Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/T509073/

Complete molecular genome analyses of equine rotavirus a strains from different continents reveal several novel genotypes and a largely conserved genotype constellation

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/ G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/ G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6- R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to nonequine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.Fil: Matthijnssens, Jelle. Katholikie Universiteit Leuven; BélgicaFil: Miño, Orlando Samuel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; ArgentinaFil: Papp, Hajnalka. Hungarian Academy of Sciences; HungríaFil: Potgieter, Christiaan. Ondersterpoort Veterinary Institute; SudáfricaFil: Novo, Luis. Katholikie Universiteit Leuven; BélgicaFil: Heylen, Elisabeth. Katholikie Universiteit Leuven; BélgicaFil: Zeller, Mark. Katholikie Universiteit Leuven; BélgicaFil: Garaicoechea, Lorena Laura. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Badaracco, Alejandra. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lengyel, György. Dr György Radó Military Medical Centre; HungríaFil: Kisfali, Péter. University Of Pécs; HungríaFil: Cullinane, Ann. Irish Equine Centre; IrlandaFil: Collins, P. J.. Cork Ins Of Technology; IrlandaFil: Ciarlet, Max. Novartis Vaccines and Diagnostics; Estados UnidosFil: O'Shea, Helen. Cork Ins Of Technology; IrlandaFil: Parreño, Gladys Viviana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bányai, Krisztián. Hungarian Academy of Sciences; HungríaFil: Barrandeguy, María Edith. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; ArgentinaFil: Van Ranst, Marc. Katholikie Universiteit Leuven; Bélgic

Salve Regina Arboretum Ten Year Plan to Reach Level III Accreditation

The Salve Regina University Arboretum, located in Newport, Rhode Island is currently registered as a Level II arboretum and is intertwined with the city of Newport Arboretum. The university now has intentions to reach Level III status, as part of a ten-year plan. This plan was developed by the students of the Spring 2018 BIO 255: Conservation Biology course, instructed by Dr. Jameson Chace, Associate Professor of biology at Salve Regina University. As part of a curriculum geared towards civic engagement, the class focused on creating and optimizing strategies that can be applied to the ten-year plan. These strategies were applied to the plan categorically: a team to inventory the current tree collection; a team to develop formal educational programming; a team for informal educational programming; a team to establish goals for conservation initiative related to the arboretum; a team dedicated to research related to arboreta; and a team to develop a list of species of special interest to add to the arboretum in the coming years. In the following document, each team’s strategies for the ten-year plan are outlined. Each of the components of this plan incorporate means to fulfill the conditions to meet Level III arboretum status so that the arboretum can apply for official registration. The aforementioned teams were tasked with designing a foundation on which to work up from. This includes formal educational programming to be applied to classroom settings and informal educational programming which can be applied to community outreach-based settings. The teams that worked to strengthen the arboretum’s mission of conservation focused on researching trees that can fit into the current landscape while providing some sort of benefit to the surrounding flora/fauna. Further, many of the species of interest, such as the chestnut, hold historical value to the greater Rhode Island region. In all, the Salve Regina Arboretum must achieve a total of 500 unique species of trees and woody plants as part of its efforts to apply for Level III status. In addition to the programming and research performed so far by the student teams, the arboretum must also hire a curator to manage the programming and to oversee the arboretum as a whole. Additionally, the arboretum must continue to actively collaborate with other arboreta and should encourage scientific research. It is important to recognize that the Salve Regina University Arboretum has already been utilized in the field of microbiology and has gained some attention at the university as a resource for further research and investigation. This ten year plan, along with resources within in it, is designed to provide a list of potential guidelines and ideas that can be applied for the arboretum’s benefit and growth. The Salve Regina University arboretum is a continually growing and developing part of the greater Newport, Rhode Island community, and will continue to strengthen its mission and that of the university which oversees its success.https://digitalcommons.salve.edu/bio255_arboretum/1000/thumbnail.jp

A Multi-Institutional Phase II Study of the Efficacy and Tolerability of Lapatinib in Patients with Advanced Hepatocellular Carcinomas

Hepatocellular carcinoma (HCC) is on the rise worldwide. HCC responds poorly to chemotherapy. Lapatinib is an inhibitor of EGFR and HER2/NEU both implicated in hepatocarcinogenesis. This trial was designed to determine the safety and efficacy of lapatinib in HCC

