bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights into the bovine rumen plasmidome
Authors: Kav Aya Brown , Sasson Goor , Jami Elie , Doron-Faigenboim Adi , Benhar Itai , Mizrahi Itzhak
Published: March 2012

Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.
Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity
Authors: Maurer Till , Garrenton Lindsay S. , Oh Angela , Pitts Keith , Anderson Daniel J. , Skelton Nicholas J. , Fauber Benjamin P. , Pan Borlan , Malek Shiva , Stokoe David , Ludlam Mary J. C. , Bowman Krista K. , Wu Jiansheng , Giannetti Anthony M. , Starovasnik Melissa A. , Mellman Ira , Jackson Peter K. , Rudolph Joachim , Wang Weiru , Fang Guowei
Published: March 2012

The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.
Redox-dependent complex formation by an ATP-dependent activator of the corrinoid/iron-sulfur protein
Authors: Hennig Sandra E. , Jeoung Jae-Hun , Goetzl Sebastian , Dobbek Holger
Published: March 2012

Movement, cell division, protein biosynthesis, electron transfer against an electrochemical gradient, and many more processes depend on energy conversions coupled to the hydrolysis of ATP. The reduction of metal sites with low reduction potentials (E
0′
 < -500 mV) is possible by connecting an energetical uphill electron transfer with the hydrolysis of ATP. The corrinoid-iron/sulfur protein (CoFeSP) operates within the reductive acetyl-CoA pathway by transferring a methyl group from methyltetrahydrofolate bound to a methyltransferase to the [Ni-Ni-Fe
4
S
4
] cluster of acetyl-CoA synthase. Methylation of CoFeSP only occurs in the low-potential Co(I) state, which can be sporadically oxidized to the inactive Co(II) state, making its reductive reactivation necessary. Here we show that an open-reading frame proximal to the structural genes of CoFeSP encodes an ATP-dependent reductive activator of CoFeSP. Our biochemical and structural analysis uncovers a unique type of reductive activator distinct from the electron-transferring ATPases found to reduce the MoFe-nitrogenase and 2-hydroxyacyl-CoA dehydratases. The CoFeSP activator contains an ASKHA domain (acetate and sugar kinases, Hsp70, and actin) harboring the ATP-binding site, which is also present in the activator of 2-hydroxyacyl-CoA dehydratases and a ferredoxin-like [2Fe-2S] cluster domain acting as electron donor. Complex formation between CoFeSP and its activator depends on the oxidation state of CoFeSP, which provides evidence for a unique strategy to achieve unidirectional electron transfer between two redox proteins.
Electroconvulsive therapy reduces frontal cortical connectivity in severe depressive disorder
Authors: Perrin Jennifer S. , Merz Susanne , Bennett Daniel M. , Currie James , Steele Douglas J. , Reid Ian C. , Schwarzbauer Christian
Published: March 2012

To date, electroconvulsive therapy (ECT) is the most potent treatment in severe depression. Although ECT has been successfully applied in clinical practice for over 70 years, the underlying mechanisms of action remain unclear. We used functional MRI and a unique data-driven analysis approach to examine functional connectivity in the brain before and after ECT treatment. Our results show that ECT has lasting effects on the functional architecture of the brain. A comparison of pre- and posttreatment functional connectivity data in a group of nine patients revealed a significant cluster of voxels in and around the left dorsolateral prefrontal cortical region (Brodmann areas 44, 45, and 46), where the average global functional connectivity was considerably decreased after ECT treatment (P< 0.05, family-wise error-corrected). This decrease in functional connectivity was accompanied by a significant improvement (P< 0.001) in depressive symptoms; the patients’ mean scores on the Montgomery Asberg Depression Rating Scale pre- and posttreatment were 36.4 (SD = 4.9) and 10.7 (SD = 9.6), respectively. The findings reported here add weight to the emerging “hyperconnectivity hypothesis” in depression and support the proposal that increased connectivity may constitute both a biomarker for mood disorder and a potential therapeutic target.
Spontaneous mutation of theDock2gene inIrf5−/−mice complicates interpretation of type I interferon production and antibody responses
Authors: Purtha Whitney E. , Swiecki Melissa , Colonna Marco , Diamond Michael S. , Bhattacharya Deepta
Published: March 2012

