Synthesis of Phosphorothioate Oligonucleotides with Stereodefined Phosphorothioate Linkages

A method for solid‐phase synthesis of stereodefined PS‐oligos via an oxathiaphospholane approach using pure P‐diastereomers of nucleoside oxathiaphospholane monomers is described. The oxathiaphospholane monomers are synthesized by phosphitylation of 5′‐O‐DMTr‐N‐protected deoxyribonucleosides with 2‐chloro‐spiro‐4,4‐pentamethylene‐1,3,2‐oxathiaphospholane followed by sulfurization. The procedure is general and may be applied to other analogs, depending on the aldehyde (or mercaptoalcohol) used. Starting from an 18O‐labeled mercaptoalcohol, the corresponding 18O‐labeled phosphitylating reagent and nucleoside monomers can be obtained and used for synthesis of labeled stereodefined PS‐oligos, which are useful for studying mechanisms of enzymatic reactions. Details are provided for chromatographic separation of the 5′‐O‐DMTr‐N‐protected‐deoxyribonucleoside‐3′‐O‐(2‐thio‐spiro‐4,4‐pentamethylene‐1,3,2‐oxathiaphospholane)s into their P‐diastereomers, and for manual solid‐phase synthesis of PS‐oligos. Oxidation of 5′‐O‐DMTr‐N‐protected‐deoxyribonucleoside‐3′‐O‐(2‐thio‐spiro‐4,4‐pentamethylene‐1,3,2‐oxathiaphospholane)s with selenium dioxide yields their 2‐oxo‐analogs, which are suitable either for elongation of stereodefined PS‐oligos with segments consisting of unmodified nucleotide units possessing phosphate internucleotide linkages, or for generating isotopomeric 18O‐labeled PO‐oligos of predetermined P‐chirality.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143684/1/cpnc0417.pd

Optimal time-critical scheduling via resource augmentation

We consider two fundamental problems in dynamic scheduling: scheduling to meet deadlines in a preemptive multiprocessor setting, and scheduling to provide good response time in a number of scheduling environments. When viewed from the perspective of traditional worst-case analysis, no good on-line algorithms exist for these problems, and for some variants no good off-line algorithms exist unless {Rho} = {Nu}{Rho}. We study these problems using a relaxed notion of competitive analysis, introduced by Kalyanasundaram and Pruhs, in which the on-line algorithm is allowed more resources than the optimal off-line algorithm to which it is compared. Using this approach, we establish that several well-known on-line algorithms, that have poor performance from an absolute worst-case perspective, are optimal for the problems in question when allowed moderately more resources. For the optimization of average flow time, these are the first results of any sort, for any {Nu}{Rho}-hard version of the problem, that indicate that it might be possible to design good approximation algorithms

Is bicarbonate in Photosystem II the equivalent of the glutamate ligand to the iron atom in bacterial reaction centers?

Photosystem II of oxygen-evolving organisms exhibits a bicarbonate-reversible formate effect on electron transfer between the primary and secondary acceptor quinones, QA and QB. This effect is absent in the otherwise similar electron acceptor complex of purple bacteria, e.g. Rhodobacter sphaeroides. This distinction has led to the suggestion that the iron atom of the acceptor quinone complex in PS II might lack the fifth and sixth ligands provided in the bacterial reaction center (RC) by a glutamate residue at position 234 of the M-subunit in Rb. sphaeroides,RCs (M232 in Rps. viridis). By site-directed mutagenesis we have altered GluM234 in RCs from Rb. sphaeroides, replacing it with valine, glutamine and glycine to form mutants M234EV, M234EQ and M234EG, respectively. These mutants grew competently under phototrophic conditions and were tested for the formate-bicarbonate effect. In chromatophores there were no detectable differences between wild type (Wt) and mutant M234EV with respect to cytochrome b-561 reduction following a flash, and no effect of bicarbonate depletion (by incubation with formate). In isolated RCs, several electron transfer activities were essentially unchanged in Wt and M234EV, M234EQ and M234EG mutants, and no formate-bicarbonate effect was observed on: (a) the fast or slow phases of recovery of the oxidized primary donor (P+) in the absence of exogenous donor, i.e., the recombination of P+QA− or P+QB−, respectively; (b) the kinetics of electron transfer from QA− to QB; or (c) the flash dependent oscillations of semiquinone formation in the presence of donor to P+ (QB turnover). The absence of a formate-bicarbonate effect in these mutants suggests that GluM234 is not responsible for the absence of the formate-bicarbonate effect in Wt bacterial RCs, or at least that other factors must be taken into account. The mutant RCs were also examined for the fast primary electron transfer along the active (A-)branch of the pigment chain, leading to reduction of QA. The kinetics were resolved to reveal the reduction of the monomer bacteriochlorophyll (τ = 3.5 ps), followed by reduction of the bacteriopheophytin (τ = 0.9 ps). Both steps were essentially unaltered from the wild type. However, the rate of reduction of QA was slowed by a factor of 2 (τ = 410 ± 30 and 47 ± 30 ps for M234EQ and M234EV, respectively, compared to 220 ps in the wild type). EPR studies of the isolated RCs showed a characteristic g = 1.82 signal for the QA semiquinone coupled to the iron atom, which was indistinguishable from the wild type. It is concluded that GluM234 is not essential to the normal functioning of the acceptor quinone complex in bacterial RCs and that the role of bicarbonate in PS II is distinct from the role of this residue in bacterial RCs

