bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural styles of mountain building: Controls of lithospheric rheologic stratification and extensional inheritance
Authors: Jammes Suzon , Huismans Ritske S.
Published: September 2012

The strength of the crust and the mantle lithosphere are strongly influenced by the temperature, the thickness and the composition of the crust and mantle lithosphere, and by inherited weaknesses. It consequently strongly depends on the geodynamic setting and is then expected to be different from one orogen to another, which might explain the diversity of deformation styles. Here we use 2D thermomechanical models at lithospheric scale to study the effect of the strength of the upper and middle crust on the geometry of contractional systems. The role of extensional inheritance is included by forward modeling the formation of rift basin or passive margin and using the resulting extensional structure as initial condition for lithospheric scale inversion. Our results demonstrate that: 1) crustal strength strongly controls the width and the elevation of orogenic wedge; 2) relative weak crust facilitates efficient propagating of thick‐skinned crustal scale thrusts; 3) contraction of a strong crust leads to the formation of long thrust sheets and an anti‐formal stack in the core of the orogen or the accretion of upper crust depending on the depth of the decoupling zone in the mid crust; 4) erosion processes favor the localization of shortening in a narrow crustal orogen; 5) rifting inheritance can explain the presence at shallower depth of lower crustal or mantle material previously upwelled and facilitates the propagation of the deformation in the external part of the chain. The range of predicted behaviors is compared to first order with the Zagros, the Alps and the Pyrenees, three natural examples for which the crustal structure is well constrained by geophysical data.
Spectral induced polarization signature of soil contaminated by organic pollutant: Experiment and modeling
Authors: Schwartz N. , Furman A.
Published: September 2012

The spectral induced polarization (SIP) signature of soil contaminated with organic pollutant was studied. Using a flow column experiment, the effect of crystal violet (CV, a polar organic pollutant) on the temporal change of the SIP response over a broad frequency range (1 mHz to 45 KHz) was determined. Complimentary measurements were used to determine the effect of CV on the chemical composition of both the pore water and the solid surface. In addition, analysis of the experimental results was carried out by using both chemical complexation and induced polarization models. Our results shows that adsorption of CV to the mineral surface resulted in release of inorganic ions to the soil solution, increasing the solution electrical conductivity and therefore also the real part of the complex conductivity. Despite the increase in the real part of the complex conductivity, the imaginary part of the complex conductivity decreased with increasing concentration of adsorbed CV. Using the Revil induced polarization model, we were able to show that the contribution of the adsorbed CV to the polarization of the soil is negligible, and that the main process affecting the polarization is the decrease in the density of the inorganic surface species. The results of this study can be used to better interpret SIP signature of soils contaminated by organic compounds.
The influence of Indian Ocean atmospheric circulation on Warm Pool hydroclimate during the Holocene epoch
Authors: Tierney J. E. , Oppo D. W. , LeGrande A. N. , Huang Y. , Rosenthal Y. , Linsley B. K.
Published: September 2012

Existing paleoclimate data suggest a complex evolution of hydroclimate within the Indo‐Pacific Warm Pool (IPWP) during the Holocene epoch. Here we introduce a new leaf wax isotope record from Sulawesi, Indonesia and compare proxy water isotope data with ocean‐atmosphere general circulation model (OAGCM) simulations to identify mechanisms influencing Holocene IPWP hydroclimate. Modeling simulations suggest that orbital forcing causes heterogenous changes in precipitation across the IPWP on a seasonal basis that may account for the differences in time‐evolution of the proxy data at respective sites. Both the proxies and simulations suggest that precipitation variability during the September–November (SON) season is important for hydroclimate in Borneo. The preëminence of the SON season suggests that a seasonally lagged relationship between the Indian monsoon and Indian Ocean Walker circulation influences IPWP hydroclimatic variability during the Holocene.
Dimensionless criteria for the production‐dissipation equilibrium of scalar fluctuations and their implications for scalar similarity
Authors: Cancelli Diana M. , Dias Nelson L. , Chamecki Marcelo
Published: September 2012

In water resources it is common to consider that two scalars have a similar behavior in the atmospheric surface layer. This is a consequence of Monin‐Obukhov similarity theory whose direct implication is that all similarity functions between two scalars are equal. However, many works show that scalar similarity does not always hold under unstable conditions, a fact for which it is often difficult to establish a physical cause. In this paper, using a data set measured during winter over a tropical lake in Brazil (Furnas Lake), we found a relation between temperature–water vapor similarity and the strength of the surface forcing; we also confirmed that the classical balance between gradient production and molecular dissipation of scalar variance and covariance is key to scalar similarity. This balance can be disrupted by large values of the third‐order transport terms, and possibly by nonstationary terms as well. In connection with the scalar variance and covariance budgets, we propose a new set of dimensionless scalar flux numbers which are able to make a good diagnosis of the aforementioned balance (or the lack thereof) for each budget. The fact that different Monin‐Obukhov functions are not equally capable of identifying scalar similarity is also demonstrated and a new bulk indicator of scalar flux similarity is proposed whose absolute value, unlike the relative transfer efficiency, is bounded above by 1; this new indicator holds also in the spectral domain. Finally, we verify that low‐frequency dissimilarity has a larger impact over scalar similarity than over scalar flux similarity.
Yearly emission factors of ammonia and particulate matter from three laying-hen housing systems
Authors: Costa Annamaria , Ferrari Sara , Guarino Marcella
Published: September 2012

