bluuebunny/crossref_metadata_2025_split huggingface dataset:
LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure NormalArabidopsisDevelopment
Authors: Perea-Resa Carlos , Hernández-Verdeja Tamara , López-Cobollo Rosa , Castellano María del Mar , Salinas Julio 
Published: December 2012

AbstractIn yeast and animals, SM-like (LSM) proteins typically exist as heptameric complexes and are involved in different aspects of RNA metabolism. Eight LSM proteins, LSM1 to 8, are highly conserved and form two distinct heteroheptameric complexes, LSM1-7 and LSM2-8,that function in mRNA decay and splicing, respectively. A search of the Arabidopsis thaliana genome identifies 11 genes encoding proteins related to the eight conserved LSMs, the genes encoding the putative LSM1, LSM3, and LSM6 proteins being duplicated. Here, we report the molecular and functional characterization of the Arabidopsis LSM gene family. Our results show that the 11 LSM genes are active and encode proteins that are also organized in two different heptameric complexes. The LSM1-7 complex is cytoplasmic and is involved in P-body formation and mRNA decay by promoting decapping. The LSM2-8 complex is nuclear and is required for precursor mRNA splicing through U6 small nuclear RNA stabilization. More importantly, our results also reveal that these complexes are essential for the correct turnover and splicing of selected development-related mRNAs and for the normal development of Arabidopsis. We propose that LSMs play a critical role in Arabidopsis development by ensuring the appropriate development-related gene expression through the regulation of mRNA splicing and decay.
PSBP-DOMAIN PROTEIN1, a Nuclear-Encoded Thylakoid Lumenal Protein, Is Essential for Photosystem I Assembly in Arabidopsis
Authors: Liu Jun , Yang Huixia , Lu Qingtao , Wen Xiaogang , Chen Fan , Peng Lianwei , Zhang Lixin , Lu Congming 
Published: December 2012

Abstract
To gain insights into the molecular details of photosystem I (PSI) biogenesis, we characterized the PsbP-domain protein1 (ppd1) mutant of Arabidopsis thaliana that specifically lacks PSI activity. Deletion of PPD1 results in an inability of the mutant to grow photoautotrophically and a specific loss of the stable PSI complex. Unaltered transcription and translation of plastid-encoded PSI genes indicate that PPD1 acts at the posttranslational level. In vivo protein labeling experiments reveal that the rate of synthesis of PSI reaction center proteins PsaA/B in ppd1 is comparable to that of wild-type plants, whereas the rate of turnover of PsaA/B proteins is higher in ppd1 than in wild-type plants. With increasing leaf age, PPD1 content decreases considerably, while PSI content remains constant. PPD1 is a nuclear-encoded thylakoid lumenal protein and is associated with PSI but is not an integral subunit of PSI. Biochemical and molecular analyses reveal that PPD1 interacts directly and specifically with PsaB and PsaA. Yeast two-hybrid experiments show that PPD1 interacts with some lumenal loops of PsaB and PsaA. Our results suggest that PPD1 is a PSI assembly factor that assists the proper folding and integration of PsaB and PsaA into the thylakoid membrane.
Model generation of coronary artery bifurcations from CTA and single plane angiography
Authors: Cárdenes Rubén , Díez José L. , Duchateau Nicolas , Pashaei Ali , Frangi Alejandro F. 
Published: December 2012

Purpose:To generate accurate and realistic models of coronary artery bifurcations before and after percutaneous coronary intervention (PCI), using information from two image modalities. Because bifurcations are regions where atherosclerotic plaque appears frequently and intervention is more challenging, generation of such realistic models could be of high value to predict the risk of restenosis or thrombosis after stent implantation, and to study geometrical and hemodynamical changes.Methods:Two image modalities have been employed to generate the bifurcation models: computer tomography angiography (CTA) to obtain the 3D trajectory of vessels, and 2D conventional coronary angiography (CCA) to obtain radius information of the vessel lumen, due to its better contrast and image resolution. In addition, CCA can be acquired right before and after the intervention in the operation room; therefore, the combination of CTA and CCA allows the generation of realistic preprocedure and postprocedure models of coronary bifurcations. The method proposed is semiautomatic, based on landmarks manually placed on both image modalities.Results:A comparative study of the models obtained with the proposed method with models manually obtained using only CTA, shows more reliable results when both modalities are used together. The authors show that using preprocedure CTA and postprocedure CCA, realistic postprocedure models can be obtained. Analysis carried out of the Murray's law in all patient bifurcations shows the geometric improvement of PCI in our models, better than using manual models from CTA alone. An experiment using a cardiac phantom also shows the feasibility of the proposed method.Conclusions:The authors have shown that fusion of CTA and CCA is feasible for realistic generation of coronary bifurcation models before and after PCI. The method proposed is efficient, and relies on minimal user interaction, and therefore is of high value to study geometric and hemodynamic changes of treated patients.
Rapid additive manufacturing of MR compatible multipinhole collimators with selective laser melting of tungsten powder
Authors: Deprez Karel , Vandenberghe Stefaan , Van Audenhaege Karen , Van Vaerenbergh Jonas , Van Holen Roel 
Published: December 2012

