bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
Authors: Greenblum Sharon , Turnbaugh Peter J. , Borenstein Elhanan
Published: December 2011

The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short of providing a comprehensive understanding of the impact of this variation on the community and on the host. Here, we introduce a
metagenomic systems biology
computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic networks. Focusing on the gut microbiome, we analyze fecal metagenomic data from 124 unrelated individuals, as well as six monozygotic twin pairs and their mothers, and generate community-level metabolic networks of the microbiome. Placing variations in gene abundance in the context of these networks, we identify both gene-level and network-level topological differences associated with obesity and inflammatory bowel disease (IBD). We show that genes associated with either of these host states tend to be located at the periphery of the metabolic network and are enriched for topologically derived metabolic “inputs.” These findings may indicate that lean and obese microbiomes differ primarily in their interface with the host and in the way they interact with host metabolism. We further demonstrate that obese microbiomes are less modular, a hallmark of adaptation to low-diversity environments. We additionally link these topological variations to community species composition. The system-level approach presented here lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health.
Curvature-driven capillary migration and assembly of rod-like particles
Authors: Cavallaro Marcello , Botto Lorenzo , Lewandowski Eric P. , Wang Marisa , Stebe Kathleen J.
Published: December 2011

Capillarity can be used to direct anisotropic colloidal particles to precise locations and to orient them by using interface curvature as an applied field. We show this in experiments in which the shape of the interface is molded by pinning to vertical pillars of different cross-sections. These interfaces present well-defined curvature fields that orient and steer particles along complex trajectories. Trajectories and orientations are predicted by a theoretical model in which capillary forces and torques are related to Gaussian curvature gradients and angular deviations from principal directions of curvature. Interface curvature diverges near sharp boundaries, similar to an electric field near a pointed conductor. We exploit this feature to induce migration and assembly at preferred locations, and to create complex structures. We also report a repulsive interaction, in which microparticles move away from planar bounding walls along curvature gradient contours. These phenomena should be widely useful in the directed assembly of micro- and nanoparticles with potential application in the fabrication of materials with tunable mechanical or electronic properties, in emulsion production, and in encapsulation.
Sucrose synthase activity in the
sus1/sus2/sus3/sus4 Arabidopsis
mutant is sufficient to support normal cellulose and starch production
Authors: Baroja-Fernández Edurne , Muñoz Francisco José , Li Jun , Bahaji Abdellatif , Almagro Goizeder , Montero Manuel , Etxeberria Ed , Hidalgo Maite , Sesma María Teresa , Pozueta-Romero Javier
Published: December 2011

Sucrose synthase (SUS) catalyzes the reversible conversion of sucrose and a nucleoside diphosphate into the corresponding nucleoside diphosphate-glucose and fructose. In
Arabidopsis
, a multigene family encodes six SUS (SUS1-6) isoforms. The involvement of SUS in the synthesis of UDP-glucose and ADP-glucose linked to
Arabidopsis
cellulose and starch biosynthesis, respectively, has been questioned by Barratt et al. [(2009)
Proc Natl Acad Sci USA
106:13124–13129], who showed that (
i
) SUS activity in wild type (WT) leaves is too low to account for normal rate of starch accumulation in
Arabidopsis
, and (
ii
) different organs of the
sus1/sus2/sus3/sus4
SUS mutant impaired in SUS activity accumulate WT levels of ADP-glucose, UDP-glucose, cellulose and starch. However, these authors assayed SUS activity under unfavorable pH conditions for the reaction. By using favorable pH conditions for assaying SUS activity, in this work we show that SUS activity in the cleavage direction is sufficient to support normal rate of starch accumulation in WT leaves. We also demonstrate that
sus1/sus2/sus3/sus4
leaves display WT
SUS5
and
SUS6
expression levels, whereas leaves of the
sus5/sus6
mutant display WT
SUS1
–
4
expression levels. Furthermore, we show that SUS activity in leaves and stems of the
sus1/sus2/sus3/sus4
and
sus5/sus6
plants is ∼85% of that of WT leaves, which can support normal cellulose and starch biosynthesis. The overall data disprove Barratt et al. (2009) claims, and are consistent with the possible involvement of SUS in cellulose and starch biosynthesis in
Arabidopsis
.
Identification of diverse modulators of central and peripheral circadian clocks by high-throughput chemical screening
Authors: Chen Zheng , Yoo Seung-Hee , Park Yong-Sung , Kim Keon-Hee , Wei Shuguang , Buhr Ethan , Ye Zeng-You , Pan Hui-Lin , Takahashi Joseph S.
Published: December 2011

