bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of surface morphology evolution of SubPc layers on the performance of SubPc/C60 organic photovoltaic cells
Authors: Kim Jinhyun , Yim Sanggyu
Published: November 2011

In this study, small-molecule organic solar cells based on choloro[subphthalocyaninato]boron (III) (SubPc) as an electron donor and fullerene (C60) as an electron acceptor were fabricated by varying the thickness, d, of the SubPc layer. The power conversion efficiency was maximized to 1.8% at d ∼ 130 Å due to the relatively large values of the short-circuit current density (JSC) and fill factor (FF). This optimal thickness was also strongly related to the surface morphology evolution of the SubPc thin films. The corrugated surface nanostructures were continually formed until the thickness of the film increased up to 130 Å, which is advantageous for the formation of an interdigitated electron donor-acceptor interface. In contrast, for films thicker than 130 Å, the corrugated surface structures were filled with subsequently deposited molecules, leading to a smoother morphology and consequently reduced JSC and FF value of the cells.
Glucose and glycine synergistically enhance the in vitro development of porcine blastocysts in a chemically defined medium
Authors: Mito Tomomi , Yoshioka Koji , Yamashita Shoko , Suzuki Chie , Noguchi Michiko , Hoshi Hiroyoshi
Published: November 2011

In the present study, the effects of glucose and/or glycine on the in vitro development of Day 5 (Day 0 = IVF) porcine blastocysts were determined. The addition of 2.5–10 mM glucose to the chemically defined culture medium porcine zygote medium (PZM)-5 significantly increased blastocyst survival rates compared with those of blastocysts cultured in the absence of glucose. The addition of 5 and 10 mM glycine to PZM-5 containing 5 mM glucose significantly enhanced the development to hatching and the number of hatched blastocysts compared with no addition of glycine. However, the addition of glycine to PZM-5 with no glucose did not improve blastocyst development. The ATP content of Day 6 blastocysts cultured with glucose was significantly higher than that of blastocysts cultured in the absence of glucose, regardless of glycine supplementation. The diameter and total cell numbers were significantly greater, and the apoptotic index was significantly lower, in Day 6 blastocysts cultured with both glucose and glycine. These results indicate that glucose is an important energy source for the porcine blastocyst and that glucose and glycine act synergistically to enhance development to the hatching and hatched blastocyst stage in vitro.
Evidence of the genetic trend for secondary sex ratio in Iranian Holsteins
Authors: Ghavi Hossein-Zadeh Navid
Published: November 2011

Calving records from the Animal Breeding Center of Iran collected from January 2000 to December 2007 and comprising 520 964 Holstein calving events from 2135 herds were analysed using animal and sire models to estimate variance components, heritabilities and genetic trends for secondary sex ratio (SSR) in the first, second and third parities. Direct heritabilities for SSR ranged from 0.00004 to 0.001 over the parities. The linear sire model estimate of heritabilities for SSR in the present study was from 0.0002 to 0.0008 over the parities. There were positive phenotypic and genetic trends for female rate in Iranian Holsteins over the years. Exploitable genetic variation in SSR can take advantage of sexual dimorphism for economically important traits, which may facilitate greater selection intensity and thus greater response to selection, as well as reducing the replacement costs. On the other hand, increasing genetic and phenotypic trends for female rate in the population under study could be partly assigned to increased use of new reproductive technologies in dairy herds; therefore, dairy farmers have the option to select from among their herd’s potential dams and produce dairy replacement heifers from only the genetically superior animals, thus promoting enhanced rates of genetic gain.
Competition is a driving force in topographic mapping
Authors: Triplett Jason W. , Pfeiffenberger Cory , Yamada Jena , Stafford Ben K. , Sweeney Neal T. , Litke Alan M. , Sher Alexander , Koulakov Alexei A. , Feldheim David A.
Published: November 2011

Topographic maps are the primary means of relaying spatial information in the brain. Understanding the mechanisms by which they form has been a goal of experimental and theoretical neuroscientists for decades. The projection of the retina to the superior colliculus (SC)/tectum has been an important model used to show that graded molecular cues and patterned retinal activity are required for topographic map formation. Additionally, interaxon competition has been suggested to play a role in topographic map formation; however, this view has been recently challenged. Here we present experimental and computational evidence demonstrating that interaxon competition for target space is necessary to establish topography. To test this hypothesis experimentally, we determined the nature of the retinocollicular projection in Math5 (Atoh7) mutant mice, which have severely reduced numbers of retinal ganglion cell inputs into the SC. We find that in these mice, retinal axons project to the anteromedialj portion of the SC where repulsion from ephrin-A ligands is minimized and where their attraction to the midline is maximized. This observation is consistent with the chemoaffinity model that relies on axon–axon competition as a mapping mechanism. We conclude that chemical labels plus neural activity cannot alone specify the retinocollicular projection; instead axon–axon competition is necessary to create a map. Finally, we present a mathematical model for topographic mapping that incorporates molecular labels, neural activity, and axon competition.
Anthropogenic fire drives the evolution of seed traits
Authors: Gómez-González Susana , Torres-Díaz Cristian , Bustos-Schindler Carlos , Gianoli Ernesto
Published: November 2011

