bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic and deterministic assembly processes in subsurface microbial communities
Authors: Stegen James C , Lin Xueju , Konopka Allan E , Fredrickson James K 
Published: March 2012

Abstract
A major goal of microbial community ecology is to understand the forces that structure community composition. Deterministic selection by specific environmental factors is sometimes important, but in other cases stochastic or ecologically neutral processes dominate. Lacking is a unified conceptual framework aiming to understand why deterministic processes dominate in some contexts but not others. Here we work toward such a framework. By testing predictions derived from general ecological theory we aim to uncover factors that govern the relative influences of deterministic and stochastic processes. We couple spatiotemporal data on subsurface microbial communities and environmental parameters with metrics and null models of within and between community phylogenetic composition. Testing for phylogenetic signal in organismal niches showed that more closely related taxa have more similar habitat associations. Community phylogenetic analyses further showed that ecologically similar taxa coexist to a greater degree than expected by chance. Environmental filtering thus deterministically governs subsurface microbial community composition. More importantly, the influence of deterministic environmental filtering relative to stochastic factors was maximized at both ends of an environmental variation gradient. A stronger role of stochastic factors was, however, supported through analyses of phylogenetic temporal turnover. Although phylogenetic turnover was on average faster than expected, most pairwise comparisons were not themselves significantly non-random. The relative influence of deterministic environmental filtering over community dynamics was elevated, however, in the most temporally and spatially variable environments. Our results point to general rules governing the relative influences of stochastic and deterministic processes across micro- and macro-organisms.
Viral clones from the GOS expedition with an unusual photosystem-I gene cassette organization
Authors: Béjà Oded , Fridman Svetlana , Glaser Fabian 
Published: March 2012

Abstract
Cyanobacteria have a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Genes encoding for photosystem-II (PSII) and photosystem-I (PSI) reaction centers are found in different cyanophage genomes, and it was suggested that the horizontal transfer of these genes might be involved in increasing phage fitness. We have further analyzed a rare viral Global Ocean Sampling (GOS) clone containing PSI genes. This clone contains the unusual PSI gene organization psaD-&gt;C-&gt;A, as opposed to the more frequently observed viral psaJF-&gt;C-&gt;A-&gt;B-&gt;K-&gt;E-&gt;D organization, and was detected only once in the GOS metagenome. Our analyses identified more occurrences with similar arrangement and indicate that this PSI viral gene organization (now psaD-&gt;C-&gt;A-&gt;B), although rare, is authentic and represents a new PSI gene arrangement.
DNAJB6 governs a novel regulatory loop determining Wnt/β-catenin signalling activity
Authors: Menezes Mitchell E. , Mitra Aparna , Shevde Lalita A. , Samant Rajeev S. 
Published: March 2012

DKK1 (dickkopf 1 homologue) is a secreted inhibitor of the Wnt signalling pathway and a critical modulator of tumour promotion and the tumour microenvironment. However, mechanisms regulating DKK1 expression are understudied. DNAJB6 {DnaJ [HSP40 (heat-shock protein 40 kDa)] homologue, subfamily B, member 6} is an HSP40 family member whose expression is compromized during progression of breast cancer and melanoma. Inhibition of the Wnt/β-catenin signalling pathway by up-regulation of DKK1 is one of the key mechanisms by which DNAJB6 suppresses tumour metastasis and EMT (epithelial–mesenchymal transition). Analysis of the DKK1 promoter to define the cis-site responsible for its up-regulation by DNAJB6 revealed the presence of two binding sites for a transcriptional repressor, MSX1 (muscle segment homeobox 1). Our investigations showed that MSX1 binds the DKK1 promoter and inhibits DKK1 transcription. Interestingly, silencing DNAJB6 resulted in up-regulation of MSX1 concomitant with increased stabilization of β-catenin. ChIP (chromatin immunoprecipitation) studies revealed that β-catenin binds the MSX1 promoter and stabilization of β-catenin elevates MSX1 transcription, indicating that β-catenin works as a transcription co-activator for MSX1. Functionally, exogenous expression of MSX1 in DNAJB6-expressing cells promotes the mesenchymal phenotype by suppression of DKK1. Thus we have identified a novel regulatory mechanism of DNAJB6-mediated DKK1 transcriptional up-regulation that can influence EMT. DKK1 is a feedback regulator of β-catenin levels and thus our studies also define an additional negative control of this β-catenin/DKK1 feedback loop by MSX1, which may potentially contribute to excessive stabilization of β-catenin.
Pancreatic Autoantibodies and Autoantibodies Against Goblet Cells in Pediatric Patients With Inflammatory Bowel Disease
Authors: Kovacs Marta , Lakatos Peter Laszlo , Papp Maria , Jacobsen Silvia , Nemes Eva , Polgar Marianne , Solyom Eniko , Bodi Piroska , Horvath Agnes , Muller Katalin Eszter , Molnar Kriszta , Szabo Doloresz , Cseh Aron , Dezsofi Antal , Arato Andras , Veres Gabor 
Published: March 2012

