (V1) of rats as they performed whisker-based tasks in the dark. During the free exploration of novel objects, V1 and S1 responses carried comparable amounts of information about object identity. During execution of an aperture tactile discrimination task, tactile recruitment was slower and less robust in V1 than in S1. However, V1 tactile responses correlated significantly with performance across sessions. Altogether, the results support the notion that primary sensory areas have a preference for a given modality but can engage in meaningful cross-modal processing depending on task demand.
Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons
Authors: Franchini Lucía F. , López-Leal Rodrigo , Nasif Sofía , Beati Paula , Gelman Diego M. , Low Malcolm J. , de Souza Flávio J. S. , Rubinstein Marcelo
Published: August 2011

The proopiomelanocortin gene (
POMC
) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific
POMC
expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific
POMC
enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using
in silico
paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (≈90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of
Pomc
expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated retroposons into functional analogs regulating neuronal
POMC
expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers.
Herd behavior in a complex adaptive system
Authors: Zhao Li , Yang Guang , Wang Wei , Chen Yu , Huang J. P. , Ohashi Hirotada , Stanley H. Eugene
Published: August 2011

In order to survive, self-serving agents in various kinds of complex adaptive systems (CASs) must compete against others for sharing limited resources with biased or unbiased distribution by conducting strategic behaviors. This competition can globally result in the balance of resource allocation. As a result, most of the agents and species can survive well. However, it is a common belief that the formation of a herd in a CAS will cause excess volatility, which can ruin the balance of resource allocation in the CAS. Here this belief is challenged with the results obtained from a modeled resource-allocation system. Based on this system, we designed and conducted a series of computer-aided human experiments including herd behavior. We also performed agent-based simulations and theoretical analyses, in order to confirm the experimental observations and reveal the underlying mechanism. We report that, as long as the ratio of the two resources for allocation is biased enough, the formation of a typically sized herd can help the system to reach the balanced state. This resource ratio also serves as the critical point for a class of phase transition identified herein, which can be used to discover the role change of herd behavior, from a ruinous one to a helpful one. This work is also of value to some fields, ranging from management and social science, to ecology and evolution, and to physics.
Single cell analysis reveals similar functional competence of dominant and nondominant CD8 T-cell clonotypes
Authors: Speiser Daniel E. , Wieckowski Sébastien , Gupta Bhawna , Iancu Emanuela M. , Baumgaertner Petra , Baitsch Lukas , Michielin Olivier , Romero Pedro , Rufer Nathalie
Published: August 2011

Immune protection from infectious diseases and cancer is mediated by individual T cells of different clonal origin. Their functions are tightly regulated but not yet fully characterized. Understanding the contribution of each T cell will improve the prediction of immune protection based on laboratory assessment of T-cell responses. Here we developed techniques for simultaneous molecular and functional assessment of single CD8 T cells directly ex vivo. We studied two groups of patients with melanoma after vaccination with two closely related tumor antigenic peptides. Vaccination induced T cells with strong memory and effector functions, as found in virtually all T cells of the first patient group, and fractions of T cells in the second group. Interestingly, high functionality was not restricted to dominant clonotypes. Rather, dominant and nondominant clonotypes acquired equal functional competence. In parallel, this was also found for EBV- and CMV-specific T cells. Thus, the nondominant clonotypes may contribute similarly to immunity as their dominant counterparts.
Insights into Krabbe disease from structures of galactocerebrosidase
Authors: Deane Janet E. , Graham Stephen C. , Kim Nee Na , Stein Penelope E. , McNair Rosamund , Cachón-González M. Begoña , Cox Timothy M. , Read Randy J.
Published: August 2011