The aim of the present study was to measure the concentration of ammonia and particulate matter (PM) that passes through a size‐selective inlet with a 50% cut‐off at 10-μm aerodynamic-equivalent diameter (PM10) and emissions into atmosphere in the following three types of laying-hen houses: traditional battery cages with aerated open-manure storage (BSP) and two best available technique (BAT) housing types, namely, an aviary-system housing (ASH) and a vertical tiered cage with manure belts and forced-air drying (VTC). Measurements were taken continuously for a period of 1 year in each house. Ammonia concentration was measured continuously in each house using an infrared photoacoustic detector with a 15-min sampling interval. PM10 was measured continuously using a scatter light photometer, corrected by the traditional gravimetric-technique concentration to lower the measurement error. The same instrument was also used to collect PM10 through a traditional gravimetric technique. This procedure was performed to adjust the particulate matter-specific gravity of PM that is typical and specific for every animal house. PM10 and ammonia measurements were carried out together with measurements of inside and outside temperature, inside and outside relative humidity and ventilation rate. For the high PM10 concentrations measured in the ASH house during a preliminary survey, concentrations of total suspended particles (TSP) and fine PM (particles <2.5 microns) were also measured to evaluate the dustiness in the building during the working hours. The ammonia concentration was 5.37 mg/m3 in the traditional BSP house (the reference for cage-housing system), 4.95 mg/m3 in the VTC and 3.85 mg/m3 in the ASH. The ammonia-emission factors were 15.445 mg/h.hen place (0.135 kg/year.hen place) for BSP, 8.258 mg/h.hen place (0.072 kg/year.hen place) for VTC, and 23.704 mg/h.hen place (0.208 kg/year.hen place) for ASH. Ammonia emission-reduction efficiency of VTC v. the BSP was 53%, according to thresholds assessed by Integrated Prevention Pollution Control. The ammonia-reduction efficiency of ASH v. that of the standard Reference Housing system for non-cage housing was 68%. Average yearly PM10 concentration was remarkably higher in the ASH, with 0.215 mg/m3 v. 0.108 mg/m3 for the VTC and 0.094 mg/m3 for BSP. In the ASH, the concentration of total suspended particles (TSP) was 0.444 mg/m3 and that of PM2.5 was 0.032 mg/m3. In this facility, a great variation of PM10 concentration occurred in the morning hours. Recorded values for the PM10 emission were 0.433 mg/h.hen for BSP and 0.081 mg/h.hen for VTC, while the ASH showed the highest PM10 emission (1.230 mg/h.hen), with clear peaks occurring in the morning hours during daily farming operations.
The in vitro rumen methane output of perennial grass species and white clover varieties, and associative effects for their binary mixtures, evaluated using a batch-culture technique
Authors: Purcell P. J. , Grant J. , Boland T. M. , Grogan D. , O'Kiely P.
Published: September 2012

Grassland swards containing white clover varieties (WCV) may result in lower enteric methane (CH4) output from grazing ruminants than swards of only perennial grass species (PGS) due to differences in their chemical composition and rumen fermentation dynamics. The objectives of the present study were to compare the chemical composition, in vitro rumen fermentation variables and CH4 output per unit of feed for a range of common PGS and WCV harvested in May from simulated grazing regimes, and to determine the effects of binary mixtures of the PGS and WCV on in vitro rumen fermentation variables and CH4 output, using a batch-culture technique. Four PGS (perennial ryegrass, cocksfoot, meadow fescue and timothy) and three WCV (Aran, Chieftain and Crusader) were incubated as sole substrates or as part of binary mixtures (PGS : WCV ratios of 0 : 1, 0.25 : 0.75, 0.5 : 0.5, 0.75 : 0.25 and 1 : 0) for 24 h at 39°C with buffered rumen fluid. All WCV had lower (P < 0.001) CH4 output per unit of apparent DM disappeared (aDMD; mean value across WCV (s.e.m.) of 27.0 (1.35) mL/g aDMD v. 36.1 (0.90) mL/g aDMD across PGS) during the in vitro rumen incubation than did all PGS. The WCV also had lower CH4 output per unit of total volatile fatty acids (corresponding values of 0.147 (0.0090) v. 0.199 (0.0073) mmol/mmol total volatile fatty acid output) and per unit of total gas produced (0.118 (0.0022) v. 0.153 (0.0024) mmol/mmol total gas produced) than did the PGS. In addition, Aran and Crusader had lower (P < 0.001) CH4 output per unit of feed DM incubated than did all PGS. There were synergistic associative effects (i.e. where the response was greater for the mixtures than the arithmetic calculation using the responses for PGS and WCV alone; P < 0.05) of mixing the PGS and WCV in binary combinations on all CH4 output variables.
Generalised pollination system of Erythrina dominguezii (Fabaceae : Papilionoideae) involving hummingbirds, passerines and bees
Authors: Etcheverry Ángela V. , Figueroa-Castro Dulce , Figueroa-Fleming Trinidad , Alemán María M. , Juárez Víctor D. , López-Spahr Diego , Yáñez Carolina N. , Gómez Carlos A.
Published: September 2012