Fire is a major disturbance affecting ecosystems worldwide. Phylogenetic studies have shown that the evolution of seed persistence (fire resistance) is associated with fire frequency or severity. However, the existence of specific seed traits resulting from natural selection mediated by fire remains a key question in plant evolution. We evaluated the role of fire in the evolution of seed traits from a microevolutionary perspective, using as a study system a native forb from the Chilean matorral, where fire is a novel, anthropogenic disturbance. We show that anthropogenic fires are shaping the evolution of seed traits such as pubescence and shape. Among-population variation in seed pubescence, shape, and pericarp thickness was strongly associated with fire frequency, and within a population, fire selected those plants with more pubescent seeds, thicker pericarps, and less rounded seeds. Seed pubescence and shape were shown to be heritable traits. Our findings provide insights into the understanding of the evolution of seed traits in fire-prone environments and demonstrate that human-made fires can be driving evolutionary changes in plant species from ecosystems where fires do not occur naturally.
Nanostructure of cellulose microfibrils in spruce wood
Authors: Fernandes Anwesha N. , Thomas Lynne H. , Altaner Clemens M. , Callow Philip , Forsyth V. Trevor , Apperley David C. , Kennedy Craig J. , Jarvis Michael C.
Published: November 2011

The structure of cellulose microfibrils in wood is not known in detail, despite the abundance of cellulose in woody biomass and its importance for biology, energy, and engineering. The structure of the microfibrils of spruce wood cellulose was investigated using a range of spectroscopic methods coupled to small-angle neutron and wide-angle X-ray scattering. The scattering data were consistent with 24-chain microfibrils and favored a “rectangular” model with both hydrophobic and hydrophilic surfaces exposed. Disorder in chain packing and hydrogen bonding was shown to increase outwards from the microfibril center. The extent of disorder blurred the distinction between the I alpha and I beta allomorphs. Chains at the surface were distinct in conformation, with high levels of conformational disorder at C-6, less intramolecular hydrogen bonding and more outward-directed hydrogen bonding. Axial disorder could be explained in terms of twisting of the microfibrils, with implications for their biosynthesis.
Inferring the rules of interaction of shoaling fish
Authors: Herbert-Read James E. , Perna Andrea , Mann Richard P. , Schaerf Timothy M. , Sumpter David J. T. , Ward Ashley J. W.
Published: November 2011

Collective motion, where large numbers of individuals move synchronously together, is achieved when individuals adopt interaction rules that determine how they respond to their neighbors’ movements and positions. These rules determine how group-living animals move, make decisions, and transmit information between individuals. Nonetheless, few studies have explicitly determined these interaction rules in moving groups, and very little is known about the interaction rules of fish. Here, we identify three key rules for the social interactions of mosquitofish (Gambusia holbrooki): (i) Attraction forces are important in maintaining group cohesion, while we find only weak evidence that fish align with their neighbor’s orientation; (ii) repulsion is mediated principally by changes in speed; (iii) although the positions and directions of all shoal members are highly correlated, individuals only respond to their single nearest neighbor. The last two of these rules are different from the classical models of collective animal motion, raising new questions about how fish and other animals self-organize on the move.
Sulfanyl stabilization of copper-bonded phenoxyls in model complexes and galactose oxidase
Authors: Verma Pratik , Pratt Russell C. , Storr Tim , Wasinger Erik C. , Stack T. Daniel P.
Published: November 2011

Integrating sulfanyl substituents into copper-bonded phenoxyls significantly alters their optical and redox properties and provides insight into the influence of cysteine modification of the tyrosine cofactor in the enzyme galactose oxidase. The model complexes [
1
SR2
]
+
are class II mixed-valent Cu
II
-phenoxyl-phenolate species that exhibit intervalence charge transfer bands and intense visible sulfur-aryl
π
 → 
π
∗
transitions in the energy range, which provides a greater spectroscopic fidelity to oxidized galactose oxidase than non-sulfur-bearing analogs. The potentials for phenolate-based oxidations of the sulfanyl-substituted
1
SR2
are lower than the alkyl-substituted analogs by up to
ca.
150 mV and decrease following the steric trend: -S
t
Bu > -S
i
 Pr > -SMe. Density functional theory calculations suggest that reducing the steric demands of the sulfanyl substituent accommodates an in-plane conformation of the alkylsulfanyl group with the aromatic ring, which stabilizes the phenoxyl hole by
ca.
8 kcal mol
-1
(1 kcal = 4.18 kJ; 350 mV) through delocalization onto the sulfur atom. Sulfur K-edge X-ray absorption spectroscopy clearly indicates a contribution of
ca.
8–13% to the hole from the sulfur atoms in [
1
SR2
]
+
. The electrochemical results for the model complexes corroborate the
ca.
350 mV (density functional theory) contribution of hole delocalization on to the cysteine–tyrosine cross-link to the stability of the phenoxyl radical in the enzyme, while highlighting the importance of the in-plane conformation observed in all crystal structures of the enzyme.
Nanoparticles enhance brain delivery of blood–brain barrier-impermeable probes for in vivo optical and magnetic resonance imaging
Authors: Koffie Robert M. , Farrar Christian T. , Saidi Laiq-Jan , William Christopher M. , Hyman Bradley T. , Spires-Jones Tara L.
Published: November 2011

