bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of land-cover change on Africa's burnt area
Authors: Grégoire J.-M. , Eva H. D. , Belward A. S. , Palumbo I. , Simonetti D. , Brink A.
Published: September 2012

As Africa contributes some 64% of the global extent of area burnt annually, uncertainty concerning fire activity in the continent is an important issue. In this study, we quantify the effect of land-cover conversion from natural vegetation to agriculture on burnt area extent. This is based on the comparison of contemporary fire distribution in 189 protected areas where agricultural activity is largely absent with that occurring in the surrounding regions, where agriculture is practised. Results indicate a decrease in the total area burnt annually in Africa linked to the loss of natural vegetation communities due to expanding agricultural lands. Land-use change within the savanna vegetation units of Africa has led to a decrease in burnt area in the order of ~8×105hayear–1, which corresponds to 0.4% of the area currently burnt in Africa. The resulting decrease in the quantity of biomass burnt in any year would be between 3.4 and 9Tg, depending on the estimates of aboveground fuel biomass. Deforestation in the humid tropical forest domains may act as a small counterbalance to the trend of decreasing burnt area linked to land-use change in the short term.
UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity
Authors: Wang Chaochen , Lee Ji-Eun , Cho Young-Wook , Xiao Ying , Jin Qihuang , Liu Chengyu , Ge Kai
Published: September 2012

To investigate the role of histone H3K27 demethylase UTX in embryonic stem (ES) cell differentiation, we have generated
UTX
knockout (KO) and enzyme-dead knock-in male ES cells. Deletion of the X-chromosome-encoded
UTX
gene in male ES cells markedly decreases expression of the paralogous
UTY
gene encoded by Y chromosome, but has no effect on global H3K27me3 level,
Hox
gene expression, or ES cell self-renewal. However,
UTX
KO cells show severe defects in mesoderm differentiation and induction of
Brachyury
, a transcription factor essential for mesoderm development. Surprisingly, UTX regulates mesoderm differentiation and
Brachyury
expression independent of its enzymatic activity. UTY, which lacks detectable demethylase activity, compensates for the loss of UTX in regulating
Brachyury
expression. UTX and UTY bind directly to
Brachyury
promoter and are required for Wnt/β-catenin signaling-induced
Brachyury
expression in ES cells. Interestingly, male
UTX
KO embryos express normal levels of
UTY
and survive until birth. In contrast, female
UTX
KO mice, which lack the
UTY
gene, show embryonic lethality before embryonic day 11.5. Female
UTX
KO embryos show severe defects in both
Brachyury
expression and embryonic development of mesoderm-derived posterior notochord, cardiac, and hematopoietic tissues. These results indicate that UTX controls mesoderm differentiation and
Brachyury
expression independent of H3K27 demethylase activity, and suggest that UTX and UTY are functionally redundant in ES cell differentiation and early embryonic development.
Neural populations in human posteromedial cortex display opposing responses during memory and numerical processing
Authors: Foster Brett L. , Dastjerdi Mohammad , Parvizi Josef
Published: September 2012

Our understanding of the human default mode network derives primarily from neuroimaging data but its electrophysiological correlates remain largely unexplored. To address this limitation, we recorded intracranially from the human posteromedial cortex (PMC), a core structure of the default mode network, during various conditions of internally directed (e.g., autobiographical memory) as opposed to externally directed focus (e.g., arithmetic calculation). We observed late-onset (>400 ms) increases in broad high γ-power (70–180 Hz) within PMC subregions during memory retrieval. High γ-power was significantly reduced or absent when subjects retrieved self-referential semantic memories or responded to self-judgment statements, respectively. Conversely, a significant deactivation of high γ-power was observed during arithmetic calculation, the duration of which correlated with reaction time at the signal-trial level. Strikingly, at each recording site, the magnitude of activation during episodic autobiographical memory retrieval predicted the degree of suppression during arithmetic calculation. These findings provide important anatomical and temporal details—at the neural population level—of PMC engagement during autobiographical memory retrieval and address how the same populations are actively suppressed during tasks, such as numerical processing, which require externally directed attention.
Geometry sensing by self-organized protein patterns
Authors: Schweizer Jakob , Loose Martin , Bonny Mike , Kruse Karsten , Mönch Ingolf , Schwille Petra
Published: September 2012

In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction–diffusion system.
Ubiquity and quantitative significance of detoxification catabolism of chlorophyll associated with protistan herbivory
Authors: Kashiyama Yuichiro , Yokoyama Akiko , Kinoshita Yusuke , Shoji Sunao , Miyashiya Hideaki , Shiratori Takashi , Suga Hisami , Ishikawa Kanako , Ishikawa Akira , Inouye Isao , Ishida Ken-ichiro , Fujinuma Daiki , Aoki Keisuke , Kobayashi Masami , Nomoto Shinya , Mizoguchi Tadashi , Tamiaki Hitoshi
Published: September 2012