Plants in the genus Erythrina are pollinated by birds, such that passerine pollination is the plesiomorphic state, whereas hummingbird pollination is the derived character. Phylogenetic studies suggest that Erythrina dominguezii belongs to a basal clade characterised as pollinated by both passerines and hummingbirds. Here, we characterise the pollination system of E. dominguezii. Floral morphology, nectar traits, breeding system, visitation rates and pollen deposition by its floral visitors were studied. Floral morphology of E. dominguezii showed traits associated with both passerine and hummingbird pollination. Nectar sugar concentration showed an intermediate value but closer to the hummingbird type; however, it was rich in hexose, which is typical of the passerine type. Approximately 5% of the flowers set fruits under free pollination. Almost 80% of recorded flowers were visited by birds, with the rest visited by hymenopterans (bumblebees and honeybees). Among avian pollinators, five species of hummingbirds and three passerine species were identified as pollinators. The hummingbird Chlorostilbon lucidus was the most efficient visitor in terms of pollen deposition and was second in frequency of visits. The passerine Icterus cayanensis was second in efficiency at depositing pollen and was the most frequent pollinator. Our results show that E. dominguezii has a generalised pollination system. In addition, we report a new case of closed flowers and secondary nectar presentation. This is the first study that compares effectiveness among different pollinators in Erythrina.
The effect of sampling rate on interpretation of the temporal characteristics of radiative and convective heating in wildland flames
Authors: Frankman David , Webb Brent W. , Butler Bret W. , Jimenez Daniel , Harrington Michael
Published: September 2012

Time-resolved radiative and convective heating measurements were collected on a prescribed burn in coniferous fuels at a sampling frequency of 500 Hz. Evaluation of the data in the time and frequency domain indicate that this sampling rate was sufficient to capture the temporal fluctuations of radiative and convective heating. The convective heating signal contained significantly larger fluctuations in magnitude and frequency than did the radiative heating signal. The data were artificially down-sampled to 100, 50, 10, 5 and 1 Hz to explore the effect of sampling rate on peak heat fluxes, time-averaged heating and integrated heating. Results show that for sampling rates less than 5 Hz the difference between measured and actual peak radiative heating rates can be as great as 24%, and is on the order of 80% for 1-Hz sampling rates. Convective heating showed degradation in the signal for sampling rates less than 100 Hz. Heating rates averaged over a 2-s moving window, as well as integrated radiative and convective heating were insensitive to sampling rate across all ranges explored. The data suggest that peak radiative and convective heating magnitudes cannot be fully temporally resolved for sampling frequencies lower than 20 and 200 Hz.
p21-Activated kinase interacts with Wnt signaling to regulate tissue polarity and gene expression
Authors: Goh Kah Yee , Ng Natalie Weili , Hagen Thilo , Inoue Takao
Published: September 2012

Wnt signaling is mediated by three classes of receptors, Frizzled, Ryk, and Ror. In
Caenorhabditis elegans
, Wnt signaling regulates the anterior/posterior polarity of the P7.p vulval lineage, and mutations in
lin-17/Frizzled
cause loss or reversal of P7.p lineage polarity. We found that
pak-1/Pak
(p21-activated kinase), along with putative activators of Pak,
nck-1/Nck
, and
ced-10/Rac
, regulates P7.p polarity. Mutations in these genes suppress the polarity defect of
lin-17
mutants. Furthermore, mutations in
pak-1
,
nck-1
, and
ced-10
cause constitutive dauer formation at 27 °C, a phenotype also observed in
egl-20/Wnt
and
cam-1/Ror
mutants. In HEK293T cells, Pak1 can antagonize canonical Wnt signaling. Moreover, overexpression of Ror2 leads to phosphorylation of Pak1. Together, these results indicate that Pak interacts with Wnt signaling to regulate tissue polarity and gene expression.
Chromatin conformation governs T-cell receptor Jβ gene segment usage
Authors: Ndifon Wilfred , Gal Hilah , Shifrut Eric , Aharoni Rina , Yissachar Nissan , Waysbort Nir , Reich-Zeliger Shlomit , Arnon Ruth , Friedman Nir
Published: September 2012

