Observation of single top quark production and measurement of |Vtb| with CDF

We report the observation of electroweak single top quark production in 3.2 fb-1 of ppbar collision data collected by the Collider Detector at Fermilab at sqrt{s}=1.96 TeV. Candidate events in the W+jets topology with a leptonically decaying W boson are classified as signal-like by four parallel analyses based on likelihood functions, matrix elements, neural networks, and boosted decision trees. These results are combined using a super discriminant analysis based on genetically evolved neural networks in order to improve the sensitivity. This combined result is further combined with that of a search for a single top quark signal in an orthogonal sample of events with missing transverse energy plus jets and no charged lepton. We observe a signal consistent with the standard model prediction but inconsistent with the background-only model by 5.0 standard deviations, with a median expected sensitivity in excess of 5.9 standard deviations. We measure a production cross section of 2.3+0.6-0.5(stat+sys) pb, extract the CKM matrix element value |Vtb|=0.91+0.11-0.11 (stat+sys)+-0.07(theory), and set a lower limit |Vtb|>0.71 at the 95% confidence level, assuming m_t=175 GeVc^2.

Measurement of the Single-Top-Quark Production Cross Section at CDF

We report a measurement of the single top quark production cross section in 2.2 ~fb-1 of p-pbar collision data collected by the Collider Detector at Fermilab at sqrt{s}=1.96 TeV. Candidate events are classified as signal-like by three parallel analyses which use likelihood, matrix element, and neural network discriminants. These results are combined in order to improve the sensitivity. We observe a signal consistent with the standard model prediction, but inconsistent with the background-only model by 3.7 standard deviations with a median expected sensitivity of 4.9 standard deviations. We measure a cross section of 2.2 +0.7 -0.6(stat+sys) pb, extract the CKM matrix element value |V_{tb}|=0.88 +0.13 -0.12 (stat+sys) +- 0.07(theory), and set the limit |V_{tb}|>0.66 at the 95% C.L.

Observation of Electroweak Single Top-Quark Production

We report the first observation of single top quark production using 3.2 fb^-1 of pbar p collision data with sqrt{s}=1.96 TeV collected by the Collider Detector at Fermilab. The significance of the observed data is 5.0 standard deviations, and the expected sensitivity for standard model production and decay is in excess of 5.9 standard deviations. Assuming m_t=175 GeV/c^2, we measure a cross section of 2.3 +0.6 -0.5 (stat+syst) pb, extract the CKM matrix element value |V_{tb}|=0.91 +-0.11 (stat+syst) 0.07(theory), and set the limit |V_{tb}|>0.71 at the 95% C.L.

Optical Tweezers for Single Molecule Biology

Molecular machinery on the micro-scale, believed to be the fundamental building blocks of life, involve forces of 1-100 pN and movements of nanometers to micrometers. Micromechanical single-molecule experiments seek to understand the physics of nucleic acids, molecular motors, and other biological systems through direct measurement of forces and displacements. Optical tweezers are a popular choice among several complementary techniques for sensitive force-spectroscopy in the field of single molecule biology. The main objective of this thesis was to design and construct an optical tweezers instrument capable of investigating the physics of molecular motors and mechanisms of protein/nucleic-acid interactions on the single-molecule level. A double-trap optical tweezers instrument incorporating acousto-optic trap-steering, two independent detection channels, and a real-time digital controller was built. A numerical simulation and a theoretical study was performed to assess the signal-to-noise ratio in a constant-force molecular motor stepping experiment. Real-time feedback control of optical tweezers was explored in three studies. Position-clamping was implemented and compared to theoretical models using both proportional and predictive control. A force-clamp was implemented and tested with a DNA-tether in presence of the enzyme lambda exonuclease. The results of the study indicate that the presented models describing signal-to-noise ratio in constant-force experiments and feedback control experiments in optical tweezers agree well with experimental data. The effective trap stiffness can be increased by an order of magnitude using the presented position-clamping method. The force-clamp can be used for constant-force experiments, and the results from a proof-of-principle experiment, in which the enzyme lambda exonuclease converts double-stranded DNA to single-stranded DNA, agree with previous research. The main objective of the thesis was thus achieved. The developed instrument and presented results on feedback control serve as a stepping stone for future contributions to the growing field of single molecule biology.

Moonlighting Proteins of Lactobacillus crispatus : Extracellular Localization, Cell Wall Anchoring and Interactions with the Host

Moonlighting functions have been described for several proteins previously thought to localize exclusively in the cytoplasm of bacterial or eukaryotic cells. Moonlighting proteins usually perform conserved functions, e. g. in glycolysis or as chaperonins, and their traditional and moonlighting function(s) usually localize to different cell compartments. The most characterized moonlighting proteins in Grampositive bacteria are the glycolytic enzymes enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which function in bacteria-host interactions, e. g. as adhesins or plasminogen receptors. Research on bacterial moonlighting proteins has focused on Gram-positive bacterial pathogens, where many of their functions have been associated with bacterial virulence. In this thesis work I show that also species of the genus Lactobacillus have moonlighting proteins that carry out functions earlier associated with bacterial virulence only. I identified enolase, GAPDH, glutamine synthetase (GS), and glucose-6-phosphate isomerase (GPI) as moonlighting proteins of Lactobacillus crispatus strain ST1 and demonstrated that they are associated with cell surface and easily released from the cell surface into incubation buffer. I also showed that these lactobacillar proteins moonlight either as adhesins with affinity for basement membrane and extracellular matrix proteins or as plasminogen receptors. The mechanisms of surface translocation and anchoring of bacterial moonlighting proteins have remained enigmatic. In this work, the surface localization of enolase, GAPDH, GS and GPI was shown to depend on environmental factors. The members of the genus Lactobacillus are fermentative organisms that lower the ambient pH by producing lactic acid. At acidic pH enolase, GAPDH, GS and GPI were associated with the cell surface, whereas at neutral pH they were released into the buffer. The release did not involve de novo protein synthesis. I showed that purified recombinant His6-enolase, His6-GAPDH, His6-GS and His6-GPI reassociate with cell wall and bind in vitro to lipoteichoic acids at acidic pH. The in-vitro binding of these proteins localizes to cell division septa and cell poles. I also show that the release of moonlighting proteins is enhanced in the presence of cathelicidin LL- 37, which is an antimicrobial peptide and a central part of the innate immunity defence. I found that the LL-37-induced detachment of moonlighting proteins from cell surface is associated with cell wall permeabilization by LL-37. The results in this thesis work are compatible with the hypothesis that the moonlighting proteins of L. crispatus associate to the cell wall via electrostatic or ionic interactions and that they are released into surroundings in stress conditions. Their surface translocation is, at least in part, a result from their release from dead or permeabilized cells and subsequent reassociation onto the cell wall. The results of this thesis show that lactobacillar cells rapidly change their surface architecture in response to environmental factors and that these changes influence bacterial interactions with the host.