Blinatumomab compared with standard of care for the treatment of adult patients with relapsed/refractory Philadelphia chromosome–positive B-precursor acute lymphoblastic leukemia

Background: A single-arm, phase 2 trial demonstrated the efficacy and safety of blinatumomab, a bispecific T-cell\u2013engaging antibody construct, in patients with relapsed/refractory (r/r) Philadelphia chromosome\u2013positive (Ph+) acute lymphoblastic leukemia (ALL), a rare hematologic malignancy with limited treatment options. This study compared outcomes with blinatumomab with those of a historical control treated with the standard of care (SOC). Methods: The blinatumomab trial enrolled adult patients with Ph+ ALL who were r/r to at least 1 second-generation tyrosine kinase inhibitor (n = 45). Propensity score analysis (PSA) was used to compare outcomes with blinatumomab with those of an external cohort of similar patients receiving SOC chemotherapy (n = 55). The PSA mitigated confounding variables between studies by adjusting for imbalances in the age at diagnosis and start of treatment, sex, duration from diagnosis to most recent treatment, prior allogeneic hematopoietic stem cell transplantation, prior salvage therapy, and number of salvage therapies. Bayesian data augmentation was applied to improve power to 80% with data from a phase 3 blinatumomab study in r/r Philadelphia chromosome\u2013negative ALL. Results: In the PSA, the rate of complete remission or complete remission with partial hematologic recovery was 36% for blinatumomab and 25% for SOC, and this resulted in an odds ratio of 1.54 (95% confidence interval [CI], 0.61-3.89) or 1.70 (95% credible interval [CrI], 0.94-2.94) with Bayesian data augmentation. Overall survival favored blinatumomab over SOC, with a hazard ratio of 0.81 (95% CI, 0.57-1.14) or 0.77 (95% CrI, 0.61-0.96) with Bayesian data augmentation. Conclusions: These results further support blinatumomab as a treatment option for patients with r/r Ph+ ALL

Tumor stroma-derived TGF-beta limits Myc-driven lymphomagenesis via Suv39h1-dependent senescence

Activated RAS/BRAF oncogenes induce cellular senescence as a tumor-suppressive barrier in early cancer development, at least in part, via an oncogene-evoked DNA damage response (DDR). In contrast, Myc activation-although producing a DDR as well-is known to primarily elicit an apoptotic countermeasure. Using the Emu-myc transgenic mouse lymphoma model, we show here in vivo that apoptotic lymphoma cells activate macrophages to secrete transforming growth factor beta (TGF-beta) as a critical non-cell-autonomous inducer of cellular senescence. Accordingly, neutralization of TGF-beta action, like genetic inactivation of the senescence-related histone methyltransferase Suv39h1, significantly accelerates Myc-driven tumor development via cancellation of cellular senescence. These findings, recapitulated in human aggressive B cell lymphomas, demonstrate that tumor-prompted stroma-derived signals may limit tumorigenesis by feedback senescence induction

Presupernova Structure of Massive Stars

Issues concerning the structure and evolution of core collapse progenitor stars are discussed with an emphasis on interior evolution. We describe a program designed to investigate the transport and mixing processes associated with stellar turbulence, arguably the greatest source of uncertainty in progenitor structure, besides mass loss, at the time of core collapse. An effort to use precision observations of stellar parameters to constrain theoretical modeling is also described.Comment: Proceedings for invited talk at High Energy Density Laboratory Astrophysics conference, Caltech, March 2010. Special issue of Astrophysics and Space Science, submitted for peer review: 7 pages, 3 figure