Genome-wide studies have identified associations between polymorphisms in the IFN regulatory factor-5 (Irf5) gene and a variety of human autoimmune diseases. Its functional role in disease pathogenesis, however, remains unclear, as studies inIrf5−/−mice have reached disparate conclusions regarding the importance of this transcription factor in type I IFN production and antibody responses. We identified a spontaneous genomic duplication and frameshift mutation in the guanine exchange factor dedicator of cytokinesis 2 (Dock2) that has arisen in at least a subset of circulatingIrf5−/−mice and inadvertently been bred to homozygosity. Retroviral expression of DOCK2, but not IRF-5, rescued defects in plasmacytoid dendritic cell and B-cell development, andIrf5−/−mice lacking the mutation inDock2exhibited normal plasmacytoid dendritic cell and B-cell development, largely intact type I IFN responses, and relatively normal antibody responses to viral infection. Thus, confirmation of the normalDock2genotype in circulatingIrf5−/−mice is warranted, and our data may partly explain conflicting results in this field.
Coordination of the transcriptome and metabolome by the circadian clock
Authors: Eckel-Mahan Kristin L. , Patel Vishal R. , Mohney Robert P. , Vignola Katie S. , Baldi Pierre , Sassone-Corsi Paolo
Published: March 2012

The circadian clock governs a large array of physiological functions through the transcriptional control of a significant fraction of the genome. Disruption of the clock leads to metabolic disorders, including obesity and diabetes. As food is a potent zeitgeber (ZT) for peripheral clocks, metabolites are implicated as cellular transducers of circadian time for tissues such as the liver. From a comprehensive dataset of over 500 metabolites identified by mass spectrometry, we reveal the coordinate clock-controlled oscillation of many metabolites, including those within the amino acid and carbohydrate metabolic pathways as well as the lipid, nucleotide, and xenobiotic metabolic pathways. Using computational modeling, we present evidence of synergistic nodes between the circadian transcriptome and specific metabolic pathways. Validation of these nodes reveals that diverse metabolic pathways, including the uracil salvage pathway, oscillate in a circadian fashion and in a CLOCK-dependent manner. This integrated map illustrates the coherence within the circadian metabolome, transcriptome, and proteome and how these are connected through specific nodes that operate in concert to achieve metabolic homeostasis.
Comanagement of coral reef social-ecological systems
Authors: Cinner Joshua E. , McClanahan Tim R. , MacNeil M. Aaron , Graham Nicholas A. J. , Daw Tim M. , Mukminin Ahmad , Feary David A. , Rabearisoa Ando L. , Wamukota Andrew , Jiddawi Narriman , Campbell Stuart J. , Baird Andrew H. , Januchowski-Hartley Fraser A. , Hamed Salum , Lahari Rachael , Morove Tau , Kuange John
Published: March 2012

In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: (
i
) comanagement is largely successful at meeting social and ecological goals; (
ii
) comanagement tends to benefit wealthier resource users; (
iii
) resource overexploitation is most strongly influenced by market access and users’ dependence on resources; and (
iv
) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.
Structural basis for lack of toxicity of the diphtheria toxin mutant CRM197
Authors: Malito Enrico , Bursulaya Badry , Chen Connie , Surdo Paola Lo , Picchianti Monica , Balducci Enrico , Biancucci Marco , Brock Ansgar , Berti Francesco , Bottomley Matthew James , Nissum Mikkel , Costantino Paolo , Rappuoli Rino , Spraggon Glen
Published: March 2012

CRM197 is an enzymatically inactive and nontoxic form of diphtheria toxin that contains a single amino acid substitution (G52E). Being naturally nontoxic, CRM197 is an ideal carrier protein for conjugate vaccines against encapsulated bacteria and is currently used to vaccinate children globally against
Haemophilus influenzae
, pneumococcus, and meningococcus. To understand the molecular basis for lack of toxicity in CRM197, we determined the crystal structures of the full-length nucleotide-free CRM197 and of CRM197 in complex with the NAD hydrolysis product nicotinamide (NCA), both at 2.0-Å resolution. The structures show for the first time that the overall fold of CRM197 and DT are nearly identical and that the striking functional difference between the two proteins can be explained by a flexible active-site loop that covers the NAD binding pocket. We present the molecular basis for the increased flexibility of the active-site loop in CRM197 as unveiled by molecular dynamics simulations. These structural insights, combined with surface plasmon resonance, NAD hydrolysis, and differential scanning fluorimetry data, contribute to a comprehensive characterization of the vaccine carrier protein, CRM197.
MicroRNAs/TP53 feedback circuitry in glioblastoma multiforme
Authors: Suh Sung-Suk , Yoo Ji Young , Nuovo Gerard J. , Jeon Young-Jun , Kim Seokho , Lee Tae Jin , Kim Taewan , Bakàcs Arianna , Alder Hansjuerg , Kaur Balveen , Aqeilan Rami I. , Pichiorri Flavia , Croce Carlo M.
Published: March 2012

