1,720,972 research outputs found
Truffles in Michigan : impacts of herbicides on their growth, effectiveness of in-field inoculations, and the discovery of a local truffle (Tuber rugosum)
No full textWith the advent of promising truffle cultivation techniques, there are many new truffle plantations (truffiere) being established and managed throughout the world; one of the biggest challenges these plantations face is weed management. There is little known about the impact popular herbicides have on truffle mycelial growth. Here, I discuss how the use of herbicides in management may impact mycelial growth. Pure culture growth assays were performed to assess the impacts glyphosate and glufosinate chemistries on three species of truffle, two species of morels, and two members of the Mortierellaceae. While there were variable responses by each species tested, most fungi experienced growth inhibition near or above the manufacturer's recommended application rates for general weed use.I also assess how introducing exotic truffle species, local ectomycorrhizal species, and commercial mycorrhizal inoculants in post-methyl bromide fumigated bare-root conifer tree nursery impacts seedling growth. To test whether inoculum benefits seedling health and growth, exotic, and commercial ectomycorrhizal inoculua were added at the time of planting for three species of conifer. The results showed a high mycorrhizal diversity on bare-root seedling roots, which generally differed from those of the added inoculum. Additionally, there were no growth or health improvements over uninoculated control blocks compared to treatment blocks.Finally, I will showcase the taxonomic discovery of a new species of truffle native to Michigan, Tuber rugosum. Also, observing slug fungivory of this new truffle led to an improved ascus technique for performing scanning electron microscopy of truffle spores. Collectively, this thesis aims to inform herbicide use in myco-agricultural lands, to inform the use of added mycorrhizal inoculants in bare-root conifer tree nurseries, and to improve our knowledge on Michigan's native truffle species.Thesis (M.S.)--Michigan State University. Plant Pathology, 2023Includes bibliographical reference
Investigation and analysis of taxonomic irregularities with the Botryosphaeriaceae
Full text linkMany members of Botryosphaeriaceae live as endophytes with a latent phase that can cause disease in native and non-native plant hosts around the world. The main Botryosphaeriaceae examined in this thesis included species in the Lasiodiplodia theobromae species complex, Neofusicoccum parvum-ribis species complex and Neofusicoccum australe. A combination of traditional morphology, pathogenicity trials, multiple gene phylogenies and microsatellite analyses were used to probe between and within species.
Within native bushland in the Kimberley, Western Australia, 13 taxa of the Botryosphaeriaceae were identified; Lasiodiplodia mahajangana was the most common species and was confirmed as a potentially significant pathogen of Adansonia gregorii. These fungi also colonised non-native Mangifera indica in the same region possibly displacing the exotic microflora of M. indica. Pathogenicity tests resulted in lesion development of mango fruit and excised stems.
Isolates in the N. parvum- ribis complex collected from eucalypt cankers in eastern Australia exhibited overlapping morphology and pathogenicity. Phylogenetic analysis of four gene regions and application of the Genealogical Sorting Index to the same data set supported two new species. Consequently, the description of Neofusicoccum occulatum is presented. Neofusicoccum parvum has been recorded in 71 host species across six continents and 21 countries. Population data analysis of N. parvum populations reflects admixture and repeat introductions of new genetic material. No specific host associations were observed.
Evaluation of EF1-α molecular data amongst members of L. theobromae species complex suggests there are an additional four taxa and two potential hybrids. The 19 Lasiodiplodia taxa have been recorded in 56 host species, across six continents and 23 countries. Nine Lasiodiplodia taxa and one hybrid have been identified in Australia. Population analysis suggests the Kimberley populations are sexually reproducing with no discernable host restriction and display moderate genetic diversity.
Neofusicoccum australe is found across nine countries and 46 host species. Phylogenetic analysis of the ITSrDNA sequence identified a single dominant ITS haplotype found in most locations and another 12 rare to moderately rare haplotypes found in one to two locations. Using microsatellite markers, populations of N. australe were found to be highly diverse and there was no discernable host or habitat restriction. The dominance of N. australe in native forest throughout the southwest of Western Australia suggests that this species is endemic to this area.
The species studied in this thesis appear to be capable latent pathogens with no obvious restriction to host colonisation or habitat. Multiple species and multiple genotypes of one species can colonise small sections of a single host. Cryptic sympatric speciation is common despite no observable telomorphs. These species appear to be highly competitive and their endophytic life strategy appears to provide effective means for dissemination via asymptomatic host tissue, which could complicate quarantine efforts that typically rely on the visual presence of disease symptoms
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Resolving the Botryosphaeria ribis-B. parva species complex : a molecular and phenotypic investigation
No full textBotryosphaeria spp. have been found around the world on numerous hosts. Recent work has indicated
that Botryosphaeria ribis and B. parva may not be distinct species but rather represent the extremes in a
complex. It has been difficult to separate these species based on phenotypic, molecular or niche
associations. fu this thesis, a selection of isolates, representing the diversity in the whole group, were
chosen from a larger subset. This thesis sought to uncover the true status of B. ribis-B. parva. Four
possible scenarios were hypothesized:
a) they were never two distinct species and are instead one species
b) they are a species complex in the process of speciation
c) they were two distinct species that have never developed reproductive isolation mechanisms and
when brought back into contact with each other hybridized and formed a species complex
d) There are many species
Multiple gene genealogies using five gene regions, ITS, EF, CHS, RPB2 and ACT, were investigated. The topology of each generated from each individual gene region reflected a different phylogenetic relationship between isolates in the B. ribis-B. parva complex. The trees were incongruent and could not be combined. This inability to combine the data sets indicated recombination amongst isolates from these two "species". Isolates were classified as either B. parva, B. ribis or "other", depending on whether they grouped with the type specimens of each "species" or not. Based on this there were isolates that consistently grouped with types of B. parva and B. ribis and there were isolates contained a combination of characters from both B. parva sensu stricto and B. ribis sensu stricto. The reticulate nature of each tree topology indicated recombination amongst isolates, lending weight to the scenario hypothesising one species.