T cells play fundamental roles in adaptive immunity, relying on a diverse repertoire of T-cell receptor (TCR) α and β chains. Diversity of the TCR β chain is generated in part by a random yet intrinsically biased combinatorial rearrangement of variable (Vβ), diversity (Dβ), and joining (Jβ) gene segments. The mechanisms that determine biases in gene segment use remain unclear. Here we show, using a high-throughput TCR sequencing approach, that a physical model of chromatin conformation at the DJβ genomic locus explains more than 80% of the biases in Jβ use that we measured in murine T cells. This model also predicts correctly how differences in intersegment genomic distances between humans and mice translate into differences in Jβ bias between TCR repertoires of these two species. As a consequence of these structural and other biases, TCR sequences are produced with different a priori frequencies, thus affecting their probability of becoming public TCRs that are shared among individuals. Surprisingly, we find that many more TCR sequences are shared among all five mice we studied than among only subgroups of three or four mice. We derive a necessary mathematical condition explaining this finding, which indicates that the TCR repertoire contains a core set of receptor sequences that are highly abundant among individuals, if their a priori probability of being produced by the recombination process is higher than a defined threshold. Our results provide evidence for an expanded role of chromatin conformation in VDJ rearrangement, from control of gene accessibility to precise determination of gene segment use.
Evidence that viral RNAs have evolved for efficient, two-stage packaging
Authors: Borodavka Alexander , Tuma Roman , Stockley Peter G.
Published: September 2012

Genome packaging is an essential step in virus replication and a potential drug target. Single-stranded RNA viruses have been thought to encapsidate their genomes by gradual co-assembly with capsid subunits. In contrast, using a single molecule fluorescence assay to monitor RNA conformation and virus assembly in real time, with two viruses from differing structural families, we have discovered that packaging is a two-stage process. Initially, the genomic RNAs undergo rapid and dramatic (approximately 20–30%) collapse of their solution conformations upon addition of cognate coat proteins. The collapse occurs with a substoichiometric ratio of coat protein subunits and is followed by a gradual increase in particle size, consistent with the recruitment of additional subunits to complete a growing capsid. Equivalently sized nonviral RNAs, including high copy potential in vivo competitor mRNAs, do not collapse. They do support particle assembly, however, but yield many aberrant structures in contrast to viral RNAs that make only capsids of the correct size. The collapse is specific to viral RNA fragments, implying that it depends on a series of specific RNA–protein interactions. For bacteriophage MS2, we have shown that collapse is driven by subsequent protein–protein interactions, consistent with the RNA–protein contacts occurring in defined spatial locations. Conformational collapse appears to be a distinct feature of viral RNA that has evolved to facilitate assembly. Aspects of this process mimic those seen in ribosome assembly.
Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi
Authors: Walton Katherine D. , Kolterud Åsa , Czerwinski Michael J. , Bell Michael J. , Prakash Ajay , Kushwaha Juhi , Grosse Ann S. , Schnell Santiago , Gumucio Deborah L.
Published: September 2012

In the adult intestine, an organized array of finger-like projections, called villi, provide an enormous epithelial surface area for absorptive function. Villi first emerge at embryonic day (E) 14.5 from a previously flat luminal surface. Here, we analyze the cell biology of villus formation and examine the role of paracrine epithelial Hedgehog (Hh) signals in this process. We find that, before villus emergence, tight clusters of Hh-responsive mesenchymal cells form just beneath the epithelium. Cluster formation is dynamic; clusters first form dorsally and anteriorly and spread circumferentially and posteriorly. Statistical analysis of cluster distribution reveals a patterned array; with time, new clusters form in spaces between existing clusters, promoting approximately four rounds of villus emergence by E18.5. Cells within mesenchymal clusters express Patched1 and Gli1, as well as Pdgfrα, a receptor previously shown to participate in villus development. BrdU-labeling experiments show that clusters form by migration and aggregation of Hh-responsive cells. Inhibition of Hh signaling prevents cluster formation and villus development, but does not prevent emergence of villi in areas where clusters have already formed. Conversely, increasing Hh signaling increases the size of villus clusters and results in exceptionally wide villi. We conclude that Hh signals dictate the initial aspects of the formation of each villus by controlling mesenchymal cluster aggregation and regulating cluster size.
Folate binding site of flavin-dependent thymidylate synthase
Authors: Koehn Eric M. , Perissinotti Laura L. , Moghram Salah , Prabhakar Arjun , Lesley Scott A. , Mathews Irimpan I. , Kohen Amnon
Published: September 2012

The DNA nucleotide thymidylate is synthesized by the enzyme thymidylate synthase, which catalyzes the reductive methylation of deoxyuridylate using the cofactor methylene-tetrahydrofolate (CH
2
H
4
folate). Most organisms, including humans, rely on the
thy
A- or
TYMS
-encoded classic thymidylate synthase, whereas, certain microorganisms, including all
Rickettsia
and other pathogens, use an alternative
thy
X-encoded flavin-dependent thymidylate synthase (FDTS). Although several crystal structures of FDTSs have been reported, the absence of a structure with folates limits understanding of the molecular mechanism and the scope of drug design for these enzymes. Here we present X-ray crystal structures of FDTS with several folate derivatives, which together with mutagenesis, kinetic analysis, and computer modeling shed light on the cofactor binding and function. The unique structural data will likely facilitate further elucidation of FDTSs’ mechanism and the design of structure-based inhibitors as potential leads to new antimicrobial drugs.
Altered Ig levels and antibody responses in mice deficient for the Fc receptor for IgM (FcμR)
Authors: Honjo Kazuhito , Kubagawa Yoshiki , Jones Dewitt M. , Dizon Brian , Zhu Zilu , Ohno Hiroshi , Izui Shozo , Kearney John F. , Kubagawa Hiromi
Published: September 2012

