bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping of seasonal freeze‐thaw transitions across the pan‐Arctic land and sea ice domains with satellite radar
Authors: Mortin J. , Schrøder T. M. , Walløe Hansen A. , Holt B. , McDonald K. C.
Published: July 2012

To monitor the pan‐Arctic seasonal freeze‐thaw transitions of the land surface and sea ice, we analyze daily backscatter data from satellite scatterometry to examine the time series on an annual basis by applying an optimal edge detection scheme, and iterate against an internal median climatology to mitigate unreasonable outliers. By applying this novel algorithm to resolution‐enhanced QuikSCAT data from 1999 to 2009, we have mapped a decade of seasonal freeze‐thaw transitions across the landmass and sea ice north of 60°N at a spatial resolution better than 5 km. The data set has been validated against surface air temperature measurements and snow depth obtained from a distributed network of weather stations and drift buoys. Most retrieved timings from surface and QuikSCAT measurements agree to less than a week at thaw transition for both land and sea ice and at freeze transition for sea ice, indicating successful retrieval over a range of surface covers. While the spatial pattern of freeze‐thaw transition changes substantially from year to year, the interannual variability of the mean transition timing over a particular surface is small.
Systematic study of rogue wave probability distributions in a fourth‐order nonlinear Schrödinger equation
Authors: Ying L. H. , Kaplan L.
Published: July 2012

Nonlinear instability and refraction by ocean currents are both important mechanisms that go beyond the Rayleigh approximation and may be responsible for the formation of freak waves. In this paper, we quantitatively study nonlinear effects on the evolution of surface gravity waves on the ocean, to explore systematically the effects of various input parameters on the probability of freak wave formation. The fourth‐order current‐modified nonlinear Schrödinger equation (CNLS4) is employed to describe the wave evolution. By solving CNLS4 numerically, we are able to obtain quantitative predictions for the wave height distribution as a function of key environmental conditions such as average steepness, angular spread, and frequency spread of the local sea state. Additionally, we explore the spatial dependence of the wave height distribution, associated with the buildup of nonlinear development.
Using passive remote sensing to retrieve the vertical variation of cloud droplet size in marine stratocumulus: An assessment of information content and the potential for improved retrievals from hyperspectral measurements
Authors: King N. J. , Vaughan G.
Published: July 2012

We present a theoretical study into the information content of solar reflectance measurements at multiple near‐infrared wavelengths in the context of deriving the vertical variation of cloud droplet size from marine stratocumulus. We employ a Bayesian optimal estimation approach to retrieve a profile of droplet effective radius as a function of optical depth in the cloud. This allows an assessment of the information content of the measurement of reflectance at different wavelengths and the potential for a new generation of hyperspectral sensors to improve the retrieval. Our results show that using the three absorbing near‐infrared channels of the Moderate Resolution Imaging Spectroradiometer (MODIS) centered at 1.6, 2.1 and 3.7 μm a retrieval of droplet sizes lower in the cloud is highly sensitive to small changes in reflectance. Consequently instrument and modeling errors must be reduced to <1% in order to gain a useful uncertainty constraint on droplet size near to cloud base. By introducing many high spectral resolution wavelength channels, such as those available from hyperspectral sensors, we find that the information content pertaining to all retrieval variables increases significantly. This results in a reduction in the uncertainty estimates on all retrieved quantities. We also test the ability of a vertical profile retrieval to provide improved liquid water path estimates by using several in situ profiling measurements of marine stratocumulus in the South‐East Pacific region. We find that a vertical profile retrieval significantly improves the liquid water path estimate when compared to a two‐band lookup table retrieval.
Kinematic and thermal evolution during two‐stage exhumation of a Mediterranean subduction complex
Authors: Behr W. M. , Platt J. P.
Published: July 2012

We examine the kinematic and thermal evolution of the Nevado‐Filabride Complex (NFC), an Early to Middle Miocene subduction complex within the Betic Cordillera of southern Spain. Thermobarometry from the NFC in the Sierra Alhamilla reveals an inverted geothermal gradient, with peak temperatures and pressures of 560°C and 13 kbar reached in the uppermost tectonic unit. The NFC cooled during exhumation, defining a linear PT path that remained within the stability field of kyanite until the aluminosilicate breakdown reaction. Geo‐ and thermochronology suggest the NFC was subducted and exhumed to the surface within ∼10 m.y., recording an early stage of fast cooling from peak T through ∼250°C, followed by a late stage of slower cooling as the rocks approached the surface. The exhumation is associated with a progressive change in kinematics, with early co‐axial fabrics showing NNE‐SSW‐trending stretching lineations, and late non‐coaxial fabrics showing SSW‐trending lineations. A new tectonic model is proposed to explain these data, in which rocks at the leading edge of the Iberian margin were subducted southeastward beneath the thin, hot, Alboran lithosphere to form the NFC. The rocks at the top of the slab began to be exhumed once they reached 48–67 km depth. They were initially exhumed rapidly along the top of the subducting slab, in a subduction channel geometry; then upon reaching the middle crust, were captured by a low‐angle detachment fault with a WSW shear sense and final exhumation was accommodated more slowly in a core‐complex geometry.
Evolution of near‐surface ramp‐flat‐ramp normal faults and implication during intramontane basin formation in the eastern Betic Cordillera (the Huércal‐Overa Basin, SE Spain)
Authors: Pedrera Antonio , Galindo‐Zaldívar Jesús , Lamas Francisco , Ruiz‐Constán Ana
Published: July 2012

