Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Abasic Sites (1)
- Activation- induced Deaminase (1)
- Antibiotic resistance (1)
- Aptamers (1)
- Atomic Force Microscopy (1)
-
- B cell lymphomas (1)
- Co-assembly (1)
- Collagen (1)
- Colored De Bruijn Graph (1)
- DNA (1)
- DNA Damage (1)
- Discoidin domain receptors (1)
- Folate receptor (1)
- Genome (1)
- Helix 69 (1)
- Protein-protein interactions (1)
- Ribosome (1)
- SELEX (1)
- Sequencing (1)
- Single Cell (1)
- Single molecule force measurements (1)
- Uracil-DNA Glycosylase (1)
- Uracils (1)
Articles 1 - 6 of 6
Full-Text Articles in Physical Sciences and Mathematics
Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy, Anwesha Sarkar
Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy, Anwesha Sarkar
Wayne State University Dissertations
Atomic Force Microscopy (AFM) provides superior imaging resolution and the ability to measure forces at the nanoscale. It is an important tool for studying a wide range of bio-molecular samples from proteins, DNA to living cells. We developed AFM measurement procedures to measure protein interactions on live cells at the single molecular level. These measurements can be interpreted by using proper statistical approaches and can yield important parameters about ligand-receptor interactions on live cells. However, the standard theory for analyzing rupture force data does not fit the experimental rupture force histograms. Most of the experimental measurements of rupture force data …
Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill
Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill
Wayne State University Dissertations
Outbreaks of advanced antibiotic-resistant strains of microbes have hastened the need to identify new viable molecular targets for the development of novel anti-infectives. For this purpose, helix 69 (H69, or m3a 19-nucleotide (nt) hairpin motif that is highly conserved throughout phylogeny and rich in modified nucleotides, including pseudouridine () and 3-methylpseudouridine (m3) was chosen as a potential target. Helix 69, which is located in domain IV of Escherichia coli 23S ribosomal RNA (rRNA), undergoes conformational changes when in close proximity to the decoding region of 16S rRNA and transfer RNAs (tRNAs) in the peptidyl-transferase center (PTC). Functionally, the exact biological …
The Loss Of Genomic Uracil Homeostasis And Aid-Dependent Accumulation Of Dna Damage In B Cell Lymphomas, Sophia Shalhout
The Loss Of Genomic Uracil Homeostasis And Aid-Dependent Accumulation Of Dna Damage In B Cell Lymphomas, Sophia Shalhout
Wayne State University Dissertations
Activation-induced deaminase (AID) is a sequence-selective DNA cytosine deaminase that introduces uracils in immunoglobulin genes. This DNA mutator is required for somatic hypermutation and class switch recombination- processes involved in the affinity maturation and diversification of antibodies. AID, however, can also lead to deleterious mutations and translocations promoting lymphomagenesis. The introduction of uracils throughout the genome of activated B cells and the ability of UNG2 glycosylase to excise these uracils is examined here. This interplay was also studied in cancerous B cells, with different results emerging in transformed cells versus healthy cells. Genomic uracil levels are found to remain at …
Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations, Gurpreet Dhindsa
Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations, Gurpreet Dhindsa
Wayne State University Dissertations
Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic Pyrophosphatase (IPPase).
RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and …
Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Wayne State University Dissertations
Recent progress in DNA amplification techniques, particularly multiple displacement
amplification (MDA), has made it possible to sequence and assemble bacterial
genomes from a single cell. However, the quality of single cell genome assembly has
not yet reached the quality of normal multi-cell genome assembly due to the coverage
bias (including uneven depth of coverage and region blackout) and errors caused by
MDA. Computational methods try to mitigates the amplification bias. In this document
we introduce a de novo co-assembly method using colored de Bruijn graph,
which can overcome the problem of blackout regions due to amplification bias. The
algorithm is …
Applications Of Machine Learning In Biology And Medicine, Saied Haidarian Shahri
Applications Of Machine Learning In Biology And Medicine, Saied Haidarian Shahri
Wayne State University Dissertations
Machine learning as a field is defined to be the set of computational algorithms that improve their performance by assimilating data.
As such, the field as a whole has found applications in many diverse disciplines from robotics and communication in engineering to economics and finance, and also biology and medicine.
It should not come as a surprise that many popular methods in use today have completely different origins.
Despite this heterogeneity, different methods can be divided into standard tasks, such as supervised, unsupervised, semi-supervised and reinforcement learning.
Although machine learning as a field can be formalized as methods trying to …