Cell line-specific efficacy of thermoradiotherapy in human and canine cancer cells in vitro

Objective Aims were to investigate sensitivity of various human and canine cancer cell lines to hyperthermia and the influence of particular treatment conditions, and to analyze the DNA-damage response and mode of cell death in cell line radiosensitized by hyperthermia. Additionally, we were interested in the involvement of HSP70 in radiosensitization. Methods Radiosensitization by hyperthermia was determined in a panel of human and canine cancer cell lines using clonogenic cell survival assay, as well as levels of heat shock proteins (HSPs) using immunoblotting. The influence of the hyperthermia-radiotherapy time gap, different temperatures and the order of treatments on clonogenicity of hyperthermia-sensitive A549 cells was investigated. Additionally, DNA damage and cell death were assessed by Comet assay and an apoptosis/necrosis assay. Further we induced transient knockdown in A549 cells to test HSP70’s involvement in radiosensitization. Results Out of eight cell lines tested, only two (A549 and Abrams) showed significant decrease in clonogenic cell survival when pre-treated with hyperthermia at 42˚C. Strong induction of HSP70 upon thermoradiotherapy (HT-RT) treatment was found in all cell lines. Transient knockdown of HSP70 in A549 cells did not result in decrease of clonogenic cell survival in response to HT-RT. Conclusion Tumor cell-type, temperature and order of treatment play an important role in radiosensitization by hyperthermia. However, hyperthermia has limited potency to radiosensitize canine cancer cells grown in a 2D cell culture setting presented here. DNA damage and apoptosis/necrosis did not increase upon combined treatment and cytosolic levels of HSP70 appear not to play critical role in the radiosensitization of A549 cells

^{63}Cu, ^{35}Cl, and ^{1}H NMR in the S=1/2 Kagom\'e Lattice ZnCu_{3}(OH)_{6}Cl_{2}

ZnCu$_{3}$(OH)$_{6}$Cl$_{2}$ ($S=1/2$) is a promising new candidate for an ideal Kagom\'e Heisenberg antiferromagnet, because there is no magnetic phase transition down to $\sim$50 mK. We investigated its local magnetic and lattice environments with NMR techniques. We demonstrate that the intrinsic local spin susceptibility {\it decreases} toward T=0, but that slow freezing of the lattice near $\sim$50 K, presumably associated with OH bonds, contributes to a large increase of local spin susceptibility and its distribution. Spin dynamics near T=0 obey a power-law behavior in high magnetic fields.Comment: Phys. Rev. Lett. (in press

ADVANCES IN SILOXANE-BASED COUPLING TECHNOLOGIES: APPROACHES TOWARD PANCRATISTATIN AND STREPTONIGRIN

The ability to form carbon-carbon bonds, arguably the most important transformation in synthetic chemistry, has been critically facilitated via the implementation of transition metal catalysts with main group element-associated carbon moieties. Specifically, organosilane coupling technology previously reported in the DeShong group provides ease of access to a wide variety of structurally important carbon-carbon bond motifs. The stability, tolerance of numerous implicit functional groups, simplicity of use, and ease of synthetic access to a multitude of organosilane coupling partners, makes the coupling technology developed in the DeShong lab markedly attractive for implementation in syntheses of complex natural product targets. Two targets of specific interest are pancratistatin and streptonigrin. Synthetic approaches toward pancratistatin via complex organosilane coupling precursors proved promising, however mechanistic studies performed in the DeShong group determined that standard 18-electron palladium(0) catalysts fail in transmetallation. Therefore, a new class of 16-electron Pd(0) catalysts have been developed and surveyed for applications in siloxane based allyl-aryl coupling protocols. The ability to "tune" these catalysts' activity by varying either the cone angle or the electronic characteristics of the alkene ligands attached to palladium has also been demonstrated. Unfortunately, attempts to prepare chiral adducts in the coupling reaction utilizing chiral bicyclooctadiene derivatives as a ligand for palladium provided no significant enantioenrichment in the coupled product. Similarly, previous work in the DeShong lab toward the synthesis of streptonigrin has been reported. Particularly, the synthesis of the structurally congested pyridyl C-ring proved difficult, requiring numerous steps at low yields. Development of new synthetic pathways toward the pyridyl C-ring was undertaken, exploiting the electronically withdrawn nature of the pyridone intermediate in order to brominate and alcohol, as well as change a methyl group to an aldehyde, via an enamine intermediate. The specific goals of this work were (1) to investigate new palladium(0) catalysts for the coupling of analogues of pancratistatin precursors, and (2) to improve upon problematic portions of our previous synthesis of streptonigrin's pyridyl C-ring