The nucleation, propagation, and associated folding of ramp‐flat‐ramp normal faults were analyzed from field examples developed in a brittle/ductile multilayer sequence of the Huércal‐Overa Basin (SE Spain). Gently dipping sandy silt layers, which display a low cohesive strength (C0 = 7 kPa, μ= 34°), favor the development of extensional detachments. A tectonic origin instead of a possible gravitational origin is supported by the perpendicularity between the paleoslope direction of the fluvial‐deltaic environment inferred from imbricated pebbles, and the senses of movement deduced from fault slicken‐lines. The link between high‐angle normal faults (HANFs) —formed at different levels in the layered sequence— with horizontal fault segments comes to develop ramp‐flat‐ramp normal faults with associated roll‐over in the hanging wall. Observed extensional duplexes are formed by parallel detachments connected through synthetic Riedel faults. These Riedel faults would produce the back‐rotation of the individual blocks (horses), i.e., extensional folding of the originally subhorizontal layers. There is no correlation between the analyzed ramp‐flat‐ramp normal faults, accommodating south‐southeastward extension during Serravallian‐lower Tortonian, and either the regional Alpujarride/Nevado‐Filabride west‐directed extensional shear zone or the top‐to‐the‐north detachments within Alpujarride units, which are clearly sealed by Serravallian‐lower Tortonian sediments. Therefore, the studied normal faults are restricted to the brittle/ductile multilayer fluvio/deltaic sequence and accommodate moderate late extension instead of belonging to a large crustal extensional system connected with a regional detachment at depth. Therefore, the basin formed in a moderate crustal thickness context where small and medium‐scale extensional systems were subordinate structures. These natural examples support the development of low‐angle normal faults at very shallow crustal levels in multilayer sequences with suitable rheological conditions.
The ‘atom‐splitting’ moment of synthetic biology
Authors: Valentine Alex J , Kleinert Aleysia , Verdier Jerome
Published: July 2012

Synthetic biology and nuclear physics share many commonalities in terms of public perception and funding. Synthetic biologists could learn valuable lessons from the history of the atomic bomb and nuclear power.
PDIp is a major intracellular oestrogen-storage protein that modulates tissue levels of oestrogen in the pancreas
Authors: Fu Xinmiao , Wang Pan , Fukui Masayuki , Long Cheng , Yin Linxiang , Choi Hye Joung , Zhu Bao Ting
Published: July 2012

E2 (17β-oestradiol), a female sex hormone, has important biological functions in a woman's body. The pancreas, often considered a non-classical E2-targeting organ, is known to be functionally regulated by E2, but little is known about how oestrogen actions are regulated in this organ. In the present study we report that PDIp (pancreas-specific protein disulfide isomerase), a protein-folding catalyst, can act as a major intracellular E2 storage protein in a rat model to modulate the pancreatic tissue level, metabolism and action of E2. The purified endogenous PDIp from both rat and human pancreatic tissues can bind E2 with a Kd value of approximately 150 nM. The endogenous PDIp-bound E2 accounts for over 80% of the total protein-bound E2 present in rat and human pancreatic tissues, and this binding protects E2 from metabolic disposition and prolongs its duration of action. Importantly, we showed in ovariectomized female rats that the E2 level in the pancreas reaches its highest level (9-fold increase over its basal level) at 24–48 h after a single injection of E2, and even at 96 h its level is still approximately 5-fold higher. In contrast, the E2 level in the uterus quickly returns to its basal level at 48 h after reaching its maximal level (approximately 2-fold increase) at 24 h. Taken together, these results show for the first time that PDIp is a predominant intracellular oestrogen storage protein in the pancreas, which offers novel mechanistic insights into the accumulation and action of oestrogen inside pancreatic cells.
Reference Correlation of the Thermal Conductivity of Toluene from the Triple Point to 1000 K and up to 1000 MPa
Authors: Assael M. J. , Mylona S. K. , Huber M. L. , Perkins R. A.
Published: June 2012

This paper contains new, representative equations for the thermal conductivity of toluene. The equations are based in part upon a body of experimental data that has been critically assessed for internal consistency and for agreement with theory whenever possible. Although there are a sufficiently large number of data at normal temperatures, data at very low and very high temperatures as well as near the critical region are scarce. In the case of the dilute-gas thermal conductivity, a theoretically based correlation was adopted in order to extend the temperature range of the experimental data. Moreover, in the critical region, the experimentally observed enhancement of the thermal conductivity is well represented by theoretically based equations containing just one adjustable parameter. The correlations are applicable for the temperature range from the triple point to 1000 K and pressures up to 1000 MPa. The overall uncertainty (considered to be estimates of a combined expanded uncertainty with a coverage factor of two) of the proposed correlation is estimated, for pressures less than 700 MPa and temperatures less than 550 K, to be less than 3% for the liquid, while for the region 550 K ≤ T ≤ 700 K the uncertainty is estimated to be 4%. For the region T > 700 K and 500 MPa ≤ p ≤ 1000 MPa, the equations can safely be used with an uncertainty of the order of 10%. Finally, the uncertainty along the saturation line is estimated to be 2% with a coverage factor of two.
Correlation for the Viscosity of Sulfur Hexafluoride (SF6) from the Triple Point to 1000 K and Pressures to 50 MPa
Authors: Quiñones-Cisneros Sergio E. , Huber Marcia L. , Deiters Ulrich K.
Published: June 2012

