bluuebunny/crossref_metadata_2025 huggingface dataset:
Refuchess: locating Bosniac repatriates after the war in Bosnia–Herzegovina
Authors: Jansen Stef
Published: January 2010

One of the central contradictions characterising the state of Bosnia–Herzegovina that emerged from the ashes of the 1992–1995 war concerns the territorial distribution of its population according to nationality. On the one hand, the foreign intervention, and the Dayton Peace Agreement it brokered, sanctioned its division into largely nationally homogenised polities, consolidating military conquests. On the other hand, large foreign funds were invested in programmes of refugee repatriation and return to redress ethnic cleansing, with considerable success in terms of property restitution. Rather than understanding these dynamics as a resurrection of a prior situation, this article considers them as part of a set of interrelated transformations. Working from ethnographic material gathered among Bosniac repatriates in the early phases of large‐scale return, it first introduces the notion ofrefuchess, the strategic deployment and movement of nationalised persons across nationalised places. It then zooms out to investigate such return movements more generally in terms of different projects of home making and in terms of their paradoxical implications on the national demographic structure of Bosnia–Herzegovina. Copyright © 2009 John Wiley & Sons, Ltd.
Hydrodynamic modelling study of a fish exclusion system for a river diversion
Authors: Ho J. , Coonrod J. , Hanna L. J. , Mefford B. W.
Published: January 2010

River diversions are often equipped with some device to exclude fish, such as fish screens. Flow pattern changes due to fish screen systems were investigated using a three‐dimensional numerical model solving the Reynolds‐averaged Navier‐Stokes (RANS) equations. A porous media obstacle, which is commonly used for ground water flow modelling, was employed to model a fish screen. Fish screens require a velocity component perpendicular to the screen (approach velocity), allowing for water diversion. Meanwhile, it is imperative that this velocity not result in pinning fish to the screen but allowing for fish to be guided to a different location. Thus the ratio of sweeping velocity to approach velocity (VR) is an important criterion in fish screen design. 20:1 VR and 10:1 VR models were tested under high and low flow rates in this study. Screen head loss coefficients for various wire Reynolds numbers were compared with laboratory model measurements to verify the mathematical results. Two different screen types were simulated: perforated plate and wedged wire. Altering global porosity and local permeability of a porous obstacle results in flow direction changes that effectively simulate different screen materials in the numerical model. Model simulations of head loss coefficients and velocity ratios showed good agreement with the laboratory model measurements. The wedged wire allows for more control of the velocity ratio along the screen system than the perforated plate. Baffles installed behind each fish screen bay promote uniform flow distribution along the screen. The porous media obstacle assumption is shown to effectively simulate the hydraulics of various configurations of fish screens at river diversion channels. Copyright © 2010 John Wiley & Sons, Ltd.
Ideas about the nature of science in pedagogically relevant contexts: Insights from a situated perspective of primary teachers' knowledge
Authors: Guerra‐Ramos Maria Teresa , Ryder Jim , Leach John
Published: January 2010

There is evidence that science teachers give naive responses to direct questions about the nature of science. However, there is also evidence that such responses underpredict the more sophisticated knowledge that teachers may use in classroom situations. The purpose of this study was to characterize the informal ideas used by teachers in situations directly relevant to their teaching of science. The sample comprised 50 Mexican primary school teachers. Three areas of informal expertise were addressed: scientists and their work; scientific inquiry; and data measurement. The teachers' thinking was explored through questionnaires and semistructured interviews using pedagogically relevant contexts. The database was analyzed first to describe ideas shared by teachers and second to identify any recurrent themes and patterns among responses. Teachers' responses were characterized around four areas of discourse: demarcation of science; scientific procedures; approaches to reliable knowledge; and professional and institutional features of science. The teachers' responses were diverse in their contextualization, that is, they incorporated specific background and contextual details to a different extent. Most responses showed limited or intermediate contextualization across all four areas of discourse, though some more sophisticated responses were noted. A general framework was developed to characterize this diversity in teachers' responses. This paper concludes with a discussion of the extent to which this sample of teachers was equipped to discuss the nature of science in pedagogical contexts and, given their starting points, how they might be supported in developing their expertise in doing this. Implications for teacher education and curriculum development are presented. © 2010 Wiley Periodicals, Inc. Sci Ed 94:282–307, 2010
Shaping the Future of Cognitive Science
Authors: Nadel Lynn
Published: January 2010

This article is categorized under:

Psychology > Theory and Methods
Married to an Unbeliever: Households, Hierarchies, and Holiness in 1 Corinthians 7:12–16
Authors: Hodge Caroline Johnson
Published: January 2010

In his Advice to the Bride and Groom, Plutarch famously pronounces: “A married woman should therefore worship and recognize the gods whom her husband holds dear, and these alone. The door must be closed to strange cults and foreign superstitions. No god takes pleasure in cult performed furtively and in secret by a woman.”1 These comments represent a patriarchal ideology that the wife (along with the whole household) should follow the worship practices of the husband. It also suggests the possibility that this counsel was not always followed and that wives might bring their own gods into a marriage, attempting to maintain ritual practices in their honor, perhaps secretly.
A New Fragment of Athanasius's Thirty-Ninth Festal Letter: Heresy, Apocrypha, and the Canon
Authors: Brakke David
Published: January 2010

