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RNA, Fungal (0):
Recent article
RNA, Fungal
Comptes Rendus Biologies (334)8-9 2011
Abstract
The steady-state mRNA level is the result of two opposing processes: transcription and degradation; both of which can provide important points to regulate gene expression. In the model organism yeast Saccharomyces cerevisiae, it is now possible to determine, at the genomic level, the...
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PMID: 21819946
PDF is available here.
PDF is available here.
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Comptes Rendus Biologies (334)8-9 2011
Abstract
We describe the assembly of two automatic annotation pipelines, integrating publicly available tools, for homology and de novo ncRNA search in genomes. We applied both pipelines to 10 Saccharomycotina genomes and were able to find and annotate 693 ncRNA genes, corresponding to 81% of the ncRNAs expe...
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PMID: 21819949
PDF is available here.
PDF is available here.
Abstract
We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel st...
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PMID: 21441097
PDF is available here.
PDF is available here.
Abstract
Paramutation refers to the process by which homologous DNA sequences communicate in trans to establish meiotically heritable expression states. Although mechanisms are unknown, current data are consistent with the hypothesis that the establishment and heritable transmission of specific chromatin sta...
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PMID: 21030647
PDF is available here.
PDF is available here.
Eukaryotic Cell (9)11 2010
Abstract
We characterize the upstream developmental regulator A. fumigatus flbB (AfuflbB). Northern blotting and cDNA analyses reveal that AfuflbB produces two transcripts predicted to encode two basic leucine zipper domain (bZIP) polypeptides, AfuFlbBβ (420 amino acids [aa]) and AfuFlbBα (390 aa). The del...
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PMID: 20852021
PDF is available here.
PDF is available here.
Antonie Van Leeuwenhoek (98)4 2010
Abstract
The molecular phylogeny and comparative morphological studies reported here provide evidence for the recognition of the genus Picoa, an hypogeous desert truffle, in the family Pyronemataceae (Ascomycota, Pezizales). Picoa juniperi and Picoa lefebvrei were reassigned to the genus Picoa based on large...
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PMID: 20559873
PDF is available here.
PDF is available here.
Abstract
We show that Dom34:Hbs1 interacts with the ribosome to promote subunit dissociation and peptidyl-tRNA drop-off. Our data further indicate that these recycling activities are shared by the homologous translation termination factor complex eRF1:eRF3, suggesting a common ancestral function. Because Dom...
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PMID: 20947765
PDF is available here.
PDF is available here.
Cell Cycle (9)20 2010
Abstract
We have recently demonstrated that histone protein levels are regulated posttranslationally by the DNA damage checkpoint kinase Rad53 and ubiquitin-proteasome dependent proteolysis in the budding yeast. However, the underlying mechanism/s via which excess histones exert their deleterious effects in...
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PMID: 20948314
PDF is available here.
PDF is available here.
Abstract
Three types of nuruk were made from rice, wheat, and a rice-glasswort (6:4) mixture. Nuruk, makgeolli, and vinegar were manufactured with rice nuruk (RN), wheat nuruk (WN), and rice-glasswort nuruk (RGN). The saccharifying activity and ethanol productivity of nuruk, polyphenol content in makgeolli,...
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PMID: 20890098
PDF is available here.
PDF is available here.
Food Microbiology (27)6 2010
Abstract
We used a reverse transcription-quantitative PCR (RT-qPCR) method with relative quantification to investigate the expression of seven hexose transporter genes (HXT1-7) and one invertase-encoding gene (SUC2) during ADY rehydration in water with or without sucrose. For this, seven candidate reference...
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PMID: 20630323
PDF is available here.
PDF is available here.
Abstract
To obtain a thiamine-auxotrophic yeast strain that overproduces alpha-ketoglutaric acid (alpha-KG) from glycerol and to investigate nutrient effects on alpha-KG production.
Yeast strain WSH-Z06, a thiamine auxotroph that gave high yields of alpha-KG from glycerol, was obtained by screening for ampic...
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PMID: 20636327
PDF is available here.
PDF is available here.
