The Aharonov-Bohm (AB) effect is a purely quantum mechanical effect. The original (classified as Type-I) AB-phase shift exists in experimental conditions where the electromagnetic fields and forces are zero. It is the absence of forces that makes the ABeffect entirely quantum mechanical. Although the AB-phase shift has been demonstrated unambiguously, the absence of forces in Type-I AB-effects has never been shown. Here, we report the observation of the absence of time delays associated with forces of the magnitude needed to explain the AB-phase shift for a macroscopic system. In 1918, Weyl proposed a scaling of space-time in an attempt to combine electromagnetism and general relativity with what he coined a gauge theory [1]. Einstein subsequently pointed out that Weyl's space-time scaling led to contradictions [2]. Yang overcame Einstein's objections by modifying Weyl's idea to use a phase change instead of a gauge change [3]. Aharonov and Bohm (AB) proposed the use of magnetic flux enclosed in an electron interferometer to detect the phase shift [4]. Chambers, following the proposal, demonstrated the now famous AB-effect [5]. Later efforts [6-9] include Tonomura's

HighlightImage Harvest is an open-source software for high-throughput image processing and analysis that is integrated with the Open Science Grid and provides computational resources to process large image datasets.

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS.

The magnetic Aharonov-Bohm (A-B) effect occurs when a point charge interacts with a line of magnetic flux, while its reciprocal, the Aharonov-Casher (A-C) effect, occurs when a magnetic moment interacts with a line of charge. For the two interacting parts of these physical systems, the equations of motion are discussed in this paper. The generally accepted claim is that both parts of these systems do not accelerate, while Boyer has claimed that both parts of these systems do accelerate. Using the Euler-Lagrange equations we predict that in the case of unconstrained motion, only one part of each system accelerates, while momentum remains conserved. This prediction requires a time-dependent electromagnetic momentum. For our analysis of unconstrained motion, the A-B effects are then examples of the Feynman paradox. In the case of constrained motion, the Euler-Lagrange equations give no forces, in agreement with the generally accepted analysis. The quantum mechanical A-B and A-C phase shifts are independent of the treatment of constraint. Nevertheless, experimental testing of the above ideas and further understanding of the A-B effects that are central to both quantum mechanics and electromagnetism could be possible.

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in NM associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification than the conventional all-in-one search approach and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures.