Different evolutionary patterns between young duplicate genes in the human genome

BACKGROUND: Following gene duplication, two duplicate genes may experience relaxed functional constraints or acquire different mutations, and may also diverge in function. Whether the two copies will evolve in different patterns remains unclear, however, because previous studies have reached conflicting conclusions. In order to resolve this issue, by providing a general picture, we studied 250 independent pairs of young duplicate genes from the whole human genome. RESULTS: We showed that nearly 60% of the young duplicate gene pairs have evolved at the amino-acid level at significantly different rates from each other. More than 25% of these gene pairs also showed significantly different ratios of nonsynonymous to synonymous rates (K(a)/K(s )ratios). Moreover, duplicate pairs with different rates of amino-acid substitution also tend to differ in the K(a)/K(s )ratio, with the fast-evolving copy tending to have a slightly higher K(s )than the slow-evolving one. Lastly, a substantial portion of fast-evolving copies have accumulated amino-acid substitutions evenly across the protein sequences, whereas most of the slow-evolving copies exhibit uneven substitution patterns. CONCLUSIONS: Our results suggest that duplicate genes tend to evolve in different patterns following the duplication event. One copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence. Such different evolutionary patterns may be largely due to different functional constraints on the two copies

Label-free monitoring of plasmonic catalysis on the nanoscale

Plasmonics is the description of specific light matter interactions of metallic structures. In general the size of such structures is well in the nanometer regime and also determines such specific characteristics as color, field confinement etc. Plasmon-induced hot electrons play a vital role in so-called plasmonic catalysis, a field that has recently attracted attention as a new reaction platform. Current reports introduce such nanoscale catalysis as an effective approach to concentrate the energy of visible light and direct it to adsorbed molecules, thereby increasing the chemical reaction rate, and controlling the reaction selectivity. In this review, we present various plasmon-catalyzed reactions specifically monitored with Raman spectroscopy, namely surface-enhanced Raman scattering (SERS), remote SERS (Re-SERS) and tip-enhanced Raman scattering (TERS). These techniques utilize the signal enhancing effect of the metal nanoparticles. However, at the same time they can be used to control the actual reactivity. In the first part, the mechanism of plasmonic catalysis is introduced. Then it is shown how catalytic reactions can be spectroscopically investigated far beyond the diffraction limit using TERS. Finally, the sensitivity of the methods is discussed

Propagating Surface Plasmon Polaritons: Towards Applications for Remote-Excitation Surface Catalytic Reactions

Plasmonics is a well-established field, exploiting the interaction of light and metals at the nanoscale; with the help of surface plasmon polaritons, remote-excitation can also be observed by using silver or gold plasmonic waveguides. Recently, plasmonic catalysis was established as a new exciting platform for heterogeneous catalytic reactions. Recent reports present remote-excitation surface catalytic reactions as a route to enhance the rate of chemical reactions, and offer a pathway to control surface catalytic reactions. In this review, we focus on recent advanced reports on silver plasmonic waveguide for remote-excitation surface catalytic reactions. First, the synthesis methods and characterization techniques of sivelr nanowire plasmonic waveguides are summarized, and the properties and physical mechanisms of plasmonic waveguides are presented in detail. Then, the applications of plasmonic waveguides including remote excitation fluorescence and SERS are introduced, and we focus on the field of remote-excitation surface catalytic reactions. Finally, forecasts are made for possible future applications for the remote-excitation surface catalysis by plasmonic waveguides in living cells

Single molecule level plasmonic catalysis – a dilution study of p-nitrothiophenol on gold dimers

Surface plasmons on isolated gold dimers can initiate intermolecular reactions of adsorbed p-nitrothiophenol. At the single molecule level when dimerization is not possible an intramolecular reaction can be observed. Experimental evidence indicates that plasmon-induced hot electrons provide the required activation energy

Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts

<p>Abstract</p> <p>Background</p> <p>The filamentous fungus <it>Ashbya gossypii </it>grows into a multicellular mycelium that is distinct from the unicellular morphology of its closely related yeast species. It has been proposed that genes important for cell cycle regulation play central roles for such phenotypic differences. Because <it>A. gossypii </it>shares an almost identical set of cell cycle genes with the typical yeast <it>Saccharomyces cerevisiae</it>, the differences might occur at the level of orthologous gene regulation. Codon usage patterns were compared to identify orthologous genes with different gene regulation between <it>A. gossypii </it>and nine closely related yeast species.</p> <p>Results</p> <p>Here we identified 3,151 orthologous genes between <it>A. gossypii </it>and nine yeast species. Two groups of genes with significant differences in codon usage (gene translation efficiency) were identified between <it>A. gossypii </it>and yeasts. 333 genes (Group I) and 552 genes (Group II) have significantly higher translation efficiency in <it>A. gossypii </it>and yeasts, respectively. Functional enrichment and pathway analysis show that Group I genes are significantly enriched with cell cycle functions whereas Group II genes are biased toward metabolic functions.</p> <p>Conclusion</p> <p>Because translation efficiency of a gene is closely related to its functional importance, the observed functional distributions of orthologous genes with different translation efficiency might account for phenotypic differentiation between <it>A. gossypii </it>and yeast species. The results shed light on the mechanisms for pseudohyphal growth in pathogenic yeast species.</p

