The Implementation and Efficacy of Scientific Literature within an Introductory Biology Lecture Course: A Study in Pedagogy, Curricula, and Standards as They Apply to Post-Secondary Science EducationTomaszewski, Shaun Allen 15 May 2009 (has links)
The current study involved students enrolled in the Fall 2007 Biosc 0150 and Spring 2008 Biosc 0160 lecture sections of a single Faculty member. Most students were incoming freshmen, and their prior exposure to the natural sciences varied. A single recitation section was used as the experimental section, taken from each lecture section. In addition to regular instruction, the students enrolled in the experimental section were also assigned readings from peer-reviewed journals. The performance of these students was then tracked, as it was expected to vary, and compared to that of the students enrolled in the control recitation sections. There was found to be a significant difference between the achieved mean course grade of the experimental section and the control section, for the Biosc 0150 lecture section, but not in the Biosc 0160 lecture section. Important trends, though, were noted in both semesters and are examined herein.
Chu, Joseph Peng-hsiang.
In 1809, A. von Thaer wrote in his book "Grundsatz der Rationell Landwirtschaft" that, except for water, the humus in the soil is the sole substance which supplies nutrients for the growth of plants. Since then, the role of humus in soil has been intensively studied and the meaning of humus has varied from the "organic fraction of soil" to "a dark incoherent and heterogeneous colloidal mass in soil" (Buckman and Brady 1960). Based on the latter meaning the term humus does not include any undecayed organic materials or micro-organisms in the soil. However, in the practical consideration of humus, the presence of microorganisms is usually neglected. For exemple, the well known humus fractionation method of Tyurin mentioned by Kononova (1958), does not consider that the treatment with solvent, alkali, and acid will fractionate not only the colloidal organic matter (humus) but also the undecayed organic materials and microorganisms. [...]
[A] Study of the methods and the conditions for the isolation of pathogenic actinomyces from lesions in animalsAvery, Robert J. January 1952 (has links)
Note: / The consistent isolation and accurate classification of the pathogenic anerobic Actinomyces from clinically and histopathologically diagnosed cases of “true” Actinomyces is not always possible. This, it is felt is due primarily to the lack of known differentiating characteristics of the so-called Smooth form of the etiological agent.
Kulp, Adam John
<p>Abstract</p><p>The envelope of Gram-negative bacteria is a tightly regulated, intricate system, and as an essential component of these species, it is often the target of antibacterial treatments. Bacteria monitor and protect their envelope through a multitude of distinct stress response pathways, each with its own specialized role in maintaining a functioning envelope. Although these response pathways are each specialized for a particular type of stress, they are co-regulated and act as a network of stress responses rather than isolated pathways. Studying these pathways, both individually and as a network, provides insight into bacterial survival and may aid the design of antimicrobials. In this work, envelope stress response pathways of Escherichia coli are explored to elucidate the activation mechanisms driving individual pathways and to describe the co-regulatory properties linking the pathways. The production of outer membrane vesicles is examined for an entire knock-out library using a new, high-throughput dot-blot method. Based on these data, novel biological pathways are implicated in the production of vesicles and the link between vesiculation and the SigmaE stress response pathway is investigated. Further experiments on the SigmaE pathway lead to the discovery of a second necessary activation signal. Finally, the CPX stress response pathway is categorized as a general envelope stress response that is suppressed by the SigmaE pathway, creating a potentially exploitable weakness in the bacteria's defense.</p> / Dissertation
01 January 2015
We have previously identified σS, an ECF sigma factor that is important in the virulence and stress response of S. aureus. Transcriptional profiling of sigS revealed that it is differentially regulated in a variety of laboratory and clinical strains of S. aureus, suggesting that there exists a regulatory network that modulates its expression. In order to identify direct regulators of sigS expression, we performed a biotin pull down assay in tandem with mass spectrometry. We identified CymR as a direct regulator and observed that sigS expression is increased in cells lacking cymR. In addition, transposon mutagenesis was performed to identify regulators of sigS expression. We identified insertions in genes that are transcriptional regulators, and elements involved in amino acid biosynthesis and DNA replication, recombination and repair as influencing sigS expression. Finally, methyl nitro-nitrosoguanidine mutagenesis in conjunction with whole genome sequencing was employed and revealed mutations in the lactose repressor, lacR, and the membrane sensor histidine kinase, kdpD, as negatively effecting sigS expression. EMSAs revealed that LacR is an indirect regulator of sigS expression, while the response regulator KdpE is a direct repressor. These results indicate that a complex regulatory network is in place for sigS that modulates its expression. In