Purpose:The construction of complex collimators with a high number of oblique pinholes is very labor intensive, expensive or is sometimes impossible with the current available techniques (drilling, milling or electric discharge machining). All these techniques are subtractive: one starts from solid plates and the material at the position of the pinholes is removed. The authors used a novel technique for collimator construction, called metal additive manufacturing. This process starts with a solid piece of tungsten on which a first layer of tungsten powder is melted. Each subsequent layer is then melted on the previous layer. This melting is done by selective laser melting at the locations where the CAD design file defines solid material.Methods:A complex collimator with 20 loftholes with 500 μm diameter pinhole opening was designed and produced (16 mm thick and 70 × 52 mm2 transverse size). The density was determined, the production accuracy was measured (GOM ATOS II Triple Scan, Nikon AZ100M microscope, Olympus IMT200 microscope). Point source measurements were done by mounting the collimator on a SPECT detector. Because there is increasing interest in dual‐modality SPECT‐MR imaging, the collimator was also positioned in a 7T MRI scanner (Bruker Pharmascan). A uniform phantom was acquired using T1, T2, and T2* sequences to check for artifacts or distortion of the phantom images due to the collimator presence. Additionally, three tungsten sample pieces (250, 500, and 750 μm thick) were produced. The density, attenuation (140 keV beam), and uniformity (GE eXplore Locus SP micro‐CT) of these samples were measured.Results:The density of the collimator was equal to 17.31 ± 0.10 g/cm3 (89.92% of pure tungsten). The production accuracy ranges from −260 to +650 μm. The aperture positions have a mean deviation of 5 μm, the maximum deviation was 174 μm and the minimum deviation was −122 μm. The mean aperture diameter is 464 ± 19 μm. The calculated and measured sensitivity and resolution of point sources at different positions in the field‐of‐view agree well. The measured and expected attenuation of the three sample pieces are in a good agreement. There was no influence of the 7T magnetic field on the collimator (which is paramagnetic) and minimal distortion was noticed on the MR scan of the uniform phantom.Conclusions:Additive manufacturing is a very promising technique for the production of complex multipinhole collimators and may also be used for producing other complex collimators. The cost of this technique is only related to the amount of powder needed and the time it takes to have the collimator built. The timeframe from design to collimator production is significantly reduced.
Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities
Authors: MacGregor Barbara J. , Biddle Jennifer F. , Siebert Jason R. , Staunton Eric , Hegg Eric L. , Matthysse Ann G. , Teske Andreas 
Published: December 2012

ABSTRACT

Orange, white, and yellow vacuolated
Beggiatoaceae
filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate
Beggiatoaceae
are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange
Beggiatoa
(“
Candidatus
Maribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by
in vitro
assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of
Beggiatoaceae
physiology, nitrite reduction is the most likely
in vivo
role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.
Efficient Bioconversion of Echinocandin B to Its Nucleus by Overexpression of Deacylase Genes in Different Host Strains
Authors: Shao Lei , Li Jian , Liu Aijuan , Chang Qing , Lin Huimin , Chen Daijie 
Published: December 2012