The immunomodulatory effect of IL-4 accelerates bone substitute material-mediated osteogenesis in aged rats via NLRP3 inflammasome inhibition

BackgroundBone defect repair by implanting bone substitute materials has been a common clinical treatment. With the understanding of substance–immune system interactions and increasing evidence indicating that the post-implantation immune response determines the fate of bone substitute materials, active modulation of host macrophage polarization is considered a promising strategy. However, whether the same regulatory effects exist when an individual immune system is altered with aging is unclear. MethodsIn this study, we mechanistically investigated the effect of immunosenescence on the active regulation of macrophage polarization by establishing a cranial bone defect model in young and aged rats implanted with Bio-Oss®. Forty-eight young and 48 aged specific pathogen-free (SPF) male SD rats were randomly divided into two groups. In the experimental group, 20 μL of IL-4 (0.5 μg/mL) was injected locally on the third to seventh postoperative days, while an equal volume of PBS was injected in the control group. Specimens were collected at 1, 2, 6, and 12 weeks postoperatively, and bone regeneration at the defect site was evaluated by micro-CT, histomorphometry, immunohistochemistry, double-labeling immunofluorescence, and RT–qPCR.ResultsThe application of exogenous IL-4 reduced activation of NLRP3 inflammasomes by promoting the polarization of M1 macrophages to M2 macrophages, thus promoting bone regeneration at the site of bone defects in aged rats. However, this effect was gradually weakened after the IL-4 intervention was discontinued.ConclusionOur data confirmed that a strategy to regulate macrophage polarization is also feasible under conditions of immunosenescence, i.e., the local inflammatory microenvironment can be regulated by reducing M1-type macrophages. However, further experiments are needed to determine an exogenous IL-4 intervention that can maintain a more sustained effect

A “built-up” composite film with synergistic functionalities on Mg–2Zn–1Mn bioresorbable stents improves corrosion control effects and biocompatibility

Control of premature corrosion of magnesium (Mg) alloy bioresorbable stents (BRS) is frequently achieved by the addition of rare earth elements. However, limited long-term experience with these elements causes concerns for clinical application and alternative methods of corrosion control are sought after. Herein, we report a “built-up” composite film consisting of a bottom layer of MgF2 conversion coating, a sandwich layer of a poly (1, 3-trimethylene carbonate) (PTMC) and 3-aminopropyl triethoxysilane (APTES) co-spray coating (PA) and on top a layer of poly (lactic-co-glycolic acid) (PLGA) ultrasonic spray coating to decorate the rare earth element-free Mg–2Zn–1Mn (ZM21) BRS for tailoring both corrosion resistance and biological functions. The developed “built-up” composite film shows synergistic functionalities, allowing the compression and expansion of the coated ZM21 BRS on an angioplasty balloon without cracking or peeling. Of special importance is that the synergistic corrosion control effects of the “built-up” composite film allow for maintaining the mechanical integrity of stents for up to 3 months, where complete biodegradation and no foreign matter residue were observed about half a year after implantation in rabbit iliac arteries. Moreover, the functionalized ZM21 BRS accomplished re-endothelialization within one month

Intention Understanding in Human-Robot Interaction Based on Visual-NLP Semantics

With the rapid development of robotic and AI technology in recent years, human-robot interaction has made great advancement, making practical social impact. Verbal commands are one of the most direct and frequently used means for human-robot interaction. Currently, such technology can enable robots to execute pre-defined tasks based on simple and direct and explicit language instructions, e.g., certain keywords must be used and detected. However, that is not the natural way for human to communicate. In this paper, we propose a novel task-based framework to enable the robot to comprehend human intentions using visual semantics information, such that the robot is able to satisfy human intentions based on natural language instructions (total three types, namely clear, vague, and feeling, are defined and tested). The proposed framework includes a language semantics module to extract the keywords despite the explicitly of the command instruction, a visual object recognition module to identify the objects in front of the robot, and a similarity computation algorithm to infer the intention based on the given task. The task is then translated into the commands for the robot accordingly. Experiments are performed and validated on a humanoid robot with a defined task: to pick the desired item out of multiple objects on the table, and hand over to one desired user out of multiple human participants. The results show that our algorithm can interact with different types of instructions, even with unseen sentence structures

Say What You Are Looking At: An Attention-Based Interactive System for Autistic Children

Gaze-following is an effective way for intention understanding in human–robot interaction, which aims to follow the gaze of humans to estimate what object is being observed. Most of the existing methods require people and objects to appear in the same image. Due to the limitation in the view of the camera, these methods are not applicable in practice. To address this problem, we propose a method of gaze following that utilizes a geometric map for better estimation. With the help of the map, this method is competitive for cross-frame estimation. On the basis of this method, we propose a novel gaze-based image caption system, which has been studied for the first time. Our experiments demonstrate that the system follows the gaze and describes objects accurately. We believe that this system is competent for autistic children’s rehabilitation training, pension service robots, and other applications.</jats:p