Culturome versus DNA metabarcoding: Diversity of grapevine endophytic mycobiome in old and young vines of different health status in New Zealand

The grapevine harbours a diverse community of fungi in the woody trunk tissue, termed the “endophytic mycota”. These communities can have a profound effect on the vine’s physiology, health, growth, and ability to adapt to stress. Some of these include pathogenic fungi as the causal agents of grapevine trunk disease (GTD), with many considered latent pathogens. For GTD, understanding the factors affecting latency is still limited. This study aimed to compare the fungal endophyte community in young and old Sauvignon blanc vines, both symptomatic and asymptomatic for GTD, using culture-dependent and culture-independent approaches. Nine vineyards were sampled, with 60 mature vines (>10 years old) and 30 young vines (<9 years old) sampled. Each age group consisted of equal numbers of apparently healthy and symptomatic vines. Trunk cores were taken from each vine using a sterilised 4-mm drill bit after removing the bark with a knife. Fungal communities were characterized by isolation and metabarcoding of the ITS1 region. For the culturome, a collection of 2116 endophytic fungi were recovered, representing 42 fungal genera. Trunk microbiota was dominated by species of the genera Alternaria, Aureobasidium, Diplodia,Epicoccum, Phaeomoniella, Eutypa, Botrytis, Cladosporium, and Diaporthe. Differences in the taxa recovered into culture were observed between vines of different ages, and symptomology. In the metabarcoding approach, 1892 OTUs were obtained. The same fungal genera were identified as the most abundant using metabarcoding. Alpha diversity analysis revealed that greater diversity was detected in old compared to young vines and in asymptomatic compared to symptomatic trunks. Beta diversity analysis demonstrated significant differentiation in the fungal communities structure for both age and health status. This study has produced new baseline information on Sauvignon blanc endophytic mycota and further work will determine the impact of these microbial communities on the latency of GTDs

Two-Particle Correlations in Relativistic Heavy-Ion Collisions

Two-particle momentum correlations between pairs of identical particles produced in relativistic heavy-ion reactions can be analyzed to extract the space-time structure of the collision fireball. We review recent progress in the application of this method, based on newly developed theoretical tools and new high-quality data from heavy-ion collision experiments. Implications for our understanding of the collision dynamics and for the search for the quark-gluon plasma are discussed.Comment: 44 pages, LaTeX, 11 Figures, uses special style files (included), prepared for Ann. Rev. Nucl. Part. Sci. 49 (1999). Error in Chapt. 1 corrected and a few references adde

The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis.

Synovial sarcomas are aggressive soft-tissue malignancies that express chromosomal translocation-generated fusion genes, SS18-SSX1 or SS18-SSX2 in most cases. Here, we report a mouse sarcoma model expressing SS18-SSX1, complementing our prior model expressing SS18-SSX2. Exome sequencing identified no recurrent secondary mutations in tumors of either genotype. Most of the few mutations identified in single tumors were present in genes that were minimally or not expressed in any of the tumors. Chromosome 6, either entirely or around the fusion gene expression locus, demonstrated a copy number gain in a majority of tumors of both genotypes. Thus, by fusion oncogene coding sequence alone, SS18-SSX1 and SS18-SSX2 can each drive comparable synovial sarcomagenesis, independent from other genetic drivers. SS18-SSX1 and SS18-SSX2 tumor transcriptomes demonstrated very few consistent differences overall. In direct tumorigenesis comparisons, SS18-SSX2 was slightly more sarcomagenic than SS18-SSX1, but equivalent in its generation of biphasic histologic features. Meta-analysis of human synovial sarcoma patient series identified two tumor-gentoype-phenotype correlations that were not modeled by the mice, namely a scarcity of male hosts and biphasic histologic features among SS18-SSX2 tumors. Re-analysis of human SS18-SSX1 and SS18-SSX2 tumor transcriptomes demonstrated very few consistent differences, but highlighted increased native SSX2 expression in SS18-SSX1 tumors. This suggests that the translocated locus may drive genotype-phenotype differences more than the coding sequence of the fusion gene created. Two possible roles for native SSX2 in synovial sarcomagenesis are explored. Thus, even specific partial failures of mouse genetic modeling can be instructive to human tumor biology

Effects of Copper Exchange Levels on Complexation of Ammonia in Cu (II)-exchanged X Zeolite

