Additional file 2: of The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover

gt1-dx. This file is an executable version of our simulation interface program, which has been tested under the platform of MS-Windows XP and MS-Windows 7.0. (EXE 3434 kb

Additional file 1: Figs-S1-S4. of The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover

This file includes four supporting figures for the paper, Figs. S1-S4, which have been cited correspondingly in the text. (PDF 471 kb

Production of Formamides from CO and Amines Induced by Porphyrin Rhodium(II) Metalloradical

It is of fundamental importance to transform carbon monoxide (CO) to petrochemical feedstocks and fine chemicals. Many strategies built on the activation of CO bond by π-back bonding from the transition metal center were developed during the past decades. Herein, a new CO activation method, in which the CO was converted to the active acyl-like metalloradical, [(por)­Rh­(CO)]^• (por = porphyrin), was reported. The reactivity of [(por)­Rh­(CO)]^• and other rhodium porphyrin compounds, such as (por)­RhCHO and (por)­RhC­(O)­NH^<i>n</i>Pr, and corresponding mechanism studies were conducted experimentally and computationally and inspired the design of a new conversion system featuring 100% atom economy that promotes carbonylation of amines to formamides using porphyrin rhodium­(II) metalloradical. Following this radical based pathway, the carbonylations of a series of primary and secondary aliphatic amines were examined, and turnover numbers up to 224 were obtained

Clinically Approved Ferric Maltol: A Potent Nanozyme with Added Effect for High-Efficient Catalytic Disinfection

Nanozyme has been proven to be an attractive and promising candidate to alleviate the current pressing medical problems. However, the unknown clinical safety and limited function beyond the catalysis of the most reported nanozymes cannot promise an ideal therapeutic outcome in further clinical application. Herein, we find that ferric maltol (FM), a clinically approved iron supplement synthesized through a facile scalable method, exhibits excellent peroxidase-like activity than natural horseradish peroxidase-like (HRP) and commonly reported Fe-based nanozymes, and also shows high antibacterial performance for methicillin-resistant Staphylococcus aureus (MRSA) elimination (100%) and wound disinfection. In addition, with added effects inherited from contained maltol, FM can accelerate skin barrier recovery. Therefore, the exploration of FM as a safe and desired nanozyme provides a timely alternative to current antibiotic therapy against drug-resistant bacteria

Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world

<div><p>The idea that life may have started with an “RNA world” is attractive. Wherein, a crucial event (perhaps at the very beginning of the scenario) should have been the emergence of a ribozyme that catalyzes its own replication, i.e., an RNA replicase. Although now there is experimental evidence supporting the chemical feasibility of such a ribozyme, the evolutionary dynamics of how the replicase could overcome the “parasite” problem (because other RNAs may also exploit this ribozyme) and thrive, as described in the scenario, remains unclear. It has been suggested that spatial limitation may have been important for the replicase to confront parasites. However, more studies showed that such a mechanism is not sufficient when this ribozyme’s altruistic trait is taken into full consideration. “Tag mechanism”, which means labeling the replicase with a short subsequence for recognition in replication, may be a further mechanism supporting the thriving of the replicase. However, because parasites may also “equip” themselves with the tag, it is far from clear whether the tag mechanism could take effect. Here, we conducted a computer simulation using a Monte-Carlo model to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world. We concluded that (1) with the tag mechanism the replicase could resist the parasites and become prosperous, (2) the main underlying reason should be that the parasitic molecules, especially those strong parasites, are more difficult to appear in the tag-driven system, and (3) the tag mechanism has a synergic effect with the spatial limitation mechanism–while the former provides “time” for the replicase to escape from parasites, the latter provides “space” for the replicase to escape. Notably, tags may readily serve as “control handles”, and once the tag mechanism was exploited, the evolution towards complex life may have been much easier.</p></div

Statistical parameters of each chronology.

<p>MS, mean sensitivity; R, inter-series correlation; SNR, signal to noise ratio; EPS, the expressed population signal; the R, SNR and EPS were all calculated for the common period, 1978–2007. P1, P2, P3, P4, the chronologies of <i>P. meyeri</i> in the lowest, the lower, the higher and the highest sites, respectively; L1, L2, L3, L4, the chronologies of <i>L. principis-rupprechtii</i> in the lowest, the lower, the higher and the highest sites, respectively.</p><p>Statistical parameters of each chronology.</p

Geographic location and forest stand characteristics of the sampling sites.

a,b<p>Data are presented as mean ± SE.</p><p>Geographic location and forest stand characteristics of the sampling sites.</p

Pearson’s correlation coefficients between each pair of chronologies.

<p>* and ** indicate the significant levels of 0.05 and 0.01, respectively; P1, P2, P3, P4, represent the chronologies of <i>P. meyeri</i> in the lowest, the lower, the higher and the highest sites, respectively; L1, L2, L3, L4 represent the chronologies of <i>L. principis-rupprechtii</i> in the lowest, the lower, the higher and the highest sites, respectively; the correlations are based on the common period 1978–2007.</p><p>Pearson’s correlation coefficients between each pair of chronologies.</p

Location and climate survey of the study area.

<p>Location and climate survey of the study area.</p

Using Defect Control To Break the Stability–Activity Trade-Off in Enzyme Immobilization via Competitive Coordination

Immobilization of enzymes within metal–organic frameworks is a powerful strategy to enhance the long-term usability of labile enzymes. However, the thus-confined enzymes suffer from the trade-off between enhanced stability and reduced activity because of the contradiction between the high crystallinity and the low accessibility. Here, by taking laccase and zeolitic imidazolate framework-8 (ZIF-8) as prototypes, we disclosed an observation that the stability–activity trade-off could be solved by controlling the defects via competitive coordination. Owing to the presence of competitive coordination between laccase and the ligand precursor of ZIF-8, there existed a three-stage process in the de novo encapsulation: nucleation–crystallization–recrystallization. Our results show that the biocomposites collected before the occurrence of recrystallization possessed both increased activity and enhanced stability. The findings here shed new light on the control of defects through the subtle use of competitive coordination, which is of great significance for the engineering application of biomacromolecules