Krabbe disease is a devastating neurodegenerative disease characterized by widespread demyelination that is caused by defects in the enzyme galactocerebrosidase (GALC). Disease-causing mutations have been identified throughout the
GALC
gene. However, a molecular understanding of the effect of these mutations has been hampered by the lack of structural data for this enzyme. Here we present the crystal structures of GALC and the GALC-product complex, revealing a novel domain architecture with a previously uncharacterized lectin domain not observed in other hydrolases. All three domains of GALC contribute residues to the substrate-binding pocket, and disease-causing mutations are widely distributed throughout the protein. Our structures provide an essential insight into the diverse effects of pathogenic mutations on GALC function in human Krabbe variants and a compelling explanation for the severity of many mutations associated with fatal infantile disease. The localization of disease-associated mutations in the structure of GALC will facilitate identification of those patients that would be responsive to pharmacological chaperone therapies. Furthermore, our structure provides the atomic framework for the design of such drugs.
Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components
Authors: Quinlan R. Jason , Sweeney Matt D. , Lo Leggio Leila , Otten Harm , Poulsen Jens-Christian N. , Johansen Katja Salomon , Krogh Kristian B. R. M. , Jørgensen Christian Isak , Tovborg Morten , Anthonsen Annika , Tryfona Theodora , Walter Clive P. , Dupree Paul , Xu Feng , Davies Gideon J. , Walton Paul H.
Published: August 2011

The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation. Perhaps the most promising approach involves the application of “cellulase-enhancing factors,” such as those from the glycoside hydrolase (CAZy) GH61 family. Here we show that GH61 enzymes are a unique family of copper-dependent oxidases. We demonstrate that copper is needed for GH61 maximal activity and that the formation of cellodextrin and oxidized cellodextrin products by GH61 is enhanced in the presence of small molecule redox-active cofactors such as ascorbate and gallate. By using electron paramagnetic resonance spectroscopy and single-crystal X-ray diffraction, the active site of GH61 is revealed to contain a type II copper and, uniquely, a methylated histidine in the copper's coordination sphere, thus providing an innovative paradigm in bioinorganic enzymatic catalysis.
Two types of
cis
-
trans
compensation in the evolution of transcriptional regulation
Authors: Takahasi K. Ryo , Matsuo Takashi , Takano-Shimizu-Kouno Toshiyuki
Published: August 2011

Because distant species often share similar macromolecules, regulatory mutations are often considered responsible for much of their biological differences. Recently, a large portion of regulatory changes has been attributed to
cis
-regulatory mutations. Here, we examined an alternative possibility that the putative contribution of
cis
-regulatory changes was, in fact, caused by compensatory action of
cis
- and
trans
-regulatory elements. First, we show by stochastic simulations that compensatory
cis
-
trans
evolution maintains the binding affinity of a transcription factor at a constant level, thereby spuriously exaggerating the contribution of
cis
-regulatory mutations to gene expression divergence. This exaggeration was not observed when changes in the binding affinity were compensated by variable transcription factor concentration. Second, using reciprocal introgressions of
Drosophila
, we show that relative expression of heterozygous alleles from two distinct species often varied significantly between different species backgrounds, indicating the possible action of
cis
-
trans
compensation. Taken together, we propose that
cis
-
trans
hybrid incompatibilities are accumulating much faster than generally considered.
Mitochondrial matrix Ca
2
+
as an intrinsic signal regulating mitochondrial motility in axons
Authors: Chang Karen T. , Niescier Robert F. , Min Kyung-Tai
Published: August 2011

The proper distribution of mitochondria is particularly vital for neurons because of their polarized structure and high energy demand. Mitochondria in axons constantly move in response to physiological needs, but signals that regulate mitochondrial movement are not well understood. Aside from producing ATP, Ca
2+
buffering is another main function of mitochondria. Activities of many enzymes in mitochondria are also Ca
2+
-dependent, suggesting that intramitochondrial Ca
2+
concentration is important for mitochondrial functions. Here, we report that mitochondrial motility in axons is actively regulated by mitochondrial matrix Ca
2+
. Ca
2+
entry through the mitochondrial Ca
2+
uniporter modulates mitochondrial transport, and mitochondrial Ca
2+
content correlates inversely with the speed of mitochondrial movement. Furthermore, the miro1 protein plays a role in Ca
2+
uptake into the mitochondria, which subsequently affects mitochondrial movement.
Controlling the dimensionality of charge transport in organic thin-film transistors
Authors: Laiho Ari , Herlogsson Lars , Forchheimer Robert , Crispin Xavier , Berggren Magnus
Published: August 2011

