Chemical Research with Undergraduate Collaborators: Building Cyclic Polymers

Undergraduate research in chemistry provides not only a meaningful experience for the students, but is essential in getting research done. This talk will focus on an ongoing project in my lab: designing large molecules of specific shapes by studying the fundamental reactions. While results will be discussed, the talk will be tailored towards a general audience. I will attempt to highlight the outstanding contributions made by Bucknell students that have worked in my lab.

Quantum Mechnical Investion of Cyclic 3',5'- Adenosine Monophosphate, the Second Hormonal Messenger

Full geometry optimizations using the PM3, AM1, 3-21G∗/HF and 6-31G∗/HF levels of theory were conducted on the syn and anti conformations of cyclic3′,5′-adenosine monophosphate (cAMP). Comparison of the anti crystal structures with the semiempirical and ab initio results revealed that the ab initio results agree well with the experimental results. The results of semiempirical calculations are in qualitative agreement with experimental and ab initio values, with the exception of the glycosyl torsion angle for the anti conformer. Sugar puckering, which is not handled properly by semiempirical methods for unconstrained sugars, nucleosides, nucleotides and nucleotide base pairs, is modeled reasonably well by the semiempirical methods for cAMP. This improvement results from the constraints introduced by the cyclization of AMP to form the phosphodiester.

Use of the Supermolecule Approach To Model the Syn and Anti Conformations of Solvated Cyclic 3‘,5‘-Adenosine Monophosphate

The supermolecule approach has been used to model the hydration of cyclic 3‘,5‘-adenosine monophosphate, cAMP. Model building combined with PM3 optimizations predict that the anti conformer of cAMP is capable of hydrogen bonding to an additional solvent water molecule compared to the syn conformer. The addition of one water to the syn superstructure with concurrent rotation of the base about the glycosyl bond to form the anti superstructure leads to an additional enthalpy of stabilization of approximately −6 kcal/mol at the PM3 level. This specific solute−solvent interaction is an example of a large solvent effect, as the method predicts that cAMP has a conformational preference for the anti isomer in solution. This conformational preference results from a change in the number of specific solute−solvent interactions in this system. This prediction could be tested by NMR techniques. The number of waters predicted to be in the first hydration sphere around cAMP is in agreement with the results of hydration studies of nucleotides in DNA. In addition, the detailed picture of solvation about this cyclic nucleotide is in agreement with infrared experimental results.

Cyclic alternating pattern in narcolepsy patients and healthy controls after partial and total sleep deprivation

To investigate the regulation NREM sleep at baseline and in morning recovery sleep after partial and total sleep deprivation (SD) in narcolepsy-cataplexy (NC) using cyclic alternating pattern (CAP).

Stochastic amplitude-modulated stretching of Rabbit flexor digitorum profundus tendons reduces stiffness compared to Cyclic Loading but does not affect Tenocyte Metabolism

Background It has been demonstrated that frequency modulation of loading influences cellular response and metabolism in 3D tissues such as cartilage, bone and intervertebral disc. However, the mechano-sensitivity of cells in linear tissues such as tendons or ligaments might be more sensitive to changes in strain amplitude than frequency. Here, we hypothesized that tenocytes in situ are mechano-responsive to random amplitude modulation of strain. Methods We compared stochastic amplitude-modulated versus sinusoidal cyclic stretching. Rabbit tendon were kept in tissue-culture medium for twelve days and were loaded for 1h/day for six of the total twelve culture days. The tendons were randomly subjected to one of three different loading regimes: i) stochastic (2 – 7% random strain amplitudes), ii) cyclic_RMS (2–4.42% strain) and iii) cyclic_high (2 - 7% strain), all at 1 Hz and for 3,600 cycles, and one unloaded control. Results At the end of the culture period, the stiffness of the “stochastic” group was significantly lower than that of the cyclic_RMS and cyclic_high groups (both, p < 0.0001). Gene expression of eleven anabolic, catabolic and inflammatory genes revealed no significant differences between the loading groups. Conclusions We conclude that, despite an equivalent metabolic response, stochastically stretched tendons suffer most likely from increased mechanical microdamage, relative to cyclically loaded ones, which is relevant for tendon regeneration therapies in clinical practice.