Athanasius of Alexandria's thirty-ninth Festal Letter remains one of the most significant documents in the history of the Christian Bible. Athanasius wrote the letter, which contains the first extant list of precisely the twenty-seven books of the current New Testament canon, in 367 c.e., during the final decade of his life. Like many of his annual Easter letters, the thirty-ninth was fairly long, but only a small portion of the text survives in Greek.1 The Greek excerpt contains Athanasius's lists of the books of the Old and New Testaments, which he calls “canonized,” and a list of a few additional books, like the Shepherd of Hermas, which he says are not canonized, but are useful in the instruction of catechumens. Most studies of the formation of the Christian canon, including very recent ones, examine only this Greek fragment and so discuss only the contents of the lists. But already in the late-nineteenth-century fragments of the much more extensive Coptic translation had been published, and a few scholars, such as Carl Schmidt and Theodor Zahn, used them to write penetrating studies of the letter.2 In 1955 Lefort published all the then-known Coptic fragments in his book of Coptic Athanasiana, and then in 1984 Coquin published another long fragment.3 These served as the basis for my 1995 translation and my 1994 article in this journal on the social context of canon formation in fourth-century Egypt.4
Growth inhibitory effects of casein hydrolysates on human cancer cell lines
Authors: Phelan Martha , Aisling Aherne S. , O'Sullivan Dara , FitzGerald Richard J. , O'Brien Nora M.
Published: January 2010

The aim of this study was to investigate the effects of unhydrolysed/intact casein and eight different sodium casein hydrolysates(a–h) on the viability and growth of human cancer cell lines. Both human Jurkat T cells and Caco-2 cells were incubated with increasing concentrations of the test compounds (0·5–10% v/v) for 24 h. Cell viability was assessed using the MTT, lactate dehydrogenase (LDH) release and Trypan Blue assays. Cell growth was monitored using the MTT, Trypan Blue and Bromodeoxyuridine (BrdU) proliferation assays. Casein hydrolysates b, c and f had an inhibitory effect on the viability and growth of both cell lines. The casein hydrolysates did not negatively affect the membrane integrity of both Jurkat and Caco-2 cells. In Jurkat cells hydrolysates a and h had an inhibitory effect on DNA synthesis after 24 h, while in Caco-2 cells DNA synthesis was not affected. In conclusion, we found that the different casein hydrolysates had cell-specific effects which target particular functions within the cell. Overall, casein hydrolysates had no effect on membrane integrity while they had varied effects on mitochondrial activity and DNA synthesis in the different cell lines.
Simultaneous pasteurization and homogenization of human milk by combining heat and ultrasound: effect on milk quality
Authors: Czank Charles , Simmer Karen , Hartmann Peter E
Published: January 2010

The combination of ultrasound and heat (thermoultrasound) is an emerging food preservation technique that retains higher quantities of bioactive components compared with current thermal pasteurization practice, but has not yet been assessed for pasteurizing human milk. Artificially contaminated human milk samples were treated with ultrasound (20 kHz, 150 watts) with and without heating. The retention of four human milk proteins was quantified by biochemical assay and laser scattering particle sizing was used to determine the extent of homogenization. While ultrasonic treatment was effective at inactivating Escherichia coli (D4 °C=5·94 min), Staphylococcus epidermidis exhibited resistance (D4 °C=16·01 min). Thermoultrasonic treatment was considerably more effective (Esch. coli D45 °C=1·74 min, D50 °C=0·89 min; Staph. epidermidis D45 °C=2·08 min, D50 °C=0·94 minutes) with a predicted retention (2·8 min treatment, 50°C) of secretory IgA lysozyme, lactoferrin and bile salt stimulated lipase of 91, 80, 77, and 45%, respectively. Homogenization of the milk samples occurred after 5 min and 2 min of ultrasonic and thermoultrasonic treatment, respectively. Thermoultrasonic treatment is an effective method for pasteurizing donor human milk and retaining a greater proportion of bioactive components compared with current practices. However, further studies are required to assess the practicality of applying this technique routinely to donor human milk.
Study on the combined effects of essential oils on microbiological quality of Fior di Latte cheese
Authors: Gammariello Daniela , Conte Amalia , Attanasio Massimiliano , Alessandro Del Nobile Matteo
Published: January 2010

The effectiveness of three natural compounds in slowing down the deterioration of microbial quality of Fior di latte cheese is addressed. In particular, the control of the growth of spoilage microorganisms and the determination of the Microbiological Stability Limit (MAL) were the main goals. A Central Composite Design (CCD) strategy was adopted to highlight possible combined effects between three essential oils: sage and two types of lemon. Results showed an increase in the MAL value for all cheese samples packaged with the antimicrobial compounds, compared with the control cheese. Moreover, the combinations of the three essential oils indicated that the substances can act in a synergistic or antagonistic way, depending on their concentrations. In particular, a synergistic effect was evident when the three compounds were used at about 3000 ppm.
Blocker filtering low-noise amplifier for SAW-less Bluetooth receiver system
Authors: Seo Heesong , Song Hyejeong , Park Changjoon , Yoon Jehyung , Choi Inyoung , Kim Bumman
Published: January 2010