A wide-ranging correlation for the viscosity surface of sulfur hexafluoride (SF6) has been developed that incorporates generalized friction theory (GFT). The approach requires, as the core thermodynamic model, a reference-quality equation of state (EoS). Here the EoS of Guder and Wagner has been selected for that purpose. All available experimental data, to the extent of our knowledge, were considered in the development of the model. The correlation performs best in the low-pressure (less than 0.33 MPa) region from 300 K to 700 K where the estimated uncertainty (considered to be combined expanded uncertainty with a coverage factor of two) is 0.3%. In the region from 300 K to 425 K for pressures less than 20 MPa, the estimated uncertainty is less than 1%. Where there were data available for validation at temperatures from 230 K to 575 K for pressures up to 50 MPa, the estimated uncertainty is 2%. The correlation extrapolates in a physically reasonable manner and may be used at pressures to 100 MPa and temperatures from the triple point to 1000 K.
Thermodynamic Properties ofo-Xylene,m-Xylene,p-Xylene, and Ethylbenzene
Authors: Zhou Yong , Wu Jiangtao , Lemmon Eric W.
Published: June 2012

Equations of state for the xylene isomers (o-xylene, m-xylene, and p-xylene) and ethylbenzene have been developed with the use of the Helmholtz energy as the fundamental property with independent variables of density and temperature. The general uncertainties of the equations of state are 0.5% in vapor pressure above the normal boiling point, and increase as the temperature decreases due to a lack of experimental data. The uncertainties in density range from 0.1% in the liquid region to 1.0% elsewhere (the critical and vapor-phase regions). The uncertainties in properties related to energy (such as heat capacity and sound speed) are estimated to be 1.0%. In the critical region, the uncertainties are higher for all properties. The behavior of the equations of state is reasonable within the region of validity and at higher and lower temperatures and pressures. Detailed analyses between the equations and experimental data are reported.
Soil CO2 concentration and efflux from three forests in subtropical China
Authors: Zhou Lixia , Fu Shenglei , Ding Mingmao , Yi Zhigang , Yi Weimin
Published: July 2012

Measurements of soil CO2 efflux and soil CO2 concentration concurrently are important for understanding the mechanism and regulation of CO2 in the soil. We have analysed CO2 concentration in a soil profile and soil CO2 efflux in three typical forests in subtropical China: monsoon evergreen broad-leaved forest (BF, 400 years old), pine and broad-leaved mixed forest (MF, 80 years old), and pine forest (PF, 70 years old). A portable soil CO2 sampler of simple sample operation was designed and used. The seasonal patterns of soil surface CO2 efflux and soil CO2 concentration were observed, and were positively correlated with rainfall, soil temperature, and moisture. The mean values of soil CO2 concentrations at the 15, 30, 45, and 60 cm soil depth were higher in BF (3368–9243 μL L–1) than in MF (1495–7662 μL L–1) and PF (1566–5730 μL L–1), while the mean values of soil surface CO2 efflux (Rsurface) were 0.55 ± 0.11 g m–2 h–1 in BF, 0.52 ± 0.10 g m–2 h–1 in MF, and 0.45 ± 0.07 g m–2 h–1 in PF. Soil CO2 concentration and Rsurface increased gradually with the age of the forests, but the incremental increase in soil CO2 concentration will be greater than that of Rsurface in MF and PF compared with BF. The data suggested that, although older forests have more C, younger forests probably will sequester C as CO2 faster than older forests.
Sirtuin 6 (SIRT6) rescues the decline of homologous recombination repair during replicative senescence
Authors: Mao Zhiyong , Tian Xiao , Van Meter Michael , Ke Zhonghe , Gorbunova Vera , Seluanov Andrei
Published: July 2012