MicroRNAs (miRNAs) are increasingly implicated in regulating cancer initiation and progression. In this study, two miRNAs, miR-25 and -32, are identified as p53-repressed miRNAs by p53-dependent negative regulation of their transcriptional regulators, E2F1 and MYC. However, miR-25 and -32 result in p53 accumulation by directly targeting Mdm2 and TSC1, which are negative regulators of p53 and the mTOR (mammalian target of rapamycin) pathway, respectively, leading to inhibition of cellular proliferation through cell cycle arrest. Thus, there is a recurrent autoregulatory circuit involving expression of p53, E2F1, and MYC to regulate the expression of miR-25 and -32, which are miRNAs that, in turn, control p53 accumulation. Significantly, overexpression of transfected miR-25 and -32 in glioblastoma multiforme cells inhibited growth of the glioblastoma multiforme cells in mouse brain in vivo. The results define miR-25 and -32 as positive regulators of p53, underscoring their role in tumorigenesis in glioblastoma.
Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells
Authors: McKinney Caleb , Perez Cesar , Mohr Ian
Published: March 2012

By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5′ UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly.
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of
Arabidopsis
seeds
Authors: Lu Jie , Zhang Changqing , Baulcombe David C. , Chen Z. Jeffrey
Published: March 2012

Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter seed size. Specifically, paternal-excess crosses (2 × 4) delay endosperm cellularization (EC) and produce larger seeds, whereas maternal-excess crosses (4 × 2) promote precocious EC and produce smaller seeds. The mechanisms for responding to the parental genome dosage imbalance and for gene expression changes in endosperm are unknown. In plants, RNA polymerase IV (PolIV or p4) encoded by
NRPD1a
is required for biogenesis of a major class of 24-nt small interfering RNAs (also known as p4-siRNAs), which are predominately expressed in developing endosperm. Here we show that p4-siRNA accumulation depends on the maternal genome dosage, and maternal p4-siRNAs target transposable elements (TEs) and TE-associated genes (
TAG
s) in seeds. The p4-siRNAs correlate negatively with expression levels of AGAMOUS-LIKE (
AGL
) genes in endosperm of interploidy crosses. Moreover, disruption of maternal
NRPD1a
expression is associated with p4-siRNA reduction and
AGL
up-regulation in endosperm of reciprocal crosses. This is unique genetic evidence for maternal siRNAs in response to parental genome imbalance and in control of transposons and gene expression during endosperm development.
Genome-wide analysis of histone H3.1 and H3.3 variants in
Arabidopsis thaliana
Authors: Stroud Hume , Otero Sofía , Desvoyes Bénédicte , Ramírez-Parra Elena , Jacobsen Steven E. , Gutierrez Crisanto
Published: March 2012

Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant
Arabidopsis thaliana
and found that the localization of these variants shows broad similarity in plants and animals, along with some unique features. H3.1 was enriched in silent areas of the genome, including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3′ end of genes, and correlated with histone modifications associated with gene activation, such as histone H3 lysine 4 methylation and H2B ubiquitylation, as well as RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin-disrupting processes like transcription.
A review of selected ecosystem services provided by coastal wetlands of the Laurentian Great Lakes
Authors: Sierszen Michael E. , Morrice John A. , Trebitz Anett S. , Hoffman Joel C.
Published: March 2012

Significant ecosystem services derive from the coastal wetlands of the Laurentian Great Lakes even though two-thirds of the original coastal wetlands have been lost since European settlement, and the remaining 126,000 ha of U.S. coastal wetlands and ≥70,000 ha of Canadian wetlands are affected by anthropogenic stressors. Published information indicates that wildlife habitat, fisheries support, and water quality improvement are significant ecosystem services provided by Great Lakes coastal wetlands that should be strongly considered during management decision making. 30 species of waterfowl, 155 breeding bird species, and 55 species of reptiles and amphibians are supported by coastal wetland habitats across the Basin. Nearly all sport and commercial Great Lakes fish species use coastal wetlands for life-cycle functions, and Great Lakes food webs are supported by wetland export of young sport and forage fish. Biological responses indicate declines in the wildlife and fishery services with increasing levels of anthropogenic disturbance. Extrapolation from a single well-studied system suggests that, Basin-wide, coastal wetlands may retain nearly 4000 tonnes P and 53,000 tonnes N per year, but additional studies are needed to support these estimates and determine stressor effects. Coastal wetlands appear to retain sediments over long time scales, but may either retain or release sediments during storm events. Extrapolation of carbon sequestration from other wetland types suggests that less than 90 g C yr−1 might be retained across the Basin. Wild rice production provides a culturally important ecosystem service, and coastal protection may be locally significant where fringing wetland remain. To support management decisions, quantitative relationships between specific stressors or land use practices and the delivery of ecosystem services are needed, as are ecosystem service indicators to measure those responses.
Saltwater intrusion in the Pearl River Estuary during winter
Authors: Zhou Wei , Luo Lin , Xu Hongzhou , Wang Dongxiao
Published: March 2012