A 2.4 GHz CMOS blocker filtering low-noise amplifier (BF-LNA) suitable for Bluetooth™ application is presented. The circuit employs a differential amplifier topology with a current mirror active load and a notch filter. Each path amplifies differentially with the common mode input signal, but there is a notch filter rejecting only the wanted signal at one path. By subtracting the two signals from each path, the large interferers are rejected and only the wanted signal is amplified. Therefore, it becomes a narrow-band amplifier with blocker filtering capability, realizing a receiver system without need of the off-chip SAW filter. The BF-LNA is designed using a 0.13-μm CMOS process. The measured performances are a gain of 11.4 dB, and a noise figure of 1.85 dB. Attenuation levels at 400 MHz apart from the target frequency are −13 and −29 dBc at each sideband. The P1dB,in and IIP3 are −8.2 and 1.46 dBm, respectively. The proposed BF-LNA can reject large interferers at the front-end of the receiver system with a good noise figure.
Investigating the southern daytime midlatitude trough's relation with the daytime Weddell Sea Anomaly during equinoxes
Authors: Horvath Ildiko , Lovell Brian C.
Published: January 2010

A detailed study with statistical investigations was conducted on the morning topside ionosphere for the 1996/1997 equinoctial period utilizing Defense Meteorological Satellite Program data and coupled thermosphere‐ionosphere plasmasphere wind simulations. Highly structured plasma densities, including a daytime Weddell Sea Anomaly (WSA; about 0900 LT) over the southeastern Pacific and localized high‐latitude plasma enhancements (about 0800 LT) in the Australian sector, were tracked. Poleward and equatorward winds, respectively, were strongest there. High‐resolution regional surface maps and field‐aligned profiles tracked their thermal structures, O+ and H+ composition, vertical drifts (VZ, m/s) and horizontal plasma flows {FY; [i+/(cm2s)]}. A daytime heavy‐ion (Ni‐O+) stagnation trough [(54.5 ± 4.5)°S; geomagnetic] appeared equatorward of both the WSA [60.0 ± 4.0)°S (center), 185–310°E; geographic] and these enhancements [>(62.0 ± 3.5)°S; 30–180°E]. Meanwhile, the plasmapause developed poleward of the WSA and equatorward of these enhancements. Plasma convection became significantly increased by enhanced electron temperatures nearby upflows underlying localized plasma enhancements. Upflow velocities, modeled as about 694.5 m/s, shows close similarities to the actual direct measurements of about 700 m/s. Both slow and enhanced plasma convections promoted stagnation events and trough formation. However, regular trough features became significantly altered by the development of a downward dipping poleward wall in the WSA region and by the absence of regular trough walls in the region of localized plasma enhancements. Statistically, the trough and localized plasma enhancement locations varied linearly with magnetic activity and showed an equatorward movement with increasing activity. A rate of (0.026 ± 0.002)°S/nT for the trough and (0.067 ± 0.003)°S/nT for the localized plasma enhancements were modeled. This higher (approximately two times) rate of movement indicates the localized plasma enhancements' more responsiveness.
A satellite‐based method for monitoring seasonality in the overstory leaf area index of Siberian larch forest
Authors: Kobayashi Hideki , Delbart Nicolas , Suzuki Rikie , Kushida Keiji
Published: January 2010

Reliable monitoring of the leaf area index (LAI) is required to further understand the carbon, water, and energy cycles of forests. In this study, we proposed a new satellite‐based method to estimate the overstory LAI (LAIo) separately from the understory LAI (LAIu) for larch forests covering eastern Siberia. We modeled forest scenes representative of larch forest structure, with particular consideration of the typical clumped shoot structure of larch. Three‐dimensional radiative transfer simulations were then conducted under various forest conditions to establish the relationships between LAIo and seasonal increases in the normalized difference water index after leaf appearance. Model‐based sensitivity analyses indicated a maximum error of up to 26% under known noise levels. Averaged at the continental scale, total LAI from our estimates, the CYCLOPES version 3.1, and the Moderate Resolution Imaging Spectroradiometer MOD15 Collection 5 (main algorithm) showed similar ranges in summer. However, spatial pattern of LAI was slightly different, with smoother variability for CYCLOPES LAI. Our LAI and CYLOPES effective LAI reproduced a realistic seasonal variation with exact timing of spring increase in LAIo. The main drawbacks of MOD15 Collection 5 were unrealistically strong temporal variability, and the fact that LAI began to increase earlier than the overstory leaf appearance date. Overall, the results show that our new method is a good alternative to MOD15 Collection 5 and CYCLOPES, as it provides separate estimates of LAIo and LAIu and true LAI instead of effective LAI.
Resilience in urban socioecological systems: residential water management as a driver of biodiversity
Authors: Katti Madhusudan , Schleder Bradley
Published: January 2010

