bluuebunny/crossref_metadata_2025 huggingface dataset:
PbS nanocrystal solar cells with high efficiency and fill factor
Authors: Szendrei K. , Gomulya W. , Yarema M. , Heiss W. , Loi M. A.
Published: November 2010

We report on the fabrication of efficient PbS solar cells, showing power conversion efficiencies approaching 4% and fill factors of 60% under AM1.5 illumination. The effect of the size of two different nanocrystals (NCs) on the performance and key parameters of the devices are discussed together with peculiar features of device functioning. The results prove that the devices are not under space-charge limitation and the device performance is influenced by charge trapping which is dependent on the size of the NCs.
Nanocrystallization of amorphous germanium films observed with nanosecond temporal resolution
Authors: Nikolova L. , LaGrange T. , Reed B. W. , Stern M. J. , Browning N. D. , Campbell G. H. , Kieffer J.-C. , Siwick B. J. , Rosei F.
Published: November 2010

Using dynamic transmission electron microscopy we measure nucleation and growth rates during laser driven crystallization of amorphous germanium (a-Ge) films supported by silicon monoxide membranes. The films were crystallized using single 532 nm laser pulses at a fluence of ∼128 mJ cm−2. Devitrification processes initiate less than 20 ns after excitation and are complete within ∼55 ns. The nucleation rate was estimated by tracking crystallite density as a function of time and reached a maximum of ∼1.6×1022 nuclei/cm3 s. This study provides information on nanocrystallization phenomena in a-Ge, which is important for the implementation of nanostructured group IV semiconductors in optoelectronics devices.
A straightforward and quantitative approach for characterizing the photoactivation performance of optical highlighter fluorescent proteins
Authors: Liu Jun , Pei Zhiguo , Wang Liang , Zhang Zhihong , Zeng Shaoqun , Huang Zhen-Li
Published: November 2010

Characterizing the photoactivation performance of highlighter fluorescence proteins (FPs) is crucial for screening better highlighter FPs and optimizing the photoactivation efficiency of a certain highlighter FP. Currently, photoactivation contrast and half-time values of photoactivation and photobleaching processes are used for such purpose. However, the relations among these parameters are not clear, and little guidance for practical experiments could be obtained from the half-time values. Here, we show that light dose dependent fluorescence curve, which is calculated from activation-intensity-dependent photoactivation and photobleaching rates, is capable of quantifying the photoactivation performance straightforwardly. Moreover, the photoactivation contrast is easily obtained from the curve.
Displacing New York
Authors: Wyly Elvin , Newman Kathe , Schafran Alex , Lee Elizabeth
Published: November 2010

The capitalization of urban property markets intensifies the contradictions between housing as use-value affordability versus exchange-value asset accumulation, and exacerbates displacement pressures. Policies designed to deal with these contradictions—public housing and rent regulations—allow some low-income renters to resist displacement, particularly in gentrifying neighborhoods. Unfortunately, the resulting empirical configuration has been interpreted in ways that cast doubt on the extent of displacement, its causal links to gentrification, and the necessity of protective policies. In this paper we present an alternative interpretation, using New York City as a case study to analyze the spatial evolution of displacement pressures amidst the restructuring of an embattled yet vital municipal welfare state.
Understanding the Social Geography of Census Undercount
Authors: Martin David
Published: November 2010

A new round of censuses is being held internationally in 2010–11 in the face of increasing challenges to the achievement of high coverage rates. Censuses are of enormous importance due to the extensive range of planning and analysis which is dependent on the accuracy of their results. Despite efforts to assess quality and make corrections, there is still evidence of population missing from published estimates. This paper uses administratively based data sources to assess probable undercount in the 2001 Census of England and Wales, specifically seeking to understand the differences between the census and alternative sources. It presents new evidence of strong social and spatial concentrations, only some of which have been addressed by official adjustments to the census. It is important both that these issues are taken into account in substantive research using published small area data and that the underlying processes are much more clearly understood by users and reviewers of the 2010–11 round of censuses.
Anxiety as Social Practice
Authors: Jackson Peter , Everts Jonathan
Published: November 2010

This paper advances a theory of anxiety as social practice. Distinguishing between individual anxieties and anxiety as a social condition, the paper suggests that anxiety has not been subject to the same level of theoretical scrutiny as related concepts such as risk, trust, or fear. Drawing on the existential philosophy of Kierkegaard, Nietzsche, and Heidegger, the paper shows how contemporary anxieties involve the recognition of our own mortality and the destabilisation of established systems of meaning. The paper then turns to practice theory to show how social anxieties can be understood as events that rupture the fabric of everyday life, creating specific subjects and objects, ‘framed’ by different communities of practice, and becoming institutionalised to varying degrees. Focusing on a range of food-related anxieties, the paper explores the geographical and historical constitution of social anxiety, examining the process of anxiety formation and the factors that inhibit or enhance its social and spatial diffusion.
Racial Desegregation and Schooling in South Africa: Contested Geographies of Class Formation
Authors: Hunter Mark
Published: November 2010

