The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at a water depth of 1525 meters, and a deep-sea plume was detected within one month. Oil contacted and ...persisted in parts of the bottom of the deep-sea in the Gulf of Mexico. As part of the response to the accident, monitoring cruises were deployed in fall 2010 to measure potential impacts on the two main soft-bottom benthic invertebrate groups: macrofauna and meiofauna. Sediment was collected using a multicorer so that samples for chemical, physical and biological analyses could be taken simultaneously and analyzed using multivariate methods. The footprint of the oil spill was identified by creating a new variable with principal components analysis where the first factor was indicative of the oil spill impacts and this new variable mapped in a geographic information system to identify the area of the oil spill footprint. The most severe relative reduction of faunal abundance and diversity extended to 3 km from the wellhead in all directions covering an area about 24 km(2). Moderate impacts were observed up to 17 km towards the southwest and 8.5 km towards the northeast of the wellhead, covering an area 148 km(2). Benthic effects were correlated to total petroleum hydrocarbon, polycyclic aromatic hydrocarbons and barium concentrations, and distance to the wellhead; but not distance to hydrocarbon seeps. Thus, benthic effects are more likely due to the oil spill, and not natural hydrocarbon seepage. Recovery rates in the deep sea are likely to be slow, on the order of decades or longer.
A survey of the endophytic fungi in fronds of Livistona chinensis was carried out in Hong Kong. The endophyte
assemblages identified using morphological characters consisted of 16 named species and ...19 ‘morphospecies’, the
latter grouped based on cultural morphology and growth rates. Arrangement of taxa into morphospecies does not
reflect species phylogeny, and therefore selected morphospecies were further identified based on ribosomal DNA
(rDNA) sequence analysis. The 5.8S gene and flanking internal transcribed spacers (ITS1 and ITS2) regions of
rDNA from 19 representative morphospecies were amplified by the polymerase chain reaction and sequenced.
Phylogenetic analysis based on 5.8S gene sequences showed that these morphospecies were filamentous
Ascomycota, belonging in the Loculoascomycetes and Pyrenomycetes. Further identification was conducted by
means of sequence comparison and phylogenetic analysis of both the ITS and 5.8S regions. Results showed that
MS704 belonged to the genus Diaporthe and its anamorph Phomopsis of the Valsaceae. MS594 was inferred to be
Mycosphaerella and its anamorph Cladosporium of the Mycosphaerellaceae. MS339, MS366, MS370, MS395,
MS1033, MS1083 and MS1092 were placed in the genus Xylaria of the Xylariaceae. MS194, MS375 and MS1028
were close to the Clypeosphaeriaceae. MS191 and MS316 were closely related to the Pleosporaceae within the
Dothideales. The other 5 morphospecies, MS786, MS1043, MS1065, MS1076 and MS1095, probably belong in
the Xylariales. The value of using DNA sequence analysis in the identification of endophytes is discussed.
Families of Sordariomycetes Maharachchikumbura, Sajeewa S. N.; Hyde, Kevin D.; Jones, E. B. Gareth ...
Fungal diversity,
07/2016, Letnik:
79, Številka:
1
Journal Article
Recenzirano
Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi characterized mainly by perithecial ascomata and inoperculate unitunicate asci. The class ...includes many important plant pathogens, as well as endophytes, saprobes, epiphytes, coprophilous and fungicolous, lichenized or lichenicolous taxa. They occur in terrestrial, freshwater and marine habitats worldwide. This paper reviews the 107 families of the class Sordariomycetes and provides a modified backbone tree based on phylogenetic analysis of four combined loci, with a maximum five representative taxa from each family, where available. This paper brings together for the first time, since Barrs’
1990
Prodromus, descriptions, notes on the history, and plates or illustrations of type or representative taxa of each family, a list of accepted genera, including asexual genera and a key to these taxa of Sordariomycetes. Delineation of taxa is supported where possible by molecular data. The outline is based on literature to the end of 2015 and the Sordariomycetes now comprises six subclasses, 32 orders, 105 families and 1331 genera. The family
Obryzaceae
and
Pleurotremataceae
are excluded from the class.
