bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasticity tradeoffs in salt tolerance mechanisms among desert Distichlis spicata genotypes
Authors: Lazarus Brynne E. , Richards James H. , Gordon Phoebe E. , Oki Lorence R. , Barnes Corey S.
Published: March 2011

We investigated genetic differences in salinity tolerance among 20 saltgrass (Distichlis spicata (L.) Greene) genotypes, including constitutive, gender-based and phenotypic plasticity traits, to better understand the basis of adaptation and acclimation by saltgrass in diverse environments. On average, the plants survived NaCl treatments up to ~1 M, with reductions in growth and health that varied with genotype. For these 20 genotypes in a greenhouse study, we showed that greater plasticity in one salt tolerance mechanism was physiologically linked to lesser plasticity in another. Under various levels of constant salinity stress, genotypes employing a strategy of greater plasticity in foliar Na and lesser plasticity in both foliar K : Na and Na turnover rate were better able to substitute Na for K in some cellular functions, especially osmotic adjustment, leading to increased salinity tolerance. Although we observed gender segregation with salinity in the Owens (Dry) Lake Playa (Inyo County, CA, USA) population planted for dust control, from which the genotypes were collected, we did not observe gender differences in salinity tolerance in the greenhouse. Significant physiological plasticity tradeoffs among genotypes, however, did affect overall salinity tolerance and may be important for this species survival in diverse managed and natural habitats.
Comparative genomics of two ecologically differential populations of Hibiscus tiliaceus under salt stress
Authors: Yang Guili , Chen Xiaoshu , Tang Tian , Zhou Renchao , Chen Sufang , Li Weijing , Ouyang Jianhua , He Lian , Shi Shuhua
Published: March 2011

Hibiscus tiliaceus L. is a mangrove associate that occupies the divergent environments of intertidal wetland (L population) and inland (T population). Thus, it is an ideal plant for the study of ecological adaptation and salt tolerance. In this study we compared responses of the two populations to salinity combining a global transcriptional analysis and physiological analysis. Microarray transcript profiling analysis showed both shared and divergent responses to salinity stress in the two populations. A total of 575 unigenes were identified as being salt-responsive in the two populations. Shared responses were exemplified by the regulated genes functioning in confining ribosomal functions, photosynthesis and cellular metabolism. A set of genes functioning in cellular transporting and cell detoxification and a crucial transcription factor AP2 domain-containing protein involved in environmental responsiveness, were differently expressed in the two populations. Physiological analysis showed that the L population was less susceptible to salt stress in photosynthesis and had a stronger capability of K+ : Na+ regulation than the T population. Both microarray and physiological data showed the L population possess higher fitness under high salinity, probably due to it its long-term adaptation to their native environment.
Pinus halepensis regeneration after a wildfire in a semiarid environment: assessment using multitemporal Landsat images
Authors: Vicente-Serrano Sergio M. , Pérez-Cabello Fernando , Lasanta Teodoro
Published: March 2011

We studied the spatial and temporal patterns of forest regeneration using a 24-year time series of Landsat images and the normalised difference vegetation index (NDVI) in a homogeneous Pinus halepensis forest, 3000 ha of which were extensively burned in 1995. We demonstrated a progressive slow and linear recovery in NDVI values, based on Landsat images between 1997 and 2007. The forest tended to recover to pre-disturbance conditions, both with respect to the magnitude of the NDVI and in terms of the spatial pattern. We found that the spatial differences in the rates of NDVI recovery were not affected by the burn severity. Moreover, burn severity did not affect the rates of NDVI recovery after the fire. Although highly homogeneous P. halepensis regeneration was the dominant pattern in the study area (more than the 70% of the burn area showed positive and significant trends), some spatial differences in the magnitude of change were observed. The forest tended to recover the spatial pattern corresponding to pre-fire conditions, although it was difficult to establish whether terrain elevation or previous tree size and density were the main governing factors, given the strong relationship between them.
An optimisation modelling approach to seasonal resource allocation for planned burning
Authors: Higgins Andrew , Whitten Stuart , Slijepcevic Alen , Fogarty Liam , Laredo Luis
Published: March 2011

Burning of fine fuels is a crucial activity in Australia as part of reducing the severity of bushfires. Seasonal planning of such planned burning is a very complex task owing to the large number of practical considerations and uncertainty of burn conditions, as well as personnel and equipment resource constraints. Practical considerations include the small number of suitable burn days for different types of burns, as well as different fuel hazard and burn types. This requires careful management of very high resource requirements during the available days. We developed a tool that will use all of the above variables to estimate the resource requirements for different levels of planned burning program. We provide a mathematical programming approach to help plan burning crews and equipment resource requirements in each district by month to minimise likely personnel requirements, under seasonal uncertainty. A key feature is that it accommodates maximum daily resource demands given uncertainty in available burn days and overlap between geographical districts. We implemented the model on a real-world problem of public land across Victoria, and solved it to optimality using GAMS/Cplex 9.
Effects of particle fracturing and moisture content on fire behaviour in masticated fuelbeds burned in a laboratory
Authors: Kreye Jesse K. , Varner J. Morgan , Knapp Eric E.
Published: March 2011