Electrolyte-gated organic thin-film transistors (OTFTs) can offer a feasible platform for future flexible, large-area and low-cost electronic applications. These transistors can be divided into two groups on the basis of their operation mechanism: (
i
) field-effect transistors that switch fast but carry much less current than (
ii
) the electrochemical transistors which, on the contrary, switch slowly. An attractive approach would be to combine the benefits of the field-effect and the electrochemical transistors into one transistor that would both switch fast and carry high current densities. Here we report the development of a polyelectrolyte-gated OTFT based on conjugated polyelectrolytes, and we demonstrate that the OTFTs can be controllably operated either in the field-effect or the electrochemical regime. Moreover, we show that the extent of electrochemical doping can be restricted to a few monolayers of the conjugated polyelectrolyte film, which allows both high current densities and fast switching speeds at the same time. We propose an operation mechanism based on self-doping of the conjugated polyelectrolyte backbone by its ionic side groups.
Implications for the hydrologic cycle under climate change due to the expansion of bioenergy crops in the Midwestern United States
Authors: Le Phong V. V. , Kumar Praveen , Drewry Darren T.
Published: August 2011

To meet emerging bioenergy demands, significant areas of the large-scale agricultural landscape of the Midwestern United States could be converted to second generation bioenergy crops such as miscanthus and switchgrass. The high biomass productivity of bioenergy crops in a longer growing season linked tightly to water use highlight the potential for significant impact on the hydrologic cycle in the region. This issue is further exacerbated by the uncertainty in the response of the vegetation under elevated CO2and temperature. We use a mechanistic multilayer canopy-root-soil model to (i) capture the eco-physiological acclimations of bioenergy crops under climate change, and (ii) predict how hydrologic fluxes are likely to be altered from their current magnitudes. Observed data and Monte Carlo simulations of weather for recent past and future scenarios are used to characterize the variability range of the predictions. Under present weather conditions, miscanthus and switchgrass utilized more water than maize for total seasonal evapotranspiration by approximately 58% and 36%, respectively. Projected higher concentrations of atmospheric CO2(550 ppm) is likely to decrease water used for evapotranspiration of miscanthus, switchgrass, and maize by 12%, 10%, and 11%, respectively. However, when climate change with projected increases in air temperature and reduced summer rainfall are also considered, there is a net increase in evapotranspiration for all crops, leading to significant reduction in soil-moisture storage and specific surface runoff. These results highlight the critical role of the warming climate in potentially altering the water cycle in the region under extensive conversion of existing maize cropping to support bioenergy demand.
Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography
Authors: Dudkina Natalya V. , Kudryashev Mikhail , Stahlberg Henning , Boekema Egbert J.
Published: August 2011

The respirasome is a multisubunit supercomplex of the respiratory chain in mitochondria. Here we report the 3D reconstruction of the bovine heart respirasome, composed of dimeric complex III and single copies of complex I and IV, at about 2.2-nm resolution, determined by cryoelectron tomography and subvolume averaging. Fitting of X-ray structures of single complexes I, III
2
, and IV with high fidelity allows interpretation of the model at the level of secondary structures and shows how the individual complexes interact within the respirasome. Surprisingly, the distance between cytochrome
c
binding sites of complexes III
2
and IV is about 10 nm. Modeling indicates a loose interaction between the three complexes and provides evidence that lipids are gluing them at the interfaces.
Heterotrimeric G protein
β
1
γ
2
subunits change orientation upon complex formation with G protein-coupled receptor kinase 2 (GRK2) on a model membrane
Authors: Boughton Andrew P. , Yang Pei , Tesmer Valerie M. , Ding Bei , Tesmer John J. G. , Chen Zhan
Published: August 2011

