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Full-Text Articles in Molecular Biology

The Mechanism Of Integration Preference To Heterochromatin Of Yeast Retrotransposon Ty5 , Weiwu Xie Jan 2003

The Mechanism Of Integration Preference To Heterochromatin Of Yeast Retrotransposon Ty5 , Weiwu Xie

Retrospective Theses and Dissertations

Ty5 is a retrotransposon in Saccharomyces cerevisiae. In wild type yeast strains, over 90% of Ty5 insertions occur at the telomeres or HM loci. These regions are bound in silent chromatin, which is analogous to heterochromatin of higher eukaryotes. Our laboratory previously described a targeting mutant of Ty5 that has an amino acid substitution near the C-terminus of integrase. Targeting to silent chromatin is reduced more than 20-fold in the mutant. We further defined the Ty5 targeting domain (TD) by saturation mutagenesis. All of the targeting mutations mapped to a stretch of six amino acids (LDSSPP). We tethered TD to ...


Functional Divergence And Genome Evolution Of Vertebrate Protein Kinases (Kinome), Jianying Gu Jan 2003

Functional Divergence And Genome Evolution Of Vertebrate Protein Kinases (Kinome), Jianying Gu

Retrospective Theses and Dissertations

The emerging complete and nearly complete genome sequences have provided a significant amount of materials for large-scale comparative genomic analysis. Novel methods have been developed to elucidate the function of gene products and functional interacting networks. Many of these post-genomic attempts have focused on unveiling the evolutionary forces that have shaped the network organization. Among various evolutionary forces, duplication of functional domain, individual gene, chromosomal segment, or entire genome has long been thought as primary resource for the function novelties in a vast number of gene families. It is therefore intriguing to quantitatively trace the changes of evolutionary constraints after ...


Molecular And Genetic Characterization Of Rf2, A Mitochondrial Aldehyde Dehydrogenase Gene Required For Male Fertility In Maize (Zea Mays L) , Xiangqin Cui Jan 2001

Molecular And Genetic Characterization Of Rf2, A Mitochondrial Aldehyde Dehydrogenase Gene Required For Male Fertility In Maize (Zea Mays L) , Xiangqin Cui

Retrospective Theses and Dissertations

T-cytoplasm induced male sterility (cms-T) is a maternally inherited inability to produce viable pollen in maize. The causal factor, the URF13 protein, is encoded by the mitochondrial genome and accumulates in the mitochondrial inner membrane. Fertility restoration of cms-T is mediated by the complementary action of two nuclear genes, rf1 and rf2. The rf2 gene was cloned via transposon tagging. Sequence analysis revealed that it has high sequence similarity to mammalian mitochondrial aldehyde dehydrogenases (mtALDHs). Sequence, mRNA, and protein analyses of the spontaneous mutant allele rf2-R213 demonstrated that the ALDH activity is necessary for rf2's function as a cms-T ...


Studying The Replication Mechanism Of The Yeast Retrotransposon Ty5 By Molecular And Computational Approaches, Xiang Gao Jan 2001

Studying The Replication Mechanism Of The Yeast Retrotransposon Ty5 By Molecular And Computational Approaches, Xiang Gao

Retrospective Theses and Dissertations

The yeast retrotransposon Ty5 is a Ty1/copia element. It is in the Hemivirus genus of the Pseudoviridae family. The ability to genetically manipulate retrotransposons and the yeast host cell was taken advantage of to explore replication mechanisms unique to Ty5 and common to most retrotransposons. Because of the abundance and diversity of retroelement sequences, along with the fact that many retroelement enzymes have evolved unique functional specificities, computational approaches were also developed to study functional divergence in replication. By screening a randomly mutagenized Ty5 library, two mutations (Y68C, D252N) causing higher transposition frequencies were identified. Both mutations increased Ty5 ...