An intensive observation and a three-dimensional finite-difference model of Environmental Fluid Dynamic Code were used to study saltwater intrusion in the Pearl River Estuary. The model simulation was carried out for December 2007 to February 2008, which covered the in situ observation. The model was forced by observed winds, tidal elevation at open boundaries, and river discharges from eight inlets in the Pearl River Estuary. The agreements with observation were verified in terms of current, salinity and tide elevation. Using the computed tidal current, the residual current was also calculated to estimate material transport. In addition, the Lagrangian method was used to track the trajectory of particles from the mouth of Humen and Modaomen inlets. By computing the flushing time of these two channels, the authors find that there exists close relationship between flushing time and saltwater intrusion. Potential impact of sea-level rise on saltwater intrusion was also studied. Sensitivity experiments indicate that sea-level rise can impact on the saltwater intrusion in the Pearl River Estuary, such as increasing salinity concentration and intrusion distance, especially during neap tide in winter (dry season).
Responses of the river plume to the external forcing in Pearl River Estuary
Authors: Luo L. , Zhou W. , Wang D.
Published: March 2012

The interaction of river flow, tidal mixing, basin morphology and wind produces a different type of river plume in the Pearl River Estuary. In this paper, a three-dimensional numerical model has been used to study the response of the river plume to different forcings in the Pearl River Estuary. The results indicate that river discharge determines the font size of river plume, while wind greatly affects its shape. Tidal current can restrict diluted water spreading seaward, but contributes little to the net transport of low salinity water. The flushing time can increase by 2 times when considering the Coriolis force, which delays the diluted water flowing out of the flushing area. Southwest winds can greatly decrease the flushing time, while northeast winds can increase it. This rule can also be valid when considering tides.
Characterization of resident and migratory dendritic cells in human lymph nodes
Authors: Segura Elodie , Valladeau-Guilemond Jenny , Donnadieu Marie-Hélène , Sastre-Garau Xavier , Soumelis Vassili , Amigorena Sebastian
Published: March 2012

Dendritic cells (DCs) initiate adaptive immune responses in lymph nodes (LNs). In mice, LN DCs can be divided into resident and tissue-derived populations, the latter of which migrate from the peripheral tissues. In humans, different subsets of DCs have been identified in the blood, spleen, and skin, but less is known about populations of resident and migratory tissue-derived DCs in LNs. We have analyzed DCs in human LNs and identified two populations of resident DCs that are present in all LNs analyzed, as well as in the spleen and tonsil, and correspond to the two known blood DC subtypes. We also identify three main populations of skin-derived migratory DCs that are present only in skin-draining LNs and correspond to the DC subsets found in the skin. Resident DCs subsets induce both Th1 and Th2 cytokines in naive allogeneic T lymphocytes, whereas the corresponding blood subsets failed to induce efficient Th2 polarization. LN-resident DCs also cross-present antigen without in vitro activation, whereas blood DCs fail to do so. Among migratory DCs, one subset was poor at both CD4+ and CD8+ T cell activation, whereas the other subsets induced only Th2 polarization. We conclude that in humans, skin-draining LNs host both resident and migratory DC subsets with distinct functional abilities.
A novel pathogenic role of the ER chaperone GRP78/BiP in rheumatoid arthritis
Authors: Yoo Seung-Ah , You Sungyong , Yoon Hyung-Ju , Kim Dong-Ho , Kim Hyun-Sook , Lee Kyungho , Ahn Jin Hee , Hwang Daehee , Lee Amy S. , Kim Ki-Jo , Park Yune-Jung , Cho Chul-Soo , Kim Wan-Uk
Published: March 2012

An accumulation of misfolded proteins can trigger a cellular survival response in the endoplasmic reticulum (ER). In this study, we found that ER stress–associated gene signatures were highly expressed in rheumatoid arthritis (RA) synoviums and synovial cells. Proinflammatory cytokines, such as TNF and IL-1β, increased the expression of GRP78/BiP, a representative ER chaperone, in RA synoviocytes. RA synoviocytes expressed higher levels of GRP78 than osteoarthritis (OA) synoviocytes when stimulated by thapsigargin or proinflammatory cytokines. Down-regulation of Grp78 transcripts increased the apoptosis of RA synoviocytes while abolishing TNF- or TGF-β–induced synoviocyte proliferation and cyclin D1 up-regulation. Conversely, overexpression of the Grp78 gene prevented synoviocyte apoptosis. Moreover, Grp78 small interfering RNA inhibited VEGF165-induced angiogenesis in vitro and also significantly impeded synoviocyte proliferation and angiogenesis in Matrigel implants engrafted into immunodeficient mice. Additionally, repeated intraarticular injections of BiP-inducible factor X, a selective GRP78 inducer, increased synoviocyte proliferation and angiogenesis in the joints of mice with experimental OA. In contrast, mice with Grp78 haploinsufficiency exhibited the suppression of experimentally induced arthritis and developed a limited degree of synovial proliferation and angiogenesis. In summary, this study shows that the ER chaperone GRP78 is crucial for synoviocyte proliferation and angiogenesis, the pathological hallmark of RA.
Elastic waves and damage quantification in brittle material with evolving damage
Authors: Zuo Q H , Deganis L E , Wang G
Published: March 2012

