404 research outputs found
Research Data for Thyroglossal duct diseases: presentation and outcomes
No full textResearch Data for Thyroglossal duct diseases: presentation and outcomes by Aso S. Muhialdeen, Abdulwahid M. Salih, Mohsin M. Ahmed, Yadgar A. Saeed, Aras J. Qaradakhy, Hiwa O. Baba, Ari M. Abdullah, Fahmi H. Kakamad, Shvan H. Mohammed, Dilan Sarmad Hiwa, Mohammed Subhan Mohammed and Zana Baqi Najmadden in Journal of International Medical Research</p
Septate endophyte colonization and host responses of grasses and forbs native to a tallgrass prairie
No full textNative tallgrass prairies support distinct dark septate endophyte (DSE) communities exemplified by periconia macrospinosa and Microdochium sp. that were recently identified as common root symbionts in this
system. Since these DSE fungi were repeatedly isolated from grasses and forbs, we aimed to test their abilities to
colonize different hosts. One Microdochium and three Periconia strains were screened for colonization and growth responses using five native grasses and six forbs
in an in vitro system. Previously published data for an additional grass (Andropogon gerardii) were included and reanalyzed. Presence of indicative inter- and intracellular structures (melanized hyphae, microsclerotia, and chlamydospores)
demonstrated that all plant species were colonized by the DSE isolates albeit to varying degrees. Microscopic observations suggested that, compared to forbs, grasses were colonized to a greater degree in vitro.
Host biomass responses varied among the host species. In broad comparisons, more grass species than forbs tended to respond positively to colonization, whereas more forb species tended to be non-responsive. Based on the suspected differences
in the levels of colonization, we predicted that tallgrass prairie grasses would support greater DSE colonization than forbs in the field. A survey of field-collected roots from 15
native species supported this hypothesis. Our study supports the “broad host range” of DSE fungi, although the differences
in the rates of colonization in the laboratory and in the field suggest a greater compatibility between grasses and DSE
fungi. Furthermore, host responses to DSE range from mutualism to parasitism, suggesting a genotype-level interplay
between the fungi and their hosts that determines the outcome of this symbiosis
Evolutionary and demographic processes in the invasive weed Microstegium vimineum
No full textMicrostegium vimineum (Trin.) A. Camus (stiltgrass) is considered among the most invasive plants in the eastern United States. There has been considerable study of this species’ ecology and management though far less attention has been paid to its molecular ecology and the evolutionary processes which may influence its invasion success. Here, I describe a newly developed molecular marker system (microsatellite) which I used to examine M. vimineum’s genetic population structure and diversity in both its native and introduced ranges. I found clear signals that M. vimineum’s mating system is the most important determinant of the species’ population structure and variability. The invasive range had lower genetic diversity overall, probably due to founder effects. Also, population and regional genetic differentiation appeared to be ‘in process’ in the invasive range. Furthermore, M. vimineum’s mixed cleistogamous/chasmogamous mating system allowed for the near fixation of microsatellite genotypes in a given population by high rates of selfing, while still permitting the persistence of allelic diversity and generation of new genotypes at low frequency via occasional outcrossing. Thus, this mating system may confer adaptive advantage to the species as it settles upon fit genotypes in a given area while retaining evolutionary potential for range expansion into new habitats. I also attempted to discern adaptively significant phenotypes in M. vimineum through the measurement of phenological variation of plants originating from across the species’ invasive range under manipulated light treatments. Flowering time and biomass were both strongly correlated with the latitude of population origin such that populations collected from more northern latitudes flowered significantly earlier at lower biomass than populations from southern locations. This pattern suggests rapid adaptive evolution of phenology over a period of less than one hundred years, and such changes have likely promoted the northward range expansion of this species. Interestingly, barriers to gene flow, including bottlenecks and inbreeding, have apparently not forestalled adaptive processes for this plant. Based on literature review and these new data, I hypothesize that adaptive evolution of phenological traits may be widespread in many invasive plant species and an essential process during range expansion.Ph. D.Includes bibliographical referencesIncludes vitaby Ari E. Nov
Arabidopsis thaliana model system reveals a continuum of responses to root endophyte colonization
No full textWe surveyed the non-mycorrhizal model plant Arabidopsis thaliana microscopically for its ability to form dark septate endophyte (DSE) symbioses in field, greenhouse, and laboratory studies. The laboratory studies were also used to estimate host growth responses to 34 Periconia macrospinosa and four Microdochium sp. isolates. Consistent with broad host range observed in previous experiments, field-, greenhouse-, and laboratory-grown A. thaliana were colonized by melanized inter- and intracellular hyphae and microsclerotia or chlamydospores indicative of DSE symbiosis. Host responses to colonization were variable and depended on the host ecotype. On average, two A. thaliana accessions (Col-0 and Cvi-0) responded negatively, whereas one (Kin-1) was unresponsive, a conclusion consistent with our previous analyses with forbs native to the field site where the fungi originate. Despite the average negative responses, examples of positive responses were also observed, a conclusion also congruent with earlier studies. Our results suggest that A. thaliana has potential as a model for more detailed dissection of the DSE symbiosis. Furthermore, our data suggest that host responses are controlled by variability in the host and endophyte genotypes