Hydraulic sustainability of soil-bentonite cutoff walls subjected to cyclic wetting and drying

This study investigated the effect of cyclic wetting and drying on the backfill used in soil-bentonite (SB) cutoff walls. For this purpose, model SB vertical cutoff wall backfills were prepared comprising of a fine grained mortar sand and 2% bentonite (by total weight) and 4% bentonite (by total weight). Results of the study indicate that the volume change is influenced by the bentonite content, that is, the increase in volume change increased with increasing bentonite content.

Role of RhoA/ROCK-dependent actin contractility in the induction of tenascin-C by cyclic tensile strain

In chick embryo fibroblasts, the mRNA for extracellular matrix protein tenascin-C is induced 2-fold by cyclic strain (10%, 0.3 Hz, 6 h). This response is attenuated by inhibiting Rho-dependent kinase (ROCK). The RhoA/ROCK signaling pathway is primarily involved in actin dynamics. Here, we demonstrate its crucial importance in regulating tenascin-C expression. Cyclic strain stimulated RhoA activation and induced fibroblast contraction. Chemical activators of RhoA synergistically enhanced the effects of cyclic strain on cell contractility. Interestingly, tenascin-C mRNA levels perfectly matched the extent of RhoA/ROCK-mediated actin contraction. First, RhoA activation by thrombin, lysophosphatidic acid, or colchicine induced tenascin-C mRNA to a similar extent as strain. Second, RhoA activating drugs in combination with cyclic strain caused a super-induction (4- to 5-fold) of tenascin-C mRNA, which was again suppressed by ROCK inhibition. Third, disruption of the actin cytoskeleton with latrunculin A abolished induction of tenascin-C mRNA by chemical RhoA activators in combination with cyclic strain. Lastly, we found that myosin II activity is required for tenascin-C induction by cyclic strain. We conclude that RhoA/ROCK-controlled actin contractility has a mechanosensory function in fibroblasts that correlates directly with tenascin-C gene expression. Previous RhoA/ROCK activation, either by chemical or mechanical signals, might render fibroblasts more sensitive to external tensile stress, e.g., during wound healing.

Cyclic nucleotide specific phosphodiesterases of Leishmania major

Background Leishmania represent a complex of important human pathogens that belong to the systematic order of the kinetoplastida. They are transmitted between their human and mammalian hosts by different bloodsucking sandfly vectors. In their hosts, the Leishmania undergo several differentiation steps, and their coordination and optimization crucially depend on numerous interactions between the parasites and the physiological environment presented by the fly and human hosts. Little is still known about the signalling networks involved in these functions. In an attempt to better understand the role of cyclic nucleotide signalling in Leishmania differentiation and host-parasite interaction, we here present an initial study on the cyclic nucleotide-specific phosphodiesterases of Leishmania major. Results This paper presents the identification of three class I cyclic-nucleotide-specific phosphodiesterases (PDEs) from L. major, PDEs whose catalytic domains exhibit considerable sequence conservation with, among other, all eleven human PDE families. In contrast to other protozoa such as Dictyostelium, or fungi such as Saccharomyces cerevisiae, Candida ssp or Neurospora, no genes for class II PDEs were found in the Leishmania genomes. LmjPDEA contains a class I catalytic domain at the C-terminus of the polypeptide, with no other discernible functional domains elsewhere. LmjPDEB1 and LmjPDEB2 are coded for by closely related, tandemly linked genes on chromosome 15. Both PDEs contain two GAF domains in their N-terminal region, and their almost identical catalytic domains are located at the C-terminus of the polypeptide. LmjPDEA, LmjPDEB1 and LmjPDEB2 were further characterized by functional complementation in a PDE-deficient S. cerevisiae strain. All three enzymes conferred complementation, demonstrating that all three can hydrolyze cAMP. Recombinant LmjPDEB1 and LmjPDEB2 were shown to be cAMP-specific, with Km values in the low micromolar range. Several PDE inhibitors were found to be active against these PDEs in vitro, and to inhibit cell proliferation. Conclusion The genome of L. major contains only PDE genes that are predicted to code for class I PDEs, and none for class II PDEs. This is more similar to what is found in higher eukaryotes than it is to the situation in Dictyostelium or the fungi that concomitantly express class I and class II PDEs. Functional complementation demonstrated that LmjPDEA, LmjPDEB1 and LmjPDEB2 are capable of hydrolyzing cAMP. In vitro studies with recombinant LmjPDEB1 and LmjPDEB2 confirmed this, and they demonstrated that both are completely cAMP-specific. Both enzymes are inhibited by several commercially available PDE inhibitors. The observation that these inhibitors also interfere with cell growth in culture indicates that inhibition of the PDEs is fatal for the cell, suggesting an important role of cAMP signalling for the maintenance of cellular integrity and proliferation.