Mechanical mastication is a fuels treatment that converts shrubs and small trees into dense fuelbeds composed of fractured woody particles. Although compaction is thought to reduce fireline intensity, the added particle surface area due to fracturing could also influence fire behaviour. We evaluated effects of particle fracturing and moisture content (ranging from 2.5 to 13%) on fire behaviour in fuelbeds composed of masticated Arctostaphylos manzanita Parry and Ceanothus velutinus Dougl. shrubs in the laboratory. Fuelbeds composed of fractured particles did not burn with greater intensity than fuelbeds composed of intact particles, as hypothesised. Flame heights ranged from 54 to 95 cm and fireline intensity from 50 to 140 kJ s–1 m–1, approximating values observed in field experiments. Masticated fuelbeds burned with shorter flame heights and longer flaming duration under higher fuel moistures, but duration of lethal heating (>60°C) above fuelbeds did not differ across the range of fuel moistures, averaging 12 min over a 0.1-m2 area. Our results suggest that expected fire behaviour increases due to particle fracturing may be overwhelmed by fuelbed bulk density. The long-duration heating of burning masticated fuels may require managers to mitigate effects to trees and soils when fuel loads are high.
Lignin content in natural
Populus
variants affects sugar release
Authors: Studer Michael H. , DeMartini Jaclyn D. , Davis Mark F. , Sykes Robert W. , Davison Brian , Keller Martin , Tuskan Gerald A. , Wyman Charles E.
Published: March 2011

The primary obstacle to producing renewable fuels from lignocellulosic biomass is a plant's recalcitrance to releasing sugars bound in the cell wall. From a sample set of wood cores representing 1,100 individual undomesticated
Populus trichocarpa
trees, 47 extreme phenotypes were selected across measured lignin content and ratio of syringyl and guaiacyl units (S/G ratio). This subset was tested for total sugar release through enzymatic hydrolysis alone as well as through combined hot-water pretreatment and enzymatic hydrolysis using a high-throughput screening method. The total amount of glucan and xylan released varied widely among samples, with total sugar yields of up to 92% of the theoretical maximum. A strong negative correlation between sugar release and lignin content was only found for pretreated samples with an S/G ratio < 2.0. For higher S/G ratios, sugar release was generally higher, and the negative influence of lignin was less pronounced. When examined separately, only glucose release was correlated with lignin content and S/G ratio in this manner, whereas xylose release depended on the S/G ratio alone. For enzymatic hydrolysis without pretreatment, sugar release increased significantly with decreasing lignin content below 20%, irrespective of the S/G ratio. Furthermore, certain samples featuring average lignin content and S/G ratios exhibited exceptional sugar release. These facts suggest that factors beyond lignin and S/G ratio influence recalcitrance to sugar release and point to a critical need for deeper understanding of cell-wall structure before plants can be rationally engineered for reduced recalcitrance and efficient biofuels production.
Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450
Authors: Oláh Julianna , Mulholland Adrian J. , Harvey Jeremy N.
Published: March 2011

Cytochrome P450 enzymes play key roles in the metabolism of the majority of drugs. Improved models for prediction of likely metabolites will contribute to drug development. In this work, two possible metabolic routes (aromatic carbon oxidation and O-demethylation) of dextromethorphan are compared using molecular dynamics (MD) simulations and density functional theory (DFT). The DFT results on a small active site model suggest that both reactions might occur competitively. Docking and MD studies of dextromethorphan in the active site of P450 2D6 show that the dextromethorphan is located close to heme oxygen in a geometry apparently consistent with competitive metabolism. In contrast, calculations of the reaction path in a large protein model [using a hybrid quantum mechanical–molecular mechanics (QM/MM) method] show a very strong preference for O-demethylation, in accordance with experimental results. The aromatic carbon oxidation reaction is predicted to have a high activation energy, due to the active site preventing formation of a favorable transition-state structure. Hence, the QM/MM calculations demonstrate a crucial role of many active site residues in determining reactivity of dextromethorphan in P450 2D6. Beyond substrate binding orientation and reactivity of Compound I, successful metabolite predictions must take into account the detailed mechanism of oxidation in the protein. These results demonstrate the potential of QM/MM methods to investigate specificity in drug metabolism.
Adaptive human behavior in epidemiological models
Authors: Fenichel Eli P. , Castillo-Chavez Carlos , Ceddia M. G. , Chowell Gerardo , Parra Paula A. Gonzalez , Hickling Graham J. , Holloway Garth , Horan Richard , Morin Benjamin , Perrings Charles , Springborn Michael , Velazquez Leticia , Villalobos Cristina
Published: March 2011

The science and management of infectious disease are entering a new stage. Increasingly public policy to manage epidemics focuses on motivating people, through social distancing policies, to alter their behavior to reduce contacts and reduce public disease risk. Person-to-person contacts drive human disease dynamics. People value such contacts and are willing to accept some disease risk to gain contact-related benefits. The cost–benefit trade-offs that shape contact behavior, and hence the course of epidemics, are often only implicitly incorporated in epidemiological models. This approach creates difficulty in parsing out the effects of adaptive behavior. We use an epidemiological–economic model of disease dynamics to explicitly model the trade-offs that drive person-to-person contact decisions. Results indicate that including adaptive human behavior significantly changes the predicted course of epidemics and that this inclusion has implications for parameter estimation and interpretation and for the development of social distancing policies. Acknowledging adaptive behavior requires a shift in thinking about epidemiological processes and parameters.
Residence time of buoyant objects in drowning machines
Authors: Gioia Gustavo , Chakraborty Pinaki , Gary Stefan F. , Zamalloa Carlo Zuñiga , Keane Richard D.
Published: March 2011

