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2017 Shukla Blue Waters Professor Report
No full text2017 annual report for Diwakar Shukla Blue Waters Professor allocation.Open Restriction set for Item 116725 on 2020-12-04T21:11:16Z with date null by [email protected] by Susan Vinson ([email protected]) on 2020-12-04T21:20:25Z
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Previous issue date: 2017Ope
Genomic analysis of sex chromosomes and sex differentiation in Caricaceae
Get PDFPapaya is an excellent model species to study mechanisms for sex determination and sex chromosome evolution in plants, due to the presence of three sex types: female, male, and hermaphrodite. Previous research has revealed the location of the sex determination region (SDR) and the existence of three sex chromosomes X, Y, and Yh in the papaya genome, including the number and identity of transcripts within this region. It is still unknown which gene or genes in the SDR are responsible for sex determination in papaya. The regulatory mechanism for sex determination and expression in papaya remains a mystery despite that multiple candidate genes have been proposed. This Dissertation focuses on three different molecular approaches to search for candidate genes responsible for sex determination in C. papaya and to elucidate possible regulatory mechanisms for sex expression in papaya flowers.
The first approach included a transcriptome analysis of papaya flower buds from different sex types at different developmental stages, including the transcriptome analysis of hermaphrodite-to-female sex reversal mutants. The analysis of differentially expressed genes between male, female, and hermaphrodite flower buds (Chapter 2) revealed the existence of several genes with strong sex-biased expression in male and hermaphrodite flowers that might be playing an important role in male organ development, specifically tapetum development in the anther developmental pathway. Other transcription factors related to flower organ development and flowering time regulation, as well as genes that are known to participate in ABA, ROS and auxin signaling pathways were identified as differentially expressed among papaya flowers. The analysis of differentially expressed genes between hermaphrodite-to-female and hermaphrodite flower buds (Chapter 3) revealed only five differentially expressed genes. Among these genes, only an uncharacterized gene with a high level of expression in hermaphrodite-to-female mutants and female flower buds was identified. Despite no match for this gene was found in other plant species, the function of this gene might be related to biological processes involved in the anther developmental pathway. None of these differentially expressed genes located in the SDR in papaya, it is possible that these genes act downstream sex determination genes as consequence of a complex regulatory cascade, regulated by a Y-specific gene acting as a stamen promoting factor.
A second approach involved identifying differences on the promoter region of genes located in the sex chromosomes (X, Y and Yh) in papaya and studying the effects of these differences on the expression of a previously proposed candidate gene for sex determination called CpMDAR4 (Chapter 4). Results showed that differences in the promoter sequence of the CpMDAR4 gene drove the expression of a reporter gene (GUS) to different flower tissues in Arabidopsis thaliana, due to the existence and location of cis-regulatory elements (POLLEN1LELAT52) responsible for anther or pollen-specific expression present on the Y chromosomes (Y and Yh). A similar expression pattern of CpMDAR4 alleles in different tissues of papaya flowers and the existence of two different isoforms for this gene on male and hermaphrodites support MDAR4 as an important candidate for sex differentiation.
Sex chromosomes are hypothesized to have evolved from the same pair of autosomes in the Caricaceae family, therefore a third approach involved the genome assembly of a species from a closely related genus (Jarilla heterophylla) and identification of conserved synteny in the SDR between both species (Chapter 5). Conserved candidate genes in the SDR between the two species (C. papaya and J. heterophylla) are more likely to be responsible for sex determination given the close phylogenetic relationship, overlapping geographical distribution in southern Mexico, and similar morphological and reproductive characteristics between these species. Results showed that J. heterophylla has a XY sex determination system, with homomorphic sex chromosomes, as was found in papaya, and genes in the SDR are conserved between these species. Only one Y-specific gene in papaya (CpY19 or CpSVP) was identified in J. heterophylla, making this gene an important candidate for sex differentiation in papaya.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2023-08-01The student, Dessiree Zerpa Catanho, accepted the attached license on 2021-06-23 at 15:56.The student, Dessiree Zerpa Catanho, submitted this Dissertation for approval on 2021-06-23 at 16:00.This Dissertation was approved for publication on 2021-06-30 at 09:00.DSpace SAF Submission Ingestion Package generated from Vireo submission #16709 on 2022-01-12 at 13:03:27Made available in DSpace on 2022-01-12T22:51:39Z (GMT). No. of bitstreams: 3
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Previous issue date: 2021-06-30Embargo set by: Seth Robbins for item 121182
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Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Variations on the Author
Get PDF“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
Get PDFWe 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
Posttranscriptional and posttranslational regulation of virulence in erwinia amylovora
Get PDFErwinia amylovora is the causal agent of fire blight, the most destructive bacterial disease of the Rosaceae family plants. Two virulence factors, the type III secretion system (T3SS) and the exopolysaccharide (EPS) amylovoran, are strictly required for its pathogenicity. Our previous studies have determined the role of several transcription factors in the regulation of E. amylovora virulence; however, molecular mechanisms of virulence regulation at the posttranscriptional and posttranslational levels have still remained elusive. In this dissertation, our goal was to understand new regulatory mechanisms in E. amylovora virulence.
First, we characterized the molecular mechanism of Lon protease-mediated virulence regulation. Mutation of the lon gene caused the amylovoran overproduction, the increased T3SS expression and the non-motile phenotype. In the absence of Lon, abundance and stability of the HrpS/HrpA and RcsA proteins were significantly increased, and the resulting accumulation of the RcsA/RcsB proteins influenced the expression of flhD, hrpS and csrB. In addition, lon expression is under the control of the RNA-binding protein CsrA, possibly at both the transcriptional and post-transcriptional levels, suggesting a possible interplay between Lon and the Csr system.