Phyllosticta is a geographically widespread genus of plant pathogenic fungi with a diverse host range. This study redefines Phyllosticta, and shows that it clusters sister to the Botryosphaeriaceae ...(Botryosphaeriales, Dothideomycetes), for which the older family name Phyllostictaceae is resurrected. In moving to a unit nomenclature for fungi, the generic name Phyllosticta was chosen over Guignardia in previous studies, an approach that we support here. We use a multigene DNA dataset of the ITS, LSU, ACT, TEF and GPDH gene regions to investigate 129 isolates of Phyllosticta, representing about 170 species names, many of which are shown to be synonyms of the ubiquitous endophyte P. capitalensis. Based on the data generated here, 12 new species are introduced, while epitype and neotype specimens are designated for a further seven species. One species of interest is P. citrimaxima associated with tan spot of Citrus maxima fruit in Thailand, which adds a fifth species to the citrus black spot complex. Previous morphological studies lumped many taxa under single names that represent complexes. In spite of this Phyllosticta is a species-rich genus, and many of these taxa need to be recollected in order to resolve their phylogeny and taxonomy.
Taxonomic novelties: New species – Phyllosticta abieticola Wikee & Crous, P. aloeicola Wikee & Crous, P. citrimaxima Wikee, Crous, K.D. Hyde & McKenzie, P. leucothoicola Wikee, Motohashi & Crous, P. mangifera-indica Wikee, Crous, K.D. Hyde & McKenzie, P. neopyrolae Wikee, Motohashi, Crous, K.D. Hyde & McKenzie, P. pachysandricola Wikee, Motohashi & Crous, P. paxistimae Wikee & Crous, P. podocarpicola Wikee, Crous, K.D. Hyde & McKenzie, P. rhaphiolepidis Wikee, C. Nakash. & Crous, P. rubra Wikee & Crous, P. vacciniicola Wikee, Crous, K.D. Hyde & McKenzie; New combinations – P. foliorum (Sacc.) Wikee & Crous, P. philoprina (Berk. & M.A. Curtis) Wikee & Crous; Epitypifications (basionyms) – P. concentrica Sacc., P. cussoniae Cejp, P. owaniana G. Winter; Neotypifications (basionyms) – Phyllosticta cordylinophila P.A. Young, Physalospora gregaria var. foliorum Sacc., Sphaeropsis hypoglossi Mont., Sphaeropsis minima Berk. & M.A. Curtis.
Ovarian tissue transplantation (OTT) is a technique well established and successfully applied in humans using mainly orthotopic or heterotopic transplantation sites. In livestock, OTT is still in its ...infancy and, therefore, different aspects of the technique, including the efficiency of different heterotopic OTT sites as well as the potential effect of age (i.e., young vs. old mares) in the ovarian graft quality, need to be investigated. The present study investigated the efficacy of the intramuscular (IM) or the novel subvulvar mucosa (SV) heterotopic autotransplantation sites to maintain the survivability of the grafts for 3 and 7 days post-OTT. Ovarian biopsy fragments were obtained in vivo and distributed to the following treatments: Fresh control group (ovarian fragments immediately fixed), SV-3, IM-3, SV-7, and IM-7. During and after graft harvesting, the macroscopic characteristics of the grafts (i.e., adherence, morphology, and bleeding) were scored, and the percentages of morphologically normal and developing preantral follicles as well as the follicular and stromal cell densities of the grafts were evaluated. The results were that similar (P > 0.05) macroscopic scores were observed between both transplantation sites 7 days post-OTT, with positive correlations (P < 0.01) found among adherence, morphology, and bleeding of the grafts. A lower (P < 0.05) percentage of morphologically normal follicles was found 7 days post-OTT in the SV site (82%) compared with the Fresh control group (99%) and IM site (95%); however, the percentages of developing follicles were similar (P > 0.05) between both transplantation sites 7 days post-OTT (30–43%). Although similar (P > 0.05) follicular densities were found in both transplantation sites in young and old mares at 3 and 7 days post-OTT, large individual variation in the follicular depletion rate was observed regardless of transplantation site. The Fresh control group and SV-7 treatments had higher (P < 0.05) stromal cell densities in young and old mares compared with both IM-7 treatments. When comparing transplant sites between young and old mares, the follicular density in old mares and the stromal cell density in young mares were greater (P < 0.05) in the SV than in the IM site. In conclusion, even though the transplantation sites differentially affected some end points, overall comparable findings of the OTT technique using both heterotopic autotransplantation sites (i.e., IM and SV) for equine ovarian tissue were observed.