Few experimental techniques can assess the orientation of peripheral membrane proteins in their native environment. Sum Frequency Generation (SFG) vibrational spectroscopy was applied to study the formation of the complex between G protein-coupled receptor (GPCR) kinase 2 (GRK2) and heterotrimeric G protein
β
1
γ
2
subunits (Gβγ) at a lipid bilayer, without any exogenous labels. The most likely membrane orientation of the GRK2-Gβγ complex differs from that predicted from the known protein crystal structure, and positions the predicted receptor docking site of GRK2 such that it would more optimally interact with GPCRs. Gβγ also appears to change its orientation after binding to GRK2. The developed methodology is widely applicable for the study of other membrane proteins in situ.
Behavioral and neural correlates of delay of gratification 40 years later
Authors: Casey B. J. , Somerville Leah H. , Gotlib Ian H. , Ayduk Ozlem , Franklin Nicholas T. , Askren Mary K. , Jonides John , Berman Marc G. , Wilson Nicole L. , Teslovich Theresa , Glover Gary , Zayas Vivian , Mischel Walter , Shoda Yuichi
Published: August 2011

We examined the neural basis of self-regulation in individuals from a cohort of preschoolers who performed the delay-of-gratification task 4 decades ago. Nearly 60 individuals, now in their mid-forties, were tested on “hot” and “cool” versions of a go/nogo task to assess whether delay of gratification in childhood predicts impulse control abilities and sensitivity to alluring cues (happy faces). Individuals who were less able to delay gratification in preschool and consistently showed low self-control abilities in their twenties and thirties performed more poorly than did high delayers when having to suppress a response to a happy face but not to a neutral or fearful face. This finding suggests that sensitivity to environmental hot cues plays a significant role in individuals’ ability to suppress actions toward such stimuli. A subset of these participants (
n
= 26) underwent functional imaging for the first time to test for biased recruitment of frontostriatal circuitry when required to suppress responses to alluring cues. Whereas the prefrontal cortex differentiated between nogo and go trials to a greater extent in high delayers, the ventral striatum showed exaggerated recruitment in low delayers. Thus, resistance to temptation as measured originally by the delay-of-gratification task is a relatively stable individual difference that predicts reliable biases in frontostriatal circuitries that integrate motivational and control processes.
Low-frequency songs lose their potency in noisy urban conditions
Authors: Halfwerk Wouter , Bot Sander , Buikx Jasper , van der Velde Marco , Komdeur Jan , ten Cate Carel , Slabbekoorn Hans
Published: August 2011

Many animal species communicate with their mates through acoustic signals, but this communication seems to become a struggle in urbanized areas because of increasing anthropogenic noise levels. Several bird species have been reported to increase song frequency by which they reduce the masking impact of spectrally overlapping noise. However, it remains unclear whether such behavioral flexibility provides a sufficient solution to noisy urban conditions or whether there are hidden costs. Species may rely on low frequencies to attract and impress females, and the use of high frequencies may, therefore, come at the cost of reduced attractiveness. We studied the potential tradeoff between signal strength and signal detection in a successful urban bird species, the great tit (
Parus major).
We show that the use of low-frequency songs by males is related to female fertility as well as sexual fidelity. We experimentally show that urban noise conditions impair male–female communication and that signal efficiency depends on song frequency in the presence of noise. Our data reveal a response advantage for high-frequency songs during sexual signaling in noisy conditions, whereas low-frequency songs are likely to be preferred. These data are critical for our understanding of the impact of anthropogenic noise on wild-ranging birds, because they provide evidence for low-frequency songs being linked to reproductive success and to be affected by noise-dependent signal efficiency.
Newly discovered landscape traps produce regime shifts in wet forests
Authors: Lindenmayer David B. , Hobbs Richard J. , Likens Gene E. , Krebs Charles J. , Banks Samuel C.
Published: August 2011