Hydraulic jumps are a common feature of rivers and waterways, where they can be found close to spillways, weirs, rocky ledges, and boulders. People adrift upstream of a hydraulic jump are liable to become trapped in the turbulent roller of the hydraulic jump. For this reason, hydraulic jumps have been termed “drowning machines” and are recognized as a public hazard. We use experiments and theory to show that on average a buoyant object spends a time
τ
/
p
trapped in a jump, where
τ
is the period of a harmonic process inherent in the jump, and
p
is the probability that the object will escape in any time interval
τ
. The probability
p
is governed by the statistical theory of extreme values and depends primarily on the ratio between the density of the object and the density of the fluid. We use our results to draw conclusions that might prove to be useful to public-safety agencies intent on carrying out tests in drowning machines. Our results can also be used to predict the amount of flotsam that accumulates at the toe of a hydraulic jump.
Cardiolipin microdomains localize to negatively curved regions of
Escherichia coli
membranes
Authors: Renner Lars D. , Weibel Douglas B.
Published: March 2011

Many proteins reside at the cell poles in rod-shaped bacteria. Several hypotheses have drawn a connection between protein localization and the large cell-wall curvature at the poles. One hypothesis has centered on the formation of microdomains of the lipid cardiolipin (CL), its localization to regions of high membrane curvature, and its interaction with membrane-associated proteins. A lack of experimental techniques has left this hypothesis unanswered. This paper describes a microtechnology-based technique for manipulating bacterial membrane curvature and quantitatively measuring its effect on the localization of CL and proteins in cells. We confined
Escherichia coli
spheroplasts in microchambers with defined shapes that were embossed into a layer of polymer and observed that the shape of the membrane deformed predictably to accommodate the walls of the microchambers. Combining this technique with epifluorescence microscopy and quantitative image analyses, we characterized the localization of CL microdomains in response to
E. coli
membrane curvature. CL microdomains localized to regions of high intrinsic negative curvature imposed by microchambers. We expressed a chimera of yellow fluorescent protein fused to the N-terminal region of MinD—a spatial determinant of
E. coli
division plane assembly—in spheroplasts and observed its colocalization with CL to regions of large, negative membrane curvature. Interestingly, the distribution of MinD was similar in spheroplasts derived from a CL synthase knockout strain. These studies demonstrate the curvature dependence of CL in membranes and test whether these structures participate in the localization of MinD to regions of negative curvature in cells.
MicroRNA-138 regulates osteogenic differentiation of human stromal (mesenchymal) stem cells in vivo
Authors: Eskildsen Tilde , Taipaleenmäki Hanna , Stenvang Jan , Abdallah Basem M. , Ditzel Nicholas , Nossent Anne Yael , Bak Mads , Kauppinen Sakari , Kassem Moustapha
Published: March 2011

Elucidating the molecular mechanisms that regulate human stromal (mesenchymal) stem cell (hMSC) differentiation into osteogenic lineage is important for the development of anabolic therapies for treatment of osteoporosis. MicroRNAs (miRNAs) are short, noncoding RNAs that act as key regulators of diverse biological processes by mediating translational repression or mRNA degradation of their target genes. Here, we show that miRNA-138 (miR-138) modulates osteogenic differentiation of hMSCs. miRNA array profiling and further validation by quantitative RT-PCR (qRT-PCR) revealed that miR-138 was down-regulated during osteoblast differentiation of hMSCs. Overexpression of miR-138 inhibited osteoblast differentiation of hMSCs in vitro, whereas inhibition of miR-138 function by antimiR-138 promoted expression of osteoblast-specific genes, alkaline phosphatase (ALP) activity, and matrix mineralization. Furthermore, overexpression of miR-138 reduced ectopic bone formation in vivo by 85%, and conversely, in vivo bone formation was enhanced by 60% when miR-138 was antagonized. Target prediction analysis and experimental validation by luciferase 3′ UTR reporter assay confirmed focal adhesion kinase, a kinase playing a central role in promoting osteoblast differentiation, as a bona fide target of miR-138. We show that miR-138 attenuates bone formation in vivo, at least in part by inhibiting the focal adhesion kinase signaling pathway. Our findings suggest that pharmacological inhibition of miR-138 by antimiR-138 could represent a therapeutic strategy for enhancing bone formation in vivo.
Geographic bias of field observations of soil carbon stocks with tropical land-use changes precludes spatial extrapolation
Authors: Powers Jennifer S. , Corre Marife D. , Twine Tracy E. , Veldkamp Edzo
Published: March 2011

