Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves

Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems

New Solutions of the Inflationary Flow Equations

The inflationary flow equations are a frequently used method of surveying the space of inflationary models. In these applications the infinite hierarchy of differential equations is truncated in a way which has been shown to be equivalent to restricting the set of models considered to those characterized by polynomial inflaton potentials. This paper explores a different method of solving the flow equations, which does not truncate the hierarchy and in consequence covers a much wider class of models while retaining the practical usability of the standard approach.Comment: References added, and a couple of comment

A Hamilton-Jacobi approach to non-slow-roll inflation

I describe a general approach to characterizing cosmological inflation outside the standard slow-roll approximation, based on the Hamilton-Jacobi formulation of scalar field dynamics. The basic idea is to view the equation of state of the scalar field matter as the fundamental dynamical variable, as opposed to the field value or the expansion rate. I discuss how to formulate the equations of motion for scalar and tensor fluctuations in situations where the assumption of slow roll is not valid. I apply the general results to the simple case of inflation from an ``inverted'' polynomial potential, and to the more complicated case of hybrid inflation.Comment: 21 pages, RevTeX (minor revisions to match published version

The Influence of Neuromusculoskeletal Model Calibration Method on Predicted Knee Contact Forces during Walking

This study explored the influence of three model calibration methods on predicted knee contact and leg muscle forces during walking. Static optimization was used to calculate muscle activations for all three methods. Approach A used muscle-tendon model parameter values (i.e., optimal muscle fiber lengths and tendon slack lengths) taken directly from literature. Approach B used a simple algorithm to calibrate muscle-tendon model parameter values such that each muscle operated within the ascending region of its normalized force-length curve. Approach C used a novel two-level optimization procedure to calibrate muscle-tendon, moment arm, and neural control model parameter values while simultaneously predicting muscle activations

The Emergence of the Modern Universe: Tracing the Cosmic Web

This is the report of the Ultraviolet-Optical Working Group (UVOWG) commissioned by NASA to study the scientific rationale for new missions in ultraviolet/optical space astronomy approximately ten years from now, when the Hubble Space Telescope (HST) is de-orbited. The UVOWG focused on a scientific theme, The Emergence of the Modern Universe, the period from redshifts z = 3 to 0, occupying over 80% of cosmic time and beginning after the first galaxies, quasars, and stars emerged into their present form. We considered high-throughput UV spectroscopy (10-50x throughput of HST/COS) and wide-field optical imaging (at least 10 arcmin square). The exciting science to be addressed in the post-HST era includes studies of dark matter and baryons, the origin and evolution of the elements, and the major construction phase of galaxies and quasars. Key unanswered questions include: Where is the rest of the unseen universe? What is the interplay of the dark and luminous universe? How did the IGM collapse to form the galaxies and clusters? When were galaxies, clusters, and stellar populations assembled into their current form? What is the history of star formation and chemical evolution? Are massive black holes a natural part of most galaxies? A large-aperture UV/O telescope in space (ST-2010) will provide a major facility in the 21st century for solving these scientific problems. The UVOWG recommends that the first mission be a 4m aperture, SIRTF-class mission that focuses on UV spectroscopy and wide-field imaging. In the coming decade, NASA should investigate the feasibility of an 8m telescope, by 2010, with deployable optics similar to NGST. No high-throughput UV/Optical mission will be possible without significant NASA investments in technology, including UV detectors, gratings, mirrors, and imagers.Comment: Report of UV/O Working Group to NASA, 72 pages, 13 figures, Full document with postscript figures available at http://casa.colorado.edu/~uvconf/UVOWG.htm