Several imaging modalities are suitable for in vivo molecular neuroimaging, but the blood–brain barrier (BBB) limits their utility by preventing brain delivery of most targeted molecular probes. We prepared biodegradable nanocarrier systems made up of poly(n-butyl cyanoacrylate) dextran polymers coated with polysorbate 80 (PBCA nanoparticles) to deliver BBB-impermeable molecular imaging probes into the brain for targeted molecular neuroimaging. We demonstrate that PBCA nanoparticles allow in vivo targeting of BBB-impermeable contrast agents and staining reagents for electron microscopy, optical imaging (multiphoton), and whole brain magnetic resonance imaging (MRI), facilitating molecular studies ranging from individual synapses to the entire brain. PBCA nanoparticles can deliver BBB-impermeable targeted fluorophores of a wide range of sizes: from 500-Da targeted polar molecules to 150,000-Da tagged immunoglobulins into the brain of living mice. The utility of this approach is demonstrated by (
i
) development of a “Nissl stain” contrast agent for cellular imaging, (
ii
) visualization of amyloid plaques in vivo in a mouse model of Alzheimer's disease using (traditionally) non–BBB-permeable reagents that detect plaques, and (
iii
) delivery of gadolinium-based contrast agents into the brain of mice for in vivo whole brain MRI. Four-dimensional real-time two-photon and MR imaging reveal that brain penetration of PBCA nanoparticles occurs rapidly with a time constant of ∼18 min. PBCA nanoparticles do not induce nonspecific BBB disruption, but collaborate with plasma apolipoprotein E to facilitate BBB crossing. Collectively, these findings highlight the potential of using biodegradable nanocarrier systems to deliver BBB-impermeable targeted molecular probes into the brain for diagnostic neuroimaging.
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage
Authors: Farrer Rhys A. , Weinert Lucy A. , Bielby Jon , Garner Trenton W. J. , Balloux Francois , Clare Frances , Bosch Jaime , Cunningham Andrew A. , Weldon Che , du Preez Louis H. , Anderson Lucy , Pond Sergei L. Kosakovsky , Shahar-Golan Revital , Henk Daniel A. , Fisher Matthew C.
Published: November 2011

Batrachochytrium dendrobatidis
(
Bd
) is a globally ubiquitous fungal infection that has emerged to become a primary driver of amphibian biodiversity loss. Despite widespread effort to understand the emergence of this panzootic, the origins of the infection, its patterns of global spread, and principle mode of evolution remain largely unknown. Using comparative population genomics, we discovered three deeply diverged lineages of
Bd
associated with amphibians. Two of these lineages were found in multiple continents and are associated with known introductions by the amphibian trade. We found that isolates belonging to one clade, the global panzootic lineage (
Bd
GPL) have emerged across at least five continents during the 20th century and are associated with the onset of epizootics in North America, Central America, the Caribbean, Australia, and Europe. The two newly identified divergent lineages, Cape lineage (
Bd
CAPE) and Swiss lineage (
Bd
CH), were found to differ in morphological traits when compared against one another and
Bd
GPL, and we show that
Bd
GPL is hypervirulent.
Bd
GPL uniquely bears the hallmarks of genomic recombination, manifested as extensive intergenomic phylogenetic conflict and patchily distributed heterozygosity. We postulate that contact between previously genetically isolated allopatric populations of
Bd
may have allowed recombination to occur, resulting in the generation, spread, and invasion of the hypervirulent
Bd
GPL leading to contemporary disease-driven losses in amphibian biodiversity.
Metabolic cycling without cell division cycling in respiring yeast
Authors: Slavov Nikolai , Macinskas Joanna , Caudy Amy , Botstein David
Published: November 2011

Despite rapid progress in characterizing the yeast metabolic cycle, its connection to the cell division cycle (CDC) has remained unclear. We discovered that a prototrophic batch culture of budding yeast, growing in a phosphate-limited ethanol medium, synchronizes spontaneously and goes through multiple metabolic cycles, whereas the fraction of cells in the G1/G0 phase of the CDC increases monotonically from 90 to 99%. This demonstrates that metabolic cycling does not require cell division cycling and that metabolic synchrony does not require carbon-source limitation. More than 3,000 genes, including most genes annotated to the CDC, were expressed periodically in our batch culture, albeit a mere 10% of the cells divided asynchronously; only a smaller subset of CDC genes correlated with cell division. These results suggest that the yeast metabolic cycle reflects a growth cycle during G1/G0 and explains our previous puzzling observation that genes annotated to the CDC increase in expression at slow growth.
Helping counts: predicting children's intentions to disclose being bullied to teachers from prior social support experiences
Authors: Boulton Michael J. , Murphy Debborah , Lloyd Julie , Besling Sabine , Coote Jennifer , Lewis Jennifer , Perrin Roxanne , Walsh Linda
Published: November 2011