ABSTRACT

Anidulafungin, which noncompetitively inhibits β-(1,3)-
d
-glucan synthase in fungal cell wall biosynthesis, is the newest antifungal drug to be developed. Echinocandin B deacylase from
Actinoplanes utahensis
NRRL 12052 catalyzes the cleavage of the linoleoyl group of echinocandin B, a key step in the process of manufacturing anidulafungin. Unfortunately, the natural yield of echinocandin B nucleus is low. In our study, the echinocandin B deacylase gene was systematically overexpressed by genetic engineering in its original producer,
A. utahensis
, and in the heterologous hosts
Streptomyces lividans
TK24 and
Streptomyces albus
. The introduction of additional copies of the gene, under the control of
PermE
* or its native promoter, into hosts showed significant increases in its transcription level and in the efficiency of the bioconversion of echinocandin B to its nucleus. The conditions for the cultivation and bioconversion of
A. utahensis
have been optimized further to improve production. As a result, while the wild-type strain initially produced 0.36 g/liter, a concentration of 4.21 g/liter was obtained after the generation of a strain with additional copies of the gene and further optimization of the reaction conditions. These results are useful for enhancing echinocandin B nucleus production in
A. utahensis
. Our study could enable the engineering of commercially useful echinocandin B nucleus-overproducing stains.
Extensive Reduction of Cell Viability and Enhanced Matrix Production in Pseudomonas aeruginosa PAO1 Flow Biofilms Treated with a
d
-Amino Acid Mixture
Authors: Sanchez Zoe , Tani Akio , Kimbara Kazuhide 
Published: December 2012

ABSTRACT

Treatment of
Pseudomonas aeruginosa
PAO1 flow biofilms with a
d
-amino acid mixture caused significant reductions in cell biomass by 75% and cell viability by 71%. No biofilm disassembly occurred, and matrix production increased by 30%, thereby providing a thick protective cover for remaining viable or persister cells.
Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a
Authors: Luo Quan , Hiessl Sebastian , Poehlein Anja , Steinbüchel Alexander 
Published: December 2012

ABSTRACTNocardia novaSH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 × 107CFU per μg of plasmid DNA was achieved. By applying this optimized protocol toN. novaSH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an α-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, β-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP.
Patterned Hydrophobic Domains in the Exopolymer Matrix of Shewanella oneidensis MR-1 Biofilms
Authors: Aldeek Fadi , Schneider Raphaël , Fontaine-Aupart Marie-Pierre , Mustin Christian , Lécart Sandrine , Merlin Christophe , Block Jean-Claude 
Published: December 2012

ABSTRACT

Water-dispersible amphiphilic surface-engineered quantum dots (QDs) were found to be strongly accumulated within discrete zones of the exopolymer network of
Shewanella oneidensis
MR-1 biofilms, but not on the cell surfaces. These microdomains showed a patterned distribution in the exopolymer matrix, which led to a restricted diffusion of the amphiphilic nanoparticles.
Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition
Authors: Eisenlord Sarah D. , Freedman Zachary , Zak Donald R. , Xue Kai , He Zhili , Zhou Jizhong 
Published: December 2012

ABSTRACT
Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.
The Rare
ospC
Allele L of Borrelia burgdorferi Sensu Stricto, Commonly Found among Samples Collected in a Coastal Plain Area of the Southeastern United States, Is Associated with Ixodes affinis Ticks and Local Rodent Hosts Peromyscus gossypinus and Sigmodon hispidus
Authors: Rudenko Nataliia , Golovchenko Maryna , Grubhoffer Libor , Oliver James H. 
Published: December 2012

ABSTRACT

The rare
ospC
allele L was detected in 30% of
Borrelia burgdorferi
sensu stricto strains cultured from a tick species,
Ixodes affinis
, and two rodent host species,
Peromyscus gossypinus
and
Sigmodon hispidus
, collected in a coastal plain area of Georgia and South Carolina, in the southeastern United States.
A
uvs-5
Strain Is Deficient for a Mitofusin Gene Homologue,
fzo1
, Involved in Maintenance of Long Life Span in Neurospora crassa
Authors: Kurashima Kiminori , Chae Michael , Inoue Hirokazu , Hatakeyama Shin , Tanaka Shuuitsu 
Published: December 2012