Cities are unique ecosystems where human social-economic-cultural activities prominently shape the landscape, influencing the distribution and abundance of other species, and consequent patterns of biodiversity. The long-term sustainability of cities is of increasing concern as they continue to grow, straining infrastructure and pushing against natural resources constraints. A key resource is water, esp. in the more rapidly urbanizing arid regions. Understanding water management is thus critical for a deeper theoretical understanding of urban ecosystems and for effective urban policy. Landscaping and irrigation at any urban residence is a product of local geophysical/ecological conditions, homeowners’ cultural preferences, socioeconomic status, neighborhood dynamics, zoning laws, and city/state/federal regulations. Since landscape structure and water availability are key determinants of habitat for other species, urban biodiversity is strongly driven by the outcome of interactions between these variables. Yet the relative importance of ecological variables vs human socioeconomic variables in driving urban biodiversity remains poorly understood. Here we analyze data from the Fresno Bird Count, a citizen science project in California’s Central Valley, to show that spatial variation in bird diversity is best explained by a multivariate model including significant negative correlations with % building and grass cover, and positive correlations with interactions between irrigation intensity, median family income, and grass height. We discuss implications of our findings for urban water management policies in general, and for Fresno’s planned switch to metering water use in 2013. Ecological theory, conservation, and urban policy all benefit if we recognize cities as coupled socioecological systems.
Limited Supermarket Availability Is Not Associated With Obesity Risk Among Participants in the Kansas WIC Program
Authors: Ford Paula B. , Dzewaltowski David A.
Published: January 2010

Socioecological theory and a growing body of research suggests that geographic, racial, ethnic, and socioeconomic disparities in the prevalence of obesity are linked to disparities in the availability of food retail outlets that provide healthy food options. We examined the availability of food stores for low‐income women in Kansas and tested whether food store availability was associated with obesity using cross‐sectional, geocoded data from women participating in the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) (n = 21,166) in Kansas. The availability and density of food stores within a 1, 3, and 5 mile radius of residence was determined, and multivariate logistic regression was used to examine the association of food store availability with obesity. The availability of convenience, grocery stores, and supermarkets varied across the urban–rural continuum, but the majority of WIC recipients lived within a 1 mile radius of a small grocery store. WIC participants in micropolitan areas had the greatest availability of food stores within a 1 mile radius of residence. Availability and density of food stores was not associated with obesity in metropolitan and rural areas, but availability and density of any type of food store was associated with an increased risk of obesity among WIC recipients in micropolitan areas. These results suggest that limited spatial availability of grocery stores and supermarkets does not contribute to obesity risk among low‐income WIC recipients in Kansas, and that urban influence moderates the contribution of food environments to obesity.
Conjugated polymers for high-efficiency organic photovoltaics
Authors: Zhan Xiaowei , Zhu Daoben
Published: January 2010

In this review we summarize the most recent developments in conjugated polymers for high-efficiency organic photovoltaic devices. We focus on correlations of polymer chemical structures with properties, which may guide rational structural design and evaluation of photovoltaic materials.
Significant Determinants of Isotope Composition During HI/Pred Synthesis of Methamphetamine
Authors: David Gabrielle E. , Hibbert D. Brynn , Frew Russell D. , Hayman Alan R.
Published: January 2010

Methamphetamine HCl was synthesized using three variations of the hydriodic acid/red phosphorus (HI/Pred) synthetic route. A Plackett-Burman experimental design was used to determine how reaction parameters affected the isotopic composition of the product. Isotope ratio mass spectrometry results showed only the source of precursor 13C was significant in determining product δ
13C; the manufacturer, reaction temperature, time, scale, and source of HI were not significant. The precursor was also the main determinant of product δ
2H, with smaller contributions from the HI source for one method. From precursor to product, large δ
2H depletion occurred for most samples. Deuterium nuclear magnetic resonance spectroscopy (2H NMR) was used to investigate the specific site of this. Significant fraction of deuterium was observed only at the benzylic position, the site of hydrogen addition during synthesis. Methamphetamine synthesized from ephedrine was shown to be depleted in this position.
Multiplexed transposon-mediated stable gene transfer in human cells
Authors: Kahlig Kristopher M. , Saridey Sai K. , Kaja Aparna , Daniels Melissa A. , George Alfred L. , Wilson Matthew H.
Published: January 2010

Generation of cultured human cells stably expressing one or more recombinant gene sequences is a widely used approach in biomedical research, biotechnology, and drug development. Conventional methods are not efficient and have severe limitations especially when engineering cells to coexpress multiple transgenes or multiprotein complexes. In this report, we harnessed the highly efficient, nonviral, and plasmid-based
piggyBac
transposon system to enable concurrent genomic integration of multiple independent transposons harboring distinct protein-coding DNA sequences. Flow cytometry of cell clones derived from a single multiplexed transfection demonstrated approximately 60% (three transposons) or approximately 30% (four transposons) stable coexpression of all delivered transgenes with selection for a single marker transposon. We validated multiplexed
piggyBac
transposon delivery by coexpressing large transgenes encoding a multisubunit neuronal voltage-gated sodium channel (SCN1A) containing a pore-forming subunit and two accessory subunits while using two additional genes for selection. Previously unobtainable robust sodium current was demonstrated through 38 passages, suitable for use on an automated high-throughput electrophysiology platform. Cotransfection of three large (up to 10.8 kb)
piggyBac
transposons generated a heterozygous SCN1A stable cell line expressing two separate alleles of the pore-forming subunit and two accessory subunits (total of four sodium channel subunits) with robust functional expression. We conclude that the
piggyBac
transposon system can be used to perform multiplexed stable gene transfer in cultured human cells, and this technology may be valuable for applications requiring concurrent expression of multiprotein complexes.
Detailed level-by-level study of dielectronic recombination for Ne-like gold
Authors: Yang J H , Cheng X L , Deng B L
Published: January 2010