ABSTRACTBackground:Significance of pancreatic autoantibodies determined by using exocrine pancreas (PAB) and antibodies against recombinant pancreas antigen (rPAB), as well as the importance of autoantibodies against goblet cells (GAB), is not known in pediatric patients with inflammatory bowel disease (IBD). Our aim was to determine the complex analysis of PAB, rPAB, GAB, antibodies against Saccharomyces cerevisiae, and perinuclear components of neutrophils in pediatric patients with IBD. Moreover, association with NOD2/CARD15 and disease phenotype was determined.Methods:A total of 152 pediatric patients (median age 13.9 years) with IBD (103 patients with Crohn disease [CD] and 49 patients with ulcerative colitis [UC]) and 104 controls were included. Serum autoantibodies were determined by indirect immunofluorescence assay. NOD2/CARD15 variants were tested by polymerase chain reaction/restriction fragment length polymorphism.Results:The presence of PAB and rPAB was significantly higher in CD (34% and 35.9%) and in UC (20.4% and 24.5%) compared with pediatric control cohort (0% and 0%, P < 0.0001). In addition, GAB positivity was significantly increased in patients with UC in comparison with CD and controls, respectively (UC, 12.2%; CD, 1.9%; controls, 1.9%; P = 0.02). Specificity of PAB and rPAB was 100%; however, sensitivity was low. The combination of PAB and/or antibodies against Saccharomyces cerevisiae/perinuclear components of neutrophils improved the sensitivity of serological markers in CD (87.4%) and in UC (79.6%); specificities were 89.3% and 93.2%, respectively. Pancreatic autoantibodies (PAB, rPAB) and GAB were not related to clinical presentation, medical therapy, or need for surgery in CD or in UC.Conclusions:Pancreatic autoantibodies and GAB were specific for IBD, but the sensitivity was limited as well because there was lack of correlation with clinical phenotype. Combinations of these antibodies have shown increased sensitivity; therefore, it may be recommended in the diagnostic procedure of IBD.
The CHD3 Remodeler PICKLE Associates with Genes Enriched for Trimethylation of Histone H3 Lysine 27
Authors: Zhang Heng , Bishop Brett , Ringenberg Whitney , Muir William M. , Ogas Joe 
Published: March 2012

AbstractIn Arabidopsis (Arabidopsis thaliana), the ATP-dependent chromatin remodeler PICKLE (PKL) determines expression of genes associated with developmental identity. PKL promotes the epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3) that facilitates repression of tissue-specific genes in plants. It has previously been proposed that PKL acts indirectly to promote H3K27me3 by promoting expression of the POLYCOMB REPRESSIVE COMPLEX2 complex that generates H3K27me3. We undertook expression and chromatin immunoprecipitation analyses to further characterize the contribution of PKL to gene expression and developmental identity. Our expression data support a critical and specific role for PKL in expression of H3K27me3-enriched loci but do not support a role for PKL in expression of POLYCOMB REPRESSIVE COMPLEX2. Moreover, our chromatin immunoprecipitation data reveal that PKL protein is present at the promoter region of multiple H3K27me3-enriched loci, indicating that PKL directly acts on these loci. In particular, we find that PKL is present at LEAFY COTYLEDON1 and LEAFY COTYLEDON2 during germination, which is when PKL acts to repress these master regulators of embryonic identity. Surprisingly, we also find that PKL is present at the promoters of actively transcribed genes that are ubiquitously expressed such as ACTIN7 and POLYUBIQUITIN10 that do not exhibit PKL-dependent expression. Taken together, our data contravene the previous model of PKL action and instead support a direct role for PKL in determining levels of H3K27me3 at repressed loci. Our data also raise the possibility that PKL facilitates a common chromatin remodeling process that is not restricted to H3K27me3-enriched regions.
Thioredoxin Redox Regulates ATPase Activity of Magnesium Chelatase CHLI Subunit and Modulates Redox-Mediated Signaling in Tetrapyrrole Biosynthesis and Homeostasis of Reactive Oxygen Species in Pea Plants
Authors: Luo Tao , Fan Tingting , Liu Yinan , Rothbart Maxi , Yu Jing , Zhou Shuaixiang , Grimm Bernhard , Luo Meizhong 
Published: March 2012