Much research on racial desegregation in South Africa uses residential data to track how richer black South Africans are moving from apartheid spaces to higher income suburbs; how racial privilege is giving way to class privilege. Drawing on geographers' relational conception of space and anthropologist Sherry Ortner's notion of a ‘class project’, in this paper I show the importance of geographies of schooling to class formation. The study tracks how schools and two groups—township residents and poorer shack residents—affect and navigate access to schools in Durban. Of importance to class formation, the study finds that children of relatively poor, but not the poorest, township dwellers can commute very long distances to attend prestigious schools. Consequently, racial mixing is more evident in South Africa's schools than in its residential areas—the opposite scenario to that found in many other countries. Yet children born to very poor residents of urban informal settlements face considerable barriers when trying to access well-resourced schools: although they are legally entitled to attend prestigious schools located close to informal settlements, they can often live with extended families hundreds of miles away in rural areas. This new geography of schooling leads to the marginalization of some children but the perception of, and potential for, intergenerational class mobility among a quite significant group of black South Africans.
Physiological basis for enhanced sucrose accumulation in an engineered sugarcane cell line
Authors: Wu Luguang , Birch Robert G.
Published: November 2010

Transgenic sugarcane (Saccharum officinarum L. interspecific hybrids) line N3.2 engineered to express a vacuole-targeted sucrose isomerase was found to accumulate sucrose to twice the level of the background genotype Q117 in heterotrophic cell cultures, without adverse effects on cell growth. Isomaltulose levels declined over successive subcultures, but the enhanced sucrose accumulation was stable. Detailed physiological characterisation revealed multiple processes altered in line N3.2 in a direction consistent with enhanced sucrose accumulation. Striking differences from the Q117 control included reduced extracellular invertase activity, slower extracellular sucrose depletion, lower activities of symplastic sucrose-cleavage enzymes (particularly sucrose synthase breakage activity), and enhanced levels of symplastic hexose-6-phosphate and trehalose-6-phosphate (T6P) in advance of enhanced sucrose accumulation. Sucrose biosynthesis by sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) was substantially faster in assays conducted to reflect the elevation in key allosteric metabolite glucose-6-phosphate (G6P). Sucrose-non-fermenting-1-related protein kinase 1 (SnRK1, which typically activates sucrose synthase breakage activity while downregulating SPS in plants) was significantly lower in line N3.2 during the period of fastest sucrose accumulation. For the first time, T6P is also shown to be a negative regulator of SnRK1 activity from sugarcane sink cells, hinting at a control circuitry for parallel activation of key enzymes for enhanced sucrose accumulation in sugarcane.
Path of water for root growth
Authors: Boyer John S. , Silk Wendy K. , Watt Michelle
Published: November 2010

Do roots obtain water for their growth directly from soil surrounding the growth zone or indirectly, via phloem, from water absorbed elsewhere? Wheat (Triticum aestivum L.) was studied with time-lapse imaging of seminal axile roots, growing in soil and air in a custom-made laboratory rhizotron, before and after excision. The growth data were combined with a theoretical estimate of the amount of water that could be supplied from the phloem. Roots readily extended into air, providing strong evidence that they obtain a portion of their growth-sustaining water internally. The time-lapse experiments indicated that in moist soil, internal sources provided 26–45% of the water for root growth, but the rest came externally from the soil surrounding the growth zone. From the theoretical analysis, the phloem could supply, on average, 64% of the total, accounting for all the internal sources. This indicates that phloem water could be used when root tips cannot access external water, such as in cracks or pores, or regions of dry soil. The distribution of phloem-delivered water for root growth should be considered in whole-plant modelling of root systems. Maximising phloem flux at root tips might confer more efficient use of soil water by crops.
Scale-dependent relationships between benthic habitat characteristics and abundances of blacklip abalone, Haliotis rubra (Leach)
Authors: Strain Elisabeth M. A. , Johnson Craig R.
Published: November 2010

Habitat characteristics can influence marine herbivore densities at a range of spatial scales. We examined the relationship between benthic habitat characteristics and adult blacklip abalone (Haliotis rubra) densities across local scales (0.0625–16 m2), at 2 depths, 4 sites and 2 locations, in Tasmania, Australia. Biotic characteristics that were highly correlated with abalone densities included cover of non-calcareous encrusting red algae (NERA), non-geniculate coralline algae (NCA), a matrix of filamentous algae and sediment, sessile invertebrates, and foliose red algae. The precision of relationships varied with spatial scale. At smaller scales (0.0625–0.25 m2), there was a positive relationship between NERA and ERA, and negative relationships between sediment matrix, sessile invertebrates and abalone densities. At the largest scale (16 m2), there was a positive relationship between NERA and abalone densities. Thus, for some biotic characteristics, the relationship between NERA and abalone densities may be scalable. There was very little variability between depths and sites; however, the optimal spatial scale differed between locations. Our results suggest a dynamic interplay between the behavioural responses of H. rubra to microhabitat and/or to abalone maintaining NERA free of algae, sediment, and sessile invertebrates. This approach could be used to describe the relationship between habitat characteristics and species densities at the optimal spatial scales.
Retention and dispersal of shelf waters influenced by interactions of ocean boundary current and coastal geography
Authors: Feng Ming , Slawinski Dirk , Beckley Lynnath E. , Keesing John K.
Published: November 2010