Chlorophylls are essential components of the photosynthetic apparati that sustain all of the life forms that ultimately depend on solar energy. However, a drawback of the extraordinary photosensitizing efficiency of certain chlorophyll species is their ability to generate harmful singlet oxygen. Recent studies have clarified the catabolic processes involved in the detoxification of chlorophylls in land plants, but little is understood about these strategies in aquatic ecosystem. Here, we report that a variety of heterotrophic protists accumulate the chlorophyll
a
catabolite 13
2
,17
3
-cyclopheophorbide
a
enol (cPPB-
a
E) after their ingestion of algae. This chlorophyll derivative is nonfluorescent in solution, and its inability to generate singlet oxygen in vitro qualifies it as a detoxified catabolite of chlorophyll
a
. Using a modified analytical method, we show that cPPB-
a
E is ubiquitous in aquatic environments, and it is often the major chlorophyll
a
derivative. Our findings suggest that cPPB-
a
E metabolism is one of the most important, widely distributed processes in aquatic ecosystems. Therefore, the herbivorous protists that convert chlorophyll
a
to cPPB-
a
E are suggested to play more significant roles in the modern oceanic carbon flux than was previously recognized, critically linking microscopic primary producers to the macroscopic food web and carbon sequestration in the ocean.
Equilibrium at the edge and atomistic mechanisms of graphene growth
Authors: Artyukhov Vasilii I. , Liu Yuanyue , Yakobson Boris I.
Published: September 2012

The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene.
Direct substitution and assisted dissociation pathways for turning off transcription by a MerR-family metalloregulator
Authors: Joshi Chandra P. , Panda Debashis , Martell Danya J. , Andoy Nesha May , Chen Tai-Yen , Gaballa Ahmed , Helmann John D. , Chen Peng
Published: September 2012

Metalloregulators regulate transcription in response to metal ions. Many studies have provided insights into how transcription is activated upon metal binding by MerR-family metalloregulators. In contrast, how transcription is turned off after activation is unclear. Turning off transcription promptly is important, however, as the cells would not want to continue expressing metal resistance genes and thus waste energy after metal stress is relieved. Using single-molecule FRET measurements we studied the dynamic interactions of the copper efflux regulator (CueR), a Cu
+
-responsive MerR-family metalloregulator, with DNA. Besides quantifying its DNA binding and unbinding kinetics, we discovered that CueR spontaneously flips its binding orientation at the recognition site. CueR also has two different binding modes, corresponding to interactions with specific and nonspecific DNA sequences, which would facilitate recognition localization. Most strikingly, a CueR molecule coming from solution can directly substitute for a DNA-bound CueR or assist the dissociation of the incumbent CueR, both of which are unique examples for any DNA-binding protein. The kinetics of the direct protein substitution and assisted dissociation reactions indicate that these two unique processes can provide efficient pathways to replace a DNA-bound holo-CueR with apo-CueR, thus turning off transcription promptly and facilely.
Endogenous viral antigen processing generates peptide-specific MHC class I cell-surface clusters
Authors: Lu Xiuju , Gibbs James S. , Hickman Heather D. , David Alexandre , Dolan Brian P. , Jin Yetao , Kranz David M. , Bennink Jack R. , Yewdell Jonathan W. , Varma Rajat
Published: September 2012

Sensitivity is essential in CD8+ T-cell killing of virus-infected cells and tumor cells. Although the affinity of the T-cell receptor (TCR) for antigen is relatively low, the avidity of T cell-antigen–presenting cell interactions is greatly enhanced by increasing the valence of the interaction. It is known that TCRs cluster into protein islands after engaging their cognate antigen (peptides bound to MHC molecules). Here, we show that mouse Kbclass I molecules segregate into preformed, long-lasting (hours) clusters on the antigen-presenting cell surface based on their bound viral peptide. Peptide-specific Kbclustering occurs when source antigens are expressed by vaccinia or vesicular stomatitis virus, either as proteasome-liberated precursors or free intracellular peptides. By contrast, Kb–peptide complexes generated by incubating cells with synthetic peptides are extensively intermingled on the cell surface. Peptide-specific complex sorting is first detected in the Golgi complex, and compromised by removing the Kbcytoplasmic tail. Peptide-specific clustering is associated with increased T-cell sensitivity: on a per-complex basis, endogenous SIINFEKL activates T cells more efficiently than synthetic SIINFEKL, and wild-type Kbpresents endogenous SIINFEKL more efficiently than tailless Kb. We propose that endogenous processing generates peptide-specific clusters of class I molecules to maximize the sensitivity and speed of T-cell immunosurveillance.
Changes in water chemistry can disable plankton prey defenses
Authors: Riessen Howard P. , Linley Robert Dallas , Altshuler Ianina , Rabus Max , Söllradl Thomas , Clausen-Schaumann Hauke , Laforsch Christian , Yan Norman D.
Published: September 2012