Abstract
The chloroplast thioredoxins (TRXs) function as messengers of redox signals from ferredoxin to target enzymes. In this work, we studied the regulatory impact of pea (Pisum sativum) TRX-F on the magnesium (Mg) chelatase CHLI subunit and the enzymatic activation of Mg chelatase in vitro and in vivo. In vitro, reduced TRX-F activated the ATPase activity of pea CHLI and enhanced the activity of Mg chelatase reconstituted from the three recombinant subunits CHLI, CHLD, and CHLH in combination with the regulator protein GENOMES UNCOUPLED4 (GUN4). Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that TRX-F physically interacts with CHLI but not with either of the other two subunits or GUN4. In vivo, virus-induced TRX-F gene silencing (VIGS-TRX-F) in pea plants did not result in an altered redox state of CHLI. However, simultaneous silencing of the pea TRX-F and TRX-M genes (VIGS-TRX-F/TRX-M) resulted in partially and fully oxidized CHLI in vivo. VIGS-TRX-F/TRX-M plants demonstrated a significant reduction in Mg chelatase activity and 5-aminolevulinic acid synthesizing capacity as well as reduced pigment content and lower photosynthetic capacity. These results suggest that, in vivo, TRX-M can compensate for a lack of TRX-F and that both TRXs act as important redox regulators of Mg chelatase. Furthermore, the silencing of TRX-F and TRX-M expression also affects gene expression in the tetrapyrrole biosynthesis pathway and leads to the accumulation of reactive oxygen species, which may also serve as an additional signal for the transcriptional regulation of photosynthesis-associated nuclear genes.
A bZIP Protein, VIP1, Is a Regulator of Osmosensory Signaling in Arabidopsis
Authors: Tsugama Daisuke , Liu Shenkui , Takano Tetsuo 
Published: March 2012

Abstract
Abscisic acid is a stress-related phytohormone that has roles in dehydration and rehydration. In Arabidopsis (Arabidopsis thaliana), two genes that inactivate abscisic acid, CYP707A1 and CYP707A3, are rapidly up-regulated upon rehydration. The factors that regulate CYP707A1/3 are not well characterized. We expressed a bZIP protein, VIP1, as a green fluorescent protein fusion protein in Arabidopsis and found that the nuclear localization of VIP1 was enhanced within 10 min after rehydration. A yeast one-hybrid assay revealed that the amino-terminal region of VIP1 has transcriptional activation potential. In a transient reporter assay using Arabidopsis protoplasts, VIP1 enhanced the promoter activities of CYP707A1/3. In gel shift and chromatin immunoprecipitation analyses, VIP1 directly bound to DNA fragments of the CYP707A1/3 promoters. Transgenic plants expressing VIP1-green fluorescent protein were found to overexpress CYP707A1/3 mRNAs. The time course of nuclear-cytoplasmic shuttling of VIP1 was consistent with the time courses of the expression of CYP707A1/3. These results suggest that VIP1 functions as a regulator of osmosensory signaling in Arabidopsis.
Elevational trends in butterfly phenology: implications for species responses to climate change
Authors: ILLÁN JAVIER GUTIÉRREZ , GUTIÉRREZ DAVID , DÍEZ SONIA B. , WILSON ROBERT J. 
Published: March 2012