Mycopathologia (170)3 2010
Abstract
In a survey of mycotic human skin and nail lesions in Chiriquí, Western Panama, Talaromyces indigoticus was isolated in one case. This ascomycete is characterised by formation of gymnothecia containing oval, spinose and yellow ascospores, which become blue in mounting fluids, and by short monoverti...
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PMID: 20349275
PDF is available here.
PDF is available here.
Molecular Cell (39)3 2010
Abstract
We developed an in vitro assay sensitive to proofreading of 5' splice site cleavage. We inactivated spliceosomes by disrupting a metal-ligand interaction at the catalytic center and discovered that, when the DEAH box ATPase Prp16 was disabled, these spliceosomes catalyzed 5' splice site cleavage but...
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PMID: 20705241
PDF is available here.
PDF is available here.
Abstract
I (RPB1) and nuclear ribosomal large subunit (LSU) rDNA gene sequences. Based on the result of this initial screen, 62 collections representing the full range of genetic diversity sampled were subjected to multigene phylogenetic species recognition based on genealogical concordance (GCPSR). The 62-t...
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PMID: 20580850
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)29 2010
Abstract
We show that the yeast eIF4G2 mutations altering eIF4E- and eIF4A-binding sites increase re-initiation at GCN4 and impair recognition of the start codons of uORF1 or uORF4 located after uORF1. The increase in re-initiation at GCN4 was partially suppressed by increasing the distance between uORF1 and...
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PMID: 20463023
PDF is available here.
PDF is available here.
Abstract
We discovered that the microtubule-mediated transport of mRNAs is essential for the fast polar growth of infectious filaments in the corn pathogen Ustilago maydis. Combining in vivo UV cross-linking and RNA live imaging revealed that the RNA-binding protein Rrm4, which constitutes an integral part o...
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PMID: 20472693
PDF is available here.
PDF is available here.
Infection and Immunity (78)7 2010
Abstract
We have developed an alternative, low-cost, and easy-to-use infection model for Aspergillus species based on embryonated eggs. The outcome of infections in the egg model is dose and age dependent and highly reproducible. We show that the age of the embryos affects the susceptibility to A. fumigatus...
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PMID: 20421382
PDF is available here.
PDF is available here.
Abstract
The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformati...
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PMID: 20547848
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We have investigated the mechanisms by which PUF3 in Saccharomyces cerevisiae accelerates deadenylation of the COX17 mRNA. PUF3 was shown to affect PAN2 deadenylation of the COX17 mRNA independent of the presence of CCR4, suggesting that PUF3 acts through a general mechanism to affect deadenylation....
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PMID: 20435044
PDF is available here.
PDF is available here.
Abstract
We show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP or ITP functioned with less efficiency and adenosine 5gamma'-(beta,gamma-imido)triphosphate did not function at all. The k(cat) of eEF3 was 1.12 min(-1), which is comparable to t...
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PMID: 20534490
PDF is available here.
PDF is available here.
Abstract
We examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO(2) modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO(2) condition...
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PMID: 20534474
PDF is available here.
PDF is available here.
Abstract
We investigated these questions using the meiotic gene expression program of Schizosaccharomyces pombe. We identified over 80 transcripts that co-purify with the meiotic-specific Meu5p RNA-binding protein. Their levels and half-lives were reduced in meu5 mutants, demonstrating that Meu5p stabilizes...
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PMID: 20531409
PDF is available here.
PDF is available here.
Abstract
After any RNA purification by any method, it is necessary to ascertain both the amount (yield) and the integrity (quality) of the RNA obtained. This is essential for any subsequent analysis and critical for any comparative analyses. This article discusses several methods for RNA quantitation and pro...
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PMID: 20516190
PDF is available here.
PDF is available here.
Abstract
The present study was aimed at characterizing the ability of lactic acid bacteria isolated from maize to repress the growth of fumonisin-producing fungi. A total of 67 isolates were screened for their antifungal activity against Fusarium proliferatum and Fusarium verticillioides by using the overlay...
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PMID: 20537273
PDF is available here.
PDF is available here.
Antonie Van Leeuwenhoek (98)1 2010
Abstract
Direct genetic testing for hybrid sterility unambiguously showed that the newly described yeast Saccharomyces arboricolus Wang et Bai is reproductively isolated from Saccharomyces cerevisiae, Saccharomyces bayanus, Saccharomyces cariocanus, Saccharomyces kudriavzevii, Saccharomyces mikatae and Sacch...