This paper presents an analysis of the elastic wave propagation in brittle materials containing a distribution of microcracks. The crack-size distribution is assumed to be isotropic and exponential. The evolution of the mean crack size is described by a rate-dependent damage model based on the mechanics of microcracks. The analysis shows that the elastic wave speeds of a brittle material are sensitive to the change in the mean size of the distributed cracks in the material. The dependence of the wave speeds on the applied strain can also be used to validate the damage model. An example of a brittle ceramic under uniaxial-strain tension is presented to show quantitatively the changes in the longitudinal and shear wave speeds as functions of the applied strain. Explicit relations between the wave speeds and the mean crack size in the material are given.
Will They Stay or Will They Go? The Political Influence of GM‐Averse Importing Companies on Biosafety Decision Makers in Africa
Authors: Gruère Guillaume P. , Takeshima Hiroyuki
Published: March 2012

Presumed but unproven trade risks are considered a significant factor in the reluctance of African countries to use potentially beneficial genetically modified (GM) crops. We model a threat from an importer to a local policy maker announcing an upcoming confined field trial of a GM crop as a dynamic game of incomplete information and illustrate our analysis with a stochastic simulation. The results show that provided the cost of threatening is small, and the cost of going out of the country is significant, the importer will threaten to go out and may effectively lower the probability of commercializing a GM crop.
The Self Selection of Complexity in Choice Experiments
Authors: Burton Michael , Rigby Dan
Published: March 2012

We investigate whether individuals will voluntarily increase the complexity of the tasks they complete within a discrete choice experiment (DCE). We do this via a ‘self selection of complexity’ design in which respondents choose whether to face choice sets comprising 3, 4 or 6 alternatives. We link this approach with the emerging Excessive Choice Effect (ECE) literature. We find that 30% of the sample opt for the largest sets. We test whether this choice of complexity reveals information about respondents' capability/commitment. We find that it does since those with lowest initial error variance levels are most likely to later select the highest level of task complexity. We argue that this result offers insights regarding the design of more cognitively efficient DCE designs. We consider the matching of respondents to the appropriate level of task complexity as analogous to the principal‐agent problem with asymmetric information. Rather than trying to understand respondents' cognitive capability or commitment ex ante we propose that participants self‐select designs that achieve the researcher's objective of minimizing error variance.
The thiamine deficiency syndrome M74, a reproductive disorder of Atlantic salmon (Salmo salar) feeding in the Baltic Sea, is related to the fat and thiamine content of prey fish
Authors: Keinänen Marja , Uddström Annika , Mikkonen Jaakko , Casini Michele , Pönni Jukka , Myllylä Timo , Aro Eero , Vuorinen Pekka J.
Published: March 2012

Keinänen, M., Uddström, A., Mikkonen, J., Casini, M., Pönni, J., Myllylä, T., Aro, E., and Vuorinen, P. J. 2012. The thiamine deficiency syndrome M74, a reproductive disorder of Atlantic salmon (Salmo salar) feeding in the Baltic Sea, is related to the fat and thiamine content of prey fish. – ICES Journal of Marine Science, 69: 516–528. This study clarifies how the diet of Baltic salmon leads to thiamine deficiency in eggs, and consequently to M74 mortality of yolk-sac fry. The main prey species, sprat (Sprattus sprattus) and herring (Clupea harengus membras), and their biomass in the Baltic Proper (BPr) and the Bothnian Sea, the two feeding grounds of salmon originating from the northern Gulf of Bothnia rivers, are compared. The thiamine concentration of both prey species is lowest in the youngest age groups. Because average fat content and energy density are greater in sprat than in herring, and greatest in youngest sprat, the supply of thiamine per unit energy is least in a diet containing many young sprat. Also, the greater is the supply of thiamine and fat from sprat in the southern BPr in the preceding year, the lower the concentration of thiamine in salmon eggs. Thiamine deficiency in eggs results from an unbalanced diet abundant in fatty prey fish, such as young sprat, from which the supply of thiamine is insufficient in proportion to the supply of energy and unsaturated fatty acids for salmon, which must undergo a long prespawning fasting period.
Spider orb webs rely on radial threads to absorb prey kinetic energy
Authors: Sensenig Andrew T. , Lorentz Kimberly A. , Kelly Sean P. , Blackledge Todd A.
Published: March 2012