Genomic instability is a hallmark of aging tissues. Genomic instability may arise from the inefficient or aberrant function of DNA double-stranded break (DSB) repair. DSBs are repaired by homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). HR is a precise pathway, whereas NHEJ frequently leads to deletions or insertions at the repair site. Here, we used normal human fibroblasts with a chromosomally integrated HR reporter cassette to examine the changes in HR efficiency as cells progress to replicative senescence. We show that HR declines sharply with increasing replicative age, with an up to 38-fold decrease in efficiency in presenescent cells relative to young cells. This decline is not explained by a reduction of the number of cells in S/G
2
/M stage as presenescent cells are actively dividing. Expression of proteins involved in HR such as Rad51, Rad51C, Rad52, NBS1, and Sirtuin 6 (SIRT6) diminished with cellular senescence. Supplementation of Rad51, Rad51C, Rad52, and NBS1 proteins, either individually or in combination, did not rescue the senescence-related decline of HR. However, overexpression of SIRT6 in “middle-aged” and presenescent cells strongly stimulated HR repair, and this effect was dependent on mono-ADP ribosylation activity of poly(ADP-ribose) polymerase (PARP1). These results suggest that in aging cells, the precise HR pathway becomes repressed giving way to a more error-prone NHEJ pathway. These changes in the processing of DSBs may contribute to age-related genomic instability and a higher incidence of cancer with age. SIRT6 activation provides a potential therapeutic strategy to prevent the decline in genome maintenance.
Magnetostriction and magnetic texture to 100.75 Tesla in frustrated SrCu
2
(BO
3
)
2
Authors: Jaime Marcelo , Daou Ramzy , Crooker Scott A. , Weickert Franziska , Uchida Atsuko , Feiguin Adrian E. , Batista Cristian D. , Dabkowska Hanna A. , Gaulin Bruce D.
Published: July 2012

Strong geometrical frustration in magnets leads to exotic states such as spin liquids, spin supersolids, and complex magnetic textures. SrCu
2
(BO
3
)
2
, a spin-1/2 Heisenberg antiferromagnet in the archetypical Shastry–Sutherland lattice, exhibits a rich spectrum of magnetization plateaus and stripe-like magnetic textures in applied fields. The structure of these plateaus is still highly controversial due to the intrinsic complexity associated with frustration and competing length scales. We discover magnetic textures in SrCu
2
(BO
3
)
2
via magnetostriction and magnetocaloric measurements in fields up to 100.75 T. In addition to observing low-field fine structure with unprecedented resolution, the data also reveal lattice responses at 73.6 T and at 82 T that we attribute, using a controlled density matrix renormalization group approach, to a unanticipated 2/5 plateau and to the long-predicted 1/2 plateau.
Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation
Authors: Lin Fangqin , Xing Ke , Zhang Jianzhi , He Xionglei
Published: July 2012

Susumu Ohno proposed in 1967 that, during the origin of mammalian sex chromosomes from a pair of autosomes, per-allele expression levels of X-linked genes were doubled to compensate for the degeneration of their Y homologs. This conjecture forms the foundation of the current evolutionary model of sex chromosome dosage compensation, but has been tested in mammals only indirectly via a comparison of expression levels between X-linked and autosomal genes in the same genome. The test results have been controversial, because examinations of different gene sets led to different conclusions that either support or refute Ohno’s hypothesis. Here we resolve this uncertainty by directly comparing mammalian X-linked genes with their one-to-one orthologs in species that diverged before the origin of the mammalian sex chromosomes. Analyses of RNA sequencing data and proteomic data provide unambiguous evidence for expression halving (i.e., no change in per-allele expression level) of X-linked genes during evolution, with the exception of only ∼5% of genes that encode members of large protein complexes. We conclude that Ohno’s hypothesis is rejected for the vast majority of genes, reopening the search for the evolutionary force driving the origin of chromosome-wide X inactivation in female mammals.
Reshaping of the maize transcriptome by domestication
Authors: Swanson-Wagner Ruth , Briskine Roman , Schaefer Robert , Hufford Matthew B. , Ross-Ibarra Jeffrey , Myers Chad L. , Tiffin Peter , Springer Nathan M.
Published: July 2012

Through domestication, humans have substantially altered the morphology of
Zea mays
ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
Modeling individual-level heterogeneity in racial residential segregation
Authors: Xie Yu , Zhou Xiang
Published: July 2012

We investigate the dynamic relationship between residential choices of individuals and resulting long-term aggregate segregation patterns, allowing for feedback effects of macrolevel neighborhood conditions on residential choices. We reinterpret past survey data on whites’ attitudes about desired neighborhoods as revealing large heterogeneity in whites’ tolerance of black neighbors. Through agent-based modeling, we improve on a previous model of residential racial segregation by introducing individual-level heterogeneity in racial tolerance. Our model predicts, in the long run, a lower level of residential racial segregation than would be true with homogeneous racial tolerance. Further analysis shows that whites’ tolerance of black neighbors is closely associated with their overall racial attitudes toward blacks.
Correlating the magic numbers of inorganic nanomolecular assemblies with a
{Pd

84

}
molecular-ring Rosetta Stone
Authors: Xu Feng , Miras Haralampos N. , Scullion Rachel A. , Long De-Liang , Thiel Johannes , Cronin Leroy
Published: July 2012

Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate
{Pd

84

}
-ring cluster 3.3 nm in diameter; [Pd
84
O
42
(OAc)
28
(PO
4
)
42
]
70-
(
{Pd

84

}
 ≡ 
{Pd

12

}

7

) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the
{Pd

84

}
-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the
{Pd

84

}
we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of
{Pd

84

}
allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families.
Molecular dissection of
Neurospora
Spore killer meiotic drive elements
Authors: Hammond Thomas M. , Rehard David G. , Xiao Hua , Shiu Patrick K. T.
Published: July 2012

