0,1479% Redundancy

This is a list of words or names that start with every digraph combination of 2 letters, except one. We have managed to put together a list 675 digraphs, with many different sources

The development of rapid genotyping methods for methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance. The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits. This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups. A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy. To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing. The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform

Hyaluronic acid alters vessel behavior in CXCL12-treated HUVECs

Hyaluronic acid (HA) is a key component of the extracellular matrix known for absorbing water, swelling, and altering solid stress of tumors. HA’s anionic behavior may provide important biochemical effects toward tumor progression as well. Tumors obtain nutrients by relying on signaling molecules such as CXCL12 to recruit blood vessels and promote vessel leakage. Recent work suggests that additional positively-charged residues on CXCL12’s β and γ isoforms cause different biochemical functionality compared to the well-studied α isoform. These studies aimed to determine whether the presence of HA in a tumor’s microenvironment could alter the relative response strength of CXCL12’s various isoforms on blood vessel sprouting and apparent vascular permeability. The vessel microenvironment was modeled using a 3-channel microfluidic device with Human Umbilical Vein Endothelial Cells (HUVECs) in the outer channels forming monolayers against a 3D collagen or collagen/HA matrix in the center channel. HUVECs were cultured with media containing recombinant CXCL12 (α, β or γ). Results show that total HUVEC sprouting area follows an α>β>γ trend in isoform-treated HUVECs within a collagen matrix, matching the binding affinity order of CXCL12 to endothelial CXCR4 receptors. The presence of HA decreased overall sprouting response but shifted pro-angiogenic potency towards CXCL12’s γ isoform. Vascular permeability studies also showed an α>β>γ trend for HUVECs in collagen. With HA added, control and α-treated HUVECs became less permeable while γ-treated HUVECs became more permeable. Overall results suggest that an HA-infused collagen matrix facilitates γ isoform binding, leading to a stronger isoform-specific vessel response. Knowing how HA impacts CXCL12 isoform potency on vessels will help in the future design of CXCL12-targeted cancer therapies.The American Heart AssociationInstitute for Materials Research at OSULumley Engineering FundPelotoniaA one-year embargo was granted for this item.Academic Major: Chemical Engineerin

Isogram Transdeletion Pyramid

There are many word articles on isograms and transdeletion pyramids, but there are none which talk about them combined, the isogram transdeletion pyramid

Automatic Pet Door and Magnetic Field Activation

Automatic pet doors are sold commercially as a completely built unit on today’s market. A low-cost design has been created to allow more flexible placement and construction of a door. This door is unlocked upon detection of a magnetic field originating from the pet’s collar. The required activation signal has been carefully characterized to allow customization of the door and collar for a particular purpose. Detailed information on the operating circuit and sensor activation are provided. Results of how the door is constructed and operated, as well as personalization, are presented

Fusion Rules for Affine Kac-Moody Algebras

This is an expository introduction to fusion rules for affine Kac-Moody algebras, with major focus on the algorithmic aspects of their computation and the relationship with tensor product decompositions. Many explicit examples are included with figures illustrating the rank 2 cases. New results relating fusion coefficients to tensor product coefficients are proved, and a conjecture is given which shows that the Frenkel-Zhu affine fusion rule theorem can be seen as a beautiful generalization of the Parasarathy-Ranga Rao-Varadarajan tensor product theorem. Previous work of the author and collaborators on a different approach to fusion rules from elementary group theory is also explained.Comment: 43 pp, LateX, 18 postscript figures. Paper for my talk at the Ramanujan International Symposium on Kac-Moody Lie Algebras and Applications, ISKMAA-2002, Jan. 28-31, 2002, Chennai, India. Important references and comments added. Final version accepted for publication. Also available from ftp://ftp.math.binghamton.edu/pub/alex/Madras_Paper_Latex.ps.g