Ab initio calculation of the dielectronic recombination (DR) rate coefficient for Ne-like gold in the ground state 2s22p6 is performed. The value of DR rate coefficient has been calculated over a wide temperature range from 1 to 105 eV. The present level-by-level calculations include the contributions of all the levels belonging to the following Na-like doubly excited configuration complexes, namely, 2s22p53ln′l′, 2s12p63ln′l′ (n′⩽12, l′⩽8), 2s22p54ln′l′, 2s12p64ln′l′ (n′=4, 5) and 1s12s22p63l3l′. There are 18 853 doubly excited levels in all these complexes. The contributions of 2s22p53ln′l′ and 2s12p63ln′l′ for n′>12 are evaluated by applying the complex-by-complex n′−3 extrapolation method, which are found to represent at most 3 and 0.04% of the total DR rate coefficient, respectively. The contribution of complex series 2s22p53ln′l′ is a little more than 90% to the total DR rate coefficient. The contributions of 2s12p63ln′l′, 2s22p54ln′l′ and 2s12p64ln′l′ complexes are about 2, 6 and 1%, respectively. The DR contributions of 2s22p53ln′l′ and 2s12p63ln′l′ complexes with l′>6 are found to be negligible (about 0.6 and 0.8%). For complex series 2s22p53ln′l′, the dominant contribution comes from the lowest complex 2s22p53l3l′ at all temperatures. For complex series 2s12p63ln′l′, the dominant contribution comes from the 2s12p63l3l′ complex at low and medium electron temperature (kT
e<10 keV), while at higher electron temperature (kT
e>10 keV) the contribution of 2s12p63l4l′ complex becomes larger. For complex series 2s22p54ln′l′ and 2s12p64ln′l′, the contribution from n′=5 complex exceeds the contribution from n′=4 complex at about 2000 eV. The effects of radiative decays to autoionizing levels possibly followed by radiative cascades (DAC) are checked for the (2s2p)73l3l′ and (2s2p)73l4l′ complexes and found to be negligible. The total DR rate coefficient is fitted to an empirical formula.
Fate Specification and Tissue-specific Cell Cycle Control of the Caenorhabditis elegans Intestine
Authors: Segref Alexandra , Cabello Juan , Clucas Caroline , Schnabel Ralf , Johnstone Iain L.
Published: January 2010

Coordination between cell fate specification and cell cycle control in multicellular organisms is essential to regulate cell numbers in tissues and organs during development, and its failure may lead to oncogenesis. In mammalian cells, as part of a general cell cycle checkpoint mechanism, the F-box protein β-transducin repeat-containing protein (β-TrCP) and the Skp1/Cul1/F-box complex control the periodic cell cycle fluctuations in abundance of the CDC25A and B phosphatases. Here, we find that the Caenorhabditis elegans β-TrCP orthologue LIN-23 regulates a progressive decline of CDC-25.1 abundance over several embryonic cell cycles and specifies cell number of one tissue, the embryonic intestine. The negative regulation of CDC-25.1 abundance by LIN-23 may be developmentally controlled because CDC-25.1 accumulates over time within the developing germline, where LIN-23 is also present. Concurrent with the destabilization of CDC-25.1, LIN-23 displays a spatially dynamic behavior in the embryo, periodically entering a nuclear compartment where CDC-25.1 is abundant.
Distinct and Temporal Roles of Nucleosomal Remodeling and Histone Deacetylation in the Repression of the hTERT Gene
Authors: Wang Shuwen , Hu Chunguang , Zhu Jiyue
Published: January 2010

hTERT, the human telomerase reverse transcriptase, is highly expressed in stem cells and embryonic tissues but undetectable in most adult somatic cells. To understand its repression mechanisms in somatic cells, we investigated the endogenous hTERT gene regulation during differentiation of human leukemic HL60 cells. Our study revealed that silencing of the hTERT promoter was a biphasic process. Within 24 h after initiation of differentiation, hTERT mRNA expression decreased dramatically, accompanied by increased expression of Mad1 gene and disappearance of a nucleosome-free region at the hTERT core promoter. Subsequent to this early repression, nucleosomal remodeling continued at the promoter and downstream region for several days, as demonstrated by micrococcal nuclease and restriction enzyme accessibility assays. This later nucleosomal remodeling correlated with stable silencing of the hTERT promoter. Progressive changes of core histone modifications occurred throughout the entire differentiation process. Surprisingly, inhibition of histone deacetylation at the hTERT promoter did not prevent hTERT repression or nucleosomal deposition, indicating that nucleosomal deposition at the core promoter, but not histone deacetylation, was the cause of transcriptional repression. Our data also suggested that succeeding nucleosomal remodeling and histone deacetylation worked in parallel to establish the stable repressive status of hTERT gene in human somatic cells.
Numb Independently Antagonizes Sanpodo Membrane Targeting and Notch Signaling in Drosophila Sensory Organ Precursor Cells
Authors: Tong Xin , Zitserman Diana , Serebriiskii Ilya , Andrake Mark , Dunbrack Roland , Roegiers Fabrice
Published: January 2010