•The subvulvar mucosa is an appealing new location for ovarian tissue heterografting.•Subvulvar and intramuscular sites were compared 3 and 7 days post-transplantation and between young and old mares.•Overall, both heterografting sites had similar follicular development.•The subvulvar site had higher stromal cell density and follicular density in young and old mares, respectively.•Large individual variation in follicular depletion was seen regardless of transplantation site.
Image processing strategies for functional magnetic resonance imaging (FMRI) data sets acquired using a gradient-recalled echo-planar imaging sequence are considered. The analysis is carried out ...using the mathematics of vector spaces. Data sets consisting of N sequential images of the same slice of brain tissue are analyzed in the time-domain and also, after Fourier transformation, in the frequency domain. A technique for thresholding is introduced that uses the shape of the response in a pixel compared with the shape of a reference waveform as the decision criterion. A method is presented to eliminate drifts in data that arise from subject movement. The methods are applied to experimental FMRI data from the motor-cortex and compared with more conventional image-subtraction methods. Several finger motion paradigms are considered in the context of the various image processing strategies. The most effective method for image processing involves thresholding by shape as characterized by the correlation coefficient of the data with respect to a reference waveform followed by formation of a cross-correlation image. Emphasis is placed not only on image formation, but also on the use of signal processing techniques to characterize the temporal response of the brain to the paradigm.
The human concentrative (Na+-linked) plasma membrane transport proteins hCNT1 and hCNT2 are selective for pyrimidine nucleosides (systemcit) and purine nucleosides (system cif), respectively. Both ...have homologs in other mammalian species and belong to a gene family (CNT) that also includes hfCNT, a newly identified broad specificity pyrimidine and purine Na+-nucleoside symporter (system cib) from the ancient marine vertebrate, the Pacific hagfish (Eptatretus stouti). We now report the cDNA cloning and characterization of cib homologs of hfCNT from human mammary gland, differentiated human myeloid HL-60 cells, and mouse liver. The 691- and 703-residue human and mouse proteins, designated hCNT3 and mCNT3, respectively, were 79% identical in amino acid sequence and contained 13 putative transmembrane helices. hCNT3 was 48, 47, and 57% identical to hCNT1, hCNT2, and hfCNT, respectively. When produced in Xenopus oocytes, both proteins exhibited Na+-dependentcib-type functional activities. hCNT3 was electrogenic, and a sigmoidal dependence of uridine influx on Na+concentration indicated a Na+:uridine coupling ratio of at least 2:1 for both hCNT3 and mCNT3 (cf 1:1 for hCNT1/2). Phorbol myristate acetate-induced differentiation of HL-60 cells led to the parallel appearance of cib-type activity and hCNT3 mRNA. Tissues containing hCNT3 transcripts included pancreas, bone marrow, trachea, mammary gland, liver, prostrate, and regions of intestine, brain, and heart. The hCNT3 gene mapped to chromosome 9q22.2 and included an upstream phorbol myristate acetate response element.
Studies of postmortem human brain are important for investigating underlying pathogenic molecular mechanisms of neuropsychiatric disorders. They are, however, confounded by pre- and postmortem ...factors. The purpose of this study was to identify sources of variation that will enable a better design of gene expression studies and higher reliability of gene expression data.
We assessed the contribution of multiple variables to messenger RNA (mRNA) expression of reference (housekeeping) genes measured by reverse transcriptase–polymerase chain reaction (RT-PCR) by multiple regression analysis in a large number (
N = 143) of autopsy samples from the hippocampus and white and grey matter of the dorsolateral prefrontal cortex (DLPFC) of patients with schizophrenia and normal control subjects.
The strongest predictor of gene expression was total RNA quality. Other significant factors included pH, postmortem interval, age and the duration of the agonal state, but the importance of these factors depended on transcript measured, brain region analyzed, and diagnosis. The quality of RNA obtained from the DLPFC white matter was also adversely affected by smoking.
Our results show that normalization of expression data of target genes with a geometric mean of multiple housekeeping genes should be used to control for differences in RNA quality between samples. The results also suggest that accurate assessment of other confounding factors and their inclusion as regressors in the analysis is critical for obtaining reliable and accurate quantification of mRNA expression.
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