Magnification of Genes Coding for Ribosomal RNA in Saccharomyces cerevisiae

When a strain of Saccharomyces cerevisiae monosomic for chromosome I and initially deficient for 25% of the genes coding for ribosomal RNA is repeatedly subcultured, the number of these genes increases to and remains stable at the number in the wild type. This strain shows 2:2; viable: inviable first division segregation and hemizygosity for the ade1 gene (a chromosome I marker), evidence that the strain is still monosomic for chromosome I. The increase in the number of genes coding for ribosomal RNA in yeast may be analogous to the magnification of the ribosomal RNA genes in Drosophila melanogaster bobbed mutants

Recognition of Ribosomal RNA Sites in DNA, I. Analysis of the E. coli System

The evidence recently presented of specific hybridization between bacterial ribosomal RNA and homologous DNA1-3 has indicated the possibility of a biochemical approach to the problem of the identification of ribosomal RNA sites in DNA. A difficulty in this approach is that while the specific role of the RNA in the hybridization is open to experimental test, the critical evidence of the unique involvement of presumptive DNA sites is not easily attainable

A model for the study of ligand binding to the ribosomal RNA helix h44.

Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region

Fungicide Resistance Genetics of Apple Scab fungus Venturia inaequalis

Apple scab, caused by the ascomycete fungus Venturia inaequalis, is considered the most devastating disease on domestic apple crops. Apples are the most important cultivated crop in temperate regions and the United States produced about 4.6 million tons of apples in 2010. Traditional methods to control fungal plant diseases like apple scab are based on the use of chemical compounds that may produce serious negative effects, mainly related with environmental pollution and the development of fungicide resistance. Identifying genes and mechanisms of fungicide resistance in V. inaequalis is imperative to developing new and more effective defenses against the spread of resistance

Three novel science activities relating to the structure of the atom, bioinformatics, and the denaturation of protein

Plan B Paper. 2013. Master of Science in Education- Physics--University of Wisconsin-River Falls. Physics Department. 30 leaves. Includes bibliographical references (leaf 10).This paper describes three novel activities that were designed to teach difficult scientific concepts to a wide age range of students (7th through 11th grade). The subject of the three activities include the structure of the atom, bioinformatics, and protein denaturation. Each section within the paper includes background information and material lists necessary for the activity, in addition to a procedure and reflection. The two models of learning used to analyze the activities were Bloom's Taxonomy and the Constructivist Theory. In Bloom's Taxonomy, there are six levels in the Cognitive domain: Knowledge, Comprehension, Application, Analysis, Synthesis, and Evaluation (in order from lowest to highest). As a student progresses from the lower levels to the higher levels, their comprehension and mastery of the subject increases. According to Constructivism, a learner needs to be active in the learning process so that they can give meaning to their experiences. This happens when the learner reconciles their experiences to something they previously held to be true

Reconstructing phylogeny from RNA secondary structure via simulated evolution

DNA sequences of genes encoding functional RNA molecules (e.g., ribosomal RNAs) are commonly used in phylogenetics (i.e. to infer evolutionary history). Trees derived from ribosomal RNA (rRNA) sequences, however, are inconsistent with other molecular data in investigations of deep branches in the tree of life. Since much of te functional constraints on the gene products (i.e. RNA molecules) relate to three-dimensional structure, rather than their actual sequences, accumulated mutations in the gene sequences may obscure phylogenetic signal over very large evolutionary time-scales. Variation in structure, however, may be suitable for phylogenetic inference even under extreme sequence divergence. To evaluate qualitatively the manner in which structural evolution relates to sequence change, we simulated the evolution of RNA sequences under various constraints on structural change

Control of Nucleotide Metabolism and Ribosomal Ribonucleic Acid Synthesis During Nitrogen Starvation of \u3cem\u3eEscherichia coli\u3c/em\u3e

Ribosomal ribonucleic acid (RNA) synthesis and ribonucleoside triphosphate metabolism were studied in cultures of Escherichia coli subjected to starvation for inorganic nitrogen. In a strain that was under stringent control, a 50-fold reduction in the formation of both 16S and 23S RNA was accompanied by a severe restriction on nucleotide biosynthesis. These inhibitions were relieved in part by incubating the starved cells with amino acids. This result suggests that regulation by the functional RNA control (RC) gene is involved in the effect. This suggestion was confirmed by showing that the effector of the stringent response, guanosine-5′-diphosphate-2′- or 3′-diphosphate (ppGpp), accumulated at the onset of starvation and disappeared immediately when the amino acids were added. Ribosomal RNA synthesis was severely restricted and the same nucleotide, ppGpp, accumulated at the onset of nitrogen starvation of a relaxed mutant too. These findings suggest that a control mechanism other than the one provided by the functional rel gene might operate to regulate RNA synthesis and that this mechanism is expressed through the synthesis of ppGpp

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat

Genomic function during the lampbrush chromosome stage of amphibian oogenesis

Throughout its lengthy developmental history the disposition of the genetic material in the amphibian oocyte nucleus differs from that in other cell types. The chromosomes in the oocyte nucleus, arrested for the whole of oogenesis at the prophase of the first meiotic division, are known to contain at least the tetraploid amount of DNA.(1,2) Oogenesis in amphibia requires months or even years to complete, depending on the species