The effectiveness of antipredator defenses is greatly influenced by the environment in which an organism lives. In aquatic ecosystems, the chemical composition of the water itself may play an important role in the outcome of predator–prey interactions by altering the ability of prey to detect predators or to implement defensive responses once the predator’s presence is perceived. Here, we demonstrate that low calcium concentrations (<1.5 mg/L) that are found in many softwater lakes and ponds disable the ability of the water flea,Daphnia pulexto respond effectively to its predator, larvae of the phantom midge,Chaoborus americanus. This low-calcium environment prevents development of the prey’s normal array of induced defenses, which include an increase in body size, formation of neck spines, and strengthening of the carapace. We estimate that this inability to access these otherwise effective defenses results in a 50–186% increase in the vulnerability of the smaller juvenile instars ofDaphnia, the stages most susceptible toChaoboruspredation. Such a change likely contributes to the observed lack of success of daphniids in most low-calcium freshwater environments, and will speed the loss of these important zooplankton in lakes where calcium levels are in decline.
Coexistence between wildlife and humans at fine spatial scales
Authors: Carter Neil H. , Shrestha Binoj K. , Karki Jhamak B. , Pradhan Narendra Man Babu , Liu Jianguo
Published: September 2012

Many wildlife species face imminent extinction because of human impacts, and therefore, a prevailing belief is that some wildlife species, particularly large carnivores and ungulates, cannot coexist with people at fine spatial scales (i.e., cannot regularly use the exact same point locations). This belief provides rationale for various conservation programs, such as resettling human communities outside protected areas. However, quantitative information on the capacity and mechanisms for wildlife to coexist with humans at fine spatial scales is scarce. Such information is vital, because the world is becoming increasingly crowded. Here, we provide empirical information about the capacity and mechanisms for tigers (a globally endangered species) to coexist with humans at fine spatial scales inside and outside Nepal’s Chitwan National Park, a flagship protected area for imperiled wildlife. Information obtained from field cameras in 2010 and 2011 indicated that human presence (i.e., people on foot and vehicles) was ubiquitous and abundant throughout the study site; however, tiger density was also high. Surprisingly, even at a fine spatial scale (i.e., camera locations), tigers spatially overlapped with people on foot and vehicles in both years. However, in both years, tigers offset their temporal activity patterns to be much less active during the day when human activity peaked. In addition to temporal displacement, tiger–human coexistence was likely enhanced by abundant tiger prey and low levels of tiger poaching. Incorporating fine-scale spatial and temporal activity patterns into conservation plans can help address a major global challenge—meeting human needs while sustaining wildlife.
Structure of the human MTERF4–NSUN4 protein complex that regulates mitochondrial ribosome biogenesis
Authors: Spåhr Henrik , Habermann Bianca , Gustafsson Claes M. , Larsson Nils-Göran , Hallberg B. Martin
Published: September 2012

Proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. Mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. This complex process is evolutionary conserved and involves several RNA processing and modification steps required for correct ribosomal RNA maturation. We recently showed that a member of the mitochondrial transcription termination factor (MTERF) family of proteins, MTERF4, recruits NSUN4, a 5-methylcytosine RNA methyltransferase, to the large ribosomal subunit in a process crucial for mitochondrial ribosome biogenesis. Here, we describe the 3D crystal structure of the human MTERF4–NSUN4 complex determined to 2.9 Å resolution. MTERF4 is composed of structurally repeated MTERF–motifs that form a nucleic acid binding domain. NSUN4 lacks an N- or C-terminal extension that is commonly used for RNA recognition by related RNA methyltransferases. Instead, NSUN4 binds to the C-terminus of MTERF4. A positively charged surface forms an RNA binding path from the concave to the convex side of MTERF4 and further along NSUN4 all of the way into the active site. This finding suggests that both subunits of the protein complex likely contribute to RNA recognition. The interface between MTERF4 and NSUN4 contains evolutionarily conserved polar and hydrophobic amino acids, and mutations that change these residues completely disrupt complex formation. This study provides a molecular explanation for MTERF4-dependent recruitment of NSUN4 to ribosomal RNA and suggests a unique mechanism by which other members of the large MTERF-family of proteins can regulate ribosomal biogenesis.
The meaning of default options for potential organ donors
Authors: Davidai Shai , Gilovich Thomas , Ross Lee D.
Published: September 2012