The convective Urca process

One possible fate of an accreting white dwarf is explosion in a type Ia supernova. However, the route to the thermonuclear runaway has always been uncertain owing to the lack of a convective model consistent with the Urca process. We derive a formalism for convective motions involving two radial flows. This formalism provides a framework for convective models that guarantees self-consistency for chemistry and energy budget, allows time-dependence and describes the interaction of convective motions with the global contraction or expansion of the star. In the one-stream limit, we reproduce several already existing convective models and allow them to treat chemistry. We also suggest as a model easy to implement in a stellar evolution code. We apply this formalism to convective Urca cores in Chandrasekhar mass white dwarfs. We stress that in degenerate matter, nuclear reactions that change the number of electrons strongly influence the convective velocities. We point out the sensitivity of the energy budget on the mixing. We illustrate our model by computing {\it stationary} convective cores with Urca nuclei. We show that even a very small mass fraction of Urca nuclei ($10^{-8}$) strongly influences the convective velocities. Finally, we present preliminary computations of the late evolution of a close to Chandrasekhar mass C+O white dwarf including the convective Urca process.Comment: 4 pages, 1 figure, to appear in the 8th Nuclei In Cosmos conference proceeding

The formation and evolution of bright spots on Ceres

The otherwise homogeneous surface of Ceres is dotted with hundreds of anomalously bright, predominantly carbonate-bearing areas, termed "faculae," with Bond albedos ranging from ∼0.02 to >0.5. Here, we classify and map faculae globally to characterize their geological setting, assess potential mechanisms for their formation and destruction, and gain insight into the processes affecting the Ceres surface and near-surface. Faculae were found to occur in four distinct geological settings, associated predominantly with impact craters: (1) crater pits, peaks, or floor fractures (floor faculae), (2) crater rims or walls (rim/wall faculae), (3) bright ejecta blankets, and (4) the mountain Ahuna Mons. Floor faculae were identified in eight large, deep, and geologically young (asteroid-derived model (ADM) ages of <420 ± 60 Ma) craters: Occator, Haulani, Dantu, Ikapati, Urvara, Gaue, Ernutet, and Azacca. The geometry and geomorphic features of the eight craters with floor faculae are consistent with facula formation via impact-induced heating and upwelling of volatile-rich materials, upwelling/excavation of heterogeneously distributed subsurface brines or their precipitation products, or a combination of both processes. Rim/wall faculae and bright ejecta occur in and around hundreds of relatively young craters of all sizes, and the geometry of exposures is consistent with facula formation via the excavation of subsurface bright material, possibly from floor faculae that were previously emplaced and buried. A negative correlation between rim/wall facula albedo and crater age indicates that faculae darken over time. Models using the Ceres crater production function suggest initial production or exposure of faculae by large impacts, subsequent dissemination of facula materials to form additional small faculae, and then burial by impact-induced lateral mixing, which destroys faculae over timescales of less than 1.25 Gyr. Cumulatively, these models and the observation of faculae limited to geologically young craters indicate relatively modern formation or exposure of faculae, indicating that Ceres' surface remains active and that the near surface may support brines in the present day

A Centre-Stable Manifold for the Focussing Cubic NLS in R1+3R^{1+3}

Consider the focussing cubic nonlinear Schr\"odinger equation in $R^3$: $$i\psi_t+\Delta\psi = -|\psi|^2 \psi.$$ It admits special solutions of the form $e^{it\alpha}\phi$, where $\phi$ is a Schwartz function and a positive ($\phi>0$) solution of $$-\Delta \phi + \alpha\phi = \phi^3.$$ The space of all such solutions, together with those obtained from them by rescaling and applying phase and Galilean coordinate changes, called standing waves, is the eight-dimensional manifold that consists of functions of the form $e^{i(v \cdot + \Gamma)} \phi(\cdot - y, \alpha)$. We prove that any solution starting sufficiently close to a standing wave in the $\Sigma = W^{1, 2}(R^3) \cap |x|^{-1}L^2(R^3)$ norm and situated on a certain codimension-one local Lipschitz manifold exists globally in time and converges to a point on the manifold of standing waves. Furthermore, we show that \mc N is invariant under the Hamiltonian flow, locally in time, and is a centre-stable manifold in the sense of Bates, Jones. The proof is based on the modulation method introduced by Soffer and Weinstein for the $L^2$-subcritical case and adapted by Schlag to the $L^2$-supercritical case. An important part of the proof is the Keel-Tao endpoint Strichartz estimate in $R^3$ for the nonselfadjoint Schr\"odinger operator obtained by linearizing around a standing wave solution.Comment: 56 page