Retention and dispersal of shelf waters under the influence of ocean boundary currents is crucial to recruitment processes of many coastal species. In this study, a Lagrangian particle tracking method based on an eddy-resolving, data-assimilating, hydrodynamic model is used to study spatial variations of local retention rates and alongshore dispersal of surface waters on the continental shelf off the west coast of Australia. The circulation on the shelf off the west coast of Australia is dominated by the southward-flowing eastern boundary current, the Leeuwin Current, which is interrupted by episodic wind-driven, northward, inshore surface transport during the austral summer, and by mesoscale eddy formations during the austral winter. Low-retention shelf regions tend to experience high alongshore currents, owing to the near-shore influence of the Leeuwin Current, protruding coastal geography, or formation of mesoscale eddies, whereas high-retention regions are sheltered from the direct influence of the Leeuwin Current by coastal geographic features. Alongshore dispersal also exhibits spatial as well as seasonal heterogeneity, with predominantly southward dispersal during the austral winter, and more symmetrical dispersal during the austral summer. Shelf retention and seasonal dispersal are linked with recruitment processes of invertebrate and fish species off the west coast of Australia.
Temporal variability in fish assemblage structure and recruitment in a freshwater-deprived estuary: The Coorong, Australia
Authors: Zampatti Brenton P. , Bice Christopher M. , Jennings Paul R.
Published: November 2010

River regulation can diminish freshwater flows to estuaries and compromise estuarine functionality. Understanding biotic responses to altered flow regimes is imperative to effectively manage aquatic ecosystems. The present study investigated temporal variation in fish assemblage structure and the recruitment of catadromous fish in the Coorong estuary at the terminus of the Murray River, in south-eastern Australia. Over the three-year study period, freshwater inflows to the estuary diminished and ultimately ceased, disconnecting freshwater and estuarine environments. It was hypothesised that these conditions would lead to (1) increases in estuarine salinities and concomitant changes in fish assemblage structure and abundance, and (2) decreased recruitment of catadromous fish. As freshwater inflow decreased, salinities immediately downstream of a series of tidal barrages increased from brackish to marine–hypersaline, species richness and diversity decreased, freshwater and diadromous species became less abundant and assemblages were increasingly characterised by marine species. Furthermore, the abundance of young-of-year catadromous fish decreased dramatically. Excessive regulation of freshwater inflows is resulting in the Coorong estuary resembling a marine embayment, leading to a loss in species diversity. We suggest, however, that even small volumes of freshwater may promote diversity in estuarine fish assemblages and some recruitment of catadromous species.
Life-history traits of the southern hemisphere eastern red scorpionfish, Scorpaena cardinalis (Scorpaenidae: Scorpaeninae)
Authors: Stewart John , Hughes Julian M.
Published: November 2010

Fishes of the family Scorpaenidae (scorpionfish/rockfish) are important to benthic rocky-reef communities and fisheries globally. The present study is the first to provide biological information for any species of the genus Scorpaena (Scorpaena cardinalis) in southern hemisphere waters, namely south-eastern Australia. Growth of S. cardinalis was estimated using size-at-age data from sectioned otoliths. Growth was slow, with fish attaining ∼22 cm after 5 years and 26 cm after 10 years. The oldest fish sampled was estimated to be 33 years old. In contrast to similar-sized congeneric species, males increased in length significantly faster and attained larger sizes than females. Variable recruitment patterns were evident from the age composition of the sampled population. Males of S. cardinalis had mean gonadosomatic index levels (0.09%) an order of magnitude smaller than did the females (2.8–4%) during the March spawning peak. S. cardinalis possesses a cystovarian Type II-3 ovary, a highly specialised form associated with external fertilisation and the production of eggs in a floating gelatinous mass. Traits such as slow growth, substantial longevity, variable recruitment patterns and a highly specialised reproductive strategy may make this species vulnerable to over-exploitation as has occurred with other members of the family Scorpaenidae elsewhere.
Does sampling method or microhabitat type determine patterns of macroinvertebrate assemblage structure detected across spatial scales in rivers?
Authors: Giri M. L. , Chester E. T. , Robson B. J.
Published: November 2010

Patterns in macroinvertebrate assemblage structure detected across spatial scales in rivers vary among studies, and it is not clear whether methodological differences in sampling methods or differences between rivers are responsible. We aimed to separate the roles of microhabitats and sampling methods in determining patterns in macroinvertebrate assemblages across spatial scales in the Johanna River, south-eastern Australia. We hypothesised that less sample-to-sample variability in the structure of macroinvertebrate assemblages would be detected using a Sürber sampler than by scrubbing stones. However, Sürber samples were more variable than individual stones, although invertebrate abundance did not differ. To examine the effect of habitat and substratum, we hypothesised that taxa richness, invertebrate abundance and sample variability would differ among leaf packs and stones. Variation among samples in taxa richness and abundance was higher among leaf packs than among cobbles, whereas variability in taxon composition was much higher among stones. Leaf packs in runs had four times as many taxa as did stones in riffles, and more individuals. Leaf packs may therefore provide a more representative sample of the assemblage than do stones. Sürber samplers may randomly subsample riffle assemblages, inflating the sample-to-sample variability detected.
Exogenously administered secreted frizzled related protein 2 (Sfrp2) reduces fibrosis and improves cardiac function in a rat model of myocardial infarction
Authors: He Wei , Zhang Lunan , Ni Aiguo , Zhang Zhiping , Mirotsou Maria , Mao Lan , Pratt Richard E. , Dzau Victor J.
Published: November 2010