Rates of participation in organ donation programs are known to be powerfully influenced by the relevant default policy in effect (“opt-in” vs. “opt-out”). Three studies provide evidence that this difference in participation may occur in part because the requirement to opt-in or opt-out results in large differences in the meaning that individuals attach to participation. American participants in Study 1 rated participation as a significantly more substantial action when agreement was purportedly obtained under opt-in rather than opt-out conditions, and nonagreement as a greater abrogation of responsibility when that decision was made under opt-out rather than under opt-in conditions. Study 2 replicated these findings with respondents who live in Germany, which employs an opt-in donation policy, and in Austria, which has an opt-out policy. Study 3 required American participants to rate various actions that differ in the effort and self-sacrifice they demand. As predicted, the placement of organ donation on the resulting multidimensional scaling dimension differed significantly depending on whether it purportedly was made in an opt-in country (where it was considered roughly akin to giving away half of one’s wealth to charity upon one’s death) or an opt-out country (where it fell between letting others get ahead of one in line and volunteering some time to help the poor). We discuss the relationship between this change of meaning account and two other mechanisms—behavioral inertia and implicit norms—that we believe underlie the default effect in decision making and other effects of policies designed to influence decision-makers.
Conditional ablation of brain-derived neurotrophic factor-TrkB signaling impairs striatal neuron development
Authors: Li Yun , Yui Daishi , Luikart Bryan W. , McKay Renée M. , Li Yanjiao , Rubenstein John L. , Parada Luis F.
Published: September 2012

Neurotrophic factors, such as brain-derived neurotrophic factor (BDNF), are associated with the physiology of the striatum and the loss of its normal functioning under pathological conditions. The role of BDNF and its downstream signaling in regulating the development of the striatum has not been fully investigated, however. Here we report that ablation of
Bdnf
in both the cortex and substantia nigra depletes BDNF in the striatum, and leads to impaired striatal development, severe motor deficits, and postnatal lethality. Furthermore, striatal-specific ablation of
TrkB
, the gene encoding the high-affinity receptor for BDNF, is sufficient to elicit an array of striatal developmental abnormalities, including decreased anatomical volume, smaller neuronal nucleus size, loss of dendritic spines, reduced enkephalin expression, diminished nigral dopaminergic projections, and severe deficits in striatal dopamine signaling through DARPP32. In addition,
TrkB
ablation in striatal neurons elicits a non–cell-autonomous reduction of tyrosine hydroxylase protein level in the axonal projections of substantia nigral dopaminergic neurons. Thus, our results establish an essential function for TrkB in regulating the development of striatal neurons.
Epistasis dominates the genetic architecture of
Drosophila
quantitative traits
Authors: Huang Wen , Richards Stephen , Carbone Mary Anna , Zhu Dianhui , Anholt Robert R. H. , Ayroles Julien F. , Duncan Laura , Jordan Katherine W. , Lawrence Faye , Magwire Michael M. , Warner Crystal B. , Blankenburg Kerstin , Han Yi , Javaid Mehwish , Jayaseelan Joy , Jhangiani Shalini N. , Muzny Donna , Ongeri Fiona , Perales Lora , Wu Yuan-Qing , Zhang Yiqing , Zou Xiaoyan , Stone Eric A. , Gibbs Richard A. , Mackay Trudy F. C.
Published: September 2012

Epistasis—nonlinear genetic interactions between polymorphic loci—is the genetic basis of canalization and speciation, and epistatic interactions can be used to infer genetic networks affecting quantitative traits. However, the role that epistasis plays in the genetic architecture of quantitative traits is controversial. Here, we compared the genetic architecture of three
Drosophila
life history traits in the sequenced inbred lines of the
Drosophila melanogaster
Genetic Reference Panel (DGRP) and a large outbred, advanced intercross population derived from 40 DGRP lines (Flyland). We assessed allele frequency changes between pools of individuals at the extremes of the distribution for each trait in the Flyland population by deep DNA sequencing. The genetic architecture of all traits was highly polygenic in both analyses. Surprisingly, none of the SNPs associated with the traits in Flyland replicated in the DGRP and vice versa. However, the majority of these SNPs participated in at least one epistatic interaction in the DGRP. Despite apparent additive effects at largely distinct loci in the two populations, the epistatic interactions perturbed common, biologically plausible, and highly connected genetic networks. Our analysis underscores the importance of epistasis as a principal factor that determines variation for quantitative traits and provides a means to uncover genetic networks affecting these traits. Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agriculture.
Sex, prions, and plasmids in yeast
Authors: Kelly Amy C. , Shewmaker Frank P. , Kryndushkin Dmitry , Wickner Reed B.
Published: September 2012