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators

After birds diverged from mammals, different ancestral autosomes evolved into sex chromosomes in each lineage. In birds, females are ZW and males are ZZ, but in mammals females are XX and males are XY. We sequenced the chicken W chromosome, compared its gene content with our reconstruction of the ancestral autosomes, and followed the evolutionary trajectory of ancestral W-linked genes across birds. Avian W chromosomes evolved in parallel with mammalian Y chromosomes, preserving ancestral genes through selection to maintain the dosage of broadly expressed regulators of key cellular processes. We propose that, like the human Y chromosome, the chicken W chromosome is essential for embryonic viability of the heterogametic sex. Unlike other sequenced sex chromosomes, the chicken W chromosome did not acquire and amplify genes specifically expressed in reproductive tissues. We speculate that the pressures that drive the acquisition of reproduction-related genes on sex chromosomes may be specific to the male germ line

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses.

Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype1-3. To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 × 10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores

Are identities oral? Understanding ethnobotanical knowledge after Irish independence (1937-1939)

BACKGROUND: The Schools' Folklore Scheme (1937-1939) was implemented at a pivotal time in Irelands' political history. It resulted in a body of ethnological information that is unique in terms of when, why and how it was collected. This material consists of over 700,000 pages of information, including ethnomedicinal and ethnobotanical traditions, reflecting an oral identity that spans generations and that in many cases was not documented in writing until the 1930s. The intention of this study is to highlight the importance of the Schools' Folklore Scheme and to demonstrate an ethnographic approach based on recollections of original participants of the scheme, to further understand the material in the collection and the impact it had on the participants. METHODS: This study involves an analysis of both oral and archival data. Eleven semi-structured interviews with original participants of the scheme were carried out between April and September 2016. Their corresponding schools' archival contributions to the scheme were located, and ethnomedicinal information was analysed and compared with the participants' recollections. RESULTS: The majority of participants' stated the scheme had a positive impact on them. Five participants' recalled collecting ethnomedicinal information, and there was a direct correlation between three of the participants' ethnomedicinal recollections and their entries in the archives. One third of all the ethnomedicinal entries analysed included the use of a plant. There were 191 plant mentions and 64 plant species named. CONCLUSIONS: Contacting the original participants offers a novel approach of analysing this archival material. It provides a unique first-hand account of this historical initiative, an insight into how the scheme was implemented and how it impacted upon the children. The ethnomedicinal and ethnobotanical information provides an understanding of the medicinal practices in Ireland during the 1930s. The plant species that were both orally recalled by participants and documented in the archives are in keeping with key ethnomedicinal systems throughout the world

Throwing new light on the hypersensitive response

The hypersensitive response (HR) is a pathogen-localised cell death believed to contribute towards suppression of disease development. Amongst the key initiators of the HR are reactive oxygen species (ROS). We observed the formation of HR elicited by Pseudomonas syringae pv. tomato (Pst) avrRpm1 in Arabidopsis to be influenced by light in a fluence-dependent manner. Higher fluence rates were required for rapid cell death, ROS generation, and the accumulation of the defence signals, salicylic and jasmonic acid, as well as expression of several defence-related genes. Conversely, lower light fluence rates (< 25 mmol m−1 s−1) initiated senescence-like symptoms around the infected area and expression of Senescence-Associated Gene 12. A defining feature of leaf senescence is chlorophyll catabolism, which proceeds via a series of intermediates including the breakdown of phaeophorbide (phaeide) to red chlorophyll catabolite (RCC) through the enzymatic action of phaeophorbide a oxygenase (PaO), which is encoded by ACD1 in Arabidopsis. Maize and Arabidopsis mutants deficient in PaO exhibit light-dependent cell death attributed to the accumulation of phototoxic phaeide. HPLC analysis of developing Pst avrRpm1 HR lesions in the Arabidopsis acd1 mutants showed accumulation of phaeide as early as 9 h following challenge. Mendel's I gene, mutations of which partially disable chlorophyll catabolism, has recently been identified. Crucially, Arabidopsis lines where I gene expression was suppressed by RNAi exhibited a delayed Pst avrRpm1 HR. We propose that certain chlorophyll catabolites are previously unsuspected components in the HR mechanism. These could contribute to ROS generation by virtue of being uncoupled from the photosynthetic reaction centres