ABSTRACT

Mitochondria are highly dynamic organelles that continuously fuse and divide. To maintain mitochondria, cells establish an equilibrium of fusion and fission events, which are mediated by dynamin-like GTPases. We previously showed that an
mus-10
strain, a mutagen-sensitive strain of the filamentous fungus
Neurospora crassa
, is defective in an F-box protein that is essential for the maintenance of mitochondrial DNA (mtDNA), long life span, and mitochondrial morphology. Similarly, a
uvs-5
mutant accumulates deletions within its mtDNA, has a shortened life span, and harbors fragmented mitochondria, the latter of which is indicative of an imbalance between mitochondrial fission and fusion. Since the
uvs-5
mutation maps very close to the locus of
fzo1
, encoding a mitofusin homologue thought to mediate mitochondrial outer membrane fusion, we determined the sequence of the
fzo1
gene in the
uvs-5
mutant. A single amino acid substitution (Q368R) was found in the GTPase domain of the FZO1 protein. Expression of wild-type FZO1 in the
uvs-5
strain rescued the mutant phenotypes, while expression of a mutant FZO1 protein did not. Moreover, when knock-in of the Q368R mutation was performed on a wild-type strain, the resulting mutant displayed phenotypes identical to those of the
uvs-5
mutant. Therefore, we concluded that the previously unidentified
uvs-5
gene is
fzo1
. Furthermore, we used immunoprecipitation analysis to show that the FZO1 protein interacts with MUS-10, which suggests that these two proteins may function together to maintain mitochondrial morphology.
Rsr1 Focuses Cdc42 Activity at Hyphal Tips and Promotes Maintenance of Hyphal Development in Candida albicans
Authors: Pulver Rebecca , Heisel Timothy , Gonia Sara , Robins Robert , Norton Jennifer , Haynes Paula , Gale Cheryl A. 
Published: December 2012

ABSTRACT

The extremely elongated morphology of fungal hyphae is dependent on the cell's ability to assemble and maintain polarized growth machinery over multiple cell cycles. The different morphologies of the fungus
Candida albicans
make it an excellent model organism in which to study the spatiotemporal requirements for constitutive polarized growth and the generation of different cell shapes. In
C. albicans
, deletion of the landmark protein Rsr1 causes defects in morphogenesis that are not predicted from study of the orthologous protein in the related yeast
Saccharomyces cerevisiae
, thus suggesting that Rsr1 has expanded functions during polarized growth in
C. albicans
. Here, we show that Rsr1 activity localizes to hyphal tips by the differential localization of the Rsr1 GTPase-activating protein (GAP), Bud2, and guanine nucleotide exchange factor (GEF), Bud5. In addition, we find that Rsr1 is needed to maintain the focused localization of hyphal polarity structures and proteins, including Bem1, a marker of the active GTP-bound form of the Rho GTPase, Cdc42. Further, our results indicate that tip-localized Cdc42 clusters are associated with the cell's ability to express a hyphal transcriptional program and that the ability to generate a focused Cdc42 cluster in early hyphae (germ tubes) is needed to maintain hyphal morphogenesis over time. We propose that in
C. albicans
, Rsr1 “fine-tunes” the distribution of Cdc42 activity and that self-organizing (Rsr1-independent) mechanisms of polarized growth are not sufficient to generate narrow cell shapes or to provide feedback to the transcriptional program during hyphal morphogenesis.
Integrated oncogeriatric approach: a systematic review of the literature using concept analysis
Authors: Tremblay Dominique , Charlebois Kathleen , Terret Catherine , Joannette Sonia , Latreille Jean 
Published: December 2012

ObjectivesThe purpose of this study was to provide a more precise definition of an integrated oncogeriatric approach (IOGA) through concept analysis.Data sourcesThe literature was reviewed from January 2005 to April 2011 integrating three broad terms: geriatric oncology, multidisciplinarity and integrated care delivery models.Study eligibility criteriaCitation selection was based on: (1) elderly cancer patients as the study population; (2) disease management and (3) case studies, intervention studies, assessments, evaluations and studies. Inclusion and exclusion criteria were refined in the course of the literature search.InterventionsInitiatives in geriatric oncology that relate to oncology services, social support services and primary care services for elderly cancer patients.ParticipantsElderly cancer patients aged 70 years old or more.Study appraisal and synthesis methodsRodgers’ concept analysis method was used for this study. The analysis was carried out according to thematic analysis based on the elements of the Chronic Care Model.ResultsThe search identified 618 citations. After in-depth appraisal of 327 potential citations, 62 articles that met our inclusion criteria were included in the analysis. Three IOGA main attributes were identified, which constitute IOGA's core aspects: geriatric assessment (GA), comorbidity burden and treatment outcomes. The IOGA concept comprises two broad antecedents: coordinated healthcare delivery and primary supportive care services. Regarding the consequents of an integrated approach in geriatric oncology, the studies reviewed remain inconclusive.ConclusionsOur study highlights the pioneering character of the multidimensional IOGA concept, for which the relationship between clinical and organisational attributes, on the one hand, and contextual antecedents, on the other, is not well understood. We have yet to ascertain IOGA's consequents.Implications of key findingsThere is clearly a need for a whole-system approach to change that will provide direction for multilevel (clinical, organisational, strategic) interventions to support interdisciplinary practice, education and research.