We describe the “landscape trap” concept, whereby entire landscapes are shifted into, and then maintained (trapped) in, a highly compromised structural and functional state as the result of multiple temporal and spatial feedbacks between human and natural disturbance regimes. The landscape trap concept builds on ideas like stable alternative states and other relevant concepts, but it substantively expands the conceptual thinking in a number of unique ways. In this paper, we (
i
) review the literature to develop the concept of landscape traps, including their general features; (
ii
) provide a case study as an example of a landscape trap from the mountain ash (
Eucalyptus regnans
) forests of southeastern Australia; (
iii
) suggest how landscape traps can be detected before they are irrevocably established; and (
iv
) present evidence of the generality of landscape traps in different ecosystems worldwide.
On the spontaneous collective motion of active matter
Authors: Wang Shenshen , Wolynes Peter G.
Published: August 2011

Spontaneous directed motion, a hallmark of cell biology, is unusual in classical statistical physics. Here we study, using both numerical and analytical methods, organized motion in models of the cytoskeleton in which constituents are driven by energy-consuming motors. Although systems driven by small-step motors are described by an effective temperature and are thus quiescent, at higher order in step size, both homogeneous and inhomogeneous, flowing and oscillating behavior emerges. Motors that respond with a negative susceptibility to imposed forces lead to an apparent negative-temperature system in which beautiful structures form resembling the asters seen in cell division.
Dendritic coding of multiple sensory inputs in single cortical neurons in vivo
Authors: Varga Zsuzsanna , Jia Hongbo , Sakmann Bert , Konnerth Arthur
Published: August 2011

Single cortical neurons in the mammalian brain receive signals arising from multiple sensory input channels. Dendritic integration of these afferent signals is critical in determining the amplitude and time course of the neurons' output signals. As of yet, little is known about the spatial and temporal organization of converging sensory inputs. Here, we combined in vivo two-photon imaging with whole-cell recordings in layer 2 neurons of the mouse vibrissal cortex as a means to analyze the spatial pattern of subthreshold dendritic calcium signals evoked by the stimulation of different whiskers. We show that the principle whisker and the surrounding whiskers can evoke dendritic calcium transients in the same neuron. Distance-dependent attenuation of dendritic calcium transients and the corresponding subthreshold depolarization suggest feed-forward activation. We found that stimulation of different whiskers produced multiple calcium hotspots on the same dendrite. Individual hotspots were activated with low probability in a stochastic manner. We show that these hotspots are generated by calcium signals arising in dendritic spines. Some spines were activated uniquely by single whiskers, but many spines were activated by multiple whiskers. These shared spines indicate the existence of presynaptic feeder neurons that integrate and transmit activity arising from multiple whiskers. Despite the dendritic overlap of whisker-specific and shared inputs, different whiskers are represented by a unique set of activation patterns within the dendritic field of each neuron.
Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs
Authors: Reyes José , Gómez-Romero Laura , Ibarra-Soria Ximena , Palacios-Flores Kim , Arriola Luis R. , Wences Alejandro , García Delfino , Boege Margareta , Dávila Guillermo , Flores Margarita , Palacios Rafael
Published: August 2011

We have entered the era of individual genomic sequencing, and can already see exponential progress in the field. It is of utmost importance to exclude false-positive variants from reported datasets. However, because of the nature of the used algorithms, this task has not been optimized to the required level of precision. This study presents a unique strategy for identifying SNPs, called COIN-VGH, that largely minimizes the presence of false-positives in the generated data. The algorithm was developed using the X-chromosome–specific regions from the previously sequenced genomes of Craig Venter and James Watson. The algorithm is based on the concept that a nucleotide can be individualized if it is analyzed in the context of its surrounding genomic sequence. COIN-VGH consists of defining the most comprehensive set of nucleotide strings of a defined length that map with 100% identity to a unique position within the human reference genome (HRG). Such set is used to retrieve sequence reads from a query genome (QG), allowing the production of a genomic landscape that represents a draft HRG-guided assembly of the QG. This landscape is analyzed for specific signatures that indicate the presence of SNPs. The fidelity of the variation signature was assessed using simulation experiments by virtually altering the HRG at defined positions. Finally, the signature regions identified in the HRG and in the QG reads are aligned and the precise nature and position of the corresponding SNPs are detected. The advantages of COIN-VGH over previous algorithms are discussed.
GCC185 plays independent roles in Golgi structure maintenance and AP-1–mediated vesicle tethering
Authors: Brown Frank C. , Schindelhaim Carmel H. , Pfeffer Suzanne R.
Published: August 2011

