Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is a major foliar disease in wheat. QTL mapping and meta-QTL analysis are effective methods to understand genetic basis of tan spot resistance, which can further facilitate resistant variety development. A number of QTL mapping studies have been conducted in hexaploid bread wheat whereas few mapping studies have been carried out in tetraploid wheat. Four interconnected tetraploid wheat mapping populations were evaluated for resistance to race 2 isolate 86-124. Twelve QTL were identified in three of the four mapping populations. To further extend understanding of tan spot resistance, meta-QTL analysis was conducted by using reported QTL from 14 previous QTL mapping studies. Three meta-QTL located on chromosomes 2A, 3B, and 5A showed large genetic effects in multiple populations and conferred resistance to multiple races. Integrating those race-nonspecific QTL could provide high and stable tan spot resistance in wheat.

MENVSC (Ecology and Resource Management) / See the attached abstract below

>Magister Scientiae - MSc / In the post-reionisation universe, intensity mapping (IM) with the 21 cm line of neutral hydrogen (HI) provides a potential means of probing the large-scale structure of the universe. With such a probe, a wide variety of interesting phenomena such as the Baryon Acoustic Oscillations (BAO) and Redshift Space Distortions (RSD) can be studied. The MeerKAT telescope has the potential to make full use of this technique, especially in the single-dish mode, which will probe the scales relevant to BAO and RSD. A useful complementary of this is HI IM with MeerKAT in interferometer-mode, which will enable the extraction of cosmological information on semi-linear and small scales. In this study, full end-to-end simulations of interferometric observations with MeerKAT for HI IM were developed. With this, the power spectrum extraction was analysed using the foreground avoidance technique. This took into account the foreground wedge from point source contamination extracted from real MIGHTEE COSMOS data, as well as RFI flagging. The errors on the power spectrum estimator were then calculated through a Monte Carlo process using 1000s of realisations of both the thermal noise and HI signal. In doing so, precision constraints on the HI power spectrum are found at z = 0:27 on scales 0:4 < k < 10 Mpc-1 for mock visibility data sets which contain the HI signal contaminated by noise, mimicking the MIGHTEE COSMOS field for total observation times & 20 hours. These results illustrate the potential of doing precision cosmology with MeerKAT’s MIGHTEE survey and interferometer-mode HI IM.

>Magister Scientiae - MSc / In the post-reionisation universe, intensity mapping (IM) with the 21 cm line of neutral hydrogen (HI) provides a potential means of probing the large-scale structure of the universe. With such a probe, a wide variety of interesting phenomena such as the Baryon Acoustic Oscillations (BAO) and Redshift Space Distortions (RSD) can be studied. The MeerKAT telescope has the potential to make full use of this technique, especially in the single-dish mode, which will probe the scales relevant to BAO and RSD. A useful complementary of this is HI IM with MeerKAT in interferometer-mode, which will enable the extraction of cosmological information on semi-linear and small scales. In this study, full end-to-end simulations of interferometric observations with MeerKAT for HI IM were developed. With this, the power spectrum extraction was analysed using the foreground avoidance technique. This took into account the foreground wedge from point source contamination extracted from real MIGHTEE COSMOS data, as well as RFI flagging. The errors on the power spectrum estimator were then calculated through a Monte Carlo process using 1000s of realisations of both the thermal noise and HI signal. In doing so, precision constraints on the HI power spectrum are found at z = 0:27 on scales 0:4 < k < 10 Mpc-1 for mock visibility data sets which contain the HI signal contaminated by noise, mimicking the MIGHTEE COSMOS field for total observation times & 20 hours. These results illustrate the potential of doing precision cosmology with MeerKAT’s MIGHTEE survey and interferometer-mode HI IM.

My work is a type of survey working as a documentation and analysis, enabling the mind to examine certain conditions of both the build and unbuilt environment. Geometric, relational, material or technical. What happens when we record what already exists? Could it be used to image what might be?

Proteins govern practically every process in living organisms through inhibiting, activating, or acting on other proteins in different ways. With the large and growing number of known interactions through high throughput screening technologies, experimental determination of atomic-level details of these interactions is nigh impossible. Computational methods such as docking can speed up efforts of understanding these interactions. However, several issues ought to be addressed before docking can replace experimental methods. This thesis describes work on assessment of the state of the art in docking methods, implementation of a machine learning algorithm to improve model ranking and integration of docking with template-based modeling to expand its usage with a special focus on antibody-antigen interactions. Firstly, the performance of docking methods was rigorously assessed by using a diverse set of protein complexes with a special focus on ClusPro, one of the leading rigid-body docking servers. Different strengths and potential areas of improvement for ClusPro and rigid-body docking methods in general were highlighted. Secondly, one of the major short-comings of docking noted in the first project, poor ranking of good models, was addressed. A regression-based machine learning algorithm was introduced to improve the ranking. Finally, a server was developed to tackle the challenge of epitope mapping by integrating template-based modeling with docking. An intuitive ensemble approach to scoring residue likelihood using docking poses and different homologues is shown to yield great success. In addition to shifting docking’s purpose of conformational search to interface identification, this server also allows users to start with protein sequence inputs. / 2022-09-28T00:00:00Z

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In the United States, the floodplain maps used in the administration of the National Flood Insurance Program are created and maintained by the Federal Emergency Management Agency. Currently, a nationwide map modernization program is underway to convert the existing paper floodplain maps into a digital format, while continuing to improve the maps and expand the scope of the studies. The flood zones depicted on these maps are developed through engineering studies, using a variety of accepted methods to model and predict flood-prone areas. These methods are classified as detailed, limited detailed, or approximate, corresponding to varying levels of expense and accuracy. Current flood map revision activities across the nation typically consist of developing new hydraulic models, or reusing existing hydraulic model results in conjunction with new, more detailed LiDAR terrain models. This research develops a profile synthesis method for redelineation of approximate flood boundaries, and evaluates the method's performance and usability. The profile synthesis method is shown to perform reliably on simple floodplain geometry, recreating a water surface profile based only on its floodplain boundaries. When applied to a real-world floodplain studied in a previous flood insurance study, the profile synthesis method is shown to perform adequately, with results comparable to an approximate hydraulic model developed in HEC-RAS. Methods similar to this profile synthesis method for reuse of existing approximate zone boundaries have not been widely documented or evaluated; nevertheless, methods such as this are believed to be common in the revision of approximate zone flood boundaries. As such, this work explores concepts which will be of interest to individuals actively involved in flood map revision and modernization. / Master of Science

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