Even deadly prions may be widespread in nature if they spread by infection faster than they kill off their hosts. The yeast prions [PSI+] and [URE3] (amyloids of Sup35p and Ure2p) were not found in 70 wild strains, while [PIN+] (amyloid of Rnq1p) was found in ∼16% of the same population. Yeast prion infection occurs only by mating, balancing the detrimental effects of carrying the prion. We estimated the frequency of outcross mating as about 1% of mitotic doublings from the known detriment of carrying the 2-μm DNA plasmid (∼1%) and its frequency in wild populations (38/70). We also estimated the fraction of total matings that are outcross matings (∼23–46%) from the fraction of heterozygosity at the highly polymorphic
RNQ1
locus (∼46%). These results show that the detriment of carrying even the mildest forms of [PSI+], [URE3], or [PIN+] is greater than 1%. We find that Rnq1p polymorphisms in wild strains include several premature stop codon alleles that cannot propagate [PIN+] from the reference allele and others with several small deletions and point mutations which show a small transmission barrier. Wild strains carrying [PIN+] are far more likely to be heterozygous at
RNQ1
and other loci than are [pin−] strains, probably reflecting its being a sexually transmitted disease. Because sequence differences are known to block prion propagation or ameliorate its pathogenic effects, we hypothesize that polymorphism of
RNQ1
was selected to protect cells from detrimental effects of the [PIN+] prion.
Tearing mode velocity braking due to resonant magnetic perturbations
Authors: Frassinetti L. , Menmuir S. , Olofsson K.E.J. , Brunsell P.R. , Drake J.R.
Published: September 2012

The effect of resonant magnetic perturbations (RMPs) on the tearing mode (TM) velocity is studied in EXTRAP T2R. Experimental results show that the RMP produces TM braking until a new steady velocity or wall locking is reached. The braking is initially localized at the TM resonance and then spreads to the other TMs and to the rest of the plasma producing a global velocity reduction via the viscous torque. The process has been used to experimentally estimate the kinematic viscosity profile, in the range 2–40 m2 s−1, and the electromagnetic torque produced by the RMP, which is strongly localized at the TM resonance. Experimental results are then compared with a theoretical model which gives a reasonable qualitative explanation of the entire process.
On scattering passive system nodes and maximal scattering dissipative operators
Authors: Staffans Olof
Published: September 2012

There is an extensive literature on a class of linear time-invariant dynamical systems called “well-posed scattering passive systems”. Such a system is generated by an operator

S
S

which is called a scattering passive system node. In the existing literature such a node is typically introduced by first giving a list of assumptions which imply that

S
S

is a system node and then adding an inequality which forces this system node to be scattering passive. Here we proceed in the opposite direction: we start by requiring that

S
S

satisfies the passivity inequality and then ask the question, what additional conditions are needed in order for

S
S

to be a system node? The answer is surprisingly simple: A necessary and sufficient condition for an operator

S
S

to be a scattering passive system node is that

S
S

is closed and maximal within the class of operators that satisfy the passivity inequality. In the absence of external inputs and outputs, this condition is identical to the standard condition which characterizes the class of operators which generate contraction semigroups on Hilbert spaces.
The emerging problem of linezolid-resistant Staphylococcus
Authors: Gu Bing , Kelesidis Theodoros , Tsiodras Sotirios , Hindler Janet , Humphries Romney M.
Published: September 2012

The oxazolidinone antibiotic linezolid has demonstrated potent antimicrobial activity against Gram-positive bacterial pathogens, including methicillin-resistant staphylococci. This article systematically reviews the published literature for reports of linezolid-resistant Staphylococcus (LRS) infections to identify epidemiological, microbiological and clinical features for these infections. Linezolid remains active against >98% of Staphylococcus, with resistance identified in 0.05% of Staphylococcus aureus and 1.4% of coagulase-negative Staphylococcus (CoNS). In all reported cases, patients were treated with linezolid prior to isolation of LRS, with mean times of 20.0 ± 47.0 months for S. aureus and 11.0 ± 8.0 days for CoNS. The most common mechanisms for linezolid resistance were mutation (G2576T) to the 23S rRNA (63.5% of LRSA and 60.2% of LRCoNS) or the presence of a transmissible cfr ribosomal methyltransferase (54.5% of LRSA and 15.9% of LRCoNS). The emergence of linezolid resistance in Staphylococcus poses significant challenges to the clinical treatment of infections caused by these organisms, and in particular CoNS.
Bioguided Fraction of Antioxidant Activity of Ethanol Extract from Tartary Buckwheat Bran
Authors: Guo Xu‐Dan , Wang Min , Gao Jin‐Ming , Shi Xin‐Wei
Published: September 2012

