Towards efficacy and efficiency in sparse delay tolerant networks

The ubiquitous adoption of portable smart devices has enabled a new way of communication via Delay Tolerant Networks (DTNs), whereby messages are routed by the personal devices carried by ever-moving people. Although a DTN is a type of Mobile Ad Hoc Network (MANET), traditional MANET solutions are ill-equipped to accommodate message delivery in DTNs due to the dynamic and unpredictable nature of people\u27s movements and their spatio-temporal sparsity. More so, such DTNs are susceptible to catastrophic congestion and are inherently chaotic and arduous. This manuscript proposes approaches to handle message delivery in notably sparse DTNs. First, the ChitChat system [69] employs the social interests of individuals participating in a DTN to accurately model multi-hop relationships and to make opportunistic routing decisions for interest-annotated messages. Second, the ChitChat system is hybridized [70] to consider both social context and geographic information for learning the social semantics of locations so as to identify worthwhile routing opportunities to destinations and areas of interest. Network density analyses of five real-world datasets is conducted to identify sparse datasets on which to conduct simulations, finding that commonly-used datasets in past DTN research are notably dense and well connected, and suggests two rarely used datasets are appropriate for research into sparse DTNs. Finally, the Catora system is proposed to address congestive-driven degradation of service in DTNs by accomplishing two simultaneous tasks: (i) expedite the delivery of higher quality messages by uniquely ordering messages for transfer and delivery, and (ii) avoid congestion through strategic buffer management and message removal. Through dataset-driven simulations, these systems are found to outperform the state-of-the-art, with ChitChat facilitating delivery in sparse DTNs and Catora unencumbered by congestive conditions --Abstract, page iv

Structural and mutagenic analysis of the RM controller protein C.Esp1396I

Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction. These two activities are tightly regulated to prevent over-methylation or auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. Here we present both structural and DNA binding data for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. High-resolution X-ray crystal structures of the mutant and native proteins showed that the fold of the proteins was unaffected by the mutations, but also revealed variation in the flexible loop conformations associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA complex by X-ray crystallography to allow us to directly compare the structure of the DNA in the mutant and native complexes

Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images

Microscopic imaging and technolog

Determining the relationship between Myers-Briggs Type Indicator (MBTI) personality type and preference of USMLE Step 1 study resources (poster)

At Cooper Medical School of Rowan University (CMSRU), the Myers Briggs Type Indicator (MBTI) assessment tool has set the foundation for student interactions in an academic environment. Medical students’ personality types have been used to form diverse and balanced active learning groups to facilitate a conducive and collaborative setting to learn. While the MBTI assessment tool has helped CMSRU medical students gain awareness of their learning preference, there is still a gap in understanding how MBTI results can help students maximize their learning of medical information to best prepare them for the USMLE Step 1 exam. To date, there is no published data on correlations between MBTI results and Step 1 study resources found to be most effective for learning

Molecular characterisation of Herpes simplex virus type 1 deoxyuridine triphosphatase

Analysis of primary sequence data revealed a subset of open reading frames that were predicted to encode HSV-I dUTPases based on five areas of local primary sequence conservation. The differences in the primary sequence organisation of these motif regions allowed the description of two distinct dUTPase classes. The class I dUTPases are encoded by a diverse range of organisms and are characterised by a trimeric arrangement with subunit protein lengths approximating 150 amino acids. The class II dUTPases are specific to the herpesviruses and are characterised by a monomeric arrangement with a protein chain length approximately double that of their class I counterparts. It has been proposed that the class II dUTPases arose by the intragenic duplication of the class I open reading frame.In this thesis the class I structures were used as a basis to investigate the HSV-1 class II dUTPase in terms of structural and evolutionary relationships.To allow a defined approach to functional analysis of the HSV-1 dUTPase a tertiary structural model was generated for the class II enzymes. Following intensive primary sequence analysis a method was devised for comparing class I and class II sequences directly. Secondary structure prediction programs were utilised to judge the basic structural similarities between the two classes allowing the proposition of several defined hypotheses. The available class I structural information was utilised in order to characterise highly conserved structural elements within the class I group. In was then possible to relate this data set to class I primary sequences and subsequently to the generation of a class II model. Various modelling techniques were used based on the constraints on the structural organisation that could achieve a functionally active monomer plus the set of hypotheses defined in the earlier work.Mutagenic analysis of the HSV-1 dUTPase was then possible using the class II model as a reference. Several targets were investigated based on predicated functionally important regions. Analysis of these mutant enzymes was performed using purified recombinant HSV-1 dUTPase expressed from the T7 E.coli expression system

Radiation damage to nucleoprotein complexes in macromolecular crystallography

Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses