The Biogenesis of SRP RNA Is Modulated by an RNA Folding Intermediate Attained during Transcription.

The signal recognition particle (SRP), responsible for co-translational protein targeting and delivery to cellular membranes, depends on the native long-hairpin fold of its RNA to confer functionality. Since RNA initiates folding during its synthesis, we used high-resolution optical tweezers to follow in real time the co-transcriptional folding of SRP RNA. Surprisingly, SRP RNA folding is robust to transcription rate changes and the presence or absence of its 5'-precursor sequence. The folding pathway also reveals the obligatory attainment of a non-native hairpin intermediate (H1) that eventually rearranges into the native fold. Furthermore, H1 provides a structural platform alternative to the native fold for RNase P to bind and mature SRP RNA co-transcriptionally. Delays in attaining the final native fold are detrimental to the cell, altogether showing that a co-transcriptional folding pathway underpins the proper biogenesis of function-essential SRP RNA.

Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time.

DNA compaction is required for the condensation and resolution of chromosomes during mitosis, but the relative contribution of individual chromatin factors to this process is poorly understood. We developed a physiological, cell-free system using high-speed Xenopus egg extracts and optical tweezers to investigate real-time mitotic chromatin fiber formation and force-induced disassembly on single DNA molecules. Compared to interphase extract, which compacted DNA by ~60%, metaphase extract reduced DNA length by over 90%, reflecting differences in whole-chromosome morphology under these two conditions. Depletion of the core histone chaperone ASF1, which inhibits nucleosome assembly, decreased the final degree of metaphase fiber compaction by 29%, while depletion of linker histone H1 had a greater effect, reducing total compaction by 40%. Compared to controls, both depletions reduced the rate of compaction, led to more short periods of decompaction, and increased the speed of force-induced fiber disassembly. In contrast, depletion of condensin from metaphase extract strongly inhibited fiber assembly, resulting in transient compaction events that were rapidly reversed under high force. Altogether, these findings support a speculative model in which condensin plays the predominant role in mitotic DNA compaction, while core and linker histones act to reduce slippage during loop extrusion and modulate the degree of DNA compaction.

Transcriptome and metabolome analysis of stress tolerance to aluminium in Vitis quinquangularis.

MAIN CONCLUSION: Transcriptional and metabolic regulation of aluminium tolerance of Chinese wild Vitis quinquangularis after Al treatment for 12 h: genes and pathways related to stress resistance are activated to cope with Al stress. The phytotoxicity of aluminium (Al) has become a major issue in inhibiting plant growth in acidic soils. Chinese wild Vitis species have excellent stress resistance. In this study, to explore the mechanism underlying Al tolerance in Chinese wild Vitis quinquangularis, we conducted a transcriptome analysis to understand the changes in gene expression and pathways in V. quinquangularis leaves after Al treatment for 12 h (Al_12 h). Compared with the control (CK) treatment, 2266 upregulated differentially expressed genes (DEGs) and 2943 downregulated DEGs were identified after Al treatment. We analysed the top 60 upregulated DEGs and found that these genes were related mostly to cell wall organization or biogenesis, transition metal ion binding, etc. Another analysis of all the upregulated DEGs showed that genes related to the ABC transport pathway, salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) hormone signalling pathway were expressed. Transcriptome and metabolome analysis revealed that genes and metabolites (phenylalanine, cinnamate and quercetin) related to the phenylalanine metabolic pathway were expressed. In summary, the results provide a new contribution to a better understanding of the metabolic changes that occur in grapes after Al stress as well as to research on improving the resistance of grape cultivars.

Successive Storage of Cations and Anions by Ligands of π-d-Conjugated Coordination Polymers Enabling Robust Sodium-Ion Batteries.

The oxidation of π-d-conjugated coordination polymers (CCPs) accompanied with anion insertion has the merits of increasing the capacity and elevating the discharge voltages. However, previous reports on this mechanism either required more investigations or showed low capacity and poor cyclablity. Herein, triphenylene-catecholate-based two-dimensional CCPs are constructed by employing inactive transition-metal ions (Zn2+ ) as nodes, forming Zn-HHTP. Substantial characterizations and theoretical calculations indicate the successive storage of cations and anions by redox reactions of only ligands, leading to a high reversible capacity of ≈150 mAh g-1 at 100 mA g-1 and a remarkable capacity retention of 90 % after 1000 cycles. On the contrary, as a control experiment, the analogous CCPs (Cu-HHTP) with Cu2+ nodes, where both ligands and metal ions undergo redox reactions, accompanied by the storage of only Na+ cations, show a much poorer cyclability. These results highlight the importance of redox reactions of only ligands for long-term cycle life and the insight into the storage mechanisms deepens our understanding on CCPs for the further design of CCPs with high performance.

Regulating the Solvation Sheath of Li Ions by Using Hydrogen Bonds for Highly Stable Lithium-Metal Anodes.

The performance of Li anodes is extremely affected by the solvation of Li ions, leading to preferential reduction of the solvation sheath and subsequent formation of fragile solid-electrolyte interphase (SEI), Li dendrites, and low coulombic efficiency (CE). Herein, we propose a novel strategy to regulate the solvation sheath, through the introduction of intermolecular hydrogen bonds with both the anions of Li salt and the solvent by small amount additives. The addition of such hydrogen bonds reduced the LUMO energy level of anions in electrolyte, promoted the formation of a robust SEI, reduced the amount of free solvent molecules, and enhanced stability of electrolytes. Based on this strategy, flat and dense lithium deposition was obtained. Even under lean electrolytes, at a current density of 1 mA cm-2 with a fixed capacity of 3 mAh cm-2 , the Li-Cu cells showed an impressive CE value of 99.2 %. The Li-LiFePO4 full cells showed long-term cycling stability for more than 1000 cycles at 1 C, with a total capacity loss of only 15 mAh g-1 .