Despite possible negative effects, many children do not tell their teachers when they have been bullied. This study examined junior school pupils' (N = 294) reports of instrumental, emotional and validation social support received after disclosing being bullied to teachers, and associations with intentions to disclose in the future. Overall, participants reported receiving modest to high levels of social support. The three social support variables accounted for a significant proportion (16.3%) of the variance in intentions to disclose. Each of them also emerged as significant non unique predictors (i.e. not controlling for their shared variance), and validation social support did so even after controlling for the influence of the other two types. These effects were stronger for boys than for girls, and some varied by age. Findings are discussed in terms of outcome‐ expectancy theory and practical implications.
Hsp42 is required for sequestration of protein aggregates into deposition sites in Saccharomyces cerevisiae
Authors: Specht Sebastian , Miller Stephanie B.M. , Mogk Axel , Bukau Bernd
Published: November 2011

The aggregation of proteins inside cells is an organized process with cytoprotective function. In Saccharomyces cerevisiae, aggregating proteins are spatially sequestered to either juxtanuclear or peripheral sites, which target distinct quality control pathways for refolding and degradation. The cellular machinery driving the sequestration of misfolded proteins to these sites is unknown. In this paper, we show that one of the two small heat shock proteins of yeast, Hsp42, is essential for the formation of peripheral aggregates during physiological heat stress. Hsp42 preferentially localizes to peripheral aggregates but is largely absent from juxtanuclear aggregates, which still form in hsp42Δ cells. Transferring the amino-terminal domain of Hsp42 to Hsp26, which does not participate in aggregate sorting, enables Hsp26 to replace Hsp42 function. Our data suggest that Hsp42 acts via its amino-terminal domain to coaggregate with misfolded proteins and perhaps link such complexes to further sorting factors.
Short‐ and long‐term outcomes of intracoronary and endogenously mobilized bone marrow stem cells in the treatment of ST‐segment elevation myocardial infarction: a meta‐analysis of randomized control trials
Authors: Zimmet Hendrik , Porapakkham Pramote , Porapakkham Pornwalee , Sata Yusuke , Haas Steven Joseph , Itescu Silviu , Forbes Andrew , Krum Henry
Published: November 2011

Aims

Bone marrow stem cell (BMSC) treatment of ST‐segment elevation myocardial infarction (STEMI) has been primarily via the intracoronary route or via endogenous mobilization using granulocyte colony‐stimulating factor (G‐CSF). Studies have provided conflicting results. We therefore performed a meta‐analysis of these treatments, examining short‐ and long‐term efficacy and safety.

Methods and results

Randomized controlled trials (RCTs) of BMSC‐based therapy for STEMI, delivered within 9 days of reperfusion, were identified by systematic search. Random effects models were used to calculate pooled effects of clinical outcomes, with meta‐regression to assess dependence of the magnitude of effect sizes on study characteristics. Twenty‐nine RCTs enrolling 1830 patients were included. Intracoronary BMSC therapy resulted in an overall improvement in left ventricular ejection fraction (LVEF) of 2.70% [95% confidence interval (CI) 1.48–3.92; P < 0.001] in the short term and 3.31% (95% CI 1.87–4.75; P < 0.001) longer term. Meta‐regression suggested a dose–response relationship between quantity of CD34+ cells delivered and increase in LVEF (P = 0.007). G‐CSF treatment resulted in a trend towards similar benefits (P = 0.20). No significant differences were observed in pooled adverse outcome rates between intervention and control groups of either treatment approach, except for lower revascularization rates with intracoronary BMSC vs. control (odds ratio 0.68, 95% CI 0.47–0.97; P = 0.03).

Conclusions

Intracoronary BMSC therapy post‐STEMI improves LVEF beyond standard medical treatment, in both the short and longer term. G‐CSF treatment shows positive but non‐significant trends. Both treatments demonstrate safety comparable with conventional medical treatment.
The Iturin-like Lipopeptides Are Essential Components in the Biological Control Arsenal of Bacillus subtilis Against Bacterial Diseases of Cucurbits
Authors: Zeriouh Houda , Romero Diego , García-Gutiérrez Laura , Cazorla Francisco M. , de Vicente Antonio , Pérez-García Alejandro
Published: November 2011