The circadian clock coordinates daily oscillations of essential physiological and behavioral processes. Conversely, aberrant clocks with damped amplitude and/or abnormal period have been associated with chronic diseases and aging. To search for small molecules that perturb or enhance circadian rhythms, we conducted a high-throughput screen of approximately 200,000 synthetic compounds using
Per2∷lucSV
reporter fibroblast cells and validated 11 independent classes of molecules with
Bmal1:luciferase
reporter cells as well as with suprachiasmatic nucleus and peripheral tissue explants. Four compounds were found to lengthen the period in both central and peripheral clocks, including three compounds that inhibited casein kinase I
ε
in vitro and a unique benzodiazepine derivative acting through a non-GABA
A
receptor target. In addition, two compounds acutely induced
Per2∷lucSV
reporter bioluminescence, delayed the rhythm, and increased intracellular cAMP levels, but caused rhythm damping. Importantly, five compounds shortened the period of peripheral clocks; among them, four compounds also enhanced the amplitude of central and/or peripheral reporter rhythms. Taken together, these studies highlight diverse activities of drug-like small molecules in manipulating the central and peripheral clocks. These small molecules constitute a toolbox for probing clock regulatory mechanisms and may provide putative lead compounds for treatment of clock-associated diseases.
Global risk of big earthquakes has not recently increased
Authors: Shearer Peter M. , Stark Philip B.
Published: December 2011

The recent elevated rate of large earthquakes has fueled concern that the underlying global rate of earthquake activity has increased, which would have important implications for assessments of seismic hazard and our understanding of how faults interact. We examine the timing of large (magnitudeM≥7) earthquakes from 1900 to the present, after removing local clustering related to aftershocks. The global rate ofM≥8 earthquakes has been at a record high roughly since 2004, but rates have been almost as high before, and the rate of smaller earthquakes is close to its historical average. Some features of the global catalog are improbable in retrospect, but so are some features of most random sequences—if the features are selected after looking at the data. For a variety of magnitude cutoffs and three statistical tests, the global catalog, with local clusters removed, is not distinguishable from a homogeneous Poisson process. Moreover, no plausible physical mechanism predicts real changes in the underlying global rate of large events. Together these facts suggest that the global risk of large earthquakes is no higher today than it has been in the past.
Credit use: Psychological perspectives on a multifaceted phenomenon
Authors: Kamleitner Bernadette , Hoelzl Erik , Kirchler Erich
Published: December 2011

Consumer borrowing is a highly topical and multifaceted phenomenon as well as a popular subject for study. We focus on consumer credit use and review the existing literature. To categorize what is known we identify four main psychological perspectives on the phenomenon: credit use as (1) a reflection of the situation, (2) a reflection of the person, (3) a cognitive process, and (4) a social process. On top of these perspectives we view credit use as a process that entails three distinct phases: (1) processes before credit acquisition, (2) processes at credit acquisition, and (3) processes after credit acquisition. We review the international literature along a two‐tier structure that aligns the psychological perspectives with a process view of credit. This structure allows us to identify systematic concentrations as well as gaps in the existing research. We consolidate what is known within each perspective and identify what seems to be most urgently missing. Some of the most important gaps relate to research studying credit acquisition from the perspective of credit use as a reflection of the person or as a social process. In particular, research on credit use as a reflection of the person appears to focus exclusively on the first stage of the credit process. We conclude with a discussion that reaches across perspectives and identifies overarching gaps, trends, and open questions. We highlight a series of implicit linkages between perspectives and the geographical regions in which studies related to the perspectives were conducted. Beyond diagnosing a geographical imbalance of research, we argue for future research that systematically addresses interrelations between perspectives. We conclude with a set of global implications and research recommendations.
Interactions between Desert Pupfish and Gila Topminnow Can Affect Reintroduction Success
Authors: Robinson Anthony T. , Ward David L.
Published: December 2011

In fisheries, recovery actions for species of concern sometimes involve reintroductions of multiple species. As an example, desert pupfish Cyprinodon macularius and Gila topminnow Poeciliopsis occidentalis historically had sympatric distributions and inhabited similar environments, and they are often reintroduced into the same waters. Success of these stockings has varied greatly, and a hypothesis developed among conservationists that desert pupfish populations were more likely to establish and persist if they were stocked first and allowed to establish before Gila topminnow were stocked. We examined historical records of desert pupfish reintroductions and conducted laboratory experiments to evaluate this hypothesis. For the reintroductions, we evaluated 29 ponds where four general stocking strategies (treatments) were implemented: (1) only desert pupfish were stocked, (2) desert pupfish were stocked first and allowed to establish and then Gila topminnow were stocked, (3) both desert pupfish and Gila topminnow were stocked simultaneously, and (4) Gila topminnow were stocked first and allowed to establish before desert pupfish were stocked. Desert pupfish established populations and persisted in 100% of desert pupfish-only and desert pupfish-first ponds and 57% of simultaneous-stocking and Gila topminnow-first ponds. In laboratory experiments utilizing 2.4-m-diameter tanks, the same four treatments plus one additional treatment (in which only Gila topminnow were stocked) were implemented; each treatment was replicated four times. Desert pupfish abundance increased in 75% of the desert pupfish-only trials and 50% of the desert pupfish-first trials but decreased in 75% of simultaneous-stocking trials and 100% of Gila topminnow-first trials. Gila topminnow increased in abundance in all treatments and trials but increased the least when desert pupfish were stocked first. Our results support the original hypothesis and emphasize the need to evaluate species interactions in multiple-species reintroductions. To increase success, desert pupfish should be stocked in isolation or stocked first and allowed to establish before Gila topminnow are stocked.