Molecular And Genetic Analysis Of Jil-1, A Chromatin Associated Protein Kinase Implicated In Transcriptional Regulation In Drosophila , Ye Jin Jan 1999

Molecular And Genetic Analysis Of Jil-1, A Chromatin Associated Protein Kinase Implicated In Transcriptional Regulation In Drosophila , Ye Jin

Retrospective Theses and Dissertations

Chromatin remodeling is an essential step for many chromatin-related fundamental cellular processes, such as gene replication, transcription, recombination and gene silencing. Two classes of protein complexes contribute to chromatin remodeling: protein complexes with ATPase activity and protein complexes capable of enzymatic modifications of chromosomal proteins, especially histones. Compared to well-studied histone acetylation which has been directly linked to gene transcription, the role of histone phosphorylation in chromatin remodeling for gene transcription is still poorly understood although there is some correlation between histone phosphorylation and gene transcription;A novel nuclear tandem protein kinase JIL-1 was cloned and identified in Kristen Johansen ...


Genome Reorganization And Non-Linear Transposition In Maize , Jianbo Zhang Jan 1999

Genome Reorganization And Non-Linear Transposition In Maize , Jianbo Zhang

Retrospective Theses and Dissertations

Transposable elements have long been considered as potential agents of large-scale genome reorganization by virtue of their ability to induce chromosomal rearrangements such as deletions, duplications, inversions, and reciprocal translocations. Previous researchers have shown that particular configurations of transposon termini can induce chromosome rearrangements at high frequencies. By analyzing two derivatives of an unstable allele of the maize P1 (pericarp color) gene carrying both a full-length Ac (Activator) transposable element and a Ac terminal fragment termed fAc (fractured Ac) that were recovered from a classical maize ear twinned sector, it were found that the twinned alleles are a large inverted ...


Transposon-Induced Homologous Recombination At The Maize P Locus And In Transgenic Arabidopsis , Yongli Xiao Jan 1999

Transposon-Induced Homologous Recombination At The Maize P Locus And In Transgenic Arabidopsis , Yongli Xiao

Retrospective Theses and Dissertations

The maize P gene encodes a Myb-homologous regulator of red phlobaphene pigment biosynthesis in the pericarp, cob and other floral tissues. The P locus has a unique structure with two 5.2kb direct repeats flanking the P gene coding region. When the transposon (Ac) inserts into one site between the two direct repeats in the P-ovov-1114 allele, homologous recombination between the two 5.2kb repeats can occur and the whole P gene coding sequence is deleted;To further study this transposon-induced homologous recombination. This study examined six alleles that carry Ac insertions at different sites in the P locus, in ...


Molecular Characterization Of Myb-Homologous Transcriptional Factors Of The Flavonoid Pathway In Zea Mays , Peifen Zhang Jan 1999

Molecular Characterization Of Myb-Homologous Transcriptional Factors Of The Flavonoid Pathway In Zea Mays , Peifen Zhang

Retrospective Theses and Dissertations

Structural genes encoding enzymes that catalyze each step of flavonoid synthesis are temporally and spatially regulated. It has been shown that specific anthocyanin pigmentation patterns in maize are achieved by the tissue-specific expression of regulatory genes. Moreover, this tissue-specific regulation is a consequence of the generation of different alleles or duplicated copies of regulatory genes during evolution;In contrast, the myb-homologous P1 gene was the only known regulatory gene required for phlobaphene biosynthesis. The isolation and characterization of the P2 gene, reported here, provides direct molecular evidence that the P region contains duplicated genes. Furthermore, the duplicated P1 (herein, P1-rr ...


Epigenetic Effects Of Matrix Attachment Regions On Transgene Expression In A Maize Callus Line , Cory Ray Brouwer Jan 1998

Epigenetic Effects Of Matrix Attachment Regions On Transgene Expression In A Maize Callus Line , Cory Ray Brouwer

Retrospective Theses and Dissertations

Matrix attachment regions (MARs) are DNA sequences that bind non-histone proteins in the chromatin scaffold and define discrete loops of DNA containing expressed genes in vivo. I have been studying the effects of flanking transgenes with MARs on transgene expression levels in BMS maize callus. Three MAR elements, two from maize (Adhl 5' MAR and Mhal 5' MAR) and one from yeast (ARS1), have very different effects on transgene expression that bear no relation to their affinity for the nuclear matrix in vitro. The main effect of MARs is to prevent silencing of some (but not all) transgenes, at least ...