Secreted frizzled related protein 2 (Sfrp2) is known as an inhibitor for the Wnt signaling. In recent studies, Sfrp2 has been reported to inhibit the activity of
Xenopus
homolog of mammalian Tolloid-like 1 metalloproteinase. Bone morphogenic protein 1 (Bmp1)/Tolloid-like metalloproteinase plays a key role in the regulation of collagen biosynthesis and maturation after tissue injury. Here, we showed both endogenous Sfrp2 and Bmp1 protein expressions were up-regulated in rat heart after myocardial infarction (MI). We hypothesize that Sfrp2 could inhibit mammalian Bmp1 activity and, hence, the exogenous administration of Sfrp2 after MI would inhibit the deposition of mature collagen and improve heart function. Using recombinant proteins, we demonstrated that Sfrp2, but not Sfrp1 or Sfrp3, inhibited Bmp1 activity in vitro as measured by a fluorogenic peptide based procollagen C-proteinase activity assay. We also demonstrated that Sfrp2 at high concentration inhibited human and rat type I procollagen processing by Bmp1 in vitro. We further showed that exogenously added Sfrp2 inhibited type I procollagen maturation in primary cardiac fibroblasts. Two days after direct injection into the rat infarcted myocardium, Sfrp2 inhibited MI-induced type I collagen deposition. As early as 2 wk after injection, Sfrp2 significantly reduced left ventricular (LV) fibrosis as shown by trichrome staining. Four weeks after injection, Sfrp2 prevented the anterior wall thinning and significantly improved cardiac function as revealed by histological analysis and echocardiographic measurement. Our study demonstrates Sfrp2 at therapeutic doses can inhibit fibrosis and improve LV function at a later stage after MI.
Oxidation-induced intramolecular disulfide bond inactivates mitogen-activated protein kinase kinase 6 by inhibiting ATP binding
Authors: Diao Yarui , Liu Wei , Wong Catherine C. L. , Wang Xi , Lee Kaman , Cheung Po-yan , Pan Lifeng , Xu Tao , Han Jiahuai , Yates John R. , Zhang Mingjie , Wu Zhenguo
Published: November 2010

Mitogen-activated protein kinase kinase 6 (MKK6) is a member of the mitogen-activated protein kinase (MAPK) kinase (MAP2K) subfamily that specifically phosphorylates and activates the p38 MAPKs. Based on both biochemical and cellular assays, we found that MKK6 was extremely sensitive to oxidation: It was inactivated by oxidation and its kinase activity was fully restored upon treatment with a reducing agent. Detailed mechanistic studies showed that cysteines 109 and 196, two of the six cysteines in MKK6, formed an intramolecular disulfide bond upon oxidation that inactivated MKK6 by inhibiting its ATP binding. This mechanism is distinct from that seen in other redox-sensitive kinases. The two cysteines involved in intramolecular disulfide formation are conserved in all seven members of the MAP2K family. Consistently, we confirmed that other MAP2Ks were also sensitive to oxidation. Our work reveals that MKK6 and other MAP2Ks are a distinct class of cellular redox sensors.
Multiple oncogenic mutations and clonal relationship in spatially distinct benign human epidermal tumors
Authors: Hafner Christian , Toll Agustí , Fernández-Casado Alejandro , Earl Julie , Marqués Miriam , Acquadro Francesco , Méndez-Pertuz Marinela , Urioste Miguel , Malats Núria , Burns Julie E. , Knowles Margaret A. , Cigudosa Juan C. , Hartmann Arndt , Vogt Thomas , Landthaler Michael , Pujol Ramón M. , Real Francisco X.
Published: November 2010

Malignant tumors result from the accumulation of genetic alterations in oncogenes and tumor suppressor genes. Much less is known about the genetic changes in benign tumors. Seborrheic keratoses (SK) are very frequent benign human epidermal tumors without malignant potential. We performed a comprehensive mutational screen of genes in the FGFR3-RAS-MAPK and phosphoinositide 3-kinase (PI3K)-AKT pathways from 175 SK, including multiple lesions from each patient. SK commonly harbored multiple bona fide oncogenic mutations in
FGFR3
,
PIK3CA, KRAS
,
HRAS
,
EGFR
, and
AKT1
oncogenes but not in tumor suppressor genes
TSC1
and
PTEN
. Despite the occurrence of oncogenic mutations and the evidence for downstream ERK/MAPK and PI3K pathway signaling, we did not find induction of senescence or a DNA damage response. Array comparative genomic hybridization (aCGH) analysis revealed that SK are genetically stable. The pattern of oncogenic mutations and X chromosome inactivation departs significantly from randomness and indicates that spatially independent lesions from a given patient share a clonal relationship. Our findings show that multiple oncogenic mutations in the major signaling pathways involved in cancer are not sufficient to drive malignant tumor progression. Furthermore, our data provide clues on the origin and spread of oncogenic mutations in tissues, suggesting that apparently independent (multicentric) adult benign tumors may have a clonal origin.
Both catabolic and anabolic heterotrophic microbial activity proceed in frozen soils
Authors: Drotz Stina Harrysson , Sparrman Tobias , Nilsson Mats B. , Schleucher Jürgen , Öquist Mats G.
Published: November 2010