The antibacterial potential of four strains of Bacillus subtilis, UMAF6614, UMAF6619, UMAF6639, and UMAF8561, previously selected on the basis of their antifungal activity and efficacy against cucurbit powdery mildew, was examined. Among these strains, UMAF6614 and UMAF6639 showed the highest antibacterial activity in vitro, especially against Xanthomonas campestris pv. cucurbitae and Pectobacterium carotovorum subsp. carotovorum. These strains produced the three families of lipopeptide antibiotics known in Bacillus spp.: surfactins, iturins, and fengycins. Using thin-layer chromatography analysis and direct bioautography, the antibacterial activity could be associated with iturin lipopeptides. This result was confirmed by mutagenesis analysis using lipopeptide-defective mutants. The antibacterial activity was practically abolished in iturin-deficient mutants, whereas the fengycin mutants retained certain inhibitory capabilities. Analyses by fluorescence and transmission electron microscopy revealed the cytotoxic effect of these compounds at the bacterial plasma membrane level. Finally, biological control assays on detached melon leaves demonstrated the ability of UMAF6614 and UMAF6639 to suppress bacterial leaf spot and soft rot; accordingly, the biocontrol activity was practically abolished in mutants deficient in iturin biosynthesis. Taken together, our results highlight the potential of these B. subtilis strains as biocontrol agents against fungal and bacterial diseases of cucurbits and the versatility of iturins as antifungal and antibacterial compounds.
Mitochondrial Haplotype Analysis for Differentiation of Isolates of Phytophthora cinnamomi
Authors: Martin F. N. , Coffey M. D.
Published: November 2011

Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.
The Response of Diatom Central Carbon Metabolism to Nitrogen Starvation Is Different from That of Green Algae and Higher Plants
Authors: Hockin Nicola Louise , Mock Thomas , Mulholland Francis , Kopriva Stanislav , Malin Gill
Published: November 2011

The availability of nitrogen varies greatly in the ocean and limits primary productivity over large areas. Diatoms, a group of phytoplankton that are responsible for about 20% of global carbon fixation, respond rapidly to influxes of nitrate and are highly successful in upwelling regions. Although recent diatom genome projects have highlighted clues to the success of this group, very little is known about their adaptive response to changing environmental conditions. Here, we compare the proteome of the marine diatom Thalassiosira pseudonana (CCMP 1335) at the onset of nitrogen starvation with that of nitrogen-replete cells using two-dimensional gel electrophoresis. In total, 3,310 protein spots were distinguishable, and we identified 42 proteins increasing and 23 decreasing in abundance (greater than 1.5-fold change; P < 0.005). Proteins involved in the metabolism of nitrogen, amino acids, proteins, and carbohydrates, photosynthesis, and chlorophyll biosynthesis were represented. Comparison of our proteomics data with the transcriptome response of this species under similar growth conditions showed good correlation and provided insight into different levels of response. The T. pseudonana response to nitrogen starvation was also compared with that of the higher plant Arabidopsis (Arabidopsis thaliana), the green alga Chlamydomonas reinhardtii, and the cyanobacterium Prochlorococcus marinus. We have found that the response of diatom carbon metabolism to nitrogen starvation is different from that of other photosynthetic eukaryotes and bears closer resemblance to the response of cyanobacteria.
Trend analysis of cancer incidence in Japan using data from selected population‐based cancer registries
Authors: Katanoda Kota , Ajiki Wakiko , Matsuda Tomohiro , Nishino Yoshikazu , Shibata Akiko , Fujita Manabu , Tsukuma Hideaki , Ioka Akiko , Soda Midori , Sobue Tomotaka
Published: November 2011

Population‐based cancer registries are operated by over 80% of prefectures in Japan. However, only a limited proportion of the registries can provide long‐term incidence data. Here, we aimed to establish a method for monitoring cancer incidence trends in Japan using data from selected prefectures. Based on the availability of long‐term (≥20 years) high‐quality data, we collected incidence data from five prefectures (Miyagi, Yamagata, Fukui, Osaka, and Nagasaki), which included an annual average of 54 539 primary cancer cases diagnosed between 1985 and 2004. Cancer mortality data for 1995–2004 were obtained from the vital statistics. Representativeness and homogeneity of the trends were examined by funnel plot analysis of log‐linear regression coefficients calculated for the most recent 10 years of data (1995–2004) of age‐standardized rates (ASR). The ASR of incidence for five prefectures in total (5‐pref total) showed a significant decrease, with an annual percent change (APC) of −1.0 (95% confidence interval [CI] −1.4: −0.6) for males and −0.4 (95% CI −0.8: −0.1) for females. Excluding data from Osaka (4‐pref total) reversed the decreasing trend; the corresponding APC was +0.4 (95% CI −0.2: +1.0) for males and +0.7 (95% CI +0.5: +0.9) for females. The APCs for the ASR of mortality for the 4‐pref total (males, −1.5; females, −1.3) were more representative of nationwide data (males, −1.4 [95% CI −1.7: −1.2]; females, −1.1 [95% CI −1.4: −0.9]) than those for the 5‐pref total (males, −1.7; females, −1.4). We conclude that using data from Miyagi, Yamagata, Fukui, and Nagasaki prefectures, with continuous monitoring of the representativeness of the data, is a provisionally relevant way to evaluate cancer incidence trends in Japan. (Cancer Sci 2012; 103: 360–368)
Fatigue in out‐patients with inflammatory bowel disease is common and multifactorial
Authors: Bager P. , Befrits R. , Wikman O. , Lindgren S. , Moum B. , Hjortswang H. , Hjollund N. H. , Dahlerup J. F.
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 133–141

Background  Patients with inflammatory bowel disease (IBD) often complain of fatigue.