Received July 12, 2011; accepted August 30, 2011
Reconstituted synaptotagmin I mediates vesicle docking, priming, and fusion
Authors: Wang Zhao , Liu Huisheng , Gu Yiwen , Chapman Edwin R.
Published: December 2011

The synaptic vesicle protein synaptotagmin I (syt) promotes exocytosis via its ability to penetrate membranes in response to binding Ca2+ and through direct interactions with SNARE proteins. However, studies using full-length (FL) membrane-embedded syt in reconstituted fusion assays have yielded conflicting results, including a lack of effect, or even inhibition of fusion, by Ca2+. In this paper, we show that reconstituted FL syt promoted rapid docking of vesicles (<1 min) followed by a priming step (3–9 min) that was required for subsequent Ca2+-triggered fusion between v- and t-SNARE liposomes. Moreover, fusion occurred only when phosphatidylinositol 4,5-bisphosphate was included in the target membrane. This system also recapitulates some of the effects of syt mutations that alter synaptic transmission in neurons. Finally, we demonstrate that the cytoplasmic domain of syt exhibited mixed agonist/antagonist activity during regulated membrane fusion in vitro and in cells. Together, these findings reveal further convergence of reconstituted and cell-based systems.
Aurora A and Aurora B jointly coordinate chromosome segregation and anaphase microtubule dynamics
Authors: Hégarat Nadia , Smith Ewan , Nayak Gowri , Takeda Shunichi , Eyers Patrick A. , Hochegger Helfrid
Published: December 2011

We established a conditional deletion of Aurora A kinase (AurA) in Cdk1 analogue-sensitive DT40 cells to analyze AurA knockout phenotypes after Cdk1 activation. In the absence of AurA, cells form bipolar spindles but fail to properly align their chromosomes and exit mitosis with segregation errors. The resulting daughter cells exhibit a variety of phenotypes and are highly aneuploid. Aurora B kinase (AurB)–inhibited cells show a similar chromosome alignment problem and cytokinesis defects, resulting in binucleate daughter cells. Conversely, cells lacking AurA and AurB activity exit mitosis without anaphase, forming polyploid daughter cells with a single nucleus. Strikingly, inhibition of both AurA and AurB results in a failure to depolymerize spindle microtubules (MTs) in anaphase after Cdk1 inactivation. These results suggest an essential combined function of AurA and AurB in chromosome segregation and anaphase MT dynamics.
Desmosomal cadherins utilize distinct kinesins for assembly into desmosomes
Authors: Nekrasova Oxana E. , Amargo Evangeline V. , Smith William O. , Chen Jing , Kreitzer Geri E. , Green Kathleen J.
Published: December 2011

The desmosomal cadherins, desmogleins (Dsgs) and desmocollins (Dscs), comprise the adhesive core of intercellular junctions known as desmosomes. Although these adhesion molecules are known to be critical for tissue integrity, mechanisms that coordinate their trafficking into intercellular junctions to regulate their proper ratio and distribution are unknown. We demonstrate that Dsg2 and Dsc2 both exhibit microtubule-dependent transport in epithelial cells but use distinct motors to traffic to the plasma membrane. Functional interference with kinesin-1 blocked Dsg2 transport, resulting in the assembly of Dsg2-deficient junctions with minimal impact on distribution of Dsc2 or desmosomal plaque components. In contrast, inhibiting kinesin-2 prevented Dsc2 movement and decreased its plasma membrane accumulation without affecting Dsg2 trafficking. Either kinesin-1 or -2 deficiency weakened intercellular adhesion, despite the maintenance of adherens junctions and other desmosome components at the plasma membrane. Differential regulation of desmosomal cadherin transport could provide a mechanism to tailor adhesion strength during tissue morphogenesis and remodeling.
A complex of Protocadherin-19 and N-cadherin mediates a novel mechanism of cell adhesion
Authors: Emond Michelle R. , Biswas Sayantanee , Blevins Cheasequah J. , Jontes James D.
Published: December 2011

During embryonic morphogenesis, adhesion molecules are required for selective cell–cell interactions. The classical cadherins mediate homophilic calcium-dependent cell adhesion and are founding members of the large and diverse cadherin superfamily. The protocadherins are the largest subgroup within this superfamily, yet their participation in calcium-dependent cell adhesion is uncertain. In this paper, we demonstrate a novel mechanism of adhesion, mediated by a complex of Protocadherin-19 (Pcdh19) and N-cadherin (Ncad). Although Pcdh19 alone is only weakly adhesive, the Pcdh19–Ncad complex exhibited robust adhesion in bead aggregation assays, and Pcdh19 appeared to play the dominant role. Adhesion by the Pcdh19–Ncad complex was unaffected by mutations that disrupt Ncad homophilic binding but was inhibited by a mutation in Pcdh19. In addition, the complex exhibited homophilic specificity, as beads coated with Pcdh19–Ncad did not intermix with Ncad- or Pcdh17–Ncad-coated beads. We propose a model in which association of a protocadherin with Ncad acts as a switch, converting between distinct binding specificities.
High-mobility group nucleosome-binding protein 1 acts as an alarmin and is critical for lipopolysaccharide-induced immune responses
Authors: Yang De , Postnikov Yuri V. , Li Yana , Tewary Poonam , de la Rosa Gonzalo , Wei Feng , Klinman Dennis , Gioannini Theresa , Weiss Jerrold P. , Furusawa Takashi , Bustin Michael , Oppenheim Joost J.
Published: December 2011