A large proportion of the global soil carbon pool is stored in soils of high-latitude ecosystems in which microbial processes and production of greenhouse gases proceed during the winter months. It has been suggested that microorganisms have limited ability to sequester substrates at temperatures around and below 0 °C and that a metabolic shift to dominance of catabolic processes occurs around these temperatures. However, there are contrary indications that anabolic processes can proceed, because microbial growth has been observed at far lower temperatures. Therefore, we investigated the utilization of the microbial substrate under unfrozen and frozen conditions in a boreal forest soil across a temperature range from −9 °C to +9 °C, by using gas chromatography-isotopic ratio mass spectrometry and
13
C magic-angle spinning NMR spectroscopy to determine microbial turnover and incorporation of
13
C-labeled glucose. Our results conclusively demonstrate that the soil microorganisms maintain both catabolic (CO
2
production) and anabolic (biomass synthesis) processes under frozen conditions and that no significant differences in carbon allocation from [
13
C]glucose into [
13
C]CO
2
and cell organic
13
C-compounds occurred between +9 °C and −4 °C. The only significant metabolic changes detected were increased fluidity of the cell membranes synthesized at frozen conditions and increased production of glycerol in the frozen samples. The finding that the processes in frozen soil are similar to those in unfrozen soil has important implications for our general understanding and conceptualization of soil carbon dynamics in high-latitude ecosystems.
Modeling electrical activity of myocardial cells incorporating the effects of ephaptic coupling
Authors: Lin Joyce , Keener James P.
Published: November 2010

Existing models of electrical activity in myocardial tissue are unable to easily capture the effects of ephaptic coupling. Homogenized models do not account for cellular geometry, while detailed spatial models are too complicated to simulate in three dimensions. Here we propose a unique model that accurately captures the geometric effects while being computationally efficient. We use this model to provide an initial study of the effects of changes in extracellular geometry, gap junctional coupling, and sodium ion channel distribution on propagation velocity in a single 1D strand of cells. In agreement with previous studies, we find that ephaptic coupling increases propagation velocity at low gap junctional conductivity while it decreases propagation at higher conductivities. We also find that conduction velocity is relatively insensitive to gap junctional coupling when sodium ion channels are located entirely on the cell ends and cleft space is small. The numerical efficiency of this model, verified by comparison with more detailed simulations, allows a thorough study in parameter variation and shows that cellular structure and geometry has a nontrivial impact on propagation velocity. This model can be relatively easily extended to higher dimensions while maintaining numerical efficiency and incorporating ephaptic effects through modeling of complex, irregular cellular geometry.
RD3, the protein associated with Leber congenital amaurosis type 12, is required for guanylate cyclase trafficking in photoreceptor cells
Authors: Azadi Seifollah , Molday Laurie L. , Molday Robert S.
Published: November 2010

Guanylate cyclases, GC1 and GC2, are localized in the light-sensitive outer segment compartment of photoreceptor cells, where they play a crucial role in phototransduction by catalyzing the synthesis of cGMP, the second messenger of phototransduction, and regulating intracellular Ca
2+
levels in combination with the cGMP-gated channel. Mutations in GC1 are known to cause Leber congenital amaurosis type 1 (LCA1), a childhood disease associated with severe vision loss. Although the enzymatic and regulatory properties of guanylate cyclases have been studied extensively, the molecular determinants responsible for their trafficking in photoreceptors remain unknown. Here we show that RD3, a protein of unknown function encoded by a gene associated with photoreceptor degeneration in humans with Leber congenital amaurosis type 12 (LCA12), the
rd3
mouse, and
rcd2
collie, colocalizes and interacts with GC1 and GC2 in rod and cone photoreceptor cells of normal mice. GC1 and GC2 are undetectable in photoreceptors of the
rd3
mouse deficient in RD3 by immunofluorescence microscopy. Cell expression studies show that RD3 mediates the export of GC1 from the endoplasmic reticulum to endosomal vesicles, and that the C terminus of GC1 is required for RD3 binding. Our results indicate that photoreceptor degeneration in the
rd3
mouse,
rcd2
dog, and LCA12 patients is caused by impaired RD3-mediated guanylate cyclase expression and trafficking. The resulting deficiency in cGMP synthesis and the constitutive closure of cGMP-gated channels might cause a reduction in intracellular Ca
2+
to a level below that required for long-term photoreceptor cell survival.
Annealing helicase 2 (AH2), a DNA-rewinding motor with an HNH motif
Authors: Yusufzai Timur , Kadonaga James T.
Published: November 2010