Accurately quantifying changes in soil carbon (C) stocks with land-use change is important for estimating the anthropogenic fluxes of greenhouse gases to the atmosphere and for implementing policies such as REDD (Reducing Emissions from Deforestation and Degradation) that provide financial incentives to reduce carbon dioxide fluxes from deforestation and land degradation. Despite hundreds of field studies and at least a dozen literature reviews, there is still considerable disagreement on the direction and magnitude of changes in soil C stocks with land-use change. We conducted a meta-analysis of studies that quantified changes in soil C stocks with land use in the tropics. Conversion from one land use to another caused significant increases or decreases in soil C stocks for 8 of the 14 transitions examined. For the three land-use transitions with sufficient observations, both the direction and magnitude of the change in soil C pools depended strongly on biophysical factors of mean annual precipitation and dominant soil clay mineralogy. When we compared the distribution of biophysical conditions of the field observations to the area-weighted distribution of those factors in the tropics as a whole or the tropical lands that have undergone conversion, we found that field observations are highly unrepresentative of most tropical landscapes. Because of this geographic bias we strongly caution against extrapolating average values of land-cover change effects on soil C stocks, such as those generated through meta-analysis and literature reviews, to regions that differ in biophysical conditions.
Mammalian phylogeny reveals recent diversification rate shifts
Authors: Stadler Tanja
Published: March 2011

Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous–Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveals that the tempo of mammalian evolution did not change until ∼33 Mya. This constant period was followed by a peak of diversification rates between 33 and 30 Mya. Thereafter, diversification rates remained high and constant until 8.55 Mya. Diversification rates declined significantly at 8.55 and 3.35 Mya. Investigation of mammalian subgroups (marsupials, placentals, and the six largest placental subgroups) reveals that the diversification rate peak at 33–30 Mya is mainly driven by rodents, cetartiodactyla, and marsupials. The recent diversification rate decrease is significant for all analyzed subgroups but eulipotyphla, cetartiodactyla, and primates. My likelihood approach is not limited to mammalian evolution. It provides a robust framework to infer diversification rate changes and mass extinction events in phylogenies, reconstructed from, e.g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling.
Mapping allostery through the covariance analysis of NMR chemical shifts
Authors: Selvaratnam Rajeevan , Chowdhury Somenath , VanSchouwen Bryan , Melacini Giuseppe
Published: March 2011

Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical shift changes caused by a set of covalently modified analogs of the allosteric effector (i.e., agonists and antagonists) reveals extended networks of coupled residues. Unexpectedly, such networks reach not only sites subject to effector-dependent structural variations, but also regions that are controlled by dynamically driven allostery. In these regions the allosteric signal is propagated mainly by dynamic rather than structural modulations, which result in subtle but highly correlated chemical shift variations. The proposed chemical shift covariance analysis (CHESCA) identifies interresidue correlations based on the combination of agglomerative clustering (AC) and singular value decomposition (SVD). AC results in dendrograms that define functional clusters of coupled residues, while SVD generates score plots that provide a residue-specific dissection of the contributions to binding and allostery. The CHESCA approach was validated by applying it to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC) and the CHESCA results are in full agreement with independent mutational data on EPAC activation. Overall, CHESCA is a generally applicable method that utilizes a selected chemical library of effector analogs to quantitatively decode the binding and allosteric information content embedded in chemical shift changes.
Genomic mechanisms of evolved physiological plasticity in killifish distributed along an environmental salinity gradient
Authors: Whitehead Andrew , Roach Jennifer L. , Zhang Shujun , Galvez Fernando
Published: March 2011

Adaptive variation tends to emerge clinally along environmental gradients or discretely among habitats with limited connectivity. However, in Atlantic killifish (
Fundulus heteroclitus
), a population genetic discontinuity appears in the absence of obvious barriers to gene flow along parallel salinity clines and coincides with a physiologically stressful salinity. We show that populations resident on either side of this discontinuity differ in their abilities to compensate for osmotic shock and illustrate the physiological and functional genomic basis of population variation in hypoosmotic tolerance. A population native to a freshwater habitat, upstream of the genetic discontinuity, exhibits tolerance to extreme hypoosmotic challenge, whereas populations native to brackish or marine habitats downstream of the discontinuity lose osmotic homeostasis more severely and take longer to recover. Comparative transcriptomics reveals a core transcriptional response associated with acute and acclimatory responses to hypoosmotic shock and posits unique mechanisms that enable extreme osmotic tolerance. Of the genes that vary in expression among populations, those that are putatively involved in physiological acclimation are more likely to exhibit nonneutral patterns of divergence between freshwater and brackish populations. It is not the well-known effectors of osmotic acclimation, but rather the lesser-known immediate-early responses, that appear important in contributing to population differences.
Nucleolar stress is an early response to myocardial damage involving nucleolar proteins nucleostemin and nucleophosmin
Authors: Avitabile Daniele , Bailey Brandi , Cottage Christopher T. , Sundararaman Balaji , Joyo Anya , McGregor Michael , Gude Natalie , Truffa Silvia , Zarrabi Aryan , Konstandin Mathias , Khan Mohsin , Mohsin Sadia , Völkers Mirko , Toko Haruhiro , Mason Matt , Cheng Zhaokang , Din Shabana , Alvarez Roberto , Fischer Kimberlee , Sussman Mark A.
Published: March 2011