Alarmins are endogenous mediators capable of promoting the recruitment and activation of antigen-presenting cells (APCs), including dendritic cells (DCs), that can potentially alert host defense against danger signals. However, the relevance of alarmins to the induction of adaptive immune responses remains to be demonstrated. In this study, we report the identification of HMGN1 (high-mobility group nucleosome-binding protein 1) as a novel alarmin and demonstrate that it contributes to the induction of antigen-specific immune responses. HMGN1 induced DC maturation via TLR4 (Toll-like receptor 4), recruitment of APCs at sites of injection, and activation of NF-κB and multiple mitogen-activated protein kinases in DCs. HMGN1 promoted antigen-specific immune response upon co-administration with antigens, and Hmgn1−/− mice developed greatly reduced antigen-specific antibody and T cell responses when immunized with antigens in the presence of lipopolysaccharide (LPS). The impaired ability of Hmgn1−/− mice to mount antigen-specific immune responses was accompanied by both deficient DC recruitment at sites of immunization and reduced production of inflammatory cytokines. Bone marrow chimera experiments revealed that HMGN1 derived from nonleukocytes was critical for the induction of antigen-specific antibody and T cell responses. Thus, extracellular HMGN1 acts as a novel alarmin critical for LPS-induced development of innate and adaptive immune responses.
3D MHD modelling of low current–high voltage dc plasma torch under restrike mode
Authors: Lebouvier A , Delalondre C , Fresnet F , Cauneau F , Fulcheri L
Published: December 2011

We present in this paper a magnetohydrodynamic (MHD) modelling of the gliding arc behaviour of a dc plasma torch operating with air under low current and high voltage conditions. The low current leads to instabilities and difficulties with simulating the process because the magnetic field is not sufficient to constrict the arc. The model is 3D, time dependent and the MHD equations are solved using CFD software Code_Saturne®. Although the arc is definitively non-local thermodynamic equilibrium (LTE), the LTE assumption is considered as a first approach. The injection of air is tangential. A hot gas channel reattachment model has been used to simulate the restriking process of the arc root. After the description of the model, the most appropriate electrical voltage breakdown parameter has been selected in comparing with experimental results. A typical operating point is then studied in detail and shows the helical shape of the arc discharge in the nozzle. Finally, the mass flow rate and the current have been varied in the range 0.16–0.5 g s−1 and 100–300 mA, respectively, corresponding to typical glidarc operating points of our experimental plasma torch. The model shows good consistency with experimental data in terms of global behaviour, arc length, mean voltage and glidarc frequency.
Time-dependent effects of low-temperature atmospheric-pressure argon plasma on epithelial cell attachment, viability and tight junction formation in vitro
Authors: Hoentsch Maxi , von Woedtke Thomas , Weltmann Klaus-Dieter , Barbara Nebe J
Published: December 2011

The application of physical plasma to living tissues is expected to promote wound healing by plasma disinfection and stimulation of tissue regeneration. However, the effects of plasma on healthy cells must be studied and understood. In our experiments we used an argon plasma jet (kINPen®09) to gain insights into time-dependent plasma effects on cell attachment, viability and tight junction formation in vitro. Murine epithelial cells mHepR1 were suspended in complete cell culture medium and were irradiated with argon plasma (direct approach) for 30, 60 and 120 s. Suspecting that physical plasma may exert its effect via the medium, cell culture medium alone was first treated with argon plasma (indirect approach) and immediately afterwards, cells were added and also cultured for 24 h. Cell morphology and vitality were verified using light microscopy and an enzyme-linked immunosorbent assay. Already after 30 s of treatment the mHepR1 cells lost their capability to adhere and the cell vitality decreased with increasing treatment time. Interestingly, the same inhibitory effect was observed in the indirect approach. Furthermore, the argon plasma-treated culture medium-induced large openings of the cell's tight junctions, were verified by the zonula occludens protein ZO-1, which we observed for the first time in confluently grown epithelial cells.
Recent changes in phenology over the northern high latitudes detected from multi-satellite data
Authors: Zeng Heqing , Jia Gensuo , Epstein Howard
Published: December 2011

Phenology of vegetation is a sensitive and valuable indicator of the dynamic responses of terrestrial ecosystems to climate change. Therefore, to better understand and predict ecosystems dynamics, it is important to reduce uncertainties in detecting phenological changes. Here, changes in phenology over the past several decades across the northern high-latitude region (≥60°N) were examined by calibrating and analyzing time series of the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Advanced Very High Resolution Radiometer (AVHRR). Over the past decade (2000–10), an expanded length of the growing season (LOS) was detected by MODIS, largely due to an earlier start of the growing season (SOS) by 4.7 days per decade and a delayed end of the growing season (EOS) by 1.6 days per decade over the northern high latitudes. There were significant differences between North America and Eurasia in phenology from 2000 to 2010 based on MODIS data (SOS: d
f = 21, F = 49.02, p < 0.0001; EOS: d
f = 21, F = 49.25, p < 0.0001; LOS: d
f = 21, F = 79.40, p < 0.0001). In northern America, SOS advanced by 11.5 days per decade, and EOS was delayed by 2.2 days per decade. In Eurasia, SOS advanced by 2.7 days per decade, and EOS was delayed by 3.5 days per decade. SOS has likely advanced due to the warming Arctic during April and May. Our results suggest that in recent decades the longer vegetation growing seasons can be attributed to more advanced SOS rather than delayed EOS. AVHRR detected longer LOS over the past three decades, largely related to delayed EOS rather than advanced SOS. These two datasets are significantly different in key phenological parameters (SOS: d
f = 17, F = 14.63, p = 0.0015; EOS: d
f = 17, F = 38.69, p < 0.0001; LOS: d
f = 17, F = 16.47, p = 0.0009) from 2000 to 2008 over the northern high latitudes. Thus, further inter-calibration between the sensors is needed to resolve the inconsistency and to better understand long-term trends of vegetation growth in the Arctic.
On a conjecture of Beltrametti and Sommese
Authors: Höring Andreas
Published: December 2011