1. Impacts of global change on the distribution, abundance, and phenology of species have been widely documented. In particular, recent climate change has led to widespread changes in animal and plant seasonality, leading to debate about its potential to cause phenological mismatches among interacting taxa.2. In mountainous regions, populations of many species show pronounced phenological gradients over short geographic distances, presenting the opportunity to test for effects of climate on phenology, independent of variation in confounding factors such as photoperiod.3. Here we show for 32 butterfly species sampled for five years over a 1700 m gradient (560–2260 m) in a Mediterranean mountain range that, on average, annual flight period is delayed with elevation by 15–22 days per kilometre. Species mainly occurring at low elevations in the region, and to some extent those flying earlier in the year, showed phenological delays of 23–36 days per kilometre, whereas the flight periods of species that occupy high elevations, or fly in late summer, were consistently more synchronised over the elevation gradient.4. Elevational patterns in phenology appear to reflect a narrowing phenological window of opportunity for larval and adult butterfly activity of high elevation and late‐flying species.5. Here, we speculate as to the causes of these patterns, and the consequences for our ability to predict species responses to climate change. Our results raise questions about the use of space–time substitutions in predicting phenological responses to climate change, since traits relating to flight period and environmental associations may influence the capacity of species to adapt to changing climates.
The transcription factor Grainy head and the steroid hormone ecdysone cooperate during differentiation of the skin of Drosophila melanogaster
Authors: Gangishetti U. , Veerkamp J. , Bezdan D. , Schwarz H. , Lohmann I. , Moussian B. 
Published: March 2012

AbstractThe arthropod epidermis is an epithelium that deposits the apical cuticle, which is a stratified extracellular matrix (ECM) protecting the animal against pathogens, preventing dehydration and also serving as an exoskeleton. Differentiation of the cuticle conceivably implies coordinated production, secretion and localization of its components. The underlying molecular mechanisms are poorly explored. In this work, we show that the transcription factor Grainy head and the steroid hormone ecdysone drive the production of two partially overlapping sets of cuticle factors. Nevertheless, Grainy head is needed to modulate the expression of ecdysone signalling factors; the significance of this cross‐talk is yet unclear. In addition, we found that ecdysone signalling negatively regulates its own impact. In conclusion, our findings suggest that at least two independently triggered pathways have evolved in parallel to cooperatively ensure the stereotypic implementation of the cuticle. As Grainy head is also essential for epithelial differentiation in vertebrates, we speculate that it acts to decode the ancient skin programme common to all animals. Full differentiation of the skin necessitates a second, complementing taxon‐specific programme that requires its own decoder, which is represented by ecdysone in arthropods, whereas the vertebrate specific one remains to be identified.
Resistance to spiromesifen in Trialeurodes vaporariorum is associated with a single amino acid replacement in its target enzyme acetyl‐coenzyme A carboxylase
Authors: Karatolos N. , Williamson M. S. , Denholm I. , Gorman K. , ffrench‐Constant R. , Nauen R. 
Published: March 2012

AbstractSpiromesifen is a novel insecticide and is classed as a tetronic acid derivative. It targets the insects' acetyl‐coenzyme A carboxylase (ACCase) enzyme, causing a reduction in lipid biosynthesis. At the time of this publication, there are no reports of resistance to this class of insecticides in insects although resistance has been observed in several mite species. The greenhouse whitefly Trialeurodes vaporariorum (Westwood) is a serious pest of protected vegetable and ornamental crops in temperate regions of the world and spiromesifen is widely used in its control. Mortality rates of UK and European populations of T. vaporariorum to spiromesifen were calculated and up to 26‐fold resistance was found. We therefore sought to examine the molecular mechanism underlying spiromesifen resistance in this important pest. Pre‐treatment with piperonyl butoxide did not synergize spiromesifen, suggesting a target‐site resistance mechanism. The full length ACCase gene was sequenced for a range of T. vaporariorum strains and a strong association was found between spiromesifen resistance and a glutamic acid substitution with lysine in position 645 (E645K) of this gene. A TaqMan allelic discrimination assay confirmed these findings. Although this resistance is not considered sufficient to compromise the field performance of spiromesifen, this association of E645K with resistance is the first report of a potential target site mechanism affecting an ACCase inhibitor in an arthropod species.
Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes
Authors: Adelman Z. N. , Anderson M. A. E. , Liu M. , Zhang L. , Myles K. M. 
Published: March 2012