GCC185 is a long coiled-coil protein localized to the trans-Golgi network (TGN) that functions in maintaining Golgi structure and tethering mannose 6-phosphate receptor (MPR)–containing transport vesicles en route to the Golgi. We report the identification of two distinct domains of GCC185 needed either for Golgi structure maintenance or transport vesicle tethering, demonstrating the independence of these two functions. The domain needed for vesicle tethering binds to the clathrin adaptor AP-1, and cells depleted of GCC185 accumulate MPRs in transport vesicles that are AP-1 decorated. This study supports a previously proposed role of AP-1 in retrograde transport of MPRs from late endosomes to the Golgi and indicates that docking may involve the interaction of vesicle-associated AP-1 protein with the TGN-associated tethering protein GCC185.
Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/β-catenin signaling
Authors: Berndt Jason D. , Aoyagi Atsushi , Yang Peitzu , Anastas Jamie N. , Tang Lan , Moon Randall T.
Published: August 2011

Receptor-like tyrosine kinase (RYK) functions as a transmembrane receptor for the Wnt family of secreted protein ligands. Although RYK undergoes endocytosis in response to Wnt, the mechanisms that regulate its internalization and concomitant activation of Wnt signaling are unknown. We discovered that RYK both physically and functionally interacts with the E3 ubiquitin ligase Mindbomb 1 (MIB1). Overexpression of MIB1 promotes the ubiquitination of RYK and reduces its steady-state levels at the plasma membrane. Moreover, we show that MIB1 is sufficient to activate Wnt/β-catenin (CTNNB1) signaling and that this activity depends on endogenous RYK. Conversely, in loss-of-function studies, both RYK and MIB1 are required for Wnt-3A–mediated activation of CTNNB1. Finally, we identify the Caenorhabditis elegans orthologue of MIB1 and demonstrate a genetic interaction between ceMIB and lin-18/RYK in vulva development. These findings provide insights into the mechanisms of Wnt/RYK signaling and point to novel targets for the modulation of Wnt signaling.
Critical role of Bcl11b in suppressor function of T regulatory cells and prevention of inflammatory bowel disease
Authors: VanValkenburgh Jeffrey , Albu Diana I. , Bapanpally Chandra , Casanova Sarah , Califano Danielle , Jones David M. , Ignatowicz Leszek , Kawamoto Shimpei , Fagarasan Sidonia , Jenkins Nancy A. , Copeland Neal G. , Liu Pentao , Avram Dorina
Published: August 2011

Dysregulated CD4+ T cell responses and alterations in T regulatory cells (Treg cells) play a critical role in autoimmune diseases, including inflammatory bowel disease (IBD). The current study demonstrates that removal of Bcl11b at the double-positive stage of T cell development or only in Treg cells causes IBD because of proinflammatory cytokine-producing CD4+ T cells infiltrating the colon. Provision of WT Treg cells prevented IBD, demonstrating that alterations in Treg cells are responsible for the disease. Furthermore, Bcl11b-deficient Treg cells had reduced suppressor activity with altered gene expression profiles, including reduced expression of the genes encoding Foxp3 and IL-10, and up-regulation of genes encoding proinflammatory cytokines. Additionally, the absence of Bcl11b altered the induction of Foxp3 expression and reduced the generation of induced Treg cells (iTreg cells) after Tgf-β treatment of conventional CD4+ T cells. Bcl11b bound to Foxp3 and IL-10 promoters, as well as to critical conserved noncoding sequences within the Foxp3 and IL-10 loci, and mutating the Bcl11b binding site in the Foxp3 promoter reduced expression of a luciferase reporter gene. These experiments demonstrate that Bcl11b is indispensable for Treg suppressor function and for maintenance of optimal Foxp3 and IL-10 gene expression, as well as for the induction of Foxp3 expression in conventional CD4+ T cells in response to Tgf-β and generation of iTreg cells.
WASp-deficient B cells play a critical, cell-intrinsic role in triggering autoimmunity
Authors: Becker-Herman Shirly , Meyer-Bahlburg Almut , Schwartz Marc A. , Jackson Shaun W. , Hudkins Kelly L. , Liu Chaohong , Sather Blythe D. , Khim Socheath , Liggitt Denny , Song Wenxia , Silverman Gregg J. , Alpers Charles E. , Rawlings David J.
Published: August 2011