This study describes the activity‐guided isolation of antioxidant agents from tartary buckwheat bran (TBB). The ethanol crude extract of oil‐free TBB was partitioned sequentially into ethyl acetate, n‐butanol, and residual aqueous fractions. The ethyl acetate fraction (EAF) had the highest phenolic and flavonoid contents and showed the strongest antioxidant activity. EAF was superior to rutin and inferior to vitamin C (Vc) in DPPH radical scavenging ability, had an advantage over rutin and Vc in ABTS radical scavenging ability, and again surpassed rutin and quercetin in reducing power. Then EAF was subjected to column chromatography, and isolated compounds were identified using nuclear magnetic resonance data by comparing with those reported in the literature. Finally, the bioassay‐guided fractionation of the crude ethanol extract of TBB afforded three known compounds (quercetin, p‐hydroxybenzoic acid, and daucosterol) responsible for antioxidant activity. p‐Hydroxybenzoic acid and daucosterol were isolated from buckwheat grain for the first time. Taken together, establishing of the three pure compounds is of paramount importance to the understanding of antioxidant activity of TBB, and there is an immense potential to process TBB or its EAF into value‐added functional foods and beverages.
Physical Characteristics of Genetically Altered Wheat Related to Technological Protein Separation
Authors: Robertson George H. , Blechl Ann E. , Hurkman William J. , Anderson Olin D. , Cao Trung K. , Tanaka Charlene K. , Gregorski Kay S. , Orts William J.
Published: September 2012

Wheat protein is a technologically challenging substrate for food and nonfood applications because of its compositional diversity and susceptibility to denaturation. Genetic modification could be used to create cultivars capable of producing more uniform or focused and novel protein compositions targeted to nonfood uses. These lines could serve as expression systems for specific high‐molecular‐weight (HMW) protein polymers and would be new crops leading to more diverse agricultural opportunities. However, fundamental changes to the molecular architecture in such wheat seeds could also result in separation and processing issues, such that conventional methods of protein enrichment may need modification or even reinvention. Enriched gluten protein fractions were prepared from Bobwhite lines modified to overproduce HMW glutenin subunits Dx5 and/or Dy10. These lines serve as experimental models to test various approaches that may be taken for protein polymer enrichment. However, conventional wheat gluten enrichment based on the glutomatic as a small model of industrial methods was incapable of producing enrichment for any of the tested meal or flour, including that from the non‐transformed parent Bobwhite. Mixing in the mixograph or farinograph failed to produce standard patterns for whole kernel meal and straight‐run flour, and the normal cohesiveness of dough expected from these devices was not observed. Microscopy of stained dough samples revealed severely limited formation of normal protein networks, a capability crucial to conventional separation technology. Particle size analysis of whole kernel meal revealed a higher resistance to milling for the altered lines. Higher drying rates, lower farinograph moisture absorption, and increased thermal transition temperatures were observed. These data suggested that the native architecture of these new forms was more tightly constructed with reduced capacity for alteration by hydration and input of mechanical energy. An alternative enrichment method featuring solvation in SDS and precipitation in acetone produced coagulated (Bobwhite) or partially coagulated protein (transgenic lines producing Dx5 or Dy10) enriched to 78–85% protein with high yield.
Survival of Fusarium oxysporum f. sp. vasinfectum Chlamydospores Under Solarization Temperatures
Authors: Bennett R. S.
Published: September 2012

Solarization is an effective soil treatment against race 4 of Fusarium oxysporum f. sp. vasinfectum. Despite the lack of effective alternatives, solarization is rarely used in cotton because of its high cost. Use of solarization might be increased if soil temperatures could be used to predict reductions in pathogen inoculum levels, thereby ensuring high levels of efficacy. However, relationships between survival of race 4 chlamydospores, soil moisture, and temperatures typical of solarized soil are not known. Survival of culture- and plant-produced chlamydospores of race 4, incubated at 40°C in dry or moist environments, indicated the importance of moisture in determining spore survival. Mortality of spores from either source was low under dry conditions and much higher under moist conditions. A 6-week exposure of culture-produced chlamydospores to temperatures from 30 to 40°C under moist conditions indicated limited mortality at temperatures ≤35°C. However, most spores were eliminated by day 6 at 40°C. A second study using a moist environment indicated high mortality of spores by 5 weeks at 37°C or by 10 days at temperatures from 39 to 41°C. These results should serve as useful guides in efforts to develop solarization protocols that maximize effectiveness based on monitored soil temperatures.
Differential Responses ofColletotrichum gloeosporioidesandC. truncatumIsolates from Different Hosts to Multiple Fungicides Based on Two Assays
Authors: Rampersad Sephra N. , Teelucksingh Lisa D.
Published: September 2012