Meiotic drive is a non-Mendelian inheritance phenomenon in which certain selfish genetic elements skew sexual transmission in their own favor. In some cases, progeny or gametes carrying a meiotic drive element can survive preferentially because it causes the death or malfunctioning of those that do not carry it. In
Neurospora
, meiotic drive can be observed in fungal spore killing. In a cross of Spore killer (
Sk
) × WT (
Sk
-sensitive), the ascospores containing the Spore killer allele survive, whereas the ones with the sensitive allele degenerate.
Sk-2
and
Sk-3
are the most studied meiotic drive elements in
Neurospora
, and they each theoretically contain two essential components: a killer element and a resistance gene. Here we report the identification and characterization of the
Sk
resistance gene,
rsk
(
resistant to Spore killer
).
rsk
seems to be a fungal-specific gene, and its deletion in a killer strain leads to self-killing.
Sk-2
,
Sk-3
, and naturally resistant isolates all use
rsk
for resistance. In each killer system,
rsk
sequences from an
Sk
strain and a resistant isolate are highly similar, suggesting that they share the same origin.
Sk-2
,
Sk-3
, and sensitive
rsk
alleles differ from each other by their unique indel patterns. Contrary to long-held belief, the killer targets not only late but also early ascospore development. The WT RSK protein is dispensable for ascospore production and is not a target of the spore-killing mechanism. Rather, a resistant version of RSK likely neutralizes the killer element and prevents it from interfering with ascospore development.
Economic impacts and impact dynamics of Bt (
Bacillus thuringiensis
) cotton in India
Authors: Kathage Jonas , Qaim Matin
Published: July 2012

Despite widespread adoption of genetically modified crops in many countries, heated controversies about their advantages and disadvantages continue. Especially for developing countries, there are concerns that genetically modified crops fail to benefit smallholder farmers and contribute to social and economic hardship. Many economic studies contradict this view, but most of them look at short-term impacts only, so that uncertainty about longer-term effects prevails. We address this shortcoming by analyzing economic impacts and impact dynamics of Bt cotton in India. Building on unique panel data collected between 2002 and 2008, and controlling for nonrandom selection bias in technology adoption, we show that Bt has caused a 24% increase in cotton yield per acre through reduced pest damage and a 50% gain in cotton profit among smallholders. These benefits are stable; there are even indications that they have increased over time. We further show that Bt cotton adoption has raised consumption expenditures, a common measure of household living standard, by 18% during the 2006–2008 period. We conclude that Bt cotton has created large and sustainable benefits, which contribute to positive economic and social development in India.
Observationally constrained estimates of carbonaceous aerosol radiative forcing
Authors: Chung Chul E. , Ramanathan V. , Decremer Damien
Published: July 2012

Carbonaceous aerosols (CA) emitted by fossil and biomass fuels consist of black carbon (BC), a strong absorber of solar radiation, and organic matter (OM). OM scatters as well as absorbs solar radiation. The absorbing component of OM, which is ignored in most climate models, is referred to as brown carbon (BrC). Model estimates of the global CA radiative forcing range from 0 to 0.7 Wm-2, to be compared with the Intergovernmental Panel on Climate Change’s estimate for the pre-Industrial to the present net radiative forcing of about 1.6 Wm-2. This study provides a model-independent, observationally based estimate of the CA direct radiative forcing. Ground-based aerosol network data is integrated with field data and satellite-based aerosol observations to provide a decadal (2001 through 2009) global view of the CA optical properties and direct radiative forcing. The estimated global CA direct radiative effect is about 0.75 Wm-2(0.5 to 1.0). This study identifies the global importance of BrC, which is shown to contribute about 20% to 550-nm CA solar absorption globally. Because of the inclusion of BrC, the net effect of OM is close to zero and the CA forcing is nearly equal to that of BC. The CA direct radiative forcing is estimated to be about 0.65 (0.5 to about 0.8) Wm-2, thus comparable to or exceeding that by methane. Caused in part by BrC absorption, CAs have a net warming effect even over open biomass-burning regions in Africa and the Amazon.
Functional single-cell hybridoma screening using droplet-based microfluidics
Authors: Debs Bachir El , Utharala Ramesh , Balyasnikova Irina V. , Griffiths Andrew D. , Merten Christoph A.
Published: July 2012

Monoclonal antibodies can specifically bind or even inhibit drug targets and have hence become the fastest growing class of human therapeutics. Although they can be screened for binding affinities at very high throughput using systems such as phage display, screening for functional properties (e.g., the inhibition of a drug target) is much more challenging. Typically these screens require the generation of immortalized hybridoma cells, as well as clonal expansion in microtiter plates over several weeks, and the number of clones that can be assayed is typically no more than a few thousand. We present here a microfluidic platform allowing the functional screening of up to 300,000 individual hybridoma cell clones within less than a day. This approach should also be applicable to nonimmortalized primary B-cells, as no cell proliferation is required: Individual cells are encapsulated into aqueous microdroplets and assayed directly for the release of antibodies inhibiting a drug target based on fluorescence. We used this system to perform a model screen for antibodies that inhibit angiotensin converting enzyme 1, a target for hypertension and congestive heart failure drugs. When cells expressing these antibodies were spiked into an unrelated hybridoma cell population in a ratio of 1∶10,000 we observed a 9,400-fold enrichment after fluorescence activated droplet sorting. A wide variance in antibody expression levels at the single-cell level within a single hybridoma line was observed and high expressors could be successfully sorted and recultivated.
High-throughput single-microparticle imaging flow analyzer
Authors: Goda Keisuke , Ayazi Ali , Gossett Daniel R. , Sadasivam Jagannath , Lonappan Cejo K. , Sollier Elodie , Fard Ali M. , Hur Soojung Claire , Adam Jost , Murray Coleman , Wang Chao , Brackbill Nora , Di Carlo Dino , Jalali Bahram
Published: July 2012