Nucleolar stress, characterized by loss of nucleolar integrity, has not been described in the cardiac context. In addition to ribosome biogenesis, nucleoli are critical for control of cell proliferation and stress responses. Our group previously demonstrated induction of the nucleolar protein nucleostemin (NS) in response to cardiac pathological insult. NS interacts with nucleophosmin (NPM), a marker of nucleolar stress with cytoprotective properties. The dynamic behavior of NS and NPM reveal that nucleolar disruption is an early event associated with stress response in cardiac cells. Rapid translocation of NS and NPM to the nucleoplasm and suppression of new preribosomal RNA synthesis occurs in both neonatal rat cardiomyocytes (NRCM) and cardiac progenitor cells (CPC) upon exposure to doxorubicin or actinomycin D. Silencing of NS significantly increases cell death resulting from doxorubicin treatment in CPC, whereas NPM knockdown alone induces cell death. Overexpression of either NS or NPM significantly decreases caspase 8 activity in cultured cardiomyocytes challenged with doxorubicin. The presence of altered nucleolar structures resulting from myocardial infarction in mice supports the model of nucleolar stress as a general response to pathological injury. Collectively, these findings serve as the initial description of myocardial nucleolar stress and establish the postulate that nucleoli acts as sensors of stress, regulating the cellular response to pathological insults.
High sensitivity nanoparticle detection using optical microcavities
Authors: Lu Tao , Lee Hansuek , Chen Tong , Herchak Steven , Kim Ji-Hun , Fraser Scott E. , Flagan Richard C. , Vahala Kerry
Published: March 2011

We demonstrate a highly sensitive nanoparticle and virus detection method by using a thermal-stabilized reference interferometer in conjunction with an ultrahigh-Q microcavity. Sensitivity is sufficient to resolve shifts caused by binding of individual nanobeads in solution down to a record radius of 12.5 nm, a size approaching that of single protein molecules. A histogram of wavelength shift versus nanoparticle radius shows that particle size can be inferred from shift maxima. Additionally, the signal-to-noise ratio for detection of Influenza A virus is enhanced to 38∶1 from the previously reported 3∶1. The method does not use feedback stabilization of the probe laser. It is also observed that the conjunction of particle-induced backscatter and optical-path-induced shifts can be used to enhance detection signal-to-noise.
Glucocorticoids enhance extinction-based psychotherapy
Authors: de Quervain Dominique J.-F. , Bentz Dorothée , Michael Tanja , Bolt Olivia C. , Wiederhold Brenda K. , Margraf Jürgen , Wilhelm Frank H.
Published: March 2011

Behavioral exposure therapy of anxiety disorders is believed to rely on fear extinction. Because preclinical studies have shown that glucocorticoids can promote extinction processes, we aimed at investigating whether the administration of these hormones might be useful in enhancing exposure therapy. In a randomized, double-blind, placebo-controlled study, 40 patients with specific phobia for heights were treated with three sessions of exposure therapy using virtual reality exposure to heights. Cortisol (20 mg) or placebo was administered orally 1 h before each of the treatment sessions. Subjects returned for a posttreatment assessment 3–5 d after the last treatment session and for a follow-up assessment after 1 mo. Adding cortisol to exposure therapy resulted in a significantly greater reduction in fear of heights as measured with the acrophobia questionnaire (AQ) both at posttreatment and at follow-up, compared with placebo. Furthermore, subjects receiving cortisol showed a significantly greater reduction in acute anxiety during virtual exposure to a phobic situation at posttreatment and a significantly smaller exposure-induced increase in skin conductance level at follow-up. The present findings indicate that the administration of cortisol can enhance extinction-based psychotherapy.
Shear rheology of lipid monolayers and insights on membrane fluidity
Authors: Espinosa Gabriel , López-Montero Iván , Monroy Francisco , Langevin Dominique
Published: March 2011

The concept of membrane fluidity usually refers to a high molecular mobility inside the lipid bilayer which enables lateral diffusion of embedded proteins. Fluids have the ability to flow under an applied shear stress whereas solids resist shear deformations. Biological membranes require both properties for their function: high lateral fluidity and structural rigidity. Consequently, an adequate account must include, in addition to viscosity, the possibility for a nonzero shear modulus. This knowledge is still lacking as measurements of membrane shear properties have remained incomplete so far. In the present contribution we report a surface shear rheology study of different lipid monolayers that model distinct biologically relevant situations. The results evidence a large variety of mechanical behavior under lateral shear flow.
An actin cytoskeleton with evolutionarily conserved functions in the absence of canonical actin-binding proteins
Authors: Paredez Alexander R. , Assaf Zoe June , Sept David , Timofejeva Ljudmilla , Dawson Scott C. , Wang Chung-Ju Rachel , Cande W. Z.
Published: March 2011