The structure and integrity of DNA is of considerable biological and biomedical importance, and it is therefore critical to identify and to characterize enzymes that alter DNA structure. DNA helicases are ATP-driven motor proteins that unwind DNA. Conversely, HepA-related protein (HARP) protein (also known as SMARCAL1 and DNA-dependent ATPase A) is an annealing helicase that rewinds DNA in an ATP-dependent manner. To date, HARP is the only known annealing helicase. Here we report the identification of a second annealing helicase, which we term AH2, for annealing helicase 2. Like HARP, AH2 catalyzes the ATP-dependent rewinding of replication protein A (RPA)-bound complementary single-stranded DNA, but does not exhibit any detectable helicase activity. Unlike HARP, however, AH2 lacks a conserved RPA-binding domain and does not interact with RPA. In addition, AH2 contains an HNH motif, which is commonly found in bacteria and fungi and is often associated with nuclease activity. AH2 appears to be the only vertebrate protein with an HNH motif. Contrary to expectations, purified AH2 does not exhibit nuclease activity, but it remains possible that AH2 contains a latent nuclease that is activated under specific conditions. These structural and functional differences between AH2 and HARP suggest that different annealing helicases have distinct functions in the cell.
RNA-mediated epigenetic regulation of DNA copy number
Authors: Nowacki Mariusz , Haye Joanna E. , Fang Wenwen , Vijayan Vikram , Landweber Laura F.
Published: November 2010

Increasing evidence suggests that parentally supplied RNA plays crucial roles during eukaryotic development. This epigenetic contribution may regulate gene expression from the earliest stages. Although present in a variety of eukaryotes, maternally inherited characters are especially prominent in ciliated protozoa, in which parental noncoding RNA molecules instruct whole-genome reorganization. This includes removal of nearly all noncoding DNA and sorting the remaining fragments, producing extremely gene-rich somatic genomes. Chromosome fragmentation and extensive replication produce variable DNA copy numbers in the somatic genome. Understanding the forces that drive and regulate copy number change is fundamental. We show that RNA molecules present in parental cells during sexual reproduction can regulate chromosome copy number in the developing nucleus of the ciliate
Oxytricha
. Experimentally induced changes in RNA abundance can both increase and decrease the levels of corresponding DNA molecules in progeny, demonstrating epigenetic inheritance of chromosome copy number. These results suggest that maternal RNA, in addition to controlling gene expression or DNA processing, can also program DNA amplification levels.
Neural crest origin of olfactory ensheathing glia
Authors: Barraud Perrine , Seferiadis Anastasia A. , Tyson Luke D. , Zwart Maarten F. , Szabo-Rogers Heather L. , Ruhrberg Christiana , Liu Karen J. , Baker Clare V. H.
Published: November 2010

Olfactory ensheathing cells (OECs) are a unique class of glial cells with exceptional translational potential because of their ability to support axon regeneration in the central nervous system. Although OECs are similar in many ways to immature and nonmyelinating Schwann cells, and can myelinate large-diameter axons indistinguishably from myelination by Schwann cells, current dogma holds that OECs arise from the olfactory epithelium. Here, using fate-mapping techniques in chicken embryos and genetic lineage tracing in mice, we show that OECs in fact originate from the neural crest and hence share a common developmental heritage with Schwann cells. This explains the similarities between OECs and Schwann cells and overturns the existing dogma on the developmental origin of OECs. Because neural crest stem cells persist in adult tissue, including skin and hair follicles, our results also raise the possibility that patient-derived neural crest stem cells could in the future provide an abundant and accessible source of autologous OECs for cell transplantation therapy for the injured central nervous system.
Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas
Authors: Sneeringer Christopher J. , Scott Margaret Porter , Kuntz Kevin W. , Knutson Sarah K. , Pollock Roy M. , Richon Victoria M. , Copeland Robert A.
Published: November 2010

EZH2, the catalytic subunit of the PRC2 complex, catalyzes the mono- through trimethylation of lysine 27 on histone H3 (H3K27). Histone H3K27 trimethylation is a mechanism for suppressing transcription of specific genes that are proximal to the site of histone modification. Point mutations of the EZH2 gene (Tyr641) have been reported to be linked to subsets of human B-cell lymphoma. The mutant allele is always found associated with a wild-type allele (heterozygous) in disease cells, and the mutations were reported to ablate the enzymatic activity of the PRC2 complex for methylating an unmodified peptide substrate. Here we demonstrate that the WT enzyme displays greatest catalytic efficiency (
k
cat
/
K
) for the zero to monomethylation reaction of H3K27 and diminished efficiency for subsequent (mono- to di- and di- to trimethylation) reactions. In stark contrast, the disease-associated Y641 mutations display very limited ability to perform the first methylation reaction, but have enhanced catalytic efficiency for the subsequent reactions, relative to the WT enzyme. These results imply that the malignant phenotype of disease requires the combined activities of a H3K27 monomethylating enzyme (PRC2 containing WT EZH2 or EZH1) together with the mutant PRC2s for augmented conversion of H3K27 to the trimethylated form. To our knowledge, this is the first example of a human disease that is dependent on the coordinated activities of normal and disease-associated mutant enzymatic function.
Conserved mechanism for sensor phosphatase control of two-component signaling revealed in the nitrate sensor NarX
Authors: Huynh TuAnh Ngoc , Noriega Chris E. , Stewart Valley
Published: November 2010