Cell surface Fc receptor for IgM antibody (FcμR) is the most recently identified member among FcRs. We determined the cellular distribution of mouse FcμR and the functional consequences ofFcmrdisruption. Surface FcμR expression was restricted to B-lineage cells, from immature B to plasma cells, except for a transient down-modulation during germinal center reactions.Fcmrablation had no significant effect on overall B- and T-cell development, but led to a reduction of marginal zone B cells and an increase in splenic B1 B cells. Preimmune serum IgM in mutant mice was significantly elevated as were natural autoantibodies. When immunized with live attenuated pneumococci, mutant mice mounted robust antibody responses against phosphorylcholine, but not protein, determinants compared with wild-type mice. By contrast, upon immunization with a hapten-carrier conjugate, nitrophenyl-coupled chicken γ-globulin (NP-CGG), the mutant mice had a diminished primary IgG1 response to both NP and CGG. These findings suggest that FcμR has an important role in IgM homeostasis and regulation of humoral immune responses.
Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic
Authors: Beauchemin Mathieu , Roy Sougata , Daoust Philippe , Dagenais-Bellefeuille Steve , Bertomeu Thierry , Letourneau Louis , Lang B. Franz , Morse David
Published: September 2012

Dinoflagellates are an important component of the marine biota, but a large genome with high–copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate
Lingulodinium polyedrum
from RNA-Seq (Illumina) reads. The catalog contains 93% of a
Lingulodinium
EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.
Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons
Authors: Chuang Trees-Juen , Chen Feng-Chi , Chen Yen-Zho
Published: September 2012

DNA cytosine methylation is a central epigenetic marker that is usually mutagenic and may increase the level of sequence divergence. However, methylated genes have been reported to evolve more slowly than unmethylated genes. Hence, there is a controversy on whether DNA methylation is correlated with increased or decreased protein evolutionary rates. We hypothesize that this controversy has resulted from the differential correlations between DNA methylation and the evolutionary rates of coding exons in different genic positions. To test this hypothesis, we compare human–mouse and human–macaque exonic evolutionary rates against experimentally determined single-base resolution DNA methylation data derived from multiple human cell types. We show that DNA methylation is significantly related to within-gene variations in evolutionary rates. First, DNA methylation level is more strongly correlated with C-to-T mutations at CpG dinucleotides in the first coding exons than in the internal and last exons, although it is positively correlated with the synonymous substitution rate in all exon positions. Second, for the first exons, DNA methylation level is negatively correlated with exonic expression level, but positively correlated with both nonsynonymous substitution rate and the sample specificity of DNA methylation level. For the internal and last exons, however, we observe the opposite correlations. Our results imply that DNA methylation level is differentially correlated with the biological (and evolutionary) features of coding exons in different genic positions. The first exons appear more prone to the mutagenic effects, whereas the other exons are more influenced by the regulatory effects of DNA methylation.
Antiparallel coiled-coil–mediated dimerization of myosin X
Authors: Lu Qing , Ye Fei , Wei Zhiyi , Wen Zilong , Zhang Mingjie
Published: September 2012

Processive movements of unconventional myosins on actin filaments generally require motor dimerization. A commonly accepted myosin dimerization mechanism is via formation of a parallel coiled-coil dimer by a stretch of amino acid residues immediately carboxyl-terminal to the motor’s lever-arm domain. Here, we discover that the predicted coiled-coil region of myosin X forms a highly stable, antiparallel coiled-coil dimer (anti-CC). Disruption of the anti-CC either by single-point mutations or by replacement of the anti-CC with a parallel coiled coil with a similar length compromised the filopodial induction activity of myosin X. We further show that the anti-CC and the single α-helical domain of myosin X are connected by a semirigid helical linker. The anti-CC–mediated dimerization may enable myosin X to walk on both single and bundled actin filaments.
Saturation wind power potential and its implications for wind energy
Authors: Jacobson Mark Z. , Archer Cristina L.
Published: September 2012

Wind turbines convert kinetic to electrical energy, which returns to the atmosphere as heat to regenerate some potential and kinetic energy. As the number of wind turbines increases over large geographic regions, power extraction first increases linearly, but then converges to a saturation potential not identified previously from physical principles or turbine properties. These saturation potentials are >250 terawatts (TW) at 100 m globally, approximately 80 TW at 100 m over land plus coastal ocean outside Antarctica, and approximately 380 TW at 10 km in the jet streams. Thus, there is no fundamental barrier to obtaining half (approximately 5.75 TW) or several times the world’s all-purpose power from wind in a 2030 clean-energy economy.
T cells engineered with a T cell receptor against the prostate antigen TARP specifically kill HLA-A2
+
prostate and breast cancer cells
Authors: Hillerdal Victoria , Nilsson Berith , Carlsson Björn , Eriksson Fredrik , Essand Magnus
Published: September 2012