Giardia intestinalis
, a human intestinal parasite and member of what is perhaps the earliest-diverging eukaryotic lineage, contains the most divergent eukaryotic actin identified to date and is the first eukaryote known to lack all canonical actin-binding proteins (ABPs). We sought to investigate the properties and functions of the actin cytoskeleton in
Giardia
to determine whether
Giardia
actin (giActin) has reduced or conserved roles in core cellular processes. In vitro polymerization of giActin produced filaments, indicating that this divergent actin is a true filament-forming actin. We generated an anti-giActin antibody to localize giActin throughout the cell cycle. GiActin localized to the cortex, nuclei, internal axonemes, and formed C-shaped filaments along the anterior of the cell and a flagella-bundling helix. These structures were regulated with the cell cycle and in encysting cells giActin was recruited to the Golgi-like cyst wall processing vesicles. Knockdown of giActin demonstrated that giActin functions in cell morphogenesis, membrane trafficking, and cytokinesis. Additionally,
Giardia
contains a single G protein, giRac, which affects the
Giardia
actin cytoskeleton independently of known target ABPs. These results imply that there exist ancestral and perhaps conserved roles for actin in core cellular processes that are independent of canonical ABPs. Of medical significance, the divergent giActin cytoskeleton is essential and commonly used actin-disrupting drugs do not depolymerize giActin structures. Therefore, the giActin cytoskeleton is a promising drug target for treating giardiasis, as we predict drugs that interfere with the
Giardia
actin cytoskeleton will not affect the mammalian host.
Rapid metabolic evolution in human prefrontal cortex
Authors: Fu Xing , Giavalisco Patrick , Liu Xiling , Catchpole Gareth , Fu Ning , Ning Zhi-Bin , Guo Song , Yan Zheng , Somel Mehmet , Pääbo Svante , Zeng Rong , Willmitzer Lothar , Khaitovich Philipp
Published: March 2011

Human evolution is characterized by the rapid expansion of brain size and drastic increase in cognitive capabilities. It has long been suggested that these changes were accompanied by modifications of brain metabolism. Indeed, human-specific changes on gene expression or amino acid sequence were reported for a number of metabolic genes, but actual metabolite measurements in humans and apes have remained scarce. Here, we investigate concentrations of more than 100 metabolites in the prefrontal and cerebellar cortex in 49 humans, 11 chimpanzees, and 45 rhesus macaques of different ages using gas chromatography–mass spectrometry (GC-MS). We show that the brain metabolome undergoes substantial changes, both ontogenetically and evolutionarily: 88% of detected metabolites show significant concentration changes with age, whereas 77% of these metabolic changes differ significantly among species. Although overall metabolic divergence reflects phylogenetic relationships among species, we found a fourfold acceleration of metabolic changes in prefrontal cortex compared with cerebellum in the human lineage. These human-specific metabolic changes are paralleled by changes in expression patterns of the corresponding enzymes, and affect pathways involved in synaptic transmission, memory, and learning.
Drosophila
histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin
Authors: Kotova Elena , Lodhi Niraj , Jarnik Michael , Pinnola Aaron D. , Ji Yingbiao , Tulin Alexei V.
Published: March 2011

According to the histone code hypothesis, histone variants and modified histones provide binding sites for proteins that change the chromatin state to either active or repressed. Here, we identify histone variants that regulate the targeting and enzymatic activity of poly(ADP-ribose) polymerase 1 (PARP1), a chromatin regulator in higher eukaryotes. We demonstrate that PARP1 is targeted to chromatin by association with the histone H2A variant (H2Av)—the
Drosophila
homolog of the mammalian histone H2A variants H2Az/H2Ax—and that subsequent phosphorylation of H2Av leads to PARP1 activation. This two-step mechanism of PARP1 activation controls transcription at specific loci in a signal-dependent manner. Our study establishes the mechanism through which histone variants and changes in the histone modification code control chromatin-directed PARP1 activity and the transcriptional activation of target genes.
Crystal structure of human natural cytotoxicity receptor NKp30 and identification of its ligand binding site
Authors: Joyce M. Gordon , Tran Paul , Zhuravleva Marina A. , Jaw Jessica , Colonna Marco , Sun Peter D.
Published: March 2011

Natural killer (NK) cells are a group of innate immune cells that carry out continuous surveillance for the presence of virally infected or cancerous cells. The natural cytotoxicity receptor (NCR) NKp30 is critical for the elimination of a large group of tumor cell types. Although several ligands have been proposed for NKp30, the lack of a conserved structural feature among these ligands and their uncertain physiological relevance has contributed to confusion in the field and hampered a full understanding of the receptor. To gain insights into NKp30 ligand recognition, we have determined the crystal structure of the extracellular domain of human NKp30. The structure displays an I-type Ig-like fold structurally distinct from the other natural cytotoxicity receptors NKp44 and NKp46. Using cytolytic killing assays against a range of tumor cell lines and subsequent peptide epitope mapping of a NKp30 blocking antibody, we have identified a critical ligand binding region on NKp30 involving its F strand. Using different solution binding studies, we show that the N-terminal domain of B7-H6 is sufficient for NKp30 recognition. Mutations on NKp30 further confirm that residues in the vicinity of the F strand, including part of the C strand and the CD loop, affect binding to B7-H6. The structural comparison of NKp30 with CD28 family receptor and ligand complexes also supports the identified ligand binding site. This study provides insights into NKp30 ligand recognition and a framework for a potential family of unidentified ligands.
Discovery and molecular characterization of a Bcl-2–regulated cell death pathway in schistosomes
Authors: Lee Erinna F. , Clarke Oliver B. , Evangelista Marco , Feng Zhiping , Speed Terence P. , Tchoubrieva Elissaveta B. , Strasser Andreas , Kalinna Bernd H. , Colman Peter M. , Fairlie W. Douglas
Published: March 2011