The kinetic energy of flying insect prey is a formidable challenge for orb-weaving spiders. These spiders construct two-dimensional, round webs from a combination of stiff, strong radial silk and highly elastic, glue-coated capture spirals. Orb webs must first stop the flight of insect prey and then retain those insects long enough to be subdued by the spiders. Consequently, spider silks rank among the toughest known biomaterials. The large number of silk threads composing a web suggests that aerodynamic dissipation may also play an important role in stopping prey. Here, we quantify energy dissipation in orb webs spun by diverse species of spiders using data derived from high-speed videos of web deformation under prey impact. By integrating video data with material testing of silks, we compare the relative contributions of radial silk, the capture spiral and aerodynamic dissipation. Radial silk dominated energy absorption in all webs, with the potential to account for approximately 100 per cent of the work of stopping prey in larger webs. The most generous estimates for the roles of capture spirals and aerodynamic dissipation show that they rarely contribute more than 30 per cent and 10 per cent of the total work of stopping prey, respectively, and then only for smaller orb webs. The reliance of spider orb webs upon internal energy absorption by radial threads for prey capture suggests that the material properties of the capture spirals are largely unconstrained by the selective pressures of stopping prey and can instead evolve freely in response to alternative functional constraints such as adhering to prey.
Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells
Authors: Györy Ildiko , Boller Sören , Nechanitzky Robert , Mandel Elizabeth , Pott Sebastian , Liu Edison , Grosschedl Rudolf
Published: March 2012

The transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into the functions of Ebf1 at distinct stages of differentiation, we conditionally inactivated Ebf1. We found that Ebf1 is required for the proliferation, survival, and signaling of pro-B cells and peripheral B-cell subsets, including B1 cells and marginal zone B cells. The proliferation defect of Ebf1-deficient pro-B cells and the impaired expression of multiple cell cycle regulators are overcome by transformation with v-Abl. The survival defect of transformed Ebf1fl/fl pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-xL. In mature B cells, Ebf1 deficiency interferes with signaling via the B-cell-activating factor receptor (BAFF-R)- and B-cell receptor (BCR)-dependent Akt pathways. Moreover, Ebf1 is required for germinal center formation and class switch recombination. Genome-wide analyses of Ebf1-mediated gene expression and chromatin binding indicate that Ebf1 regulates both common and distinct sets of genes in early and late stage B cells. By regulating important components of transcription factor and signaling networks, Ebf1 appears to be involved in the coordination of cell proliferation, survival, and differentiation at multiple stages of B lymphopoiesis.
Isolation and Proteomic Characterization of the Arabidopsis Golgi Defines Functional and Novel Components Involved in Plant Cell Wall Biosynthesis
Authors: Parsons Harriet T. , Christiansen Katy , Knierim Bernhard , Carroll Andrew , Ito Jun , Batth Tanveer S. , Smith-Moritz Andreia M. , Morrison Stephanie , McInerney Peter , Hadi Masood Z. , Auer Manfred , Mukhopadhyay Aindrila , Petzold Christopher J. , Scheller Henrik V. , Loqué Dominique , Heazlewood Joshua L.
Published: March 2012

The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.
Disruption of a Rice Pentatricopeptide Repeat Protein Causes a Seedling-Specific Albino Phenotype and Its Utilization to Enhance Seed Purity in Hybrid Rice Production
Authors: Su Ning , Hu Mao-Long , Wu Dian-Xing , Wu Fu-Qing , Fei Gui-Lin , Lan Ying , Chen Xiu-Ling , Shu Xiao-Li , Zhang Xin , Guo Xiu-Ping , Cheng Zhi-Jun , Lei Cai-Lin , Qi Cun-Kou , Jiang Ling , Wang Haiyang , Wan Jian-Min
Published: March 2012

The pentatricopeptide repeat (PPR) gene family represents one of the largest gene families in higher plants. Accumulating data suggest that PPR proteins play a central and broad role in modulating the expression of organellar genes in plants. Here we report a rice (Oryza sativa) mutant named young seedling albino (ysa) derived from the rice thermo/photoperiod-sensitive genic male-sterile line Pei'ai64S, which is a leading male-sterile line for commercial two-line hybrid rice production. The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. Map-based cloning revealed that YSA encodes a PPR protein with 16 tandem PPR motifs. YSA is highly expressed in young leaves and stems, and its expression level is regulated by light. We showed that the ysa mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions. We further demonstrated that ysa can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to approximately 537 kg ha−1.
(E)-2-(2,3-Dimethylanilino)-N′-[2-methyl-5-(prop-1-en-2-yl)cyclohex-2-enylidene]benzohydrazide
Authors: Bhat Mashooq A. , Abdel-Aziz Hatem A. , Ghabbour Hazem A. , Hemamalini Madhukar , Fun Hoong-Kun
Published: March 2012