Copper (II)-exchanged faujasite-X zeolites at various loadings of copper per unit cell of zeolites were prepared and then exposed to ammonia. The copper ammine complexes of the various copper levels per unit cell were characterized and analyzed by a combination of diffuse reflectance, X-ray powder diffraction, FT-infrared spectroscopy, electron paramagnetic resonance and nuclear magnetic resonance spectroscopic methods. At low copper exchange levels (&lt;5 copper atoms per unit cell), the major complex is [Cu(Ozeo)2(NH3)2]2+ and it is strongly bound to the zeolite framework walls at single four ring sites (site III). Above five copper atoms per unit cell, the major complex becomes [Cu(NH3)4]2+ and it is least interacting with the zeolite framework walls. The [Cu(NH3)4]2+ complex which was formed at higher copper levels per unit cell was most favoured by the presence of maximal amount of ammonia.Keywords: Cation Exchange, Catalysis, Copper, Complexation, Copper AmminesAttached PDF and Supplementary Fil

Simulating Reionization: Character and Observability

In recent years there has been considerable progress in our understanding of the nature and properties of the reionization process. In particular, the numerical simulations of this epoch have made a qualitative leap forward, reaching sufficiently large scales to derive the characteristic scales of the reionization process and thus allowing for realistic observational predictions. Our group has recently performed the first such large-scale radiative transfer simulations of reionization, run on top of state-of-the-art simulations of early structure formation. This allowed us to make the first realistic observational predictions about the Epoch of Reionization based on detailed radiative transfer and structure formation simulations. We discuss the basic features of reionization derived from our simulations and some recent results on the observational implications for the high-redshift Ly-alpha sources.Comment: 3 pages, to appear in the Proceedings of First Stars III, Santa Fe, July 2007, AIP Conference Serie

Demand-side financing: can it help deliver eye care for all?

Demand-side financing mechanisms in eye care can be a tool to achieve universal eye health coverage by increasing access and utilisation of key eye health services

Experiences of hospice dementia care: A qualitative study of bereaved carers and hospice clinicians

BACKGROUND: Nearly 50 million people worldwide have dementia and the increasing numbers requiring end-of-life and palliative care, has led to national efforts to define standards of care for this patient group. Little research, however, has been done to date about the experience of hospice care for people with dementia accessing these services. This study explores the views of hospice dementia care for bereaved carers of people with dementia and hospice clinicians. METHODS: We used purposive sampling for participant recruitment. Semi-structured qualitative interviews were conducted with bereaved carers and hospice clinical staff. Interviews were audio recorded and the transcriptions were analysed through thematic analysis. A total of 12 participants were interviewed from one service in the Northwest region in the UK. All were female and white British. RESULTS: Participants described their experience of hospice dementia care in three main themes: Pre-access to service, roles and responsibility within hospice care, ease and difficulty of last period of end-of-life care. CONCLUSION: Rapid response teams delivering hospice home care could represent a better option to inpatient care and may be preferred by patients. This type of service, however, may require joined-up care with other community services, and this type of care needs to be considered and planned. Future studies should evaluate this type of community care

Spectral Classification; Old and Contemporary

Beginning with a historical account of the spectral classification, its refinement through additional criteria is presented. The line strengths and ratios used in two dimensional classifications of each spectral class are described. A parallel classification scheme for metal-poor stars and the standards used for classification are presented. The extension of spectral classification beyond M to L and T and spectroscopic classification criteria relevant to these classes are described. Contemporary methods of classifications based upon different automated approaches are introduced.Comment: To be published in "Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars: Ed Aruna Goswami & Eswar Reddy, Springer Verlag, 2009, 17 pages, 10 figure

Gravity current propagation up a valley

The advance of the front of a dense gravity current propagating in a rectangular channel and V-shaped valley both horizontally and up a low slope is examined through theory, full-depth lock-release laboratory experiments and hydrostatic numerical simulations. Consistent with theory, experiments and simulations show that the front speed is relatively faster in the valley than in the channel. The front speed measured shortly after release from the lock is 5% to 22% smaller than theory with greater discrepancy found in up-sloping V-shaped valleys. By contrast, the simulated speed is about 6% larger than theory showing no dependence on slope for rise-angles up to θ = 8◦. Unlike gravity currents in a channel, the current head is observed in experiments to be more turbulent when propagating in a V-shaped valley. The turbulence is presumably enhanced due to the lateral flows down the sloping sides of the valley. As a consequence, lateral momentum transport contributes to the observed lower initial speeds. A WKB-like theory predicting the deceleration of the current as it runs upslope agrees remarkably well with simulations and with most experiments, within errors.The authors gratefully acknowledge the National Science Foundation (grant OCE-0824636) and the Office of Naval Research (grant N00014-09 1-0844) for their support of the 2013 WHOI Geophysical Fluid Dynamics Summer School, where much of the research presented in this paper was performed