Anthracnose is one of the most important postharvest diseases of many economically important crops worldwide. This study was conducted with the objective of investigating the sensitivity of Colletotrichum gloeosporioides and C. truncatum isolates to multiple fungicides with different modes of action. The study analyzed quantitative sensitivity data derived from conventional amended agar (AA) assays and qualitative spore responses obtained from a novel microtiter bioassay that is based on reduction of a viability dye, Alamar blue (AB). Generally, for AA assays, the percent growth inhibition (%RGI) increased with increasing concentration for all isolates and all fungicides, except for copper hydroxide. C. truncatum isolates reacted differently to increasing concentrations of the various fungicides depending on whether the isolates originated from pepper or papaya. C. truncatum from pepper had generally less %RGI than C. truncatum isolates from papaya. C. gloeosporioides isolates from papaya had generally higher %RGI than C. truncatum isolates for all concentrations tested for pyraclostrobin, chlorothalonil, and fosetyl-aluminum. C. gloeosporioides isolates from pepper had generally higher %RGI than C. truncatum isolates for all concentrations tested for most fungicides. In all cases, Colletotrichum sp. and fungicide had significant (P ≤ 0.001) effects on the log concentration of fungicide for which relative growth was inhibited by 50 and 90% (log EC50 and log EC90, respectively) calculated for all isolates, regardless of whether values were compared for only C. gloeosporioides isolates or only C. truncatum isolates. Correlation analyses of log EC50 and log EC90 values of all the isolates revealed a nonsignificant association for pyraclostrobin. In AB assays, all fungicides had an equivalent effect at inhibiting spore germination at the lower concentrations. According to binary logistic regression analyses, species, isolate, and fungicide concentration had significant predictive value in determining whether an AB test would be positive. Sequence alignments between C. gloeosporioides isolates and C. gloeosporioides f. sp. aeschynomene revealed no base substitutions at codons 198, 199, 200, and 240; however, sequence comparisons between C. truncatum isolates and C. gloeosporioides f. sp. aeschynomene revealed two codon changes located outside of the identified codon 198 or 200 associated with the benzimidazole-resistant phenotype of C. gloeosporioides isolates.
William Thomas Tutte. 14 May 1917 — 2 May 2002
Authors: Younger D. H.
Published: September 2012

William Tutte, born in Newmarket, completed a master’s degree in chemistry at Cambridge at the end of 1940, whereupon he was recruited to work at Bletchley Park as a cryptographer. He became the primary person responsible for breaking the Fish code used for high-level Army communication. After the war he returned to Cambridge as a Fellow of Trinity College, for three years of study for a PhD in mathematics. On completing his degree in 1948, he joined the Faculty of the University of Toronto, where he rose to pre-eminence in combinatorics. In 1962 he moved to the University of Waterloo, where he had a significant role in the development of the university and its Faculty of Mathematics.
A paradox of state-dependent diffusion and how to resolve it
Authors: Tupper P. F. , Yang Xin
Published: September 2012

Consider a particle diffusing in a confined volume which is divided into two equal regions. In one region, the diffusion coefficient is twice the value of the diffusion coefficient in the other region. Will the particle spend equal proportions of time in the two regions in the long term? Statistical mechanics would suggest yes, since the number of accessible states in each region is presumably the same. However, another line of reasoning suggests that the particle should spend less time in the region with faster diffusion, since it will exit that region more quickly. We demonstrate with a simple microscopic model system that both predictions are consistent with the information given. Thus, specifying the diffusion rate as a function of position is not enough to characterize the behaviour of a system, even assuming the absence of external forces. We propose an alternative framework for modelling diffusive dynamics in which both the diffusion rate and equilibrium probability density for the position of the particle are specified by the modeller. We introduce a numerical method for simulating dynamics in our framework that samples from the equilibrium probability density exactly and is suitable for discontinuous diffusion coefficients.
Exploratory behaviour and stressor hyper-responsiveness facilitate range expansion of an introduced songbird
Authors: Liebl Andrea L. , Martin Lynn B.
Published: September 2012

Global anthropogenic changes are occurring at an unprecedented rate; one change, human-facilitated introduction of species outside their native range, has had significant ecological and economic impacts. Surprisingly, what traits facilitate range expansions post-introduction is relatively unknown. This information could help predict future expansions of introduced species as well as native species shifting their ranges as climate conditions change. Here, we asked whether specific behavioural and physiological traits were important in the ongoing expansion of house sparrows (
Passer domesticus
) across Kenya. We predicted that birds at the site of initial introduction (Mombasa, introduced approx. 1950) would behave and regulate corticosterone, a stress hormone, differently than birds at the range edge (Kakamega, approx. 885 km from Mombasa; colonized within the last 5 years). Specifically, we predicted greater exploratory behaviour and stronger corticosterone response to stressors in birds at the range edge, which may facilitate the identification, resolution and memory of stressors. Indeed, we found that distance from Mombasa (a proxy for population age) was a strong predictor of both exploratory behaviour and corticosterone release in response to restraint (but only while birds were breeding). These results suggest that certain behavioural and neuroendocrine traits may influence the ability of species to colonize novel habitats.
Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends
Authors: Smith Andrew B. , Lloyd Graeme T. , McGowan Alistair J.
Published: September 2012

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling—a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.
Auditory sequence analysis and phonological skill
Authors: Grube Manon , Kumar Sukhbinder , Cooper Freya E. , Turton Stuart , Griffiths Timothy D.
Published: September 2012