Characterization Of Three Root Hair Mutants In Maize , Tsui-Jung Wen Jan 1998

Characterization Of Three Root Hair Mutants In Maize , Tsui-Jung Wen

Retrospective Theses and Dissertations

Root hairs are thought to play an important role in the uptake of water and nutrients from the environment. Several root hair defective mutants were isolated from Mutator-tagged stocks and EMS-mutagenized lines of maize. These mutants all condition either non-elongated root-hair initials (rth1, rth3-1, rth3-2, rth3-3, rth4, rth5, rth6) or shorter-than-normal root hairs (rth2). The morphology of rth1, rth2, and rth3 root hairs were analyzed via SEM. The rth1, rth2, and rth3 genes map to chromosomes 1L, 5L, and 1S, respectively. The rth3 gene was cloned using Mu-tagged allele. The partial cDNA sequence of this gene suggests that it may ...


Host Regulation Of The Replication Of The Yeast Retrotransposon Ty5 , Ning Ke Jan 1997

Host Regulation Of The Replication Of The Yeast Retrotransposon Ty5 , Ning Ke

Retrospective Theses and Dissertations

The replication of retroelements may have deleterious effects on the hosts. Therefore, elements and their hosts have coevolved mechanisms to regulate retroelement replication. This regulation can occur at the transcriptional, translational, or post-translational levels as well as through targeted integration or cDNA recombination. I have studied host regulation of the Saccharomyces retrotransposon Ty5. I have found that Ty5 transcription is carefully controlled. Transcription of Ty5 is haploid specific and is repressed 10 fold in diploid strains. Ty5 transcription is also regulated by the pheromone response pathway, which is activated during mating. In addition, Ty5 transcription is regulated by flanking sequences ...


Genetic And Biochemical Analysis Of Aspergillus Awamori Glucoamylase Thermostability , Martin John Allen Jan 1997

Genetic And Biochemical Analysis Of Aspergillus Awamori Glucoamylase Thermostability , Martin John Allen

Retrospective Theses and Dissertations

Aspergillus awamori glucoamylase (GA) is an enzyme involved in industrial corn starch processing. Genetic and biochemical approaches were used to study the mechanisms governing GA thermostability. Three proline substitution (Xaa → Pro) mutations were constructed that were predicted to increase the enzyme's stability by decreasing its conformational entropy of unfolding. When expressed in Saccharomyces cerevisiae Ser30 → Pro increased, Asp345 → Pro did not alter and Glu408 → Pro greatly decreased GA stability as measured by resistance to irreversible thermoinactivation relative to the wild-type enzyme. The Ser30 → Pro mutation was combined with other previously identified stabilizing mutations to examine whether combining such mutations ...


Cloning And Characterization Of A Soybean Snf2 Yeast Homolog , Weiping Chen Jan 1997

Cloning And Characterization Of A Soybean Snf2 Yeast Homolog , Weiping Chen

Retrospective Theses and Dissertations

It is of great economic and scientific interest to understand plant disease resistance genes at the molecular level. Phytophthora sojae, a fungal pathogen of soybean is of particular interest since the root and stem rot resulting from its infection causes great economic loss. It is the goal of this project to clone Phytophthora resistance genes from soybean. This was done by designing primers from the conserved regions of known plant disease resistance genes using a modified differential display for near isogenic lines; L85-3044 a resistant line and Williams, a susceptible line. Several polymorphic bands were identified, including a unique 0 ...