The asymmetric unit of the title compound, C25H29N3O, comprises two crystallographically independent molecules. The dihedral angles between the benzene rings in the two molecules are 59.7 (2) and 61.27 (18)°. The cyclohexene rings adopt sofa and half-chair conformations. In the crystal, molecules are connectedviaN—H...O and weak C—H...O hydrogen bonds, forming chains along theaaxis. In each molecule, there is an intramolecular N—H...O hydrogen bond.
N-(2,2-Dimethylpropanoyl)-N′-(2-methoxyphenyl)thiourea
Authors: Kadir Maisara A. , Yamin Bohari M. , Yusof M. Sukeri M.
Published: March 2012

In the title compound, C13H18N2O2S, the carbonylthiourea fragment is nearly planar with an r.m.s. deviation of 0.0096 Å. The dihedral angle between carbonylthiourea group and the benzene ring is 19.16 (16)°. There are two intramolecular N—H...O hydrogen bonds, which lead to two pseudo-six-membered rings. Weak intramolecular C—H...S hydrogen bonding also occurs.
1-Benzyl-1H-benzotriazole
Authors: Selvarathy Grace P. , Jebas Samuel Robinson , Ravindran Durai Nayagam B. , Schollmeyer Dieter
Published: March 2012

In the title compound, C13H11N3, the benzotriazole ring system is essentially planar, with a maximum deviation of 0.0173 (18) Å, and forms a dihedral angle of 75.08 (8)Å with the phenyl ring. In the crystal, pairs of weak C—H...N hydrogen bonds form inversion dimers. In addition, there are weak C—H...π(arene) interactions and weak π–π stacking interactions, with a centroid–centroid distance of 3.673 (11) Å.
Bis(4-benzoyl-3-methyl-1-phenyl-4,5-dihydro-1H-pyrazol-5-olato-κ2O,O′)(methanol-κO)dioxidouranium(VI) methanol monosolvate
Authors: Dehbi Ouarda , Keraghel Saida , Bouacida Sofiane , Benghanem Fatiha , Ourari Ali
Published: March 2012

In the title compound, [U(C17H13N2O2)2O2(CH3OH)]·CH3OH, the UVIion is coordinated by seven O atoms in a distorted pentagonal–bipyramidal geometry with two 3-methyl-1-phenyl-4-benzoyl-4,5-dihydro-1H-pyrazol-5-olate groups with two O atoms in a bidentate chelating coordination mode and by three O atoms, one of which is from a methanol ligand. The crystal packing can be described by alternating layers of complex molecules along theaaxis. The structure is stabilized by O—H...N and O—H...O hydrogen bonding and van der Waals interactions.
Bis(cyclohexylammonium) tetrabromidocuprate(II)
Authors: Han Meng Ting
Published: March 2012

The structure of the title salt, (C6H14N)2[CuBr4], is built up from cyclohexylammonium cations and tetrabromidocuprate anions, the latter being located on an inversion center. In the crystal, anions and cations are interconnected by N—H...Br hydrogen bonds, forming ribbons parallel to [0-11].
6,6-Dimethyl-2H,5H,6H,7H-1,3-dithiolo[4,5-f][1,5,3]dithiasilepin-2-one
Authors: Li Hongqi , Zhang Xuebin , Zhang Zhongbao , Chen Zhen , Peng Jiajian
Published: March 2012

In the structure of the title compound, C7H10OS4Si, the carbonyl O atom lies in the plane of the five-membered dithiole ring with a deviation of only 0.022 (2) Å. The seven-membered ring adopts a chair conformation. The crystal packing is stabilized by S...O [3.096 (4) Å] and S...S [3.620 (4) Å] contacts, together with C—H...S interactions.
5,7,13,15-Tetraoxo-2,2,10,10-tetrakis(trifluoromethyl)-4,8,12,16-tetraoxa-1(1,4),3(1,4),6(1,2),9(1,4),11(1,4),14(1,2)-hexabenzenahexadecaphane tetrahydrofuran monosolvate
Authors: Guo Qing-Zhong , Du Yi
Published: March 2012

The title compound, C46H24F12O8·C4H8O, consists of a cyclic aryl ester dimer and a tetrahydrofuran molecule. In the structure of the cyclic dimer, one carbonyl group stretches above the cavity and the other below.
5,6-Dimethyl-4-phenyl-2H-pyran-2-one
Authors: Xu Hai-Yun , Guo Sheng-Hai , Li Kun , Fan Xue-Sen
Published: March 2012

In the title compound, C13H12O2, the dihedral angle between the pyranone and phenyl rings is 57.55 (9)°. In the crystal, the molecules are linked by π–π stacking interactions between the parallel pyranone rings of neighboring molecules with distances of 3.5778 (11) Å and 3.3871 (11) Å between the planes. C—H...O interactions also occur.
(Acridine-κN)(pyridine-2,6-dicarboxylato-κ3O2,N,O6)palladium(II)
Authors: Ha Kwang
Published: March 2012