Second, we examined the role of ClpXP protease in virulence regulation and its potential interaction with Lon. Mutation in clpXP diminished the T3SS expression, amylovoran production and motility, resulting in delayed disease progress. Highly accumulated RpoS proteins were detected in the clpXP mutant, and mutation of rpoS in the clpXP mutant background restored virulence to the wild-type level. These suggest that ClpXP-dependent RpoS degradation positively affects virulence traits. In addition, lack of both ClpXP and Lon resulted in significantly reduced virulence independently of RpoS level, suggesting that ClpXP and Lon are indispensable for full virulence.
Third, transcriptional regulation mechanism of the hrpS gene, encoding the essential T3SS activator, was examined. We found that the hrpS gene contains two promoters driven by HrpX/HrpY and the Rcs system, respectively. IHF also positively regulates hrpS expression through directly binding to the hrpX promoter and positively regulating hrpX/hrpY expression. Moreover, hrpX expression was down-regulated in the ppGpp-deficient mutant and the dksA mutant, but up-regulated when the wild-type strain was treated with serine hydroxamate, suggesting that ppGpp might induce hrpX/hrpY and hrpS expression. Furthermore, CsrA positively regulates hrpS expression mainly through the Rcs system. These results suggest that E. amylovora recruits multiple stimuli-sensing systems to regulate hrpS and T3SS gene expression.
Fourth, we examined the global effect of CsrA and determined potential molecular mechanisms of CsrA-dependent virulence regulation in E. amylovora. Using REMSA, direct interaction between CsrA protein and csrB sRNA was confirmed, while CsrA did not bind to the transcripts of T3SS activators, hrpL and hrpS. Transcriptomic analyses under the T3SS-inducing condition revealed that mutation in csrA led to differential expression in more than 20% genes in the genome. Of these, T3SS genes and those required for cell growth and viability were significantly down-regulated, explaining the pleiotropic defects in the csrA mutant. On the other hand, the csrB mutant exhibited significant up-regulation of the major virulence genes, further suggesting antagonistic effects of csrB on CsrA. Through REMSA combined with site-directed mutagenesis and LacZ reporter gene assay, three CsrA targets (flhD, rcsB and relA) were identified that positively regulate E. amylovora virulence. Overall, this dissertation demonstrates that E. amylovora employs multiple layers of gene regulatory networks to effectively control the expression of virulence factors.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2020-05-01The student, Jae Hoon Lee, accepted the attached license on 2018-03-29 at 15:09.The student, Jae Hoon Lee, submitted this Dissertation for approval on 2018-03-29 at 15:20.This Dissertation was approved for publication on 2018-04-09 at 13:58.DSpace SAF Submission Ingestion Package generated from Vireo submission #12099 on 2018-08-31 at 17:25:42Made available in DSpace on 2018-09-04T20:46:53Z (GMT). No. of bitstreams: 3
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Previous issue date: 2018-04-09Embargo set by: Seth Robbins for item 107356
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Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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
Computational dissection of nitrate transport mechanism
No full text"Nitrogen is an essential nutrient in plants and a major driving force for crop yields and food production. Annually, about 110 million tonnes of nitrogenous fertilizers are applied globally to enhance crop yields. However, over half of the nitrogen added to the soil is lost to the environment, with an average of only 25%-50% being taken up by the plants. Excess nitrogenous fertilizers have already caused biodiversity loss, environmental pollution, and climate change. So how can we increase crop yields to match the rapidly growing global population while minimizing the environmental pollution caused by nitrogenous fertilizers? One solution is improving plant nitrogen uptake efficiency (NUE), that is, enhancing crop production per unit of added nitrogen. For plants, nitrate is one of the two major nitrogen sources, which is taken up from the soil through nitrate transporters.
Despite recent breakthroughs in structural biology, our knowledge of the molecular nature and regulation of nitrate transporters is far from complete. The major reason is that structural biology only provides few ""snapshots"" of protein structures, whereas proteins undergo complex dynamical processes to perform their functions. Molecular dynamics (MD) simulations are a powerful tool to decipher the mechanism of nitrate transporters because they can capture the dynamical behavior of biological systems in full atomic details, which is very challenging with any experimental technique.
There are two major focuses of this thesis. First, we develop computational algorithms to enhance the efficiency and accuracy of MD simulations. We leverage coevolutionary relationships conserved in protein sequences to predict the slow dynamical changes of proteins, which can be used to guide MD sampling of the protein conformational space. We also propose a method called FingerprintContacts to predict alternative protein conformations by combining coevolutionary signals and machine learning. To analyze high dimensional MD simulation data, we present a genetic algorithm-based feature selection technique, which can select relevant features in an automatic and systematic way. Second, we integrate these algorithms with MD simulations to explore the fundamental transport mechanism of two representative transporters in atomistic detail: plant dual-affinity nitrate transporter (NRT1.1) and bacterial nitrate/nitrite exchanger (NarK). We not only characterize the complete substrate translocation cycles in atomic details, but also identify key residues involved in substrate recognition, binding, exchange, and translocation. We expect the detailed molecular mechanism could guide future crop engineering strategies."Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-08-01The student, Jiangyan Feng, accepted the attached license on 2021-05-18 at 11:16.The student, Jiangyan Feng, submitted this Dissertation for approval on 2021-05-18 at 11:39.This Dissertation was approved for publication on 2021-05-20 at 08:48.DSpace SAF Submission Ingestion Package generated from Vireo submission #16649 on 2022-01-12 at 12:51:24Made available in DSpace on 2022-01-12T22:34:39Z (GMT). No. of bitstreams: 2
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Previous issue date: 2021-05-20Embargo set by: Seth Robbins for item 121040
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