Patients with the immunodeficiency Wiskott-Aldrich syndrome (WAS) frequently develop systemic autoimmunity. Here, we demonstrate that mutation of the WAS gene results in B cells that are hyperresponsive to B cell receptor and Toll-like receptor (TLR) signals in vitro, thereby promoting a B cell–intrinsic break in tolerance. Whereas this defect leads to autoantibody production in WAS protein–deficient (WASp−/−) mice without overt disease, chimeric mice in which only the B cell lineage lacks WASp exhibit severe autoimmunity characterized by spontaneous germinal center formation, class-switched autoantibodies, renal histopathology, and early mortality. Both T cell help and B cell–intrinsic TLR engagement play important roles in promoting disease in this model, as depletion with anti-CD4 antibodies or generation of chimeric mice with B cells deficient in both WASp and MyD88 prevented development of autoimmune disease. These data highlight the potentially harmful role for cell-intrinsic loss of B cell tolerance in the setting of normal T cell function, and may explain why WAS patients with mixed chimerism after stem cell transplantation often develop severe humoral autoimmunity.
Cannabinoid receptor 2 positions and retains marginal zone B cells within the splenic marginal zone
Authors: Muppidi Jagan R. , Arnon Tal I. , Bronevetsky Yelena , Veerapen Natacha , Tanaka Masato , Besra Gurdyal S. , Cyster Jason G.
Published: August 2011

Specialized B cells residing in the splenic marginal zone (MZ) continuously survey the blood for antigens and are important for immunity to systemic infections. However, the cues that uniquely attract cells to the MZ have not been defined. Previous work demonstrated that mice deficient in cannabinoid receptor 2 (CB2) have decreased numbers of MZ B cells but it has been unclear whether CB2 regulates MZ B cell development or positioning. We show that MZ B cells are highly responsive to the CB2 ligand 2-arachidonylglycerol (2-AG) and that CB2 antagonism rapidly displaces small numbers of MZ B cells to the blood. Antagonism for longer durations depletes MZ B cells from the spleen. In mice deficient in sphingosine-1-phosphate receptor function, CB2 antagonism causes MZ B cell displacement into follicles. Moreover, CB2 overexpression is sufficient to position B cells to the splenic MZ. These findings establish a role for CB2 in guiding B cells to the MZ and in preventing their loss to the blood. As a consequence of their MZ B cell deficiency, CB2-deficient mice have reduced numbers of CD1d-high B cells. We show that CB2 deficiency results in diminished humoral responses to a CD1d-restricted systemic antigen.
Testicular Pain
Authors: Booker Matthew
Published: August 2011

Testicular and scrotal pain are common presenting complaints in the GP surgery. Often, men present after acute onset of pain, but more commonly male patients attend after a gradual progression of more vague testicular symptoms or when discomfort begins to impact upon normal activities of daily living. Testicular symptoms can be a cause of great anxiety among patients, particularly as men (most notably younger men) are often embarrassed or reluctant to consult, which GPs need to be sensitive to. This article discusses some of the common and important testicular pathologies and emphasizes how a structured approach to the history and examination helps in making a clinical diagnosis.