Compressed sensing based cyclic feature spectrum sensing for cognitive radios

Spectrum sensing is currently one of the most challenging design problems in cognitive radio. A robust spectrum sensing technique is important in allowing implementation of a practical dynamic spectrum access in noisy and interference uncertain environments. In addition, it is desired to minimize the sensing time, while meeting the stringent cognitive radio application requirements. To cope with this challenge, cyclic spectrum sensing techniques have been proposed. However, such techniques require very high sampling rates in the wideband regime and thus are costly in hardware implementation and power consumption. In this thesis the concept of compressed sensing is applied to circumvent this problem by utilizing the sparsity of the two-dimensional cyclic spectrum. Compressive sampling is used to reduce the sampling rate and a recovery method is developed for re- constructing the sparse cyclic spectrum from the compressed samples. The reconstruction solution used, exploits the sparsity structure in the two-dimensional cyclic spectrum do-main which is different from conventional compressed sensing techniques for vector-form sparse signals. The entire wideband cyclic spectrum is reconstructed from sub-Nyquist-rate samples for simultaneous detection of multiple signal sources. After the cyclic spectrum recovery two methods are proposed to make spectral occupancy decisions from the recovered cyclic spectrum: a band-by-band multi-cycle detector which works for all modulation schemes, and a fast and simple thresholding method that works for Binary Phase Shift Keying (BPSK) signals only. In addition a method for recovering the power spectrum of stationary signals is developed as a special case. Simulation results demonstrate that the proposed spectrum sensing algorithms can significantly reduce sampling rate without sacrifcing performance. The robustness of the algorithms to the noise uncertainty of the wireless channel is also shown.

Cyclic automorphic graph decompositions

Chapter 1 introduces the tools and mechanics necessary for this report. Basic definitions and topics of graph theory which pertain to the report and discussion of automorphic decompositions will be covered in brief detail. An automorphic decomposition D of a graph H by a graph G is a G-decomposition of H such that the intersection of graph (D) @H. H is called the automorhpic host, and G is the automorphic divisor. We seek to find classes of graphs that are automorphic divisors, specifically ones generated cyclically. Chapter 2 discusses the previous work done mainly by Beeler. It also discusses and gives in more detail examples of automorphic decompositions of graphs. Chapter 2 also discusses labelings and their direct relation to cyclic automorphic decompositions. We show basic classes of graphs, such as cycles, that are known to have certain labelings, and show that they also are automorphic divisors. In Chapter 3, we are concerned with 2-regular graphs, in particular rCm, r copies of the m-cycle. We seek to show that rCm has a ρ-labeling, and thus is an automorphic divisor for all r and m. we discuss methods including Skolem type difference sets to create cycle systems and their correlation to automorphic decompositions. In the Appendix, we give classes of graphs known to be graceful and our java code to generate ρ-labelings on rCm.