To produce genetically engineered T cells directed against prostate and breast cancer cells, we have cloned the T-cell receptor recognizing the HLA-A2–restricted T-cell recptor γ-chain alternate reading-frame protein (TARP)
4–13
epitope. TARP is a protein exclusively expressed in normal prostate epithelium and in adenocarcinomas of the prostate and breast. Peripheral blood T cells transduced with a lentiviral vector encoding the TARP-TCR proliferated well when exposed to peptide-specific stimuli. These cells exerted peptide-specific IFN-γ production and cytotoxic activity. Importantly, HLA-A2
+
prostate and breast cancer cells expressing TARP were also killed, demonstrating that the TARP
4–13
epitope is a physiologically relevant target for T-cell therapy of prostate and breast cancer. In conclusion, we present the cloning of a T cell receptor (TCR) directed against a physiologically relevant HLA-A2 epitope of TARP. To our knowledge this report on engineering of T cells with a TCR directed against an antigen specifically expressed by prostate cells is unique.
Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo
Authors: Zandi Sasan , Åhsberg Josefine , Tsapogas Panagiotis , Stjernberg Jenny , Qian Hong , Sigvardsson Mikael
Published: September 2012

To better understand the process of B-lymphocyte lineage restriction, we have investigated molecular and functional properties in early B-lineage cells from
Pax-5
–deficient animals crossed to a B-lineage–restricted reporter mouse, allowing us to identify B-lineage–specified progenitors independently of conventional surface markers. Pax-5 deficiency resulted in a dramatic increase in the frequency of specified progenitor B-cells marked by expression of a
λ5
(
Igll1
) promoter-controlled reporter gene. Gene expression analysis of ex vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on B-cell specification. However, single-cell in vitro differentiation analysis of ex vivo isolated cells revealed that specified B-lineage progenitors still displayed a high degree of plasticity for development into NK or T lineage cells. In contrast, we were unable to detect any major changes in myeloid lineage potential in specified Pax-5–deficient cells. By comparison of gene expression patterns in ex vivo isolated Pax-5– and Ebf-1–deficient progenitors, it was possible to identify a set of B-cell–restricted genes dependent on Ebf-1 but not Pax-5, supporting the idea that B-cell specification and commitment is controlled by distinct regulatory networks.
Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding
Authors: Wang Jin , Oliveira Ronaldo J. , Chu Xiakun , Whitford Paul C. , Chahine Jorge , Han Wei , Wang Erkang , Onuchic José N. , Leite Vitor B.P.
Published: September 2012

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δ
E
, the energetic roughness Δ
E
, and the scale of landscape measured by the entropy
S
. We show that the dimensionless ratio between the gap, roughness, and entropy of the system

accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated with the thermodynamic stability against trapping, as characterized by the ratio of folding temperature versus trapping temperature. Furthermore, Λ also monotonically correlates with the folding kinetic rates. These results provide the quantitative bridge between the landscape topography and experimental folding measurements.
A mouse model for HIV-1 entry
Authors: Pietzsch John , Gruell Henning , Bournazos Stylianos , Donovan Bridget M. , Klein Florian , Diskin Ron , Seaman Michael S. , Bjorkman Pamela J. , Ravetch Jeffrey V. , Ploss Alexander , Nussenzweig Michel C.
Published: September 2012

Passive transfer of neutralizing antibodies against HIV-1 can prevent infection in macaques and seems to delay HIV-1 rebound in humans. Anti-HIV antibodies are therefore of great interest for vaccine design. However, the basis for their in vivo activity has been difficult to evaluate systematically because of a paucity of small animal models for HIV infection. Here we report a genetically humanized mouse model that incorporates a luciferase reporter for rapid quantitation of HIV entry. An antibody’s ability to block viral entry in this in vivo model is a function of its bioavailability, direct neutralizing activity, and effector functions.
Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein
Authors: Welch Brett D. , Liu Yuanyuan , Kors Christopher A. , Leser George P. , Jardetzky Theodore S. , Lamb Robert A.
Published: September 2012

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein.
Hypoxia-inducible factor 1-dependent expression of platelet-derived growth factor B promotes lymphatic metastasis of hypoxic breast cancer cells
Authors: Schito Luana , Rey Sergio , Tafani Marco , Zhang Huafeng , Wong Carmen Chak-Lui , Russo Andrea , Russo Matteo A. , Semenza Gregg L.
Published: September 2012