Aim  To investigate the prevalence and characteristics of fatigue among IBD out‐patients in Scandinavia and to provide normative values for fatigue in IBD patients.

Methods  A cross‐sectional study was conducted on 425 IBD patients from six out‐patient centres in Denmark, Norway and Sweden. Fatigue was measured using the Multidimensional Fatigue Inventory. The patients were also screened for anaemia and iron deficiency. Each centre included approximately 5% of their IBD cohort. The patients were enrolled consecutively from the out‐patient clinics, regardless of disease activity and whether the visit was scheduled. The fatigue analysis was stratified for age and gender.

Results  Using the 95th percentile of the score of the general population as a cut‐off, approximately 44% of the patients were fatigued. When comparing the IBD patients with disease activity to the IBD patients in remission, all dimensions of fatigue were statistically significant (P < 0.05). Being anaemic or iron deficient was not associated with increased fatigue. Being a male patient with ulcerative colitis treated with corticosteroids was a strong determinant for increased fatigue. The normative ranges for IBD fatigue were calculated.

Conclusions  Fatigue in IBD is common regardless of anaemia or iron deficiency. Fatigue in IBD is most marked for patients <60 years of age. Stratifying for gender and age is necessary when analysing fatigue, as fatigue is expressed differently between groups.
Primary hyperoxaluria in Coton de Tulear
Authors: Vidgren G. , Vainio‐Siukola K. , Honkasalo S. , Dillard K. , Anttila M. , Vauhkonen H.
Published: November 2011

Primary hyperoxaluria (PH) is a rare autosomal recessive disorder of glyoxylate metabolism in humans. It is characterized by the accumulation of oxalate and subsequent precipitation of calcium oxalate crystals, primarily in the kidneys. Deficiencies in glyoxylate‐metabolizing enzymes alanine‐glyoxylate aminotransferase (AGXT) or glyoxylate reductase/hydroxypyruvate reductase (GRHPR) occur in 95% of PH cases. Seven Coton de Tulear puppies from four apparently unrelated litters were examined owing to sudden illness at the age of 3–4 weeks. A complete necropsy was performed. The typical finding was tubular necrosis with extensive oxalate crystal deposition. Based on history and necropsy findings, PH was suspected. Eight microsatellite loci flanking AGXT and GRHPR were analysed, and based on segregation results, AGXT was suspected as to be the candidate gene. AGXT exon sequencing revealed a single base change (c.996G>A) that changed one conserved residue (p.Gly102Ser). The mutation was tested in of 118 Finnish Coton de Tulear dogs, ten (8.5%) of which were revealed as carriers. This preliminary study reports PH as a cause of neonatal death in Finnish Coton de Tulear and suggests that genetic testing of dogs be carried out before breeding to prevent the birth of affected offspring.
Psychosocial aspects of haemophilia: a systematic review of methodologies and findings
Authors: CASSIS F. R. M. Y , QUEROL F. , FORSYTH A. , IORIO A. ,   ON BEHALF OF THE HERO INTERNATIONAL ADVISORY BOARD
Published: November 2011

Summary.  Psychosocial factors have a significant impact on quality of life for patients with chronic diseases such as haemophilia. Interventions to support the psychosocial needs of patients and their families, such as offering information and assistance, clarifying doubts, and teaching coping strategies to minimize the impact of disabilities, may help to maximize patient outcomes and improve quality of life for their families. The aim of this study was to evaluate the current literature on psychosocial aspects of haemophilia. Literature searches were performed using the PubMed database to identify studies evaluating psychosocial stressors in persons with haemophilia. Articles pertaining to the HIV epidemic were excluded from the analysis, as were those published before 1997. The literature reviews identified 24 studies, covering a range of different populations, generally with small cohorts (n < 100). Most studies were questionnaire based, with almost no overlap in terms of the instruments used. Only one study combined questionnaire techniques with qualitative methods. Except for two European studies, all publications reported data from a single country. Overall, studies tended to show that quality of life is reduced in persons with haemophilia, with a potential impact on education and employment, particularly when prophylactic treatment is not available. Carrier status in women may have a psychosocial impact and affect reproductive choices. Data on psychosocial aspects of the haemophilia life cycle are lacking in the published literature, along with data from developing countries. There is a need for more international, multifaceted research to explore and quantify the social and psychological aspects of life with haemophilia.
Tree diversity enhances tree transpiration in a Panamanian forest plantation
Authors: Kunert Norbert , Schwendenmann Luitgard , Potvin Catherine , Hölscher Dirk
Published: November 2011

1. Tree plantations play an important role in meeting the growing demand for wood, but there is concern about their high rates of water use. Recent approaches to reforestation in the tropics involve the establishment of multispecies plantations, but few studies have compared water use in mixed vs. monospecific stands.