In Drosophila , mitotic neural progenitor cells asymmetrically segregate the cell fate determinant Numb in order to block Notch signaling in only one of the two daughter cells. Sanpodo, a membrane protein required for Notch signaling in asymmetrically dividing cells, is sequestered from the plasma membrane to intracellular vesicles in a Numb-dependent way after neural progenitor cell mitosis. However, the significance of Numb-dependent Sanpodo regulation is unclear. In this study, we conducted a structure–function analysis to identify the determinants of Sanpodo targeting in vivo. We identified an NPAF motif in the amino-terminal cytoplasmic tail of Sanpodo, which is conserved among insect Sanpodo homologues. The Sanpodo NPAF motif is predicted to bind directly to the Numb phosphotyrosine-binding domain and is critical for Numb binding in vitro. Deletion or mutation of the NPAF motif results in accumulation of Sanpodo at the plasma membrane in Numb-positive cells in vivo. Genetic analysis of Sanpodo NPAF mutants shows that Numb-dependent Sanpodo endocytic targeting can be uncoupled from Notch signaling regulation. Our findings demonstrate that Sanpodo contains an evolutionarily conserved motif that has been linked to Numb-dependent regulation in vertebrates and further support the model that Numb regulates Notch signaling independently of Sanpodo membrane trafficking in neural progenitor cells.
Bioinformatics challenges for genome-wide association studies
Authors: Moore Jason H. , Asselbergs Folkert W. , Williams Scott M.
Published: January 2010

Motivation: The sequencing of the human genome has made it possible to identify an informative set of >1 million single nucleotide polymorphisms (SNPs) across the genome that can be used to carry out genome-wide association studies (GWASs). The availability of massive amounts of GWAS data has necessitated the development of new biostatistical methods for quality control, imputation and analysis issues including multiple testing. This work has been successful and has enabled the discovery of new associations that have been replicated in multiple studies. However, it is now recognized that most SNPs discovered via GWAS have small effects on disease susceptibility and thus may not be suitable for improving health care through genetic testing. One likely explanation for the mixed results of GWAS is that the current biostatistical analysis paradigm is by design agnostic or unbiased in that it ignores all prior knowledge about disease pathobiology. Further, the linear modeling framework that is employed in GWAS often considers only one SNP at a time thus ignoring their genomic and environmental context. There is now a shift away from the biostatistical approach toward a more holistic approach that recognizes the complexity of the genotype–phenotype relationship that is characterized by significant heterogeneity and gene–gene and gene–environment interaction. We argue here that bioinformatics has an important role to play in addressing the complexity of the underlying genetic basis of common human diseases. The goal of this review is to identify and discuss those GWAS challenges that will require computational methods.

Contact:  jason.h.moore@dartmouth.edu
Role of the Host-Selective ACT-Toxin Synthesis Gene ACTTS2 Encoding an Enoyl-Reductase in Pathogenicity of the Tangerine Pathotype of Alternaria alternata
Authors: Ajiro Naoya , Miyamoto Yoko , Masunaka Akira , Tsuge Takashi , Yamamoto Mikihiro , Ohtani Kouhei , Fukumoto Takeshi , Gomi Kenji , Peever Tobin L. , Izumi Yuriko , Tada Yasuomi , Akimitsu Kazuya
Published: January 2010

The tangerine pathotype of Alternaria alternata produces host-selective ACT-toxin and causes Alternaria brown spot disease of tangerines and tangerine hybrids. Sequence analysis of a genomic BAC clone identified a previously uncharacterized portion of the ACT-toxin biosynthesis gene cluster (ACTT). A 1,034-bp gene encoding a putative enoyl-reductase was identified by using rapid amplification of cDNA ends and polymerase chain reaction and designated ACTTS2. Genomic Southern blots demonstrated that ACTTS2 is present only in ACT-toxin producers and is carried on a 1.9 Mb conditionally dispensable chromosome by the tangerine pathotype. Targeted gene disruption of ACTTS2 led to a reduction in ACT-toxin production and pathogenicity, and transcriptional knockdown of ACTTS2 using RNA silencing resulted in complete loss of ACT-toxin production and pathogenicity. These results indicate that ACTTS2 is an essential gene for ACT-toxin biosynthesis in the tangerine pathotype of A. alternata and is required for pathogenicity of this fungus.
Variation in Competitive Ability Among Isolates ofAspergillus flavusfrom Different Vegetative Compatibility Groups During Maize Infection
Authors: Mehl H. L. , Cotty P. J.
Published: January 2010