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PMID: 20379848
PDF is available here.
PDF is available here.
Antonie Van Leeuwenhoek (98)1 2010
Abstract
We describe it as Ogataea cecidiorum and designate type culture KBP Y-3846 (= CBS 11522(T) = VKM Y-2982(T) = VKPM Y-3482(T) = MUCL 52544(T) = NCAIM Y.01965(T)) as the type strain. The new species was registered in MycoBank under MB 515233....
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PMID: 20373142
PDF is available here.
PDF is available here.
Abstract
We have found that the ribosome can translate mutated lariat intermediates. By glycerol gradient analysis, we have found that the spliceosome can dissociate mutated lariat intermediates in vivo in a manner that requires the DEAH box ATPase Prp43p. Through an in vitro assay, we demonstrate that Prp43...
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PMID: 20463285
PDF is available here.
PDF is available here.
Abstract
We report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3'...
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PMID: 20421314
PDF is available here.
PDF is available here.
Abstract
We describe an extensive Cid14 protein-protein interaction network and its biochemical dissection. Cid14 most stably interacts with the zinc-knuckle protein Air1 to form the Cid14-Air1 complex (CAC). Providing a link to ribosomal RNA processing, Cid14 sediments with 60S ribosomal subunits and copuri...
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PMID: 20403971
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (26)3 2010
Abstract
Four dsRNA bands were extracted from Pleurotus ostreatus TD300 by the dsRNA isolation technique with sizes of 8.2 kb, 2.5 kb, 2.1 kb, and 1.1 kb, respectively. Four virus-eliminated methods, i. e. hyphal tips cut (HTC), protoplast regeneration (PR), single spore hybridization (SSH), and frozen and l...
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PMID: 20572349
PDF is available here.
PDF is available here.
Abstract
We have examined the cryptochrome from the filamentous fungus Neurospora crassa and demonstrate that Neurospora cry encodes a DASH-type cryptochrome that appears capable of binding flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF). The cry transcript and CRY protein levels are st...
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PMID: 20305004
PDF is available here.
PDF is available here.
Abstract
We report the first two proven cases of cavitary pulmonary zygomycosis caused by Rhizopus homothallicus. The diagnosis in each case was based on histology, culture of the causal agent, and the nucleotide sequence of the D1/D2 region of the 28S ribosomal DNA.
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PMID: 20200286
PDF is available here.
PDF is available here.
Biotechnology Letters (32)5 2010
Abstract
A new 10-hydroxycamptothecin (HCPT)-producing fungus was isolated from Camptotheca acuminata. The strain was classified as a Xylaria sp. based on the internal transcribed spacer and 18S rDNA gene analysis. All elicitors tested, except methyl jasmonate, increased HCPT production in submerged culture....
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PMID: 20112128
PDF is available here.
PDF is available here.
Abstract
We report a case of disseminated Scedosporium/Pseudallescheria infection due to Pseudallescheria boydii sensu stricto after lung transplantation in a patient with cystic fibrosis. Dissemination occurred under voriconazole. Despite surgery and combination therapy with voriconazole, caspofungin, and t...
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PMID: 20220160
PDF is available here.
PDF is available here.
Abstract
We use a fluorescence in situ hybridization (FISH) technique that allows the detection of single-RNA molecules in individual yeast cells. We use this method complemented with theoretical modeling to determine the rate of switching from OFF to ON (activation rate) and the average number of RNA molecu...
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PMID: 20393578
PDF is available here.
PDF is available here.
Abstract
We report here the (1)H, (15)N, (13)C and partial (31)P chemical shift assignments for the minimal functional 27nt neomycin sensing riboswitch RNA in complex with the 4,5-linked neomycin analog ribostamycin and the 4,6-linked aminoglycoside tobramycin....
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PMID: 20306311
PDF is available here.
PDF is available here.
Journal of Molecular Biology (397)3 2010
Abstract
We monitored Mss-116-facilitated folding of ai5gamma intron ribozymes and a catalytically active self-splicing RNA containing full-length intron and short exons. We found that the protein directly stimulates folding of these RNAs by accelerating formation of the compact near-native state. This proce...