Genetic Construction And Biochemical Analysis Of Thermostability Mutants Of Glucoamylase From Aspergillus Awamori , Yuxing Li Jan 1996

Genetic Construction And Biochemical Analysis Of Thermostability Mutants Of Glucoamylase From Aspergillus Awamori , Yuxing Li

Retrospective Theses and Dissertations

To study the molecular basis of Aspergillus awamori glucoamylase (GA) thermostability, eighteen mutants were constructed by site-directed mutagenesis and expressed in Saccharomyces cerevisiae based on thermostability theories. Four lysine residues, K61, K279, K352 and K404, were replaced with arginine, with all but K404 well exposed to the solvent and far away from the enzyme activity site. Mutations K61F/D65E and H254W/E326Q were made to fill a packing void around the inner set of six [alpha]-helices of GA and to displace water molecules inside the void. Five residues (A27, A393, A435, Ser436 and Ser460) were replaced with proline. Two ...


Integration Specificity Of The Retrovirus-Like Transposable Element Ty5 Of Saccharomyces , Sige Zou Jan 1996

Integration Specificity Of The Retrovirus-Like Transposable Element Ty5 Of Saccharomyces , Sige Zou

Retrospective Theses and Dissertations

The retrotransposons and retroviruses display a strong preference in selecting integration sites. The molecular mechanisms underlying this process, however, are largely unknown. I have characterized a new retrotransposon, called Ty5, in diverse strains of Saccharomyces cerevisiae and related species. A functional element, Ty5-6p, was identified from S. paradoxus. To investigate Ty5 target preference, the locations of 13 native insertions were determined in S. cerevisiae and S. paradoxus. Twelve were found near the telomeres and the mating locus HMR. To determine if this distribution is a consequence of targeted integration, a Ty5 transposition assay was developed in S. cerevisiae using Ty5-6p ...


Molecular Analyses Of Group 1 Late Embryogenic Abundant (Lea) Genes In Soybean (Glycine Max (L.) Merr.) , Éberson Sanches Calvo Jan 1995

Molecular Analyses Of Group 1 Late Embryogenic Abundant (Lea) Genes In Soybean (Glycine Max (L.) Merr.) , Éberson Sanches Calvo

Retrospective Theses and Dissertations

The entire soybean Sle gene family was cloned and characterized. The five Sle genes (Sle1-5) could be divided into two classes based on sequence identity. Sle1-4 map to 4 different linkage groups. Sle1 and Sle5 are expressed weeks earlier in seed development than Sle2 and Sle3. Sle4 is a pseudogene. Maximal levels of Sle mRNA accumulate in the seeds, before desiccation had occurred, and decline rapidly upon seed imbibition. Desiccation does not induce Sle expression in seeds. Unlike most of its homologs, ABA is not necessary to induce Sle expression in cultured embryos and only moderately increases Sle mRNA levels ...


Telomeric Nucleic Acids: C-Strand Structure And A Telomerase Rna Mutant , Shawn Cameron Ahmed Jan 1994

Telomeric Nucleic Acids: C-Strand Structure And A Telomerase Rna Mutant , Shawn Cameron Ahmed

Retrospective Theses and Dissertations

Telomeres, the ends of linear chromosomes, are composed of simple tandem repeats which are usually G·C rich. Telomeres are essential for chromosome stability, organizing the nuclear architecture and ensuring complete replication of the chromosomal terminus. To understand how telomeres carry out these fundamental cellular roles, one must understand the structural and dynamic properties of telomeric repeat sequences. Structural and genetic approaches were taken to learn more about telomeric nucleic acids;The structural portion of my research concerned an unusual DNA structure formed by the C-rich strand of telomeric DNA. Telomeric C-strand sequences form non-Watson-Crick structures in supercoiled plasmids at ...


Soybean Cultivar Development: A Genome Perspective , Lisa Lou Lorenzen Jan 1994

Soybean Cultivar Development: A Genome Perspective , Lisa Lou Lorenzen

Retrospective Theses and Dissertations

The purpose of this dissertation was to retrospectively analyze the process of soybean cultivar development from a molecular perspective, by following the inheritance of RFLP markers in a pedigree analysis. Five methods of analysis are included in this dissertation;Sixty-four plant introductions, cultivars, and breeding lines were analyzed to define a core set of 97 probes with a high likelihood of detecting a polymorphism in elite germplasm. The ability to trace regions of chromosomes from parent to offspring and the application of pedigree-based mapping was demonstrated, which is the cosegregation of phenotypic traits and RFLP markers based on pedigree information ...