Lymphatic dissemination from the primary tumor is a major mechanism by which breast cancer cells access the systemic circulation, resulting in distant metastasis and mortality. Numerous studies link activation of hypoxia-inducible factor 1 (HIF-1) with tumor angiogenesis, metastasis, and patient mortality. However, the role of HIF-1 in lymphatic dissemination is poorly understood. In this study, we show that HIF-1 promotes lymphatic metastasis of breast cancer by direct transactivation of the gene encoding platelet-derived growth factor B (PDGF-B), which has proliferative and chemotactic effects on lymphatic endothelial cells. Lymphangiogenesis and lymphatic metastasis in mice bearing human breast cancer orthografts were blocked by administration of the HIF-1 inhibitor digoxin or the tyrosine kinase inhibitor imatinib. Immunohistochemical analysis of human breast cancer biopsies demonstrated colocalization of HIF-1α and PDGF-B, which were correlated with lymphatic vessel area and histological grade. Taken together, these data provide experimental support for breast cancer clinical trials targeting HIF-1 and PDGF-B.
Nonsteroidal anti-inflammatory drug sensitizes
Mycobacterium tuberculosis
to endogenous and exogenous antimicrobials
Authors: Gold Ben , Pingle Maneesh , Brickner Steven J. , Shah Nilesh , Roberts Julia , Rundell Mark , Bracken W. Clay , Warrier Thulasi , Somersan Selin , Venugopal Aditya , Darby Crystal , Jiang Xiuju , Warren J. David , Fernandez Joseph , Ouerfelli Ouathek , Nuermberger Eric L. , Cunningham-Bussel Amy , Rath Poonam , Chidawanyika Tamutenda , Deng Haiteng , Realubit Ronald , Glickman J. Fraser , Nathan Carl F.
Published: September 2012

Existing drugs are slow to eradicate
Mycobacterium tuberculosis
(Mtb) in patients and have failed to control tuberculosis globally. One reason may be that host conditions impair Mtb’s replication, reducing its sensitivity to most antiinfectives. We devised a high-throughput screen for compounds that kill Mtb when its replication has been halted by reactive nitrogen intermediates (RNIs), acid, hypoxia, and a fatty acid carbon source. At concentrations routinely achieved in human blood, oxyphenbutazone (OPB), an inexpensive anti-inflammatory drug, was selectively mycobactericidal to nonreplicating (NR) Mtb. Its cidal activity depended on mild acid and was augmented by RNIs and fatty acid. Acid and RNIs fostered OPB’s 4-hydroxylation. The resultant 4-butyl-4-hydroxy-1-(4-hydroxyphenyl)-2-phenylpyrazolidine-3,5-dione (4-OH-OPB) killed both replicating and NR Mtb, including Mtb resistant to standard drugs. 4-OH-OPB depleted flavins and formed covalent adducts with
N
-acetyl-cysteine and mycothiol. 4-OH-OPB killed Mtb synergistically with oxidants and several antituberculosis drugs. Thus, conditions that block Mtb’s replication modify OPB and enhance its cidal action. Modified OPB kills both replicating and NR Mtb and sensitizes both to host-derived and medicinal antimycobacterial agents.
Selection of antibodies that regulate phenotype from intracellular combinatorial antibody libraries
Authors: Zhang Hongkai , Wilson Ian A. , Lerner Richard A.
Published: September 2012

A method is presented that uses combinatorial antibody libraries to endow cells with new binding energy landscapes for the purpose of regulating their phenotypes. Antibodies that are expressed in cells infected with a lentiviral combinatorial antibody library are selected directly for function rather than only for binding. The potential diversity space can be very large because more than one lentivirus can infect a single cell. Thus, the initial combinatorial diversity of ∼1.0 × 10
11
members generated by the random association of antibody heavy and light chains is greatly increased by the reassortment of the antibody Fv domains themselves inside cells. The power of the system is illustrated by its ability to select unusual antibodies. Here, the selected antibodies are potent erythropoietin agonists whose ontogeny depends on recombination at the protein level of pairs of antibodies expressed in the same cell to generate heterodimeric bispecific antibodies. The obligate synergy between the different binding specificities of the antibody’s monomeric subunits appears to replicate the asymmetric binding mechanism of authentic erythropoietin.
The word frequency effect in first- and second-language word recognition: A lexical entrenchment account
Authors: Diependaele Kevin , Lemhöfer Kristin , Brysbaert Marc
Published: September 2012

We investigate the origin of differences in the word frequency effect between native speakers and second-language speakers. In a large-scale analysis of English word identification times we find that group-level differences are fully accounted for by the individual language proficiency scores. Furthermore, exactly the same quantitative relation between word frequency and proficiency is found for monolinguals and three different bilingual populations (Dutch–English, French–English, and German–English). We conclude that the larger frequency effects for second-language processing than for native-language processing can be explained by within-language characteristics and thus need not be the consequence of “being bilingual” (i.e., a qualitative difference). More specifically, we argue that language proficiency increases lexical entrenchment, which leads to a reduced frequency effect, irrespective of bilingualism, language dominance, and language similarity.
Translocation of CaMKII to dendritic microtubules supports the plasticity of local synapses
Authors: Lemieux Mado , Labrecque Simon , Tardif Christian , Labrie-Dion Étienne , LeBel Éric , De Koninck Paul
Published: September 2012