AbstractSmall RNA regulatory pathways are used to control the activity of transposons, regulate gene expression and resist infecting viruses. We examined the biogenesis of mRNA‐derived endogenous short‐interfering RNAs (endo‐siRNAs) in the disease vector mosquito Aedes aegypti. Under standard conditions, mRNA‐derived endo‐siRNAs were produced from the bidirectional transcription of tail−tail overlapping gene pairs. Upon infection with the alphavirus, Sindbis virus (SINV), another class of mRNA‐derived endo‐siRNAs was observed. Genes producing SINV‐induced endo‐siRNAs were not enriched for overlapping partners or nearby genes, but were enriched for transcripts with long 3′ untranslated regions. Endo‐siRNAs from this class derived uniformly from the entire length of the target transcript, and were found to regulate the transcript levels of the genes from which they were derived. Strand‐specific quantitative PCR experiments demonstrated that antisense strands of targeted mRNA genes were produced to exonic, but not intronic regions. Finally, small RNAs mapped to both sense and antisense strands of exon−exon junctions, suggesting double‐stranded RNA precursors to SINV‐induced endo‐siRNAs may be synthesized from mature mRNA templates. These results suggest additional complexity in small RNA pathways and gene regulation in the presence of an infecting virus in disease vector mosquitoes.
Detection and speciation of brominated flame retardants in high‐impact polystyrene (HIPS) polymers
Authors: HOLBROOK R.D. , DAVIS J.M. , SCOTT K.C.K. , SZAKAL C. 
Published: March 2012

SummaryPolymeric materials have been suggested as possible environmental sources of persistent organic pollutants such as flame retardants. In situ, micrometre‐scale characterization techniques for polymer matrix containing flame retardants may provide some insight into the dominant environmental transfer mechanism(s) of these brominated compounds. In this work, we demonstrate that micro X‐ray fluorescence spectroscopy (μXRF), focused ion beam scanning electron microscopy (FIB‐SEM) combined with energy dispersive X‐ray spectroscopy (EDS), and time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) are promising techniques for the elemental and chemical identification of brominated fire retardant compounds (such as the deca‐congener of polybrominated diphenyl ether, BDE‐209) within polymeric materials (e.g. high‐impact polystyrene or HIPS). Data from μXRF demonstrated that bromine (Br) inclusions were evenly distributed throughout the HIPS samples, whereas FIB SEM‐EDS analysis revealed that small antimony (Sb) and Br inclusions are present, and regionally higher concentrations of Br surround the Sb inclusions (compared to the bulk material). Four prominent mass‐to‐charge ratio peaks (m/z 485, 487, 489 and 491) that correspond to BDE‐209 were identified by ToF‐SIMS and can be used to chemically distinguish this molecule on the surface of polymeric materials with respect to other brominated organic molecules. These techniques can be important in any study that investigates the route of entry to the environmental surroundings of BDE‐containing materials.
Neurosurgery in the age of Cushing: the achievement of Leonard Lindon
Authors: Simpson Donald 
Published: March 2012

AbstractLeonard Lindon was the first neurosurgeon on the staff of the Royal Adelaide Hospital, and headed this hospital's neurosurgical service from 1931 to 1951, with an interruption from war service. Like other early neurosurgeons, Lindon began as a general surgeon. In 1929, when he was well established in his surgical practice, he took unpaid leave from his hospital duties to undertake a study tour of neurosurgical centres in Europe and North America.Lindon visited the London Hospital, where Hugh Cairns, like him, an Adelaide medical graduate and veteran of Gallipoli, was establishing a modern neurosurgical service. Lindon also visited Harvey Cushing in Boston, USA. Cushing was then at the zenith of his reputation as the master of a safe neurosurgical operative technique; he was also famous for his contributions in the neurosciences. Lindon was deeply impressed by Cushing's philosophy and his operative methods. When Lindon returned to Adelaide in 1930, he prepared a plan for a neurosurgical unit in Adelaide, and over the next 20 years, he achieved some of his aims. In this plan, Lindon gave priority to the management of head injuries as a role for neurosurgeons.