Optical microscopy is one of the most widely used diagnostic methods in scientific, industrial, and biomedical applications. However, while useful for detailed examination of a small number (< 10,000) of microscopic entities, conventional optical microscopy is incapable of statistically relevant screening of large populations (> 100,000,000) with high precision due to its low throughput and limited digital memory size. We present an automated flow-through single-particle optical microscope that overcomes this limitation by performing sensitive blur-free image acquisition and nonstop real-time image-recording and classification of microparticles during high-speed flow. This is made possible by integrating ultrafast optical imaging technology, self-focusing microfluidic technology, optoelectronic communication technology, and information technology. To show the system’s utility, we demonstrate high-throughput image-based screening of budding yeast and rare breast cancer cells in blood with an unprecedented throughput of 100,000 particles/s and a record false positive rate of one in a million.
Sulfonation of glycopeptide antibiotics by sulfotransferase StaL depends on conformational flexibility of aglycone scaffold
Authors: Shi Rong , Munger Christine , Kalan Lindsay , Sulea Traian , Wright Gerard D. , Cygler Miroslaw
Published: July 2012

Although glycopeptide antibiotics (GPAs), including vancomycin and teicoplanin, represent the most important class of anti-infective agents in the treatment of serious Gram-positive bacterial infections, their usefulness is threatened by the emergence of resistant strains. GPAs are complex natural products consisting of a heptapeptide skeleton assembled via nonribosomal peptide synthesis and constrained through multiple crosslinks, with diversity resulting from enzymatic modifications by a variety of tailoring enzymes, which can be used to produce GPA analogues that could overcome antibiotic resistance. GPA-modifying sulfotransferases are promising tools for generating the unique derivatives. Despite significant sequence and structural similarities, these sulfotransferases modify distinct side chains on the GPA scaffold. To provide insight into the spatial diversity of modifications, we have determined the crystal structure of the ternary complex of bacterial sulfotransferase StaL with the cofactor product 3′-phosphoadenosine 5′-phosphate and desulfo-A47934 aglycone substrate. Desulfo-A47934 binds with the hydroxyl group on the 4-hydroxyphenylglycine in residue 1 directed toward the 3′-phosphoadenosine 5′-phosphate and hydrogen-bonded to the catalytic His67. Homodimeric StaL can accommodate GPA substrate in only one of the two active sites because of potential steric clashes. Importantly, the aglycone substrate demonstrates a flattened conformation, in contrast to the cup-shaped structures observed previously. Analysis of the conformations of this scaffold showed that despite the apparent rigidity due to crosslinking between the side chains, the aglycone scaffold displays substantial flexibility, important for enzymatic modifications by the GPA-tailoring enzymes. We also discuss the potential of using the current structural information in generating unique GPA derivatives.
Self-assembly of tunable protein suprastructures from recombinant oleosin
Authors: Vargo Kevin B. , Parthasarathy Ranganath , Hammer Daniel A.
Published: July 2012

Using recombinant amphiphilic proteins to self-assemble suprastructures would allow precise control over surfactant chemistry and the facile incorporation of biological functionality. We used cryo-TEM to confirm self-assembled structures from recombinantly produced mutants of the naturally occurring sunflower protein, oleosin. We studied the phase behavior of protein self-assembly as a function of solution ionic strength and protein hydrophilic fraction, observing nanometric fibers, sheets, and vesicles. Vesicle membrane thickness correlated with increasing hydrophilic fraction for a fixed hydrophobic domain length. The existence of a bilayer membrane was corroborated in giant vesicles through the localized encapsulation of hydrophobic Nile red and hydrophilic calcein. Circular dichroism revealed that changes in nanostructural morphology in this family of mutants was unrelated to changes in secondary structure. Ultimately, we envision the use of recombinant techniques to introduce novel functionality into these materials for biological applications.
Chronic reduction in inhibition reduces receptive field size in mouse auditory cortex
Authors: Seybold Bryan A. , Stanco Amelia , Cho Kathleen K. A. , Potter Gregory B. , Kim Carol , Sohal Vikaas S. , Rubenstein John L. R. , Schreiner Christoph E.
Published: July 2012

