Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes. CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution

Nanometer-Sized Electrochemical Sensors

Nanometer-sized glass-sealed metal ultramicroelectrodes (UMEs) have been prepared using a laser-based micropipet puller. The tip was exposed to solution either by etching away a small portion of glass insulator or by micropolishing. The characterization of the UMEs was carried out by a combination of steady-state voltammetry, scanning electron microscopy (SEM), and scanning electrochemical microscopy (SECM). The cyclic voltammograms obtained have a regular shape with very small capacitive and resistive background. The effective electrode radii obtained from voltammetry were between 2 and 500 nm. From the SEM micrographs, the shape of polished tips appears to be close to a microdisk, while the geometry of etched electrodes is closer to conical. Accordingly, the SECM current-distance curves (i T -d) obtained with polished electrodes fit well the theory for a disk-shaped tip, while a 20-nm-radius etched electrode was shown to be a fairly sharp cone with a height-to-radius ratio of about 2.5. The experimental data were compared to the theory developed for disk-shaped, conical, and recessed tips to demonstrate suitability of the produced electrodes for quantitative electrochemical experiments. The prospects of steady-state measurements of the rates of fast heterogeneous reactions are discussed. Submicrometer-sized ion selective electrodes (ISEs) were prepared by coating etched Ag tips with silver iodide. The concentration response of such ISEs remained stable and linear after coating of the ISEs with protective Nafion film. The introduction of micrometer-sized electrodes led to significant advances in studies of fast heterogeneous and homogeneous reactions, measurements in various microenvironments, and highresolution electrochemical imaging. 1 Even smaller, i.e., nanometer-sized, ultramicroelectrodes (UMEs) are required for characterization of the electrode/electrolyte interfacial processes with nanometer-scale resolution. 2 The initial stages of many important processes, such as metal corrosion and heterogeneous nucleation, include formation of nanometer-sized transient structures. 3 To probe such structures electrochemically, one needs a comparably sized electrode. Another important application of ultrasmall electrodes is single-molecule detection. 4 During the last several years, a few research groups have been exploring different methodologies of manufacturing nanometer-sized disks, bands, cones, and arrays of UMEs. [5][6][7][8][9][10] The main difficulty in using such electrodes for quantitative measurements is the shape uncertainty. In this paper, we develop procedures for easier preparation and better characterization of nanometer-sized electrochemical sensors. The voltammetric response of an UME does not provide sufficient information about the geometry of either the conductor exposed to electrolyte or the insulating sheath. The diffusion to a small electrode (hemisphere, cone, disk) rapidly becomes hemispherical when the electrode is in the bulk solution far from any object. 11 Thus, the shape of a reversible steady-state voltammogram is the same for any microelectrode geometry. In contrast, an irregularly shaped UME employed in kinetic measurements may result in highly erroneous values for rate constants extracted from experimental data. 12 Figure 1 presents several electrode shapes that can result from different preparation procedures. A perfect microdisk UME ( where c°is the bulk concentration of the mediator species, D is the diffusion coefficient, F is the Faraday constant, and n is the number of electrons transferred. Such electrodes have commonly been employed in both steady-state and non-steady-state measure

Structural correlations in heterogeneous electron transfer at monolayer and multilayer graphene electrodes

As a new form of carbon, graphene is attracting intense interest as an electrode material with widespread applications. In the present study, the heterogeneous electron transfer (ET) activity of graphene is investigated using scanning electrochemical cell microscopy (SECCM), which allows electrochemical currents to be mapped at high spatial resolution across a surface for correlation with the corresponding structure and properties of the graphene surface. We establish that the rate of heterogeneous ET at graphene increases systematically with the number of graphene layers, and show that the stacking in multilayers also has a subtle influence on ET kinetics. © 2012 American Chemical Society

Electrochemical Synthesis of Silver-Tetracyanoquinodimethane Nanorods at Agar Supported Water/1,2-Dichloroethane Interface

具有高导电性和独特电学性质的金属有机络合物AgTCNQ是一种重要的电荷转移盐.本文采用琼脂作为胶凝剂构成水|1,2-二氯乙烷液液界面；施加电压时银离子由水相穿过水凝胶进入有机相，与TCNQ-反应生成AgTCNQ纳米棒.结果表明液/液界面电化学方法为合成有机金属功能材料的有效途径.Silver-tetracyanoquinodimethane (AgTCNQ) is an important charge transfer salt due to its high conductivity and other electronic properties. In this communication, we report the synthesis of AgTCNQ at the liquid/liquid interface. Agar was used as a gelling agent to support water/1,2-dichloroethane (DCE) interface. Silver ions were transferred from the hydrogel into DCE phase, where they combined with TCNQ- to form AgTCNQ nanorods. The developed method can provide a new route for synthesis of functional materials based on the electrochemistry at the liquid/liquid interface.This work was supported by National Science Foundation of China (No. 20973142, No. 21061120456, and No. 21021002), National Basic Research Program of China (2011CB933700) and the National Science Foundation (CHE-1026582; MVM).This work was supported by National Science Foundation of China (No. 20973142, No. 21061120456, and No. 21021002), National Basic Research Program of China (2011CB933700) and the National Science Foundation (CHE-1026582; MVM).作者联系地址：1. 厦门大学化学化工学院化学系, 福建厦门361005; 2. 厦门大学固体表面物理化学国家重点实验室, 福建厦门361005; 3. 纽约市立大学皇后学院化学与生物化学系袁美国纽约11367Author's Address: 1. Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China; 2. State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, Fujian, China; 3. Department of Chemistry and Biochemistry, Queens College-CUNY, Flushing, New York 11367, USA通讯作者E-mail：[email protected]

Intrinsic electrochemical activity of single walled carbon nanotube–Nafion assemblies

The intrinsic electrochemical properties and activity of single walled carbon nanotube (SWNT) network electrodes modified by a drop-cast Nafion film have been determined using the one electron oxidation of ferrocene trimethyl ammonium (FcTMA+) as a model redox probe in the Nafion film. Facilitated by the very low transport coefficient of FcTMA+ in Nafion (apparent diffusion coefficient of 1.8 × 10−10 cm2 s−1), SWNTs in the 2-D network behave as individual elements, at short (practical) times, each with their own characteristic diffusion, independent of neighbouring sites, and the response is diagnostic of the proportion of SWNTs active in the composite. Data are analysed using candidate models for cases where: (i) electron transfer events only occur at discrete sites along the sidewall (with a defect density typical of chemical vapour deposition SWNTs); (ii) all of the SWNTs in a network are active. The first case predicts currents that are much smaller than seen experimentally, indicating that significant portions of SWNTs are active in the SWNT–Nafion composite. However, the predictions for a fully active SWNT result in higher currents than seen experimentally, indicating that a fraction of SWNTs are not connected and/or that not all SWNTs are wetted completely by the Nafion film to provide full access of the redox mediator to the SWNT surface

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

The authors propose that short repeat sequences may play an important role in causing the pervasive clustering of mutations across diverse genomes from prokaryotes to humans

Nanoelectrochemistry

This book provides an overview of nanoscale electrochemistry in the context of well-established concepts and principles of electrochemistry. It presents fundamental theory with the emphasis on differences between charge-transfer and mass-transfer processes on the nanoscale and analogous reactions occurring at macroscopic electrochemical interfaces. The rigorous theoretical treatment enables readers to gain an in-depth understanding of nanoelectrochemical systems discussed. The book also covers modern electrochemical tools and techniques that enable the fabrication and characterization of elec

Scanning electrochemical microscopy

x, 660 p. : ill. (some col.) ; 27 cm