Synthesis, structure, and magnetic properties of spin-1/2 kagomé antiferromagnets

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Vita.Includes bibliographical references.Stoichiometrically pure S = 1/2 Cu2+ kagomé materials have been synthesized. Such materials provide an ideal venue for exploration of quantum states on a kagomé because they exhibit strong geometric spin frustration and are predicted to show no magnetic long-range ordering (LRO). The three broad classes of kagomé layered materials presented herein--covalently linked layers, hydrogen-bonded layers, and electrostatically linked layers--reflect optimization of structure to maximize frustration while simultaneously minimizing interlayer exchange to inhibit three-dimensional (3-D) LRO. The covalently linked layered system, Cu(1,3-benzenedicarboxylate), featuring in-plane monodentate [mu]-carboxylate bridges, is the first known structurally perfect S = 1/2 metal-organic framework (MOF) kagomé and bears the shortest metal-metal distance of any such material. The frustrated material features antiferromagnetic nearest-neighbor exchange (T = -33 K) but undergoes ferromagnetic ordering (Tc = 2 K), perhaps due to an out-of-plane spin polarization mechanism. The hydrogen-bonded layered system (CdCu3(OH)6(NO3)2.0.5H2O), featuring in-plane [mu]-hydroxy bridges, shows even stronger antiferromagnetic exchange (T = -114 ± 27 K), but still exhibits magnetic ordering behavior (Tc = 5 K), likely arising from interlayer exchange through hydrogen bonds. Electrostatically linked systems featuring in-plane [mu]-hydroxy bridges--the rare minerals claringbullite (Cu4(OH)xClyFz where x + y + z = 8), clinoatacamite (Cu2(OH)3Cl), and herbertsmithite (ZnCu3(OH)6Cl2)--have been prepared and characterized both structurally and magnetically. The former two minerals are frustrated systems but still show 3-D LRO arising from ferromagnetic interactions between the kagomé planes and interlayer copper(II) ions. Herbertsmithite, in contrast, features 2-D kagomé layers isolated by diamagnetic zinc(II) ions and exhibits no LRO to 50 mK, despite strong nearest-neighbor antiferromagnetic coupling (T = -314 K). Herbertsmithite displays no spin gap in its excitation spectrum at low temperature, a signature of a spin liquid phase with long correlations.(cont.) Continued efforts are directed at growth of large single crystals for probative neutron scattering studies. Current and future study of these stoichiometrically pure spin-frustrated systems will provide critical insight into the behavior of strongly correlated electrons.by Emily A. Nytko.Ph.D

Dynamic Scaling in the Susceptibility of the Spin-1\2 Kagome Lattice Antiferromagnet Herbertsmithite

The spin-1/2 kagome lattice antiferromagnet herbertsmithite, ZnCu$_{3}$(OH)$_{6}$Cl$_{2}$, is a candidate material for a quantum spin liquid ground state. We show that the magnetic response of this material displays an unusual scaling relation in both the bulk ac susceptibility and the low energy dynamic susceptibility as measured by inelastic neutron scattering. The quantity $\chi T^\alpha$ with $\alpha \simeq 0.66$ can be expressed as a universal function of $H/T$ or $\omega/T$. This scaling is discussed in relation to similar behavior seen in systems influenced by disorder or by the proximity to a quantum critical point.Comment: 5 pages, 3 figures v2: updated to match published version

Generalizing Reduction-Based Algebraic Multigrid

Algebraic Multigrid (AMG) methods are often robust and effective solvers for solving the large and sparse linear systems that arise from discretized PDEs and other problems, relying on heuristic graph algorithms to achieve their performance. Reduction-based AMG (AMGr) algorithms attempt to formalize these heuristics by providing two-level convergence bounds that depend concretely on properties of the partitioning of the given matrix into its fine- and coarse-grid degrees of freedom. MacLachlan and Saad (SISC 2007) proved that the AMGr method yields provably robust two-level convergence for symmetric and positive-definite matrices that are diagonally dominant, with a convergence factor bounded as a function of a coarsening parameter. However, when applying AMGr algorithms to matrices that are not diagonally dominant, not only do the convergence factor bounds not hold, but measured performance is notably degraded. Here, we present modifications to the classical AMGr algorithm that improve its performance on matrices that are not diagonally dominant, making use of strength of connection, sparse approximate inverse (SPAI) techniques, and interpolation truncation and rescaling, to improve robustness while maintaining control of the algorithmic costs. We present numerical results demonstrating the robustness of this approach for both classical isotropic diffusion problems and for non-diagonally dominant systems coming from anisotropic diffusion