2. We hypothesized that tree species diversity enhances stand transpiration. Tree water use rates were estimated in monocultures (n = 5), two‐species mixtures (n = 3), three‐species mixtures (n = 3) and five‐species mixtures (n = 4). Sap flux densities were monitored with thermal dissipation probes in 60 trees for 1 year in a 7‐year‐old native tree plantation in Panama. We also estimated changes in the amount of wood produced per unit water transpired (i.e. water use efficiency, WUEwood).

3. Annual stand transpiration rates in two‐/three‐species mixtures (464 ± 271 mm year−1) and five‐species mixtures (900 ± 76 mm year−1) were 14% and 56% higher than those of monocultures (398 ± 293 mm year−1), respectively. Trees growing in mixtures had larger diameters, conductive sapwood and basal area than those in monocultures, which partly explained the enhanced stand transpiration in mixtures.

4. The five‐species mixtures maintained equally high stand transpiration rates during wet (2·64 ± 0·30 mm day−1) and dry seasons (2·51 ± 0·21 mm day−1), whereas monocultures and two‐species mixtures had significantly lower transpiration rates during the dry season, because of the presence of dry season deciduous species.

5. The WUEwood of the five‐species mixtures (2·1 g DM kg−1 H2O) was about half that of either monocultures, two‐ or three‐species mixtures.

6. The comparably high stand transpiration rates in the five‐species plots may arise from enhanced vegetation‐atmosphere‐energy exchange through higher canopy roughness and/or complementary use of soil water.

7. Synthesis and applications. Stand transpiration increased linearly with tree species richness and basal area in monocultures, two‐ and three‐species mixtures, but the ratio of stand transpiration to basal area was larger for five‐species mixtures. In conclusion, species selection and consideration of species richness and composition is crucial in the design of plantations to maximize wood production while conserving water resources.
cAMP‐CRP co‐ordinates the expression of the protein acetylation pathway with central metabolism in Escherichia coli
Authors: Castaño‐Cerezo Sara , Bernal Vicente , Blanco‐Catalá Jorge , Iborra José L. , Cánovas Manuel
Published: November 2011

Lysine acetylation is a well‐established post‐translational modification widely conserved and distributed in bacteria. Although multiple regulatory roles have been proved, little is known about its regulation. Here, we present evidence that the transcription of the Gcn5‐like acetyltransferase YfiQ of Escherichia coli (proposed name: PatZ) is regulated by cAMP‐CRP and its implications on acetate metabolism regulation. The acetate scavenging acetyl‐CoA synthetase (Acs) is regulated at the transcriptional and post‐translational levels. Post‐translational regulation depends on a protein acetyltransferase (yfiQ) and an NAD+‐dependent deacetylase (cobB). We have studied their expression under different environmental conditions. cobB is constitutively expressed from a promoter located upstream nagK. The expression of yfiQ occurs from its own promoter; it is upregulated in the stationary phase and in the presence of non‐PTS carbon sources and is positively regulated by cAMP‐CRP. Two putative CRP binding sites are necessary for its full activity. Gene deletion revealed that cobB is essential for growth on acetate, yfiQ deletion restoring growth of the cobB mutant. The fine tuning of metabolic enzymes results from the integration of multiple mechanisms, and redundant systems may exist. Despite the existence of divergent catabolite repression systems, this may be a conserved strategy common to both Gram‐positive and ‐negative bacteria.
Sulfoquinovose synthase – an important enzyme in the N‐glycosylation pathway of Sulfolobus acidocaldarius
Authors: Meyer Benjamin H. , Zolghadr Behnam , Peyfoon Elham , Pabst Martin , Panico Maria , Morris Howard R. , Haslam Stuart M. , Messner Paul , Schäffer Christina , Dell Anne , Albers Sonja‐Verena
Published: November 2011

Recently, the Surface (S)‐layer glycoprotein of the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius was found to be N‐glycosylated with a heterogeneous family of glycans, with the largest having a composition Glc1Man2GlcNAc2 plus 6‐sulfoquinovose. However, genetic analyses of genes involved in the N‐glycosylation process in Crenarchaeota were missing so far. In this study we identify a gene cluster involved in the biosynthesis of sulfoquinovose and important for the assembly of the S‐layer N‐glycans. A successful markerless in‐frame deletion of agl3 resulted in a decreased molecular mass of the S‐layer glycoprotein SlaA and the flagellin FlaB, indicating a change in the N‐glycan composition. Analyses with nanoLC ES‐MS/MS confirmed the presence of only a reduced trisaccharide structure composed of Man1GlcNAc2, missing the sulfoquinovose, a mannose and glucose. Biochemical studies of the recombinant Agl3 confirmed the proposed function as a UDP‐sulfoquinovose synthase. Furthermore, S. acidocaldarius cells lacking agl3 had a significantly lower growth rate at elevated salt concentrations compared with the background strain, underlining the importance of the N‐glycosylation to maintain an intact and stable cell envelope, to enable the survival of S. acidocaldarius in its extreme environment.
CDKB2 is involved in mitosis and DNA damage response in rice
Authors: Endo Masaki , Nakayama Shigeki , Umeda‐Hara Chikage , Ohtsuki Namie , Saika Hiroaki , Umeda Masaaki , Toki Seiichi
Published: November 2011