a continuation of studies on σS regulation, we next explored interplay with the products of genes conserved within the sigS locus. We determined that this region is conserved amongst all the sequenced staphylococci, and includes four genes: SAUSA300_1721 (a conserved hypothetical protein), as well as sigS, ecfX, and ecfY. In order to investigate the relationship between EcfX and σS we performed protein pull down assays and observed that these two protein interact. Further to this, transcriptional analysis of sigS in an ecfX mutant reveal that expression of sigS is decreased, indicating that it is an activator. Architectural analysis of the sigS locus via RNAseq revealed that the majority of transcription in this region comes from ecfY, a gene that is downstream and divergent to sigS. We demonstrate that inactivation of ecfY leads to a significant increase in sigS expression, and that ecfY null strains are more resistant to DNA damaging agents such as UV, H2O2, MMS, and ethidium bromide, which we have previously demonstrated that a sigS mutant is highly sensitive to. Our studies also revealed that an ecfY null strain is better able to survive intracellularly following phagocytosis by RAW 264.7 cell and demonstrates increased survival in whole-human blood, which is again opposed to that previously observed for sigS deficient strains. Because the ecfY null strain overexpresses sigS, we investigated the regulon of this sigma factor using this mutant in conjunction with RNAseq analysis. We identified that genes putatively under the control of σS are involved in DNA damage and repair, virulence, amino acid starvation and nucleic acid biosynthesis. Collectively, our results indicate that σS is regulated via a unique mechanism: positively through an apparent need for an activator protein (EcfX) and negatively via RNA-RNA interaction (the 3’ UTR of ecfY). We suggest that the evidence presented here greatly adds not only to our understanding of the regulatory circuits extant within S. aureus, but also to alternative sigma factor biology in general. Finally, we evaluated the efficacy of a novel library of quinazoline-based compounds against a highly drug resistant strain of S. aureus. We performed structure activity and structure property relationship assays in order to identify lead compounds. These methods lead to the identification of N2,N4-disubstituted quinazoline-2,4-diamines that had low minimum inhibitory concentrations, along with favorable physiochemical properties. Evaluation of their biological activity demonstrated limited potential for resistance of to our quinazoline based compounds, low toxicity to human epithelial cells, and strong efficacy in vivo. Taken together, our findings support the use of quinazoline derivatives as potential new antimicrobials against multidrug resistant S. aureus.
25 October 2012
Mycobacterium tuberculosis threatens global health. Its thick, impermeable cell wall renders it tolerant to high doses of many antibiotics. While we understand the biochemical functions of many cell wall-modifying enzymes, we often do not understand their physiological functions: their spatiotemporal roles in the cell cycle, their substrate preferences, or their individual effects on the macromolecular architecture of the cell wall complex. Mycobacterium tuberculosis possesses five peptidoglycan transpeptidases, five lytic transglycosylases, and numerous other peptidoglycan-modifying enzymes that lack precisely-understood roles. The lytic transglycosylases of Mycobacterium tuberculosis are collectively dispensable for in vitro growth. We sought to learn what other classes of peptidoglycan-degrading enzyme might substitute for the lytic transglycosylases or become essential in their absence. A high-throughput chemical screen was performed on a strain lacking all five lytic transglycosylases to identify compounds that specifically killed this strain and not wild-type Mycobacterium tuberculosis. Among the compounds identified were several members of the cephalosporin class of \(\beta\)-lactam antibiotics. It was shown that the cephalosporins had greater access to the periplasmic \(\beta\)-lactamase of Mycobacterium tuberculosis in the lytic transglycosylase-deficient strain and that this strain had enhanced sensitivity to several antibiotics with unrelated mechanisms of action. Together, greater periplasmic access and broadly heightened susceptibility in the deficient strain suggested a role for the lytic transglycosylases in maintaining the mycolic acid permeability barrier. To identify the specific penicillin-binding protein target of the cephalosporins, we isolated spontaneously-occurring resistant mutants. These strains contained polymorphisms in ponA2, a bifunctional penicillin-binding protein. The polymorphisms conferred sensitivity to heat stress, a phenotype associated with ponA2 loss of function. To clarify the relation between loss of function and cephalosporin resistance, a ponA2 deletion strain was created, which exhibited both cephalosporin resistance and sensitivity to carbapenems, another class of \(\beta\)-lactam. Restoration of the wild-type ponA2 allele suppressed both cephalosporin resistance and carbapenem sensitivity. Inactivation of other transpeptidases did not confer resistance to any \(\beta\)-lactams. The association of penicillin-binding protein inactivation with \(\beta\)-lactam resistance is unusual. One model to explain it is that upon deletion of ponA2, Mycobacterium tuberculosis compensates for its loss by upregulating a cephalosporin-resistant, meropenem-sensitive transpeptidase.