Cloning And Molecular Characterization Of Two Nuclear Genes For Zea Mays Mitochondrial Chaperonin 60 , Pamela Sue Close Jan 1993

Cloning And Molecular Characterization Of Two Nuclear Genes For Zea Mays Mitochondrial Chaperonin 60 , Pamela Sue Close

Retrospective Theses and Dissertations

Hsp60 is a mitochondrial protein first identified in Tetrahymena thermophila and Saccharomyces cerevisiae. It belongs to a class of proteins called "molecular chaperones" which prevent aggregation and precipitation of partially or completely unfolded polypeptides;Two cDNAs for maize cpn60 were identified and sequenced. Southern blots of maize DNA showed two bands hybridizing with mt-cpn60 in maize inbreds. One copy was present in Arabidopsis. Both maize genes are contained within the nuclear genome. The chromosomal location of the cpn60 genes have been mapped by RFLPs. A maize B73 genomic library has been constructed and screened for cpn60 clones and two major ...


Characterization Of Cis-Acting Replication Control Elements In Ribosomal Rna Genes Of Tetrahymena Thermophila , Wen-Ling Shaiu Jan 1993

Characterization Of Cis-Acting Replication Control Elements In Ribosomal Rna Genes Of Tetrahymena Thermophila , Wen-Ling Shaiu

Retrospective Theses and Dissertations

This dissertation describes the identification and characterization of specific cis-acting replication control elements in the replication origin of Tetrahymena rDNA. Earlier studies of a mutant rDNA allele, C3-rmm1, identified a cis-acting sequence (the Type I repeat) within the 5[superscript]' non-transcribed spacer of rDNA that affects rDNA replication (Larson et al. 1986). Characterization of two additional, independently-isolated mutants (C3-rmm3 and C3-rmm4) and a revertant of C3-rmm4 strongly argue that the Type I repeat is indeed a cis-acting replication control element. Mutations causing rDNA replication defects were identified in copies of the Type I repeat that are separated by >600 bp ...


Analysis Of Three Plasmids From Filamentous, Nitrogen-Fixing Cyanobacteria , Douglas Kevin Walton Jan 1991

Analysis Of Three Plasmids From Filamentous, Nitrogen-Fixing Cyanobacteria , Douglas Kevin Walton

Retrospective Theses and Dissertations

The cyanobacteria are an ancient and diverse group of prokaryotes capable of oxygenic photosynthesis. They display both unicellular and filamentous cell types and some have the ability to fix atmospheric dinitrogen, and the ability to differentiate specialized cells. In addition, many of the cyanobacteria possess plasmids. To date, only one plasmid, from a unicellular non-nitrogen-fixer, has been characterized in detail. The current lack of information concerning cyanobacterial plasmids, and their subsequent use as vectors, has hindered genetic analysis, particularly in the filamentous species;In this study, the properties of two plasmids and one plasmid origin of replication from filamentous, nitrogen-fixing ...


Study Of En At The Wx-844 Allele: Modifier Of En Excision, Weak En, And Transposition Of En , Sudhansu Dash Jan 1991

Study Of En At The Wx-844 Allele: Modifier Of En Excision, Weak En, And Transposition Of En , Sudhansu Dash

Retrospective Theses and Dissertations

The wx-844 allele contains a fully active and complete En transposable element inserted within the Wx gene. The mutability of this allele is very high and the somatic mutability is seen in the endosperm as dark staining Wx sectors in a background of non-staining wx regions;The very high coarse pattern of waxy mutability is modified into a reduced fine pattern in the presence of the I-102 element located within the A gene in the non-autonomously mutable a-m(r) 102 allele. The modifying effect of the I-102 element on En induced excision has been found to be a general phenomenon ...