Optimized Sparse Matrix Operations for Reverse Mode Automatic Differentiation

Sparse matrix representations are ubiquitous in computational science and machine learning, leading to significant reductions in compute time, in comparison to dense representation, for problems that have local connectivity. The adoption of sparse representation in leading ML frameworks such as PyTorch is incomplete, however, with support for both automatic differentiation and GPU acceleration missing. In this work, we present an implementation of a CSR-based sparse matrix wrapper for PyTorch with CUDA acceleration for basic matrix operations, as well as automatic differentiability. We also present several applications of the resulting sparse kernels to optimization problems, demonstrating ease of implementation and performance measurements versus their dense counterparts

Estimated generic prices for novel treatments for drug resistant tuberculosis

Background: Estimated annual incidence of MDR-TB is 480,000, representing 5% of TB incidence, but 20% of mortality. Multiple drugs have recently been developed or re-purposed for the treatment of MDR-TB. Currently, treatment for MDR-TB costs thousands of dollars per course. Objectives: To estimate generic prices for novel TB drugs that would be possible given large-scale competitive manufacture. Methods: Prices for linezolid, moxifloxacin, and clofazimine were estimated based on per-kilogram prices of active pharmaceutical ingredient (API). Other costs were added, including formulation, packaging and a profit margin. The costs of projection for sutezolid were estimated to be equivalent to those for linezolid, based on chemical similarit y. Generic prices for bedaquiline, delamanid, and pretomanid were estimated by assessing routes of synthesis, costs/kg of chemical reagents, routes of synthesis, and per-step yields. Costing algorithms reflected variable regulatory requirements, efficiency of scale based on demand, and were validated by testing predictive ability against widely-available TB medicines. Results: Estimated generic prices were USD $8-$17/month for bedaquiline, $5-$16/month for delamanid, $11-$3 /month for pretomanid, $4-$9/month for linezolid, $4-$9/month for sutezolid, $4-$11/month for clofazimine, and $4-$8/month for moxifloxacin. Estimated generic prices were 87%-94% lower than current lowest available prices for bedaquiline, 95%-98% for delamanid, 94%-97% for linezolid. Estimated generic prices were $168-$395 per course for the STREAM trial modified Bangladesh regimens (current cost s $734-$1,799), $53-$276 for pretomanid-based three-drug regimens, and $238-$507 for a delamanid-based four-drug regimen. Conclusions: Competitive large-scale generic manufacture could allow supplies of treatment for 5-10 times more MDR-TB cases within current procurement budgets

Temozolomide is additive with cytotoxic effect of irradiation in canine glioma cell lines

Background: Similar to human glioblastoma patients, glial tumours in dogs have high treatment resistance and a guarded prognosis. In human medicine, the addition of temozolomide to radiotherapy leads to a favourable outcome in vivo as well as a higher antiproliferative effect on tumour cells in vitro. Objectives: The aim of the study was to determine the radio- and temozolomide-sensitivity of three canine glial tumour cell lines and to investigate a potential additive cytotoxic effect in combined treatment. Additionally, we wanted to detect the level of MGMT promoter methylation in these cell lines and to investigate a potential association between MGMT promoter methylation and treatment resistance. Methods: Cells were treated with various concentrations of temozolomide and/or irradiated with 4 and 8 Gy. Radiosensitization by temozolomide was evaluated using proliferation assay and clonogenic assay, and MGMT DNA methylation was investigated using bisulfite next-generation sequencing. Results: In all tested canine cell lines, clonogenicity was inhibited significantly in combined treatment compared to radiation alone. All canine glial cell lines tested in this study were found to have high methylation levels of MGMT promoter. Conclusions: Hence, an additive effect of combined treatment in MGMT negative canine glial tumour cell lines in vitro was detected. This motivates to further investigate the association between treatment resistance and MGMT, such as MGMT promoter methylation status