Two-component signal transduction mediates a wide range of phenotypes in microbes and plants. The sensor transmitter module controls the phosphorylation state of the cognate-response-regulator receiver domain. Whereas the two-component autokinase and phosphotransfer reactions are well-understood, the mechanism by which sensors accelerate the rate of phospho-response regulator dephosphorylation, termed “transmitter phosphatase activity,” is unknown. We identified a conserved DxxxQ motif adjacent to the phospho-accepting His residue in the HisKA_3 subfamily of two-component sensors. We used site-specific mutagenesis to make substitutions for these conserved Gln and Asp residues in the nitrate-responsive NarX sensor and analyzed function both in vivo and in vitro. Results show that the Gln residue is critical for transmitter phosphatase activity, but is not essential for autokinase or phosphotransfer activities. The documented role of an amide moiety in phosphoryl group hydrolysis suggests an analogous catalytic function for this Gln residue in HisKA_3 members. Results also indicate that the Asp residue is important for both autokinase and transmitter phosphatase activities. Furthermore, we noted that sensors of the HisKA subfamily exhibit an analogous E/DxxT/N motif, the conserved Thr residue of which is critical for transmitter phosphatase activity of the EnvZ sensor. Thus, two-component sensors likely use similar mechanisms for receiver domain dephosphorylation.
Concomitant deletions of tumor suppressor genes
MEN1
and
AIP
are essential for the pathogenesis of the brown fat tumor hibernoma
Authors: Nord Karolin H. , Magnusson Linda , Isaksson Margareth , Nilsson Jenny , Lilljebjörn Henrik , Domanski Henryk A. , Kindblom Lars-Gunnar , Mandahl Nils , Mertens Fredrik
Published: November 2010

Hibernomas are benign tumors with morphological features resembling brown fat. They consistently display cytogenetic rearrangements, typically translocations, involving chromosome band 11q13. Here we demonstrate that these aberrations are associated with concomitant deletions of
AIP
and
MEN1
, tumor suppressor genes that are located 3 Mb apart and that underlie the hereditary syndromes pituitary adenoma predisposition and multiple endocrine neoplasia type I.
MEN1
and
AIP
displayed a low expression in hibernomas whereas the expression of genes up-regulated in brown fat—
PPARA
,
PPARG
,
PPARGC1A
, and
UCP1
—was high. Thus, loss of
MEN1
and
AIP
is likely to be pathogenetically essential for hibernoma development. Simultaneous loss of two tumor suppressor genes has not previously been shown to result from a neoplasia-associated translocation. Furthermore, in contrast to the prevailing assumption that benign tumors harbor relatively few genetic aberrations, the present analyses demonstrate that a considerable number of chromosome breaks are involved in the pathogenesis of hibernoma.
Configurational approach to identifying the earliest hominin butchers
Authors: Domínguez-Rodrigo Manuel , Pickering Travis Rayne , Bunn Henry T.
Published: November 2010

The announcement of two approximately 3.4-million-y-old purportedly butchered fossil bones from the Dikika paleoanthropological research area (Lower Awash Valley, Ethiopia) could profoundly alter our understanding of human evolution. Butchering damage on the Dikika bones would imply that tool-assisted meat-eating began approximately 800,000 y before previously thought, based on butchered bones from 2.6- to 2.5-million-y-old sites at the Ethiopian Gona and Bouri localities. Further, the only hominin currently known from Dikika at approximately 3.4 Ma is
Australopithecus afarensis
, a temporally and geographically widespread species unassociated previously with any archaeological evidence of butchering. Our taphonomic configurational approach to assess the claims of
A. afarensis
butchery at Dikika suggests the claims of unexpectedly early butchering at the site are not warranted. The Dikika research group focused its analysis on the morphology of the marks in question but failed to demonstrate, through recovery of similarly marked in situ fossils, the exact provenience of the published fossils, and failed to note occurrences of random striae on the cortices of the published fossils (incurred through incidental movement of the defleshed specimens across and/or within their abrasive encasing sediments). The occurrence of such random striae (sometimes called collectively “trampling” damage) on the two fossils provide the configurational context for rejection of the claimed butchery marks. The earliest best evidence for hominin butchery thus remains at 2.6 to 2.5 Ma, presumably associated with more derived species than
A
.
afarensis
.
ALS-linked mutant superoxide dismutase 1 (SOD1) alters mitochondrial protein composition and decreases protein import
Authors: Li Quan , Vande Velde Christine , Israelson Adrian , Xie Jing , Bailey Aaron O. , Dong Meng-Qui , Chun Seung-Joo , Roy Tamal , Winer Leah , Yates John R. , Capaldi Roderick A. , Cleveland Don W. , Miller Timothy M.
Published: November 2010

Mutations in superoxide dismutase 1 (SOD1) cause familial ALS. Mutant SOD1 preferentially associates with the cytoplasmic face of mitochondria from spinal cords of rats and mice expressing SOD1 mutations. Two-dimensional gels and multidimensional liquid chromatography, in combination with tandem mass spectrometry, revealed 33 proteins that were increased and 21 proteins that were decreased in SOD1
G93A
rat spinal cord mitochondria compared with SOD1
WT
spinal cord mitochondria. Analysis of this group of proteins revealed a higher-than-expected proportion involved in complex I and protein import pathways. Direct import assays revealed a 30% decrease in protein import only in spinal cord mitochondria, despite an increase in the mitochondrial import components TOM20, TOM22, and TOM40. Recombinant SOD1
G93A
or SOD1
G85R
, but not SOD1
WT
or a Parkinson's disease-causing, misfolded α-synuclein
E46K
mutant, decreased protein import by >50% in nontransgenic mitochondria from spinal cord, but not from liver. Thus, altered mitochondrial protein content accompanied by selective decreases in protein import into spinal cord mitochondria comprises part of the mitochondrial damage arising from mutant SOD1.
Increased expression of leukotriene C4synthase and predominant formation of cysteinyl-leukotrienes in human abdominal aortic aneurysm
Authors: Di Gennaro Antonio , Wågsäter Dick , Mäyränpää Mikko I. , Gabrielsen Anders , Swedenborg Jesper , Hamsten Anders , Samuelsson Bengt , Eriksson Per , Haeggström Jesper Z.
Published: November 2010