Aspergillus flavus, the primary causal agent of aflatoxin contamination, includes many genetically diverse vegetative compatibility groups (VCGs). Competitive ability during infection of living maize kernels was quantified for isolates from 38 VCGs. Kernels were inoculated with both a common VCG, CG136, and another VCG; after 7 days (31°C), conidia were washed from kernels, and aflatoxins and DNA were extracted from kernels and conidia separately. CG136-specific single-nucleotide polymorphisms were quantified by pyrosequencing; VCGs co-inoculated with CG136 produced 46 to 85 and 51 to 84% of A. flavus DNA from kernels and conidia, respectively. Co-inoculation with atoxigenic isolates reduced aflatoxin up to 90% and, in some cases, more than predicted by competitive exclusion alone. Conidia contained up to 42 ppm aflatoxin B1, indicating airborne conidia as potentially important sources of environmental exposure. Aflatoxin-producing potential and sporulation were negatively correlated. For some VCGs, sporulation during co-infection was greater than that predicted by kernel infection, suggesting that some VCGs increase dispersal while sacrificing competitive ability during host tissue colonization. The results indicate both life strategy and adaptive differences among A. flavus isolates and provide a basis for selection of biocontrol strains with improved competitive ability, sporulation, and aflatoxin reduction on target hosts.
Divergence Between Sympatric Rice- and Maize-Infecting Populations of Rhizoctonia solani AG-1 IA from Latin America
Authors: González-Vera A. D. , Bernardes-de-Assis J. , Zala M. , McDonald B. A. , Correa-Victoria F. , Graterol-Matute E. J. , Ceresini P. C.
Published: January 2010

The basidiomycetous fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice. Particularly in Venezuela, the fungus also causes banded leaf and sheath blight (BLSB) on maize, which is considered an emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent fields. Our goals in this study were to elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination. In total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Portuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriquí State) were genotyped using 10 microsatellite loci. Allopatric populations from Venezuela, Colombia, and Panama were significantly differentiated (ΦST of 0.16 to 0.34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% was distributed geographically among the sympatric Venezuelan fields. We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela. Rice- and maize-derived isolates were able to infect both rice and maize but were more aggressive on their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with migration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago. Our findings also suggest that maize-infecting populations have a mainly recombining reproductive system whereas the rice-infecting populations have a mixed reproductive system in Latin America.
Resistance to Fusarium Head Blight and Seedling Blight in Wheat Is Associated with Activation of a Cytochrome P450 Gene
Authors: Li X. , Zhang J. B. , Song B. , Li H. P. , Xu H. Q. , Qu B. , Dang F. J. , Liao Y. C.
Published: January 2010

One plant genotype displays a resistance phenotype at one development stage but a susceptible reaction to the same pathogen at another stage, which is referred to here as resistance inversion. In wheat, Fusarium head blight (FHB)-resistant cv. Sumai3 showed a Fusarium seedling blight (FSB)-susceptible reaction whereas FHB-susceptible cv. Annong8455 exhibited FSB resistance when challenged with a Fusarium asiaticum strain that produces deoxynivalenol (DON). The resistance to FHB and FSB in wheat was closely associated with expression of a plant cytochrome P450 gene in response to FHB pathogens and mycotoxins. Quantitative real-time polymerase chain reaction analyses showed that expression of nine defense-related genes in spikes and seedlings was induced by the fungal infection, in which a massive accumulation of a plant cytochrome P450 gene, CYP709C1, was clearly associated with the resistance reaction in both seedling and spike. The FHB-resistant Sumai3 accumulated 7-fold more P450 transcripts than did the FHB-susceptible Annong8455, while 84-fold more P450 transcripts were accumulated in the FSB-resistant Annong8455 than the FSB-susceptible Sumai3. A Fusarium strain with a disrupted Tri5 gene, which is not able to produce the first enzyme essential for trichothecene mycotoxin biosynthesis, also induced more P450 transcripts in FHB- and FSB-resistant cultivars. The fungal activation of the P450 gene was more profound in the FSB-resistant reaction than the FHB-resistant reaction relative to their susceptible counterparts. DON triggered a differential expression of the P450 gene with comparable patterns in spikes and seedlings in a resistance-dependent manner. These results may provide a basis for dissecting mechanisms underlying FHB and FSB resistance reactions in wheat and revealing functions of the cytochrome P450 in plant detoxification and defense.
Nucleosome landscape and control of transcription in the human malaria parasite
Authors: Ponts Nadia , Harris Elena Y. , Prudhomme Jacques , Wick Ivan , Eckhardt-Ludka Colleen , Hicks Glenn R. , Hardiman Gary , Lonardi Stefano , Le Roch Karine G.
Published: January 2010