In the title complex, [Pd(C7H3NO4)(C13H9N)], the PdIIion is four-coordinated in a distorted square-planar environment by one N and two O atoms from the tridentate pyridine-2,6-dicarboxylate (dipic) anionic ligand and one N atom of the acridine (acr) ligand. The dipic and acr ligands are nearly planar [maximum deviation = 0.069 (3) Å in dipic and 0.091 (4) Å in acr] and the dihedral angle between their mean planes is 58.67 (7)°. The Pd—O bond lengths are nearly equal, but the Pd—N bond lengths are slightly different. There is a short C—H...O interaction in the molecule involving the two ligands. In the crystal, complex molecules are linked through C—H...O interactions, forming a three-dimensional network. There are also a number of intermolecular π–π interactions present, the shortest ring centroid–centroid distance being 3.622 (3) Å.
3′,4′-Dimethoxybiphenyl-4-carbonitrile
Authors: Li Xin-Min , Hou Yan-Jun , Mei Peng , Chu Wen-Yi , Sun Zhi-Zhong
Published: March 2012

The title compound, C15H13NO2, was prepared through a palladium-catalysed Suzuki–Miyaura coupling reaction. The dihedral angle between the biphenyl rings is 40.96 (6)°. The methoxy groups are twisted slightly out of the plane of the benzene ring [C—C—C—C torsion angles = −3.61 (18) and 12.6 (2)°]. The packing of the molecules is stabilized by van der Waals interactions.
Species composition of skates (Rajidae) in commercial fisheries around the British Isles and their discarding patterns
Authors: Silva J. F. , Ellis J. R. , Catchpole T. L.
Published: March 2012

Recent regulations have required European nations to report commercial landings of Rajidae (skates) to species level since 2008. Morphological similarities between some species, variability in colouration and regional differences in common names may compromise the accuracy of some of these data. An increased proportion of rajid landings reported by the U.K. (England, Wales and Northern Ireland) are now reported to species level (42% in 2008, rising to 92% in 2010). Recent landings (2007–2010) of Rajidae by the U.K. indicated that the majority of reported landings were made by otter trawl (55·9%), tangle and gillnet (18·7%) and beam trawl (15·5%). Approximately 70% of recent landings originated from four ICES Divisions: the Irish Sea (VIIa), western English Channel (VIIe), Bristol Channel (VIIf) and southern North Sea (IVc). Recent species‐specific landings of Rajidae are appraised in terms of the species reported and the overall composition, and potential problems identified. Data from observer trips have been used to estimate the species composition of Rajidae taken in some of the main commercial fisheries operating around the British Isles, and these data are compared to landings. Although there was typically broad agreement between these data sets in terms of the main species landed, misidentification issues were apparent and Rajidae with highly patchy distributions may be under‐represented in observer data. Data from observer trips were also used to examine the discard and retention pattern. Most rajid species were first retained from total lengths, LT, of 27–34 cm, with 50% retention occurring at between 49 and 51 cm and near‐full retention at LT of 60–67 cm. Beam trawls captured a higher proportion of smaller individuals, whilst gillnets (>150 mm mesh size) caught proportionally more larger rajids.
Systematic review: the prognostic role of alpha‐fetoprotein following liver transplantation for hepatocellular carcinoma
Authors: Hakeem A. R. , Young R. S. , Marangoni G. , Lodge J. P. A. , Prasad K. R.
Published: March 2012

Background

Liver transplantation (LT) offers a possible cure for carefully selected patients with hepatocellular carcinoma (HCC). Studies report that preoperative alpha‐fetoprotein (AFP) is a prognostic indicator that can predict survival and recurrence in these patients.

Aim

To undertake a systematic review of available literature on preoperative AFP as a predictor of survival and recurrence following LT for HCC.

Methods

A literature search was performed using Medline, Embase, Cochrane Library, CINAHL and Google scholar databases to identify studies reporting AFP as a prognostic marker in LT for HCC. Primary outcomes of interest were overall survival and recurrence. Secondary outcomes were correlation of pre‐LT AFP with vascular invasion and grade of tumour differentiation.

Results

A total of 13 studies met the inclusion criteria (12 159 patients). The majority were male (9603, 78.9%). All were observational studies and only one prospective. Methodological quality was rated as poor for all studies, with selection and observer bias apparent for most cohorts. Reported survival rates and recurrence rates varied widely between the studies although overall demonstrated better outcomes for those with lower (<1000 ng/mL) pre‐LT AFP levels. Similarly, rates of vascular invasion and poor tumour differentiation were higher in those with high pre‐LT AFP levels.

Conclusions

A quantity of AFP >1000 ng/mL is associated with poorer outcomes from liver transplantation for hepatocellular carcinoma. The quality of studies was generally poor and precluded valid statistical meta‐analysis. There is a need to improve the performance and reporting of primary prognostic studies to facilitate high quality systematic review and meta‐analysis.