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PMID: 20138894
PDF is available here.
PDF is available here.
Genome Research (20)4 2010
Abstract
We present low-quantity RNA sequencing (LQ-RNAseq), a high-throughput sequencing-based technique allowing whole transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3' polyA tail...
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PMID: 20133332
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1804)4 2010
Abstract
We have previously shown that glutaredoxin 2 (Grx2) from Saccharomyces cerevisiae localizes at 3 different subcellular compartments, cytosol, mitochondrial matrix and outer membrane, as the result of different postranslational processing of one single gene. Having set the mechanism responsible for t...
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PMID: 20036764
PDF is available here.
PDF is available here.
Abstract
To report the first case of fungal keratitis caused by presumed Carpoligna species.
A 37-year-old gardener sustained a full-thickness, stellate corneal laceration while cutting wood outdoors with a circular saw. Two months after surgical repair, he developed a severe infectious keratitis with descem...
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PMID: 20168220
PDF is available here.
PDF is available here.
Abstract
Cellobiohydrolase genes cbhI and cbhII were isolated from Trichoderma viride AS3.3711 and T. viride CICC 13038, respectively, using RT-PCR technique. The cbhI gene from T. viride AS3.3711 contains 1,542 nucleotides and encodes a 514-amino acid protein with a molecular weight of approximately 53.96 k...
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PMID: 19669931
PDF is available here.
PDF is available here.
Methods in Molecular Biology (638)638 2010
Abstract
We describe the application of a PCR-based differential screening method to plant-fungal interactions. Suppression subtraction hybridization (SSH) provides a sensitive method to isolate fungal genes expressed in planta. Total RNA is isolated from infected plants for comparison with the pathogen in a...
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PMID: 20238264
PDF is available here.
PDF is available here.
Methods in Molecular Biology (638)638 2010
Abstract
For an increasing number of microorganisms of scientific and industrial interest, the genome sequences have become available, which in turn has enabled genome-wide microarray studies. Global level transcriptomic analysis has flooded the research community with gene expression data from diverse biolo...
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PMID: 20238268
PDF is available here.
PDF is available here.
Methods in Molecular Biology (638)638 2010
Abstract
We focus on detection of the accumulating product with the Syber Green dye, but other detection technologies, such as hybridization probes, might be considered as well. Accurate qPCR analysis with Syber Green depends mainly on optimal PCR reaction, and therefore it is important to design primers tha...
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PMID: 20238263
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
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PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
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PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Mycopathologia (169)3 2010
Abstract
A fungus causing tar spots on leaves of Comarostaphylis arbutoides (Ericaceae) in Panama is described as a new species, Rhytisma panamense. The fungus forms gregarious black stromata on pale yellow spots on the adaxial side of leaves. Its ascomata develop from unilocular or multilocu...
|
PMID: 19885738
PDF is available here.
PDF is available here.
Abstract
We measured the direct and interactive effects of climatic change on soil fungal and bacterial communities (abundance and composition) in a multifactor climate change experiment that exposed a constructed old-field ecosystem to different atmospheric CO2 concentration (ambient, +300 ppm), temperature...
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PMID: 20023089
PDF is available here.
PDF is available here.
Abstract
We report for the first time the taxonomic and phylogenetic description of three C. lamprauges isolates recovered from sheep with rhinopharyngeal entomophthoramycosis. The distinctive clinical and pathological features of C. lamprauges are compared with those of other Conidiobolus spp. affecting she...
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PMID: 20007391
PDF is available here.
PDF is available here.
Abstract
Proper 3' end processing of a nascent transcript is critical for the functionality of the mature RNA. Although it has long been thought that virtually all long RNA polymerase II transcripts terminate in a poly(A) tail that is generated by endonucleolytic cleavage followed by polyadenylation, noncano...
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PMID: 20007330
PDF is available here.
PDF is available here.
Abstract
We describe a straightforward approach to prepare an adequate tRNA substrate for Dnmt2 and a method to measure its tRNA methyltransferase activity....
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PMID: 21048666
PDF is available here.
PDF is available here.