In eukaryotic cells, chromatin reorganizes within promoters of active genes to allow the transcription machinery and various transcription factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum, specific transcription factors are apparently underrepresented with regards to the size of the genome, and mechanisms underlying transcriptional regulation are controversial. Here, we investigate the modulation of DNA accessibility by chromatin remodeling during the parasite infection cycle. We have generated genome-wide maps of nucleosome occupancy across the parasite erythrocytic cycle using two complementary assays—the formaldehyde-assisted isolation of regulatory elements to extract protein-free DNA (FAIRE) and the MNase-mediated purification of mononucleosomes to extract histone-bound DNA (MAINE), both techniques being coupled to high-throughput sequencing. We show that chromatin architecture undergoes drastic upheavals throughout the parasite's cycle, contrasting with targeted chromatin reorganization usually observed in eukaryotes. Chromatin loosens after the invasion of the red blood cell and then repacks prior to the next cycle. Changes in nucleosome occupancy within promoter regions follow this genome-wide pattern, with a few exceptions such as the var genes involved in virulence and genes expressed at early stages of the cycle. We postulate that chromatin structure and nucleosome turnover control massive transcription during the erythrocytic cycle. Our results demonstrate that the processes driving gene expression in Plasmodium challenge the classical eukaryotic model of transcriptional regulation occurring mostly at the transcription initiation level.
Medicinal plants of Erute county, Lira district, Uganda with particular reference to their conservation
Authors: Oryema Christine , Ziraba Remigius Bukenya , Omagor Nelson , Opio Alfonse
Published: January 2010

A medicinal plant study was carried out in eighteen parishes and 54 villages of Erute county, Lira district, Uganda. Parishes and villages were selected using stratified random sampling techniques. Questionnaires, interviews and discussions with the local people were used to obtain information on the names of the plants, their medicinal uses and conservation methods. The number of the medicinal plants species used was 180 belonging to 144 genera and 57 families of flowering plants. The major families recorded for medicinal purpose included Fabaceae (37 species), Asteraceae (26 species), Euphorbiaceae (eleven species), Vitaceae (eight species), Verbenaceae (seven species), Poaceae (six species), Solanaceae (five species), and Rubiaceae (four species). There is a need for putting in place measures to conserve these plants. Unfortunately, most of the healers or users were not interested in cultivation of the plants. The situation could worsen with the social changes and demand for land for agriculture in the district.
A low oxygen consumption pneumatic ventilator for emergency construction during a respiratory failure pandemic*
Authors: Williams D. , Flory S. , King R. , Thornton M. , Dingley J.
Published: January 2010

The UK influenza pandemic plan predicts up to 750 000 additional deaths with hospitals prioritising patients against inadequate resources. We investigated three prototype low‐cost, gas‐efficient, pneumatic ventilators in a test lung model at different compliance and rate settings. Mean (SD) oxygen consumption was 0.913 (0.198) and 1.119 (0.267) l.min−1 at tidal volumes of 500 ml and 700 ml respectively. Values of FIo2 increased marginally as lung compliance reduced, reflecting the increased ventilator workload and consequent increased enrichment of breathing gas by waste oxygen from the pneumatic mechanism. We also demonstrated that a stable nitric oxide concentration could be delivered by this design following volumetric principles. It is possible to make a gas‐efficient ventilator costing less than £200 from industrial components for use where oxygen is available at 2‐4 bar, with no pressurised air or electrical requirements. Such a device could be mass‐produced for crises characterised by an overwhelming demand for mechanical ventilation and a limited oxygen supply.
Construction of integrated genetic linkage maps of the tiger shrimp (Penaeus monodon) using microsatellite and AFLP markers
Authors: You E.‐M. , Liu K.‐F. , Huang S.‐W. , Chen M. , Groumellec M. L. , Fann S.‐J. , Yu H.‐T.
Published: January 2010

The linkage maps of male and female tiger shrimp (P. monodon) were constructed based on 256 microsatellite and 85 amplified fragment length polymorphism (AFLP) markers. Microsatellite markers obtained from clone sequences of partial genomic libraries, tandem repeat sequences from databases and previous publications and fosmid end sequences were employed. Of 670 microsatellite and 158 AFLP markers tested for polymorphism, 341 (256 microsatellite and 85 AFLP markers) were used for genotyping with three F1 mapping panels, each comprising two parents and more than 100 progeny. Chi‐square goodness‐of‐fit test (χ2) revealed that only 19 microsatellite and 28 AFLP markers showed a highly significant segregation distortion (P < 0.005). Linkage analysis with a LOD score of 4.5 revealed 43 and 46 linkage groups in male and female linkage maps respectively. The male map consisted of 176 microsatellite and 49 AFLP markers spaced every ∼11.2 cM, with an observed genome length of 2033.4 cM. The female map consisted of 171 microsatellite and 36 AFLP markers spaced every ∼13.8 cM, with an observed genome length of 2182 cM. Both maps shared 136 microsatellite markers, and the alignment between them indicated 38 homologous pairs of linkage groups including the linkage group representing the sex chromosome. The karyotype of P. monodon is also presented. The tentative assignment of the 44 pairs of P. monodon haploid chromosomes showed the composition of forty metacentric, one submetacentric and three acrocentric chromosomes. Our maps provided a solid foundation for gene and QTL mapping in the tiger shrimp.