Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

Comparative genomics has proven a fruitful approach to acquire many functional and evolutionary insights into core cellular processes. Here it is argued that in order to perform accurate and interesting comparative genomics, one first and foremost has to be able to recognize, postulate, and revise different evolutionary scenarios. After all, these studies lack a simple protocol, due to different proteins having different evolutionary dynamics and demanding different approaches. The authors here discuss this challenge from a practical (what are the observations?) and conceptual (how do these indicate a specific evolutionary scenario?) viewpoint, with the aim to guide investigators who want to analyze the evolution of their protein(s) of interest. By sharing how the authors draft, test, and update such a scenario and how it directs their investigations, the authors hope to illuminate how to execute molecular evolution studies and how to interpret them. Also see the video abstract here https://youtu.be/VCt3l2pbdbQ

EFFECT OF AMYLOID FIBRILS ON ELECTROKINETIC PROPERTIES OF LIPID VESICLES

The influence of the lysozyme and serum albumin in their native and amyloid forms on the electrokinetic behavior of the negatively charged uni- and multilamellar liposomes from the zwitterionic lipid phosphatidylcholine and anionic lipid cardiolipin has been investigated using the microelectrophoresis technique. The zeta - potential, the surface electrostatic potential and surface charge density of the lipid vesicles have been determined upon varying the lipid-to-protein molar ratio. The complex dependencies of the electrophoretic mobility on the protein concentration and reversal of the surface charge observed for the multilamellar vesicles have been explained by the multilayer protein adsorption on the liposomal surface. It has been found that the native and fibrillar proteins differ in their ability to modify the charge state of the model membranes

Towards better understanding of C60 organosols

It is of common knowledge that fullerenes form colloids in polar solvents. However, the coagulation via electrolytes and the origin of the negative charge of species are still unexplored. Using a ‘radical scavenger’ and electrospray ionization spectroscopy (ESI), we proved the formation of ion-radical C60˙− and its (probable) transformation into C602− or (C60)22−. The coagulation of C60 organosols by NaClO4 and other perchlorates and nitrates in acetonitrile and its mixture with benzene obeys the Schulze–Hardy rule. At higher Ca(ClO4)2 and La(ClO4)3 concentrations, instead of coagulation, stable re-charged colloidal particles appeared, up to a zeta-potential of +(20–42) mV, as compared with −(33–35) mV of the initial organosols. The influence of both HClO4 and CF3SO3H was similar. This phenomenon is attributed to poor solvation of inorganic cations in cationo- and protophobic acetonitrile, which was proven using [2.2.2] cryptand. Further increasing the concentration of Ca(ClO4)2 led again to coagulation, thus demonstrating a novel type of ‘coagulation zones’