The processing of excitatory synaptic inputs involves compartmentalized dendritic Ca2+ oscillations. The downstream signaling evoked by these local Ca2+ transients and their impact on local synaptic development and remodeling are unknown. Ca2+/calmodulin-dependent protein kinase II (CaMKII) is an important decoder of Ca2+ signals and mediator of synaptic plasticity. In addition to its known accumulation at spines, we observed with live imaging the dynamic recruitment of CaMKII to dendritic subdomains adjacent to activated synapses in cultured hippocampal neurons. This localized and transient enrichment of CaMKII to dendritic sites coincided spatially and temporally with dendritic Ca2+ transients. We show that it involved an interaction with microtubular elements, required activation of the kinase, and led to localized dendritic CaMKII autophosphorylation. This process was accompanied by the adjacent remodeling of spines and synaptic AMPA receptor insertion. Replacement of endogenous CaMKII with a mutant that cannot translocate within dendrites lessened this activity-dependent synaptic plasticity. Thus, CaMKII could decode compartmental dendritic Ca2+ transients to support remodeling of local synapses.
Different cyclin types collaborate to reverse the S-phase checkpoint and permit prompt mitosis
Authors: Yuan Kai , Farrell Jeffrey A. , O’Farrell Patrick H.
Published: September 2012

Precise timing coordinates cell proliferation with embryonic morphogenesis. As Drosophila melanogaster embryos approach cell cycle 14 and the midblastula transition, rapid embryonic cell cycles slow because S phase lengthens, which delays mitosis via the S-phase checkpoint. We probed the contributions of each of the three mitotic cyclins to this timing of interphase duration. Each pairwise RNA interference knockdown of two cyclins lengthened interphase 13 by introducing a G2 phase of a distinct duration. In contrast, pairwise cyclin knockdowns failed to introduce a G2 in embryos that lacked an S-phase checkpoint. Thus, the single remaining cyclin is sufficient to induce early mitotic entry, but reversal of the S-phase checkpoint is compromised by pairwise cyclin knockdown. Manipulating cyclin levels revealed that the diversity of cyclin types rather than cyclin level influenced checkpoint reversal. We conclude that different cyclin types have distinct abilities to reverse the checkpoint but that they collaborate to do so rapidly.
Schistosome-derived omega-1 drives Th2 polarization by suppressing protein synthesis following internalization by the mannose receptor
Authors: Everts Bart , Hussaarts Leonie , Driessen Nicole N. , Meevissen Moniek H.J. , Schramm Gabriele , van der Ham Alwin J. , van der Hoeven Barbara , Scholzen Thomas , Burgdorf Sven , Mohrs Markus , Pearce Edward J. , Hokke Cornelis H. , Haas Helmut , Smits Hermelijn H. , Yazdanbakhsh Maria
Published: September 2012

Omega-1, a glycosylated T2 ribonuclease (RNase) secreted by Schistosoma mansoni eggs and abundantly present in soluble egg antigen, has recently been shown to condition dendritic cells (DCs) to prime Th2 responses. However, the molecular mechanisms underlying this effect remain unknown. We show in this study by site-directed mutagenesis of omega-1 that both the glycosylation and the RNase activity are essential to condition DCs for Th2 polarization. Mechanistically, we demonstrate that omega-1 is bound and internalized via its glycans by the mannose receptor (MR) and subsequently impairs protein synthesis by degrading both ribosomal and messenger RNA. These experiments reveal an unrecognized pathway involving MR and interference with protein synthesis that conditions DCs for Th2 priming.
Extrafollicular B cell activation by marginal zone dendritic cells drives T cell–dependent antibody responses
Authors: Chappell Craig P. , Draves Kevin E. , Giltiay Natalia V. , Clark Edward A.
Published: September 2012

Dendritic cells (DCs) are best known for their ability to activate naive T cells, and emerging evidence suggests that distinct DC subsets induce specialized T cell responses. However, little is known concerning the role of DC subsets in the initiation of B cell responses. We report that antigen (Ag) delivery to DC-inhibitory receptor 2 (DCIR2) found on marginal zone (MZ)–associated CD8α− DCs in mice leads to robust class-switched antibody (Ab) responses to a T cell–dependent (TD) Ag. DCIR2+ DCs induced rapid up-regulation of multiple B cell activation markers and changes in chemokine receptor expression, resulting in accumulation of Ag-specific B cells within extrafollicular splenic bridging channels as early as 24 h after immunization. Ag-specific B cells primed by DCIR2+ DCs were remarkably efficient at driving naive CD4 T cell proliferation, yet DCIR2-induced responses failed to form germinal centers or undergo affinity maturation of serum Ab unless toll-like receptor (TLR) 7 or TLR9 agonists were included at the time of immunization. These results demonstrate DCIR2+ DCs have a unique capacity to initiate extrafollicular B cell responses to TD Ag, and thus define a novel division of labor among splenic DC subsets for B cell activation during humoral immune responses.