Analyses of ITS and LSU gene regions provide congruent results on fungal community responses
No full textThe Internal Transcribed Spacer (ITS) regions and the Large Subunit (LSU) of the nuclear ribosomal RNA (rRNA) gene complex are commonly used to elucidate questions in fungal community ecology. Here, we compared the congruence across these gene regions using two ecological experiments (primary successional dynamics at a receding glacier forefront and community dynamics in stored Sorghum biomass), in which both ITS1 and LSU were sequenced from the same DNA extracts. We analyzed richness, diversity and evenness estimators along with community shifts inferred from ordination analyses. Our analyses show that ITS and LSU provide similar results and consistent conclusions. Taken together, we conclude that either gene region is appropriate for testing ecological hypotheses as long as there are no a priori hypotheses that preclude the use of one gene region over the other
Twenty years of research on fungus-microbe-plant interactions on Lyman Glacier forefront – lessons learned and questions yet unanswered
No full textRetreating glaciers and the periglacial areas they vacate for organismal colonization produce a harsh environment of extreme radiation, nutrient limitations, and temperature oscillations. They provide a model system for studying mechanisms that drive establishment and early assembly of communities. Here, we synthesize more than twenty years of research at the Lyman Glacier forefront in the North Cascades Mountains, comparing the results and conclusions for plant and microbial communities. Compared to plant communities, the trajectories and processes of microbial community development are difficult to deduce. However, the combination of high throughput sequencing, more revealing experimental designs, and analyses of phylogenetic community provide insights into mechanisms that shape early microbial communities. While the inoculum is likely
randomly drawn from regional pools and accumulates over time, our data provide no
support for increases in richness over time since deglaciation as is commonly observed for plant communities. Re‐analyses of existing datasets suggest that microbial, particularly fungal, communities are insensitive to time since substrate exposure from underneath the retreating glacier but responsive to plant establishment both in biomass and community composition. Further research on functional aspects, organismal activity, or ecosystem services in early successional environments will provide deeper appreciation for the dynamics of these communities
Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem
No full textPrescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000+ reads per sample after subsampling) indicate that frequent fires (3 year fire interval) shift soil fungus communities whereas infrequent fires (6 year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that 1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities, but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; 2) frequent prescribed fires elicit a shift in soil fungal communities; and, 3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives
Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape
No full textNon-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two hosts, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the non-native host communities may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems
Spaces of contestation: the everyday experiences of ten African migrants in Cape Town
No full textIncludes bibliographical references.Xenophobia in South Africa is so overt that it has take a covert form. The 'xenocide' events that took place in 2008 were called xenophobic acts. It is the recurrent denialism of xenophobia on an everyday basis that this project has explored through the narrative accounts of ten African migrants in Cape Town. The lived everyday experiences of ten African migrants have brought forward the central argument of this thesis. From the data, it is evident that as a reponse to everyday pressures of prejudices and xenophobia in social and physical spaces, African migrants have developed mutable, unsettled and vagrant identities in order to cope with everyday low level violence. This argument emerged as four key stressors have been identified as the components of a more substantial explanation of xenophobia in South Africa. The four key components are: the enforcement of identity (national and group), the demarcation of spaces of belonging, the experiences of economic insecurity, and lastly a 'culture of violence' in South Africa. This thesis argues that these four stressors are the result of an on-going active process of xenophobic attitudes
Automatic TUG test segmentation
No full textThesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 44-45).The Timed-Up and Go test (TUG) is a well-known medical test that is used as an indicator of mental and physical health. I developed the TUG-Segmenter, an automatic segmentation tool that can divide recorded TUG test data into the six main phases of the test: Sitting, Standing-Up, Walking-Forward, Turning, Walking-Back, and Sitting-Down. I created an annotation tool as well that greatly speeds up the creation of ground truth from TUG test data. Using both these tools I was able to evaluate the accuracy of the TUG-Segmenter in terms of the duration of the segmented phases ( 83.4 % accurate ) and the start times of the segmented phases ( 83.6 % accurate). Lastly, I found a 0.3 cm difference for jitteriness and an 8.5 mm/s difference for speed between healthy elderly subjects and healthy young subjects when comparing the features extracted from the individual TUG test phases.by Ari M. Green.M. Eng
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