DNA damage checkpoints delay mitotic cell‐cycle progression in response to DNA stress, stalling the cell cycle to allow time for repair. CDKB is a plant‐specific cyclin‐dependent kinase (CDK) that is required for the G2/M transition of the cell cycle. In Arabidopsis, DNA damage leads the degradation of CDKB2, and the subsequent G2 arrest gives cells time to repair damaged DNA. G2 arrest also triggers transition from the mitotic cycle to endoreduplication, leading to the presence of polyploid cells in many tissues. In contrast, in rice (Oryza sativa), polyploid cells are found only in the endosperm. It was unclear whether endoreduplication contributes to alleviating DNA damage in rice (Oryza sativa). Here, we show that DNA damage neither down‐regulates Orysa;CDKB2;1 nor induces endoreduplication in rice. Furthermore, we found increased levels of Orysa;CDKB2;1 protein upon DNA damage. These results suggest that CDKB2 functions differently in Arabidopsis and rice in response to DNA damage. Arabidopsis may adopt endoreduplication as a survival strategy under genotoxic stress conditions, but rice may enhance DNA repair capacity upon genotoxic stress. In addition, polyploid cells due to endomitosis were present in CDKB2;1 knockdown rice, suggesting an important role for Orysa;CDKB2;1 during mitosis.
Using the genomic relationship matrix to predict the accuracy of genomic selection
Authors: Goddard M.E. , Hayes B.J. , Meuwissen T.H.E.
Published: November 2011

Estimated breeding values (EBVs) using data from genetic markers can be predicted using a genomic relationship matrix, derived from animal’s genotypes, and best linear unbiased prediction. However, if the accuracy of the EBVs is calculated in the usual manner (from the inverse element of the coefficient matrix), it is likely to be overestimated owing to sampling errors in elements of the genomic relationship matrix. We show here that the correct accuracy can be obtained by regressing the relationship matrix towards the pedigree relationship matrix so that it is an unbiased estimate of the relationships at the QTL controlling the trait. This method shows how the accuracy increases as the number of markers used increases because the regression coefficient (of genomic relationship towards pedigree relationship) increases. We also present a deterministic method for predicting the accuracy of such genomic EBVs before data on individual animals are collected. This method estimates the proportion of genetic variance explained by the markers, which is equal to the regression coefficient described above, and the accuracy with which marker effects are estimated. The latter depends on the variance in relationship between pairs of animals, which equals the mean linkage disequilibrium over all pairs of loci. The theory was validated using simulated data and data on fat concentration in the milk of Holstein cattle.
Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments
Authors: Ma Yingfei , Paulsen Ian T. , Palenik Brian
Published: November 2011

Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry‐sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.
Oncological outcome after laparoscopic abdominoperineal excision of the rectum
Authors: Jefferies M. T. , Evans M. D. , Hilton J. , Chandrasekaran T. V. , Beynon J. , Khot U.
Published: November 2011

Aim  Abdominoperineal excision of the rectum (APER) for cancer has been associated with higher circumferential resection margin (CRM) involvement and failure of local disease control. The aim of this study was to investigate whether the introduction of laparoscopic APER altered the incidence of CRM involvement.

Method  Consecutive patients undergoing open or laparoscopic APER for adenocarcinomas of the rectum were studied. Patient demographics, preoperative staging, neoadjuvant treatment, operative findings, length of stay and pathological details were collected from operative and radiology databases and compared.

Results  There were 16 laparoscopic and 25 open APER performed over a 3‐year period. Neoadjuvant therapy was given to 43.8% (7/16) of the laparoscopic group and 56.0% (14/25) of the open group. Complete laparoscopic resection was possible in 14 (87.5%) of 16 patients. The median harvested number of nodes was 14 (4–33) in both groups. The median length of stay was 7 (3–13) and 15 (9–40) days in the laparoscopic and open groups (P < 0.001). The CRM was clear in all cases. There was no local recurrence in either group at a median follow‐up of 23 months. There were no in‐hospital deaths and no significant differences in overall survival. There were no significant differences in preoperative or postoperative histopathological T stage between the two groups (P = 0.057 and P = 0.121).

Conclusion  Laparoscopic APER for selected rectal cancers can achieve comparable oncological outcome to open surgery but is associated with a much shorter length of stay. Patient and tumour characteristics must be taken into consideration when deciding on a laparoscopic approach for low rectal cancer.