Let

X
X

be a projective manifold of dimension

n
n

. Beltrametti and Sommese conjectured that if

A
A

is an ample divisor such that

K
X

+
(
n
−
1
)
A

K_X+ (n-1)A

is nef, then

K
X

+
(
n
−
1
)
A

K_X+(n-1)A

has non-zero global sections. We prove a weak version of this conjecture in arbitrary dimension. In dimension three, we prove the stronger non-vanishing conjecture of Ambro, Ionescu and Kawamata and give an application to Seshadri constants.
Corrigendum to “The Weil-Steinberg character of finite classical groups”
Authors: Hiss G. , Zalesski A.
Published: December 2011

This paper corrects the statement and the proof of Theorem 1.5 of the paper quoted in the title (Represent. Theory 13 (2009), 427–459).
Characterization and Optimization of Extrusion Cooking for the Manufacture of Third‐Generation Snacks with Winter Squash (Cucurbita moschata D.) Flour
Authors: Delgado‐Nieblas Carlos , Aguilar‐Palazuelos Ernesto , Gallegos‐Infante Alberto , Rocha‐Guzmán Nuria , Zazueta‐Morales José , Caro‐Corrales José
Published: December 2011

The aim of this work was to study the effects of barrel temperature (BT, 93.5–140.5°C), feed moisture (FM, 21.3–34.7%), and winter squash flour content (SFC, 0.43–15.6%) on physicochemical properties of microwave‐expanded third‐generation snack foods obtained by extrusion. Physicochemical properties used for optimization were expansion index (EI), penetration force (PF), specific mechanical energy (SME), and total color difference (ΔE). Response surface methodology was used for the analysis of data. The highest values of EI and lowest values of PF were found at high BT and low FM. The lowest values of SME were obtained at high levels of FM throughout the range of BT and SFC, whereas the highest values of ΔE were obtained at high SFC and low FM. Increasing levels of SFC increased ΔE values, whereas EI and SME values decreased. The best processing conditions (EI > 6.0, PF < 9.5 N, SME < 172 kJ/kg, and ΔE < 18) were found in the range of BT, 122–141°C; FM, 24.7–29.5%; and SFC, 0–10.9%. Under optimal process conditions, the retention of total carotenoids was higher than 60%. It is possible to manufacture third‐generation snack foods with good physicochemical properties, which could bring a health benefit because of the presence of carotenoids and dietary fiber in winter squash flour.
Influence of Instrument Rigidity and Specimen Geometry on Calculations of Compressive Strength Properties of Wheat Endosperm
Authors: Delwiche Stephen R. , Morris Craig F. , Mabille Frédéric , Abécassis Joël
Published: December 2011

Endosperm texture is one of the most important quality features in wheat; it defines milling energy requirements and end‐use suitability. From an engineering perspective, texture can be quantified by measuring the physical property of the resistance force to crushing of precisely machined specimens of endosperm. In such procedures, cylindrical or parallelepiped blocks are crushed under a constant rate of strain, in which values are reported of maximum stress, strain at maximum stress, Young's modulus, and the energy of compression to the point of maximum stress. Generally overlooked, however, is the instrument itself, which can significantly affect the apparent values of the latter three properties. Because no instrument is infinitely rigid, departures between apparent and actual strength properties occur. In this study, the physical principles for compressive strength measurement with respect to corrections for instrument rigidity are developed. Results show that the departures are exacerbated in specimens of small slenderness ratio and elevated hardness. This issue is demonstrated in a small collaborative study involving three laboratories and three instruments with low, intermediate, and high rigidity. Specimens were prepared from wheat kernels from hard and soft near‐isogenic lines derived from the cultivar Alpowa. For strain at maximum stress, the implementation of a correction for instrument rigidity reduced the range across laboratories from 6.03–47.7% (before correction) to 4.49–7.35% (after correction) for the hard genotype, and the corresponding ranges for the soft genotype were 3.29–18.6% and 2.07–6.01%, respectively. For Young's modulus, instrument rigidity correction resulted in a tenfold correction for the hard genotype measured on the least rigid instrument, going from 0.21 GPa (before) to 4.9 GPa (after). Likewise, with this instrument, the imparted energy density to maximum stress was reduced from an average apparent value of 23 MJ/m3 (before) to 3.8 MJ/m3 (after). Because of these large differences between apparent and actual values for these physical‐strength properties, it is recommended that future strength property measurements should account for instrument rigidity by implementation of the correction procedure described herein.
A Zinc-Finger-Family Transcription Factor, AbVf19, Is Required for the Induction of a Gene Subset Important for Virulence in Alternaria brassicicola
Authors: Srivastava Akhil , Ohm Robin A. , Oxiles Lindsay , Brooks Fred , Lawrence Christopher B. , Grigoriev Igor V. , Cho Yangrae
Published: December 2011

Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen with a broad host range within the family Brassicaceae. It produces secondary metabolites that marginally affect virulence. Cell wall–degrading enzymes (CDWE) have been considered important for pathogenesis but none of them individually have been identified as significant virulence factors in A. brassicicola. In this study, knockout mutants of a gene, AbVf19, were created and produced considerably smaller lesions than the wild type on inoculated host plants. The presence of tandem zinc-finger domains in the predicted amino acid sequence and nuclear localization of AbVf19-reporter protein suggested that it was a transcription factor. Gene expression comparisons using RNA-seq identified 74 genes being downregulated in the mutant during a late stage of infection. Among the 74 downregulated genes, 28 were putative CWDE genes. These were hydrolytic enzyme genes that composed a small fraction of genes within each family of cellulases, pectinases, cutinases, and proteinases. The mutants grew slower than the wild type on an axenic medium with pectin as a major carbon source. This study demonstrated the existence and the importance of a transcription factor that regulates a suite of genes that are important for decomposing and utilizing plant material during the late stage of plant infection.
Sanitation of a South African Forestry Nursery Contaminated with Fusarium circinatum Using Hydrogen Peroxide at Specific Oxidation Reduction Potentials
Authors: Van Wyk Schalk J. P. , Boutigny Anne-Laure , Coutinho Teresa A. , Viljoen Altus
Published: December 2011

Pitch canker, caused by Fusarium circinatum, was first reported in a forestry nursery in the Mpumalanga Province of South Africa in 1990, and it has since spread to almost all forestry nurseries in the country, where it causes significant economic losses. The aim of the current study was to (i) identify sources of F. circinatum contamination in the Karatara forestry nursery in the Western Cape Province and (ii) manage the disease by implementing an oxidation reduction potential (ORP)-based sanitation method using hydrogen peroxide. The irrigation water, planting tray inserts and seeds were screened for fungal contamination. Fusarium circinatum colonies were identified morphologically and confirmed by polymerase chain reaction using species-specific primers. Both the irrigation water and planting tray inserts served as sources of inoculum that introduced the pathogen into the nursery. The irrigation water was amended with hydrogen peroxide at an ORP level of 400 mV for an exposure time of 6 h because it was observed that such a treatment effectively killed all F. circinatum spores and was not phytotoxic to pine seedlings under laboratory conditions. In addition, the contaminated planting tray inserts were cleaned in water amended with hydrogen peroxide at an ORP value of 360 mV for 6 h, which was shown to efficiently eliminate all inoculum from planting tray inserts. Since the introduction of the ORP-based sanitation method at Karatara nursery, losses of pine seedlings were reduced to insignificant levels, and field losses were minimized.
First Report of Bidens mottle virus Causing Mosaic and Leaf Deformation in Garland Chrysanthemum and Lettuce in Taiwan
Authors: Chen Y. K. , Lee J. Y.
Published: December 2011

Garland chrysanthemum (Chrysanthemum coronarium) and lettuce (Lactuca sativa) are winter vegetables in Taiwan. Turnip mosaic virus (TuMV) and Lettuce mosaic virus (LMV) were potyviruses commonly isolated from garland chrysanthemum and lettuce, respectively (1). Symptoms of mosaic and deformation in leaves and stunting of plants have been observed in both Compositae crops in the fields since 2007 in the Chiayi area and with an increasing incidence in recent years (26 and 33% in garland chrysanthemum and lettuce, respectively). Filamentous virus particles (approximately 780 × 13 nm) in the crude sap and pinwheel inclusions in infected cells can be observed in the preparations of both diseased hosts with electron microscopy. However, TuMV, LMV, and other potyviruses (Bean yellow mosaic virus, Papaya ringspot virus, and Zucchini yellow mosaic virus) were not detectable in diseased samples by ELISA and western blotting tests, indicating a new potyvirus infection. Virus cultures were isolated from infected garland chrysanthemum and lettuce separately via mechanical inoculations in Chenopodium quinoa. Each isolate was mechanically inoculated to their original host individually and all caused symptoms similar to that observed in the field, indicating their pathogenicity to their original host. A cDNA fragment consisting of partial nuclear inclusion (NIb) and coat protein (CP) genes were amplified with potyvirus degenerate primers (forward: 5′-GGBAAYAATAGTGGNCAACC and reverse: 5′-GGGGAGGTGCCGTTCTCDATRCACCA) and was found to share 90% nucleotide sequence identity to that of Bidens mottle virus (BiMoV; GenBank Accession No. AF538686). The sequences of the CP gene and 3′ untranslated region (3′-UTR) of tested viruses were further amplified with a specific primer of BiMoV CP and oligo-dT in reverse transcription-PCR. The amplified fragments were cloned, sequenced, and the combined cDNA sequences were deposited in GenBank (Accession No. AB491763 for isolate garland chrysanthemum and Accession No. AB491764 for isolate lettuce). Sequence analysis showed that both cloned sequences shared more than 97% nucleotide similarity to that of BiMoV. The amino acid sequence of the CP of both isolates shared a 99.3% identity and a 98.9 to 99.3% identity to that of other BiMoV isolates deposited in GenBank. BiMoV was first described to be infecting lettuce and Cichorium endivia in the United States (4) and was first reported in sunflower and calendula in Taiwan recently (2,3). To our knowledge, this is the first report of the occurrence of BiMoV in garland chrysanthemum and lettuce in Taiwan.