Schistosomiasis is an infectious disease caused by parasites of the phylum platyhelminthe. Here, we describe the identification and characterization of a Bcl-2–regulated apoptosis pathway in
Schistosoma japonicum
and
S. mansoni.
Genomic, biochemical, and cell-based mechanistic studies provide evidence for a tripartite pathway, similar to that in humans including BH3-only proteins that are inhibited by prosurvival Bcl-2–like molecules, and Bax/Bak-like proteins that facilitate mitochondrial outer-membrane permeabilization. Because Bcl-2 proteins have been successfully targeted with “BH3 mimetic” drugs, particularly in the treatment of cancer, we investigated whether schistosome apoptosis pathways could provide targets for future antischistosomal drug discovery efforts. Accordingly, we showed that a schistosome prosurvival protein, sjA, binds ABT-737, a well-characterized BH3 mimetic. A crystal structure of sjA bound to a BH3 peptide provides direct evidence for the feasibility of developing BH3 mimetics to target Bcl-2 prosurvival proteins in schistosomes, suggesting an alternative application for this class of drugs beyond cancer treatment.
Effect of helium on structure and compression behavior of SiO
2
glass
Authors: Shen Guoyin , Mei Qiang , Prakapenka Vitali B. , Lazor Peter , Sinogeikin Stanislav , Meng Yue , Park Changyong
Published: March 2011

The behavior of volatiles is crucial for understanding the evolution of the Earth’s interior, hydrosphere, and atmosphere. Noble gases as neutral species can serve as probes and be used for examining gas solubility in silicate melts and structural responses to any gas inclusion. Here, we report experimental results that reveal a strong effect of helium on the intermediate range structural order of SiO
2
glass and an unusually rigid behavior of the glass. The structure factor data show that the first sharp diffraction peak position of SiO
2
glass in helium medium remains essentially the same under pressures up to 18.6 GPa, suggesting that helium may have entered in the voids in SiO
2
glass under pressure. The dissolved helium makes the SiO
2
glass much less compressible at high pressures. GeO
2
glass and SiO
2
glass with H
2
as pressure medium do not display this effect. These observations suggest that the effect of helium on the structure and compression of SiO
2
glass is unique.
Aquaporin water channel AgAQP1 in the malaria vector mosquito
Anopheles gambiae
during blood feeding and humidity adaptation
Authors: Liu Kun , Tsujimoto Hitoshi , Cha Sung-Jae , Agre Peter , Rasgon Jason L.
Published: March 2011

Altered patterns of malaria endemicity reflect, in part, changes in feeding behavior and climate adaptation of mosquito vectors. Aquaporin (AQP) water channels are found throughout nature and confer high-capacity water flow through cell membranes. The genome of the major malaria vector mosquito
Anopheles gambiae
contains at least seven putative AQP sequences. Anticipating that transmembrane water movements are important during the life cycle of
A. gambiae
, we identified and characterized the
A. gambiae
aquaporin 1 (AgAQP1) protein that is homologous to AQPs known in humans,
Drosophila
, and sap-sucking insects. When expressed in
Xenopus laevis
oocytes, AgAQP1 transports water but not glycerol. Similar to mammalian AQPs, water permeation of AgAQP1 is inhibited by HgCl
2
and tetraethylammonium, with Tyr185 conferring tetraethylammonium sensitivity. AgAQP1 is more highly expressed in adult female
A. gambiae
mosquitoes than in males. Expression is high in gut, ovaries, and Malpighian tubules where immunofluorescence microscopy reveals that AgAQP1 resides in stellate cells but not principal cells. AgAQP1 expression is up-regulated in fat body and ovary by blood feeding but not by sugar feeding, and it is reduced by exposure to a dehydrating environment (42% relative humidity). RNA interference reduces AgAQP1 mRNA and protein levels. In a desiccating environment (<20% relative humidity), mosquitoes with reduced AgAQP1 protein survive significantly longer than controls. These studies support a role for AgAQP1 in water homeostasis during blood feeding and humidity adaptation of
A. gambiae
, a major mosquito vector of human malaria in sub-Saharan Africa.
A hierarchy of signals regulates entry of membrane proteins into the ciliary membrane domain in epithelial cells
Authors: Francis Stephen S. , Sfakianos Jeff , Lo Bryan , Mellman Ira
Published: March 2011