Inhibitory interneurons regulate the responses of cortical circuits. In auditory cortical areas, inhibition from these neurons narrows spectral tuning and shapes response dynamics. Acute disruptions of inhibition expand spectral receptive fields. However, the effects of long-term perturbations of inhibitory circuitry on auditory cortical responses are unknown. We ablated ∼30% of dendrite-targeting cortical inhibitory interneurons after the critical period by studying mice with a conditional deletion of
Dlx1
. Following the loss of interneurons, baseline firing rates rose and tone-evoked responses became less sparse in auditory cortex. However, contrary to acute blockades of inhibition, the sizes of spectral receptive fields were reduced, demonstrating both higher thresholds and narrower bandwidths. Furthermore, long-latency responses at the edge of the receptive field were absent. On the basis of changes in response dynamics, the mechanism for the reduction in receptive field size appears to be a compensatory loss of cortico-cortically (CC) driven responses. Our findings suggest chronic conditions that feature changes in inhibitory circuitry are not likely to be well modeled by acute network manipulations, and compensation may be a critical component of chronic neuronal conditions.
Antiplatelet therapy prevents hepatocellular carcinoma and improves survival in a mouse model of chronic hepatitis B
Authors: Sitia Giovanni , Aiolfi Roberto , Di Lucia Pietro , Mainetti Marta , Fiocchi Amleto , Mingozzi Francesca , Esposito Antonio , Ruggeri Zaverio M. , Chisari Francis V. , Iannacone Matteo , Guidotti Luca G.
Published: July 2012

Chronic infection with hepatitis B virus (HBV) is a major risk factor for the development of hepatocellular carcinoma (HCC). The pathogenesis of HBV-associated HCC involves both viral and host factors. The latter include a functionally inefficient CD8+T-cell response that fails to clear the infection from the liver but sustains a chronic necroinflammatory process that contributes to the development of HCC. According to this scenario, amelioration of immune-mediated chronic liver injury may prevent HCC. Because platelets facilitate immune-mediated liver injury by promoting the hepatic accumulation of virus-specific CD8+T cells, we evaluated the long-term consequences of antiplatelet therapy in an HBV transgenic mouse model of chronic immune-mediated necroinflammatory liver disease that progresses to HCC. Treatment with aspirin and clopidogrel during the chronic phase of the disease diminished the number of intrahepatic HBV-specific CD8+T cells and HBV-nonspecific inflammatory cells, the severity of liver fibrosis, and the development of HCC. Antiplatelet therapy improved overall survival without causing significant side effects. In contrast, the same antiplatelet regimen had no antitumor effect when HCC was induced nonimmunologically by chronic exposure to a hepatotoxic chemical. The unprecedented observation that antiplatelet therapy inhibits or delays immune-mediated hepatocarcinogenesis suggests that platelets may be key players in the pathogenesis of HBV-associated liver cancer and supports the notion that immune-mediated necroinflammatory reactions are an important cause of hepatocellular transformation during chronic hepatitis.
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
Authors: Bowman Gregory R. , Geissler Phillip L.
Published: July 2012

Cryptic allosteric sites—transient pockets in a folded protein that are invisible to conventional experiments but can alter enzymatic activity via allosteric communication with the active site—are a promising opportunity for facilitating drug design by greatly expanding the repertoire of available drug targets. Unfortunately, identifying these sites is difficult, typically requiring resource-intensive screening of large libraries of small molecules. Here, we demonstrate that Markov state models built from extensive computer simulations (totaling hundreds of microseconds of dynamics) can identify prospective cryptic sites from the equilibrium fluctuations of three medically relevant proteins—β-lactamase, interleukin-2, and RNase H—even in the absence of any ligand. As in previous studies, our methods reveal a surprising variety of conformations—including bound-like configurations—that implies a role for conformational selection in ligand binding. Moreover, our analyses lead to a number of unique insights. First, direct comparison of simulations with and without the ligand reveals that there is still an important role for an induced fit during ligand binding to cryptic sites and suggests new conformations for docking. Second, correlations between amino acid sidechains can convey allosteric signals even in the absence of substantial backbone motions. Most importantly, our extensive sampling reveals a multitude of potential cryptic sites—consisting of transient pockets coupled to the active site—even in a single protein. Based on these observations, we propose that cryptic allosteric sites may be even more ubiquitous than previously thought and that our methods should be a valuable means of guiding the search for such sites.
RIM genes differentially contribute to organizing presynaptic release sites
Authors: Kaeser Pascal S. , Deng Lunbin , Fan Mingming , Südhof Thomas C.
Published: July 2012