References: (1) Y. K. Chen et al. Plant Pathol. Bull. 5:55,1996. (2) C.-H. Huang and F.-J. Jan. Plant Dis. 95:362, 2011. (3) J. Y. Liao et al. Arch. Virol. 154:723, 2009. (4) F. Youssef et al. Arch. Virol 153:227, 2008.
Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases
Authors: Lee Hyung Joo , Kweon Jiyeon , Kim Eunji , Kim Seokjoong , Kim Jin-Soo
Published: December 2011

Despite the recent discoveries of and interest in numerous structural variations (SVs)—which include duplications and inversions—in the human and other higher eukaryotic genomes, little is known about the etiology and biology of these SVs, partly due to the lack of molecular tools with which to create individual SVs in cultured cells and model organisms. Here, we present a novel method of inducing duplications and inversions in a targeted manner without pre-manipulation of the genome. We found that zinc finger nucleases (ZFNs) designed to target two different sites in a human chromosome could introduce two concurrent double-strand breaks, whose repair via non-homologous end-joining (NHEJ) gives rise to targeted duplications and inversions of the genomic segments of up to a mega base pair (bp) in length between the two sites. Furthermore, we demonstrated that a ZFN pair could induce the inversion of a 140-kbp chromosomal segment that contains a portion of the blood coagulation factor VIII gene to mimic the inversion genotype that is associated with some cases of severe hemophilia A. This same ZFN pair could be used, in theory, to revert the inverted region to restore genomic integrity in these hemophilia A patients. We propose that ZFNs can be employed as molecular tools to study mechanisms of chromosomal rearrangements and to create SVs in a predetermined manner so as to study their biological roles. In addition, our method raises the possibility of correcting genetic defects caused by chromosomal rearrangements and holds new promise in gene and cell therapy.
Management of children with high‐risk Hodgkin lymphoma
Authors: Kelly Kara M.
Published: December 2011

Most children and adolescents with newly diagnosed high‐risk Hodgkin lymphoma (HL) will achieve remission and cure with conventional chemotherapy with or without radiation therapy. However, these therapies can lead to long‐term side effects. Therapy is titrated on the basis of risk group stratification using clinical prognostic factors and, in most cases, then refined through assessment of interim or end of chemotherapy response, primarily using functional imaging with fluorodeoxyglucose positron emission tomography. No study has clearly demonstrated the factors that are sufficient in identifying the patients at highest risk for relapse that may benefit from therapy intensification. This review summarizes recent clinical trials in paediatric high‐risk HL, along with key findings from studies in adults with high‐risk HL that are applicable to the paediatric population. New directions in prognostic classification and targeted therapies are reviewed. Considerations for clinical practice at the current time outside the clinical trial setting are provided.
Night and day: short‐term variation in nitrogen chemistry and nitrous oxide emissions from streams
Authors: BAULCH HELEN M. , DILLON PETER J. , MARANGER ROXANE , VENKITESWARAN JASON J. , WILSON HENRY F. , SCHIFF SHERRY L.
Published: December 2011

1. Diel variation in metabolism contributes to variation in oxygen (O2) concentrations in streams. This variation in O2 and other parameters (e.g. pH) can in turn affect the rates of microbial nitrogen (N) processing, concentrations of nitrogenous solutes and production of the greenhouse gas nitrous oxide (N2O). We investigated diel variability in emissions of N2O and the magnitude of short‐term variability in N solutes across 10 streams.

2. Nitrous oxide fluxes varied on average 2.3‐fold over diel cycles. Concentrations would be underestimated by sampling around noon, but N2O fluxes would not show a consistent bias. Time‐weighted mean daily N2O flux was strongly related to nitrate concentration (r2 = 0.58). Diel patterns in N2O and dissolved N species were often complex (rather than simple sinusoidal curves), probably reflecting complex underlying processes.

3. Reliance on samples obtained around noon would overestimate daily mean nitrate concentrations by 5% and underestimate ammonium by 32% (average bias across all streams and dates).

4. Dissolved organic N did not show consistent day–night variation. However, the magnitude of diel variability was similar to that observed for dissolved inorganic N. Organic and inorganic N concentrations were often similar. Both appear to be dynamic components of stream N budgets.

5. The Intergovernmental Panel on Climate Change (IPCC) relies upon an emission factor to estimate indirect agricultural N2O emissions from streams and ground water. The measured emission factor (defined as the ratio of concentrations of N2O‐N to ‐N) was typically below the recently revised IPCC default figure. Measured values varied on average 1.8‐fold over approximately 24‐h periods and were slightly higher at night than by day. The emission factor was actually highest in streams that were net sinks for N2O, highlighting a conceptual problem in the current IPCC method.