The membrane of the primary cilium is continuous with the plasma membrane but compositionally distinct. Although some membrane proteins concentrate in the cilium, others such as podocalyxin/gp135 are excluded. We found that exclusion reflects a saturable selective retention mechanism. Podocalyxin is immobilized by its PDZ interaction motif binding to NHERF1 and thereby to the apical actin network via ERM family members. The retention signal was dominant, autonomous, and transferable to membrane proteins not normally excluded from the cilium. The NHERF1-binding domains of cystic fibrosis transmembrane conductance regulator and Csk-binding protein were also found to act as transferable retention signals. Addition of a retention signal could inhibit the ciliary localization of proteins (e.g., Smoothened) containing signals that normally facilitate concentration in the ciliary membrane. Proteins without a retention signal (e.g., green fluorescent protein–glycosylphosphatidylinositol) were found in the cilium, suggesting entry was not impeded by a diffusion barrier or lipid microdomain. Thus, a hierarchy of interactions controls the composition of the ciliary membrane, including selective retention, selective inclusion, and passive diffusion.
Loss of the extraproteasomal ubiquitin receptor Rings lost impairs ring canal growth in Drosophila oogenesis
Authors: Morawe Tobias , Honemann-Capito Mona , von Stein Walter , Wodarz Andreas
Published: March 2011

In Drosophila melanogaster oogenesis, there are 16 germline cells that form a cyst and stay connected to each other by ring canals. Ring canals allow the cytoplasmic transport of proteins, messenger ribonucleic acids, and yolk components from the nurse cells into the oocyte. In this paper, we describe the protein Rings lost (Rngo) and show that it is required for ring canal growth in germline cysts. rngo is an essential gene, and germline clones of a rngo-null allele show defects in ovary development, including mislocalization of ring canal proteins and fusion of germline cells. Rngo appears to be a ubiquitin receptor that possesses a ubiquitin-like domain, a ubiquitin-associated domain, and a retroviral-like aspartate protease (RVP) domain. Rngo binds to ubiquitin and to the 26S proteasome and colocalizes with both in germline cells, and its RVP domain is required for dimerization of Rngo and for its function in vivo. Our results thus show, for the first time, a function for a ubiquitin receptor in Drosophila development.
Replication stress induces 53BP1-containing OPT domains in G1 cells
Authors: Harrigan Jeanine A. , Belotserkovskaya Rimma , Coates Julia , Dimitrova Daniela S. , Polo Sophie E. , Bradshaw Charles R. , Fraser Peter , Jackson Stephen P.
Published: March 2011

Chromosomal deletions and rearrangements in tumors are often associated with common fragile sites, which are specific genomic loci prone to gaps and breaks in metaphase chromosomes. Common fragile sites appear to arise through incomplete DNA replication because they are induced after partial replication inhibition by agents such as aphidicolin. Here, we show that in G1 cells, large nuclear bodies arise that contain p53 binding protein 1 (53BP1), phosphorylated H2AX (γH2AX), and mediator of DNA damage checkpoint 1 (MDC1), as well as components of previously characterized OPT (Oct-1, PTF, transcription) domains. Notably, we find that incubating cells with low aphidicolin doses increases the incidence and number of 53BP1-OPT domains in G1 cells, and by chromatin immunoprecipitation and massively parallel sequencing analysis of γH2AX, we demonstrate that OPT domains are enriched at common fragile sites. These findings invoke a model wherein incomplete DNA synthesis during S phase leads to a DNA damage response and formation of 53BP1-OPT domains in the subsequent G1.
Putting the brakes on the unfolded protein response
Authors: Sicheri Frank , Silverman Robert H.
Published: March 2011

The unfolded protein response is an ancient cellular pathway for rapidly responding to endoplasmic reticulum stress. Two studies in this issue (Rubio et al. 2011. J. Cell. Biol. doi:10.1083/jcb.201007077 and Chawla et al. 2011. J. Cell. Biol. doi:10.1083/jcb.201008071) provide insight into how the unfolded protein response is tamped down to restore normal endoplasmic reticulum function. Although both papers implicate the Ire1 kinase domain as the key effector of the off-switch mechanism, alternate models for how this is achieved are proposed.
Prostaglandin E2 suppresses the differentiation of retinoic acid–producing dendritic cells in mice and humans
Authors: Stock Angus , Booth Sarah , Cerundolo Vincenzo
Published: March 2011

The production of retinoic acid (RA) by dendritic cells (DCs) is critical for the induction of gut-tropic immune responses by driving the expression of intestinal-specific homing receptors, such as α4β7 and CCR9, upon T and B cell activation. However, how RA production is regulated during DC development remains unclear. We describe an unexpected role for prostaglandin E2 (PGE2) as a negative regulator of retinal dehydrogenases (RALDH), the enzymes responsible for RA synthesis. The presence of PGE2 during DC differentiation inhibited RALDH expression in mouse and human DCs, abrogating their ability to induce CCR9 expression upon T cell priming. Furthermore, blocking PGE2 signaling increased the frequency of RALDH+ DCs in vitro, and reducing PGE2 synthesis in vivo promoted the systemic emergence of RA-producing DCs and the priming of CCR9+ T cells in nonintestinal sites such as the spleen. Finally, we found that PGE2 stimulated the expression of the inducible cyclic AMP early repressor, which appears to directly inhibit RALDH expression in DCs, thus providing mechanistic insight into how PGE2 signaling down-modulates RALDH. Given the role of PGE2 in regulating the development of RA-producing DCs, modulating this pathway may prove a novel means to control the development of gut-tropic immune responses.