01 January 1999
In an effort to understand the molecular mechanisms of DNA alkylation repair, I initiated molecular cloning of a novel gene, ' NGS1'. The <i>Saccharomyces cerevisiae ngs1-1</i> mutant was previously identified by its enhanced sensitivity to simple DNA alkylating agents such as methyl methanesulfonate but not to UV. Molecular cloning and sequencing of 'NGS1' as a putative DNA alkylation repair gene revealed that it is identical to 'MRE11'/'RAD58', a gene that is involved in meiotic recombination and DNA recombinational repair. In order to investigate functional domains of the Mre11 protein, I determined the nucleotide sequence alterations of a number of 'mre11' mutant alleles, including 'ngs1-1', 'mre11-1' ('ts'), 'mre11-2', 'mre11-3' and 'mre11-58'. The location of various 'ngs1'/' mre11'/'rad58' mutations combined with the deletion analysis indicates that the functional domain(s) resides in the highly conserved N-terminus of Mre11. I also investigated various roles of Mre11 in spontaneous and DNA damage-inducedmitotic recombination. The assays used in this study show that the <math> <f> mre<it>11<g>D</g></it></f> </math> mutation enhances inter-chromosomal recombination but decreases the intra-chromosomal deletion frequency. In addition, 'MRE11' appears to play different roles during spontaneous and alkylation-induced homologous mitotic recombination. Physical interactions between members of the 'RAD52' epistasis group have been detected genetically and biochemically. These protein interactions also appear to be important at the early stage of meiotic recombination. Mre11 has been shown to interact with itself, Rad50 and Xrs2 in a yeast two-hybrid system. Preliminary studies employing deletion analysis predicted that the self-interaction domain of Mre11 resided at the N-terminus of the protein. To determine domain(s) required for Mre11 complex formation, and to elucidate the relationship between this complex formation and 'MRE11' DNA repair function, I employed a combined yeast two-hybrid and functional analyses. My results indicate that both Mre11 dimerization and interaction with Rad50 are essential for recombinational repair. I found that the N-terminus of the Mre11 protein constitutes the core homodimerization and heterodimerization domain and is sufficient for Mre11 DNA repair activity. Collectively, these studies support the hypothesis that Mre11 self-association as well as its assembly into a multi-protein complex consisting of Mre11 and Rad50 are essential for effective DNA recombinational repair. Using the sequence of yeast 'MRE11', isolated the full-length ' hMRE11B' cDNA from a human HeLa cell cDNA library. Compared to the previously identified 'hMRE11', 'hMRE11B' contains an additional 84 base pair sequence that results in a 28 amino acid insertion close to the C-terminus. Overexpression of 'hMRE11B' does not complement the alkylation sensitivity of the 'mre11' null and temperature sensitive mutant strains. My results suggest that species-specific protein interaction determines the functional specificity of 'MRE11 ' and that the participation of the C-terminus of Mre11 protein plays an important role in this regard. (Abstract shortened by UMI.)
Broomfield, Stacey D.
01 January 2001
The 'mms2-1' mutant was initially isolated by its sensitivity to the alkylating agent methyl methanesulfonate (MMS). I screened a yeast genomic library and identified the 'MMS2' gene. Disruption of 'MMS2' results in enhanced sensitivity to both MMS and UV and 'mms2-1' was found to be a missense mutation with partial loss of functions. Mms2 shares homology with ubiquitin-conjugating enzymes (Ubcs), but does not function as a typical Ubc in ubiquitination. The only other 'ubc' mutant that displays a UV and MMS sensitivity is 'ubc2' ('rad6') which is involved in postreplication repair (PRR) and mutagenesis. Epistatic analysis placed 'MMS2' within the 'RAD6' pathway but is parallel to the error-prone PRR subpathway consisting of 'REV1, REV3' and 'REV7 '. Mms2 is defined as a member of error-free PRR, since 'mms2 '[Delta] cells display an increase in the spontaneous and UV-induced mutations, and these phenotypes depend on 'REV3. mms2'[Delta] and 'rev3'[Delta] are synergistic with respect to killing by DNA damaging agents, indicating that they function in alternative pathways. Study of 'rad6'[Delta]'1-9, po130-46, po13-13, rad5'[Delta] and 'rad30'[Delta] alleles has placed these genes in the error-free PRR pathway. I found that 'rad6'[Delta]' 1-9' is epistatic to 'mms2'[Delta], while ' pol30-46, rad5'[Delta] and 'rad30'[Delta] all display an additive effect with 'mms2'. A 'srs2'[Delta] mutation is able to rescue the UV sensitivities of the 'rad6'[Delta] and 'rad18'[Delta] mutants, and is epistatic to 'mms2 '[Delta] and 'rev3'[Delta]. Furthermore, 'srs2 '[Delta] suppresses the MMS sensitivity of 'pol30-46' and 'rad5'[Delta], indicating that Srs2 controls the entire PRR pathway. In addition to PRR, the Ubc activity of Rad6 is involved in other cellular functions including sporulation, telomere silencing and protein degradation. The 'mms2'[Delta] mutation results in moderate defects in sporulation and protein degradation but has no effect on telomere silencing. This indicates that Mms2 may act as an accessory protein for Rad6, or alternatively, may provide an similar activity via a pathway distinct from Rad6. Two human Mms2 homologues, 'hMMS2' and 'CROC1', have been isolated. 'hMMS2' can suppress the yeast ' mms2'[Delta] UV and MMS sensitivity and elevated mutation rate. Further analysis is required to assess whether 'hMMS2' and ' CROC1' possess analogous activities in mammalian cells.
Sreenath, H K
Xylanases production by streptomyces
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