6. Typical sampling programmes rely on daytime‐only sampling, which might cause bias in results. In our study streams, the bias was generally small. Diel variation in nitrate concentrations was related to mean temperature; variation in ammonium and N2O concentrations was greatest at low concentrations of nitrite and ammonium.
The outcome of the invasion of Florida lakes by Daphnia lumholtzi
Authors: HAVENS KARL E. , BEAVER JOHN R. , EAST THERESE L. , WORK KIRSTEN , PHLIPS EDWARD J. , CICHRA MARY F. , CROTEAU AMANDA C. , RODUSKY ANDREW J. , FULTON ROLLAND S. , ROSATI TEODORO C.
Published: December 2011

1. We examined 7–12 years of monthly to quarterly historical data from 15 lakes in FL, U.S.A. to determine the extent and outcome of invasion by the alien cladoceran Daphnia lumholtzi Sars.

2. The alien species was found in 10 of the 15 lakes, including Florida’s three largest lakes: Okeechobee, George and Apopka. All the surveyed lakes had resident populations of the smaller native species Daphnia ambigua Scourfield.

3. In most of the lakes, D. ambigua occurred seven to ninefold more often in plankton samples than D. lumholtzi, and at 10‐ to 100‐fold higher maximal densities. One exception was a small lake in central Florida (Lake Jesup), where D. lumholtzi attained high densities on several occasions in the 10 years of sampling.

4. In Lake Okeechobee, where data were of sufficient quality and quantity to perform statistical analyses, the results of canonical correlation analysis indicated that high densities of D. lumholtzi were correlated with lower concentrations of suspended solids, high algal biomass and higher temperature, whereas the opposite conditions were correlated with high densities of D. ambigua.

5. Based on the majority of data, D. lumholtzi has successfully invaded many lakes in Florida, yet it has not become a substantive component of the zooplankton. Additional research is needed to determine whether resources, fish predation or some other factor is responsible for this outcome of invasion.
Shifted hyperbola moveout approximation revisited
Authors: Stovas Alexey , Fomel Sergey
Published: December 2011

The shifted hyperbola approximation is widely used in seismic applications. Mostly, this approximation is applied to reflection moveout in multilayered media. The traditional domain for this application is the t ‐ x domain. In this paper, we discuss the use of this approximation in the τ ‐ p and t ‐ p domains. The accuracy of the shifted hyperbola approximation defined in different domains is illustrated by analytical and numerical examples.
Virtual signals combination – phase analysis for 2D and 3D data representation (acoustic medium)
Authors: Poletto Flavio , Bellezza Cinzia , Wapenaar Kees , Craglietto Aronne
Published: December 2011

We formulate the Kirchhoff‐Helmholtz representation theory for the combination of seismic interferometry signals synthesized by cross‐correlation and by cross‐convolution in acoustic media. The approach estimates the phase of the virtual reflections from the boundary encompassing a volume of interest and subtracts these virtual reflections from the total seismic‐interferometry wavefield. The reliability of the combination result, relevant for seismic exploration, depends on the stationary‐phase and local completeness in partial coverage regions. The analysis shows the differences in the phase of the corresponding seismic interferometry (by cross‐correlation) and virtual reflector (by cross‐convolution) signals obtained by 2D and 3D formulations, with synthetic examples performed to remove water layer multiples in ocean bottom seismic (OBS) acoustic data.
Different evolutionary histories underlie congruent species richness gradients of birds and mammals
Authors: Hawkins Bradford A. , McCain Christy M. , Davies T. Jonathan , Buckley Lauren B. , Anacker Brian L. , Cornell Howard V. , Damschen Ellen I. , Grytnes John‐Arvid , Harrison Susan , Holt Robert D. , Kraft Nathan J. B. , Stephens Patrick R.
Published: December 2011

Aim  The global species richness patterns of birds and mammals are strongly congruent. This could reflect similar evolutionary responses to the Earth’s history, shared responses to current climatic conditions, or both. We compare the geographical and phylogenetic structures of both richness gradients to evaluate these possibilities.

Location  Global.

Methods  Gridded bird and mammal distribution databases were used to compare their species richness gradients with the current environment. Phylogenetic trees (resolved to family for birds and to species for mammals) were used to examine underlying phylogenetic structures. Our first prediction is that both groups have responded to the same climatic gradients. Our phylogenetic predictions include: (1) that both groups have similar geographical patterns of mean root distance, a measure of the level of the evolutionary development of faunas, and, more directly, (2) that richness patterns of basal and derived clades will differ, with richness peaking in the tropics for basal clades and in the extra‐tropics for derived clades, and that this difference will hold for both birds and mammals. We also explore whether alternative taxonomic treatments for mammals can generate patterns matching those of birds.

Results  Both richness gradients are associated with the same current environmental gradients. In contrast, neither of our evolutionary predictions is met: the gradients have different phylogenetic structures, and the richness of birds in the lowland tropics is dominated by many basal species from many basal groups, whereas mammal richness is attributable to many species from both few basal groups and many derived groups. Phylogenetic incongruence is robust to taxonomic delineations for mammals.

Main conclusions  Contemporary climate can force multiple groups into similar diversity patterns even when evolutionary trajectories differ. Thus, as widely appreciated, our understanding of biodiversity must consider responses to both past and present climates, and our results are consistent with predictions that future climate change will cause major, correlated changes in patterns of diversity across multiple groups irrespective of their evolutionary histories.