This work tests the relationship between auditory and phonological skill in a non-selected cohort of 238 school students (age 11) with the specific hypothesis that sound-sequence analysis would be more relevant to phonological skill than the analysis of basic, single sounds. Auditory processing was assessed across the domains of pitch, time and timbre; a combination of six standard tests of literacy and language ability was used to assess phonological skill. A significant correlation between general auditory and phonological skill was demonstrated, plus a significant, specific correlation between measures of phonological skill and the auditory analysis of short sequences in pitch and time. The data support a limited but significant link between auditory and phonological ability with a specific role for sound-sequence analysis, and provide a possible new focus for auditory training strategies to aid language development in early adolescence.
Poly[[bis{μ2-N2,N6-bis[(pyridin-3-yl)methyl]pyridine-2,6-dicarboxamide}dichloridonickel(II)]N,N-dimethylformamide tetrasolvate]
Authors: Guo Yi-Ping , Li Dong-Ying , Li Guo-Ting
Published: September 2012

In the title compound, {[NiCl2(C19H17N5O2)2]·4C3H7NO}n, the NiIIatom is located on an inversion centre and is in a six-coordinated octahedral geometry, formed by four pyridine N atoms from fourN2,N6-bis[(pyridin-3-yl)methyl]pyridine-2,6-dicarboxamide (BPDA) ligands occupying the equatorial plane and two chloride anions at the axial sites. The bidentate bridging BPDA ligands link the NiIIatoms into a two-dimensional corrugated grid-like flexible layer with a (4,4)-connected topology, which consists of left- and right-handed helical chains sharing the common NiIIatoms. Investigation of the thermal stability shows that the network is stable up to 573 K.
Age‐related loss of nitric oxide synthase in skeletal muscle causes reductions in calpain S‐nitrosylation that increase myofibril degradation and sarcopenia
Authors: Samengo Giuseppina , Avik Anna , Fedor Brian , Whittaker Daniel , Myung Kyu H. , Wehling‐Henricks Michelle , Tidball James G.
Published: September 2012

Sarcopenia, the age‐related loss of muscle mass, is a highly‐debilitating consequence of aging. In this investigation, we show sarcopenia is greatly reduced by muscle‐specific overexpression of calpastatin, the endogenous inhibitor of calcium‐dependent proteases (calpains). Further, we show that calpain cleavage of specific structural and regulatory proteins in myofibrils is prevented by covalent modification of calpain by nitric oxide (NO) through S‐nitrosylation. We find that calpain in adult, non‐sarcopenic muscles is S‐nitrosylated but that aging leads to loss of S‐nitrosylation, suggesting that reduced S‐nitrosylation during aging leads to increased calpain‐mediated proteolysis of myofibrils. Further, our data show that muscle aging is accompanied by loss of neuronal nitric oxide synthase (nNOS), the primary source of muscle NO, and that expression of a muscle‐specific nNOS transgene restores calpain S‐nitrosylation in aging muscle and prevents sarcopenia. Together, the findings show that in vivo reduction of calpain S‐nitrosylation in muscle may be an important component of sarcopenia, indicating that modulation of NO can provide a therapeutic strategy to slow muscle loss during old age.
Management of raised glucose, a clinical decision tool to reduce length of stay of patients with hyperglycaemia
Authors: Herring R. , Russell‐Jones D. L. , Pengilley C. , Hopkins H. , Tuthill B. , Wright J. , Hordern S. V. , Pengilley C. , Hopkins H. , Tuthill B. , Davidson S.
Published: September 2012

Diabet. Med. 30, 81–87 (2013)

Objective  To assess whether the introduction of a management of raised glucose clinical decision tool could improve assessment of patients with hyperglycaemia by non‐specialist physicians, leading to early discharge and improved quality of inpatient care.

Methods  Participants were adults aged 18 years or over presenting to the Medical Assessment Unit with a capillary blood glucose level > 11.1 mmol/l. Phase 1 of the study (phase 1) evaluated current clinical practice and potential impact of the clinical decision tool. Phase 2 evaluated the effectiveness of the management of raised glucose tool in clinical practice. Primary outcome measures were inpatient length of stay and same‐calendar‐day discharges. Secondary outcome measures were diabetes specialist input, patient assessment, intravenous insulin infusion use and patient satisfaction.

Results  Implementation of the management of raised glucose clinical decision tool allowed safe, same‐calendar‐day discharges of 40% of patients with hyperglycaemia as their primary reason for attendance. Median length of stay was lower in the phase 1 than in phase 2 (1.0 vs. 3.5 days, P < 0.01). Early discharge did not result in an increase in readmissions. There was improvement in hyperglycaemia assessment for all patients (P < 0.01), a reduction in the use of intravenous insulin infusions (P < 0.01) and high level of patient satisfaction.

Conclusion  The management of raised glucose clinical decision tool resulted in a significant increase in the number of same‐calendar‐day discharges and reduction in hospital length of stay without adverse impact on readmission rates. Additionally, the tool was associated with improvements in inpatient diabetes care and patient satisfaction.