SSR data was used to help support the conclusions drawn from the multiple gene genealogies and to try and identify possible gene flow and assess level of genetic diversity amongst isolates. Eight SSR markers that had previously been developed for B.parva were used Distance analysis indicated no association with host or geographic location. The data indicated limited gene differentiation amongst isolates from the Australasian region suggestion the movement throughout the region on eucalypts. Whilst there was evidence of gene flow between South Africa and Australasia, the highest diversity and most unique alleles were found in South Africa from a group of isolates collected from a native Syzygium species. Perhaps this could be the origin of B. parva. The IA values indicated clonality despite high genotypic diversity (73 different genotypes out of 100 isolates). The SSR data did not support the maintenance of two distinct species of B. rib is and B. parva.
Pathogenicity tests showed no significant differences between isolates previously identified as B. parva sensu stricto and B. ribis sensu stricto, one group of isolates did show a significant reduction in pathogenicity but no correlation between host or geographical region could be made to support this. Both hyaline, fusoid (Fusicoccum) and pigmented, irregular (formerly Dichomera) spore types were found amongst isolates in this group however, there were no differences between isolates of the types of B. parva and B. ribis. The appearance of Dichomera spore type is very interesting and further investigations of Dichomera-like spores in the genus Botryosphaeria should be undertaken. Phenotypic evidence does not support the maintenance of two distinct species, nor does it provide any evidence of hybridisation.
There are no significant, consistent morphological differences, multiple gene genealogies generate reticulate incongruent phylogenies (indicating recombination) and SSR data indicates substantial gene flow and shared alleles. Under the Morphological Species Concept, the Biological Species Concept and the Phylogenetic Species Concepts the separation of two distinct species is not supported. Therefore the results of this thesis indicates that B. parva should be synonymized into B. ribis (B. ribis was
described before B. parva)
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
DISSECTING THE MULTIMODAL SIGNALING NETWORK MEDIATED BY CYCLIC-DI-GMP IN ERWINIA AMYLOVORA
Full text linkErwinia amylovora is the bacterial phytopathogenic causal agent of fire blight, an economically impactful disease that affects apple and pear production worldwide. The successful orchestration of infection by E. amylovora within the host entails a coordinated implementation of several different virulence strategies. A key step in the disease cycle of E. amylovora is the transition from a primarily Type III secretion system (T3SS) effectors-dependent phase in the leaf apoplast to a biofilm-dependent phase within xylem vessels. Cyclic-di-GMP (c-di-GMP), a ubiquitous bacterial second messenger mediates this phase transition into a sessile, attached lifestyle within biofilms in E. amylovora. This body of work encompasses several aspects of the complex and multifactorial signaling network dependent on c-di-GMP in E. amylovora. Diguanylate cycles enzymes (encoded by edc genes) dimerize GTP subunits to synthesize c-di-GMP and phosphodiesterase enzymes (encoded by pde genes) hydrolyze c-di-GMP. We found that the deletion of the three active pde genes in E. amylovora, singly and in combinations of two and all three genes, led to a measurable increase in intracellular c-di-GMP levels. In addition, the elevated c-di-GMP levels correlated with increased production of amylovoran, which is the most abundant exopolysaccharide (EPS), and, a pathogenicity factor in E. amylovora. The expression of T3SS, quantified by the transcriptional level of hrpL as well as by virulence measurements in the apple and pear models, was found to be negatively regulated by c- di-GMP. While biofilm formation generally increased with elevated levels of c-di-GMP, the total pde deletion mutant, \u394pdeABC, showed a relative depreciation in the ability to form biofilms, owing to the physical autoaggregative characteristic of this strain when grown in liquid media. Autoaggregation also impaired cell separation post division, leading to the presence of filamentous cells within cellular aggregates. In addition to the EPSs amylovoran and cellulose, EagA, a peptidoglycan hydrolase was found to be a major contributor to the facilitation of autoaggregation in E. amylovora. The eagA/znuABC zinc uptake gene cluster, was found to be transcriptionally regulated by c-di-GMP and the zinc-dependent repressor Zur. Further, we evaluated the impact of a systemic deletion of all genetic components involved in c-di-GMP metabolism, including active and degenerate dgc and pde encoding genes. The resulting mutant, Ea1189\u39412 was found to be impaired in surface sensing and attachment, which are key steps in the initiation of biofilm formation both in-vitro and in-planta. The transcriptomic profile of WT Ea1189 and Ea1189\u39412 at various stages of biofilm development revealed marked differences in critical metabolic and signal transduction pathways. The correlational clustering of phenotypic data gathered from single gene complemented strains generated from Ea1189\u39412, enabled the functional categorization of each of the systemic components.Thesis (Ph.D.)--Michigan State University. Plant Pathology - Doctor of Philosophy, 2021Includes bibliographical reference
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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