Tight coupling of Ca
2+
channels to the presynaptic active zone is critical for fast synchronous neurotransmitter release. RIMs are multidomain proteins that tether Ca
2+
channels to active zones, dock and prime synaptic vesicles for release, and mediate presynaptic plasticity. Here, we use conditional knockout mice targeting all RIM isoforms expressed by the
Rims1
and
Rims2
genes to examine the contributions and mechanism of action of different RIMs in neurotransmitter release. We show that acute single deletions of each
Rims
gene decreased release and impaired vesicle priming but did not alter the extracellular Ca
2+
-responsiveness of release (which for
Rims
gene mutants is a measure of presynaptic Ca
2+
influx). Moreover, single deletions did not affect the synchronization of release (which depends on the close proximity of Ca
2+
channels to release sites). In contrast, deletion of both
Rims
genes severely impaired the Ca
2+
responsiveness and synchronization of release. RIM proteins may act on Ca
2+
channels in two modes: They tether Ca
2+
channels to active zones, and they directly modulate Ca
2+
-channel inactivation. The first mechanism is essential for localizing presynaptic Ca
2+
influx to nerve terminals, but the role of the second mechanism remains unknown. Strikingly, we find that although the RIM2 C
2
B domain by itself significantly decreased Ca
2+
-channel inactivation in transfected HEK293 cells, it did not rescue any aspect of the RIM knockout phenotype in cultured neurons. Thus, RIMs primarily act in release as physical Ca
2+
-channel tethers and not as Ca
2+
-channel modulators. Different RIM proteins compensate for each other in recruiting Ca
2+
channels to active zones, but contribute independently and incrementally to vesicle priming.
MicroRNAs bind to Toll-like receptors to induce prometastatic inflammatory response
Authors: Fabbri Muller , Paone Alessio , Calore Federica , Galli Roberta , Gaudio Eugenio , Santhanam Ramasamy , Lovat Francesca , Fadda Paolo , Mao Charlene , Nuovo Gerard J. , Zanesi Nicola , Crawford Melissa , Ozer Gulcin H. , Wernicke Dorothee , Alder Hansjuerg , Caligiuri Michael A. , Nana-Sinkam Patrick , Perrotti Danilo , Croce Carlo M.
Published: July 2012

MicroRNAs (miRNAs) are small noncoding RNAs, 19–24 nucleotides in length, that regulate gene expression and are expressed aberrantly in most types of cancer. MiRNAs also have been detected in the blood of cancer patients and can serve as circulating biomarkers. It has been shown that secreted miRNAs within exosomes can be transferred from cell to cell and can regulate gene expression in the receiving cells by canonical binding to their target messenger RNAs. Here we show that tumor-secreted miR-21 and miR-29a also can function by another mechanism, by binding as ligands to receptors of the Toll-like receptor (TLR) family, murine
TLR7
and human TLR8, in immune cells, triggering a TLR-mediated prometastatic inflammatory response that ultimately may lead to tumor growth and metastasis. Thus, by acting as paracrine agonists of TLRs, secreted miRNAs are key regulators of the tumor microenvironment. This mechanism of action of miRNAs is implicated in tumor–immune system communication and is important in tumor growth and spread, thus representing a possible target for cancer treatment.
The versatile molecular complex component LC8 promotes several distinct steps of flagellar assembly
Authors: Gupta Anjali , Diener Dennis R. , Sivadas Priyanka , Rosenbaum Joel L. , Yang Pinfen
Published: July 2012

LC8 is present in various molecular complexes. However, its role in these complexes remains unclear. We discovered that although LC8 is a subunit of the radial spoke (RS) complex in Chlamydomonas flagella, it was undetectable in the RS precursor that is converted into the mature RS at the tip of elongating axonemes. Interestingly, LC8 dimers bound in tandem to the N-terminal region of a spoke phosphoprotein, RS protein 3 (RSP3), that docks RSs to axonemes. LC8 enhanced the binding of RSP3 N-terminal fragments to purified axonemes. Likewise, the N-terminal fragments extracted from axonemes contained LC8 and putative spoke-docking proteins. Lastly, perturbations of RSP3’s LC8-binding sites resulted in asynchronous flagella with hypophosphorylated RSP3 and defective associations between LC8, RSs, and axonemes. We propose that at the tip of flagella, an array of LC8 dimers binds to RSP3 in RS precursors, triggering phosphorylation, stalk base formation, and axoneme targeting. These multiple effects shed new light on fundamental questions about LC8-containing complexes and axoneme assembly.
Bnip3 and AIF cooperate to induce apoptosis and cavitation during epithelial morphogenesis
Authors: Qi Yanmei , Tian Xiaoxiang , Liu Jie , Han Yaling , Graham Alan M. , Simon M. Celeste , Penninger Josef M. , Carmeliet Peter , Li Shaohua
Published: July 2012

Apoptosis is an essential step in cavitation during embryonic epithelial morphogenesis, but its mechanisms are largely unknown. In this paper, we used embryonic stem cell–differentiated embryoid bodies (EBs) as a model and found that Bnip3 (Bcl-2/adenovirus E1B 19-kD interacting protein), a BH3-only proapoptotic protein, was highly up-regulated during cavitation in a hypoxia-dependent manner. Short hairpin RNA silencing of Bnip3 inhibited apoptosis of the core cells and delayed cavitation. We show that the Bnip3 up-regulation was mediated mainly by hypoxia-inducible factor (HIF)–2. Ablation of HIF-2α or HIF-1β, the common β subunit of HIF-1 and -2, suppressed Bnip3 up-regulation and inhibited apoptosis and cavitation. We further show that apoptosis-inducing factor (AIF) cooperated with Bnip3 to promote lumen clearance. Bnip3 silencing in AIF-null EBs nearly blocked apoptosis and cavitation. Moreover, AIF also regulated Bnip3 expression through mitochondrial production of reactive oxygen species and consequent HIF-2α stabilization. These results uncover a mechanism of cavitation through hypoxia-induced apoptosis of the core cells mediated by HIFs, Bnip3, and AIF.