Leukotrienes (LTs) are arachidonic acid-derived lipid mediators involved in the pathogenesis and progression of diverse inflammatory disorders. The cysteinyl-leukotrienes LTC4, LTD4, and LTE4are important mediators of asthma, and LTB4has recently been implicated in atherosclerosis. Here we report that mRNA levels for the three key enzymes/proteins in the biosynthesis of cysteinyl-leukotrienes, 5-lipoxygenase (5-LO), 5-LO-activating protein (FLAP), and LTC4synthase (LTC4S), are significantly increased in the wall of human abdominal aortic aneurysms (AAAs). In contrast, mRNA levels of LTA4hydrolase, the enzyme responsible for the biosynthesis of LTB4, are not increased. Immunohistochemical staining of AAA wall revealed focal expression of 5-LO, FLAP, and LTC4S proteins in the media and adventitia, localized in areas rich in inflammatory cells, including macrophages, neutrophils, and mast cells. Human AAA wall tissue converts arachidonic acid and the unstable epoxide LTA4into significant amounts of cysteinyl-leukotrienes and to a lesser extent LTB4. Furthermore, challenge of AAA wall tissue with exogenous LTD4increases the release of matrix metalloproteinase (MMP) 2 and 9, and selective inhibition of the CysLT1 receptor by montelukast blocks this effect. The increased expression of LTC4S, together with the predominant formation of cysteinyl-leukotrienes and effects on MMPs production, suggests a mechanism by which LTs may promote matrix degradation in the AAA wall and identify the components of the cysteinyl-leukotriene pathway as potential targets for prevention and treatment of AAA.
Consciousness of the first order in blindsight
Authors: Sahraie Arash , Hibbard Paul B. , Trevethan Ceri T. , Ritchie Kay L. , Weiskrantz Lawrence
Published: November 2010

At suprathreshold levels, detection and awareness of visual stimuli are typically synonymous in nonclinical populations. But following postgeniculate lesions, some patients may perform above chance in forced-choice detection paradigms, while reporting not to see the visual events presented within their blind field. This phenomenon, termed “blindsight,” is intriguing because it demonstrates a dissociation between detection and perception. It is possible, however, for a blindsight patient to have some “feeling” of the occurrence of an event without seeing per se. This is termed blindsight type II to distinguish it from the type I, defined as discrimination capability in the total absence of any acknowledged awareness. Here we report on a well-studied patient, D.B., whose blindsight capabilities have been previously documented. We have found that D.B. is capable of detecting visual patterns defined by changes in luminance (first-order gratings) and those defined by contrast modulation of textured patterns (textured gratings; second-order stimuli) while being aware of the former but reporting no awareness of the latter. We have systematically investigated the parameters that could lead to visual awareness of the patterns and show that mechanisms underlying the subjective reports of visual awareness rely primarily on low spatial frequency, first-order spatial components of the image.
Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences
Authors: Scaduto Diane I. , Brown Jeremy M. , Haaland Wade C. , Zwickl Derrick J. , Hillis David M. , Metzker Michael L.
Published: November 2010

Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases,
State of Washington v Anthony Eugene Whitfield
, case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and
State of Texas v Philippe Padieu
, case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant.
Modulation of experimental autoimmune encephalomyelitis through TRAF3-mediated suppression of interleukin 17 receptor signaling
Authors: Zhu Shu , Pan Wen , Shi Peiqing , Gao Hanchao , Zhao Fang , Song Xinyang , Liu Yan , Zhao Lihua , Li Xiaoxia , Shi Yufang , Qian Youcun
Published: November 2010

Interleukin 17 (IL-17) plays critical roles in the pathogenesis of various autoimmune diseases, including experimental autoimmune encephalomyelitis (EAE). How the signals triggered by this powerful inflammatory cytokine are controlled to avoid abnormal inflammatory responses is not well understood. In this study, we report that TRAF3 is a receptor proximal negative regulator of IL-17 receptor (IL-17R) signaling. TRAF3 greatly suppressed IL-17–induced NF-κB and mitogen-activated protein kinase activation and subsequent production of inflammatory cytokines and chemokines. Mechanistically, the binding of TRAF3 to IL-17R interfered with the formation of the receptor signaling activation complex IL-17R–Act1–TRAF6, resulting in suppression of downstream signaling. TRAF3 markedly inhibited IL-17–induced expression of inflammatory cytokine and chemokine genes in vivo and consequently delayed the onset and greatly reduced the incidence and severity of EAE. Thus, TRAF3 is a negative regulator of IL-17R proximal signaling.