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold.

During cell division, chromosomes must be folded into their compact mitotic form to ensure their segregation. This process is thought to be largely controlled by the action of condensin SMC protein complexes on chromatin fibers. However, how condensins organize metaphase chromosomes is not understood. We have combined micromanipulation of single human mitotic chromosomes, sub-nanonewton force measurement, siRNA interference of condensin subunit expression, and fluorescence microscopy, to analyze the role of condensin in large-scale chromosome organization. Condensin depletion leads to a dramatic (~ 10-fold) reduction in chromosome elastic stiffness relative to the native, non-depleted case. We also find that prolonged metaphase stalling of cells leads to overloading of chromosomes with condensin, with abnormally high chromosome stiffness. These results demonstrate that condensin is a main element controlling the stiffness of mitotic chromosomes. Isolated, slightly stretched chromosomes display a discontinuous condensing staining pattern, suggesting that condensins organize mitotic chromosomes by forming isolated compaction centers that do not form a continuous scaffold.

The SMC1-SMC3 cohesin heterodimer structures DNA through supercoiling-dependent loop formation.

Cohesin plays a critical role in sister chromatid cohesion, double-stranded DNA break repair and regulation of gene expression. However, the mechanism of how cohesin directly interacts with DNA remains unclear. We report single-molecule experiments analyzing the interaction of the budding yeast cohesin Structural Maintenance of Chromosome (SMC)1-SMC3 heterodimer with naked double-helix DNA. The cohesin heterodimer is able to compact DNA molecules against applied forces of 0.45 pN, via a series of extension steps of a well-defined size ≈130 nm. This reaction does not require ATP, but is dependent on DNA supercoiling: DNA with positive torsional stress is compacted more quickly than negatively supercoiled or nicked DNAs. Un-nicked torsionally relaxed DNA is a poor substrate for the compaction reaction. Experiments with mutant proteins indicate that the dimerization hinge region is crucial to the folding reaction. We conclude that the SMC1-SMC3 heterodimer is able to restructure the DNA double helix into a series of loops, with a preference for positive writhe.

Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end.

Enzyme rates are usually considered to be dependent on local properties of the molecules involved in reactions. However, for large molecules, distant constraints might affect reaction rates by affecting dynamics leading to transition states. In single-molecule experiments we have found that enzymes that relax DNA torsional stress display rates that depend strongly on how the distant ends of the molecule are constrained; experiments with different-sized particles tethered to the end of 10-kb DNAs reveal enzyme rates inversely correlated with particle drag coefficients. This effect can be understood in terms of the coupling between molecule extension and local molecular stresses: The rate of bead thermal motion controls the rate at which transition states are visited in the middle of a long DNA. Importantly, we have also observed this effect for reactions on unsupercoiled DNA; other enzymes show rates unaffected by bead size. Our results reveal a unique mechanism through which enzyme rates can be controlled by constraints on macromolecular or supramolecular substrates.

Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg.

PURPOSE: The incidence of aneuploidy in eggs from women of advanced reproductive age can exceed 60%, making the mammalian egg a unique model system to study the mechanisms of chromosome segregation errors. METHODS: Here we applied a novel biophysical chromosome stretching approach to quantify mechanical stiffness of meiotic chromosomes in the mammalian egg and then documented how these properties changed in a mouse model of physiologic reproductive aging. RESULTS: We found significant differences in chromosome micromechanics, and thus in higher order chromosome structure, coincident with advanced reproductive age, a time that is also unequivocally associated with an increase in egg aneuploidy. CONCLUSIONS: These findings have important implications for both reproductive and cancer biology where aneuploidy plays a central role in aging related disease states.

Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase.

Structural and topological data suggest that serine site-specific DNA recombinases exchange duplex DNAs by rigid-body relative rotation of the two halves of the synapse, mediated by a flat protein-protein interaction surface. We present evidence for this rotational motion for a simple serine recombinase, the Bxb1 phage integrase, from a single-DNA-based supercoil-release assay that allows us to follow crossover site cleavage, rotation, religation, and product release in real time. We have also used a two-DNA braiding-relaxation experiment to observe the effect of synapse rotation in reactions on two long molecules. Relaxation and unbraiding are rapid (averaging 54 and 70 turns/s, respectively) and complete, with no discernible pauses. Nevertheless, the molecular friction associated with rotation is larger than that of type-I topoisomerases in a similar assay. Surprisingly we find that the synapse can stay rotationally "open" for many minutes.

Switching and non-switching dead-beat sliding mode control with monotonic convergence.

Performance requirements necessitate control designs that assure not only transient response specifications but also steady-state accuracy. Monotonic convergence of the tracking error is crucial for an efficient control design to prevent the performance degradation caused by overshooting. This needs a balanced consideration of both reaching conditions and the monotonic convergence, in the context of sliding mode control. In this paper, the dynamic behaviour of the dead-beat sliding mode control is characterized and the signum function is replaced by employing a non-switching one, in order to reduce chattering. The paper conducts a thorough analysis of monotonic convergence of both the switching and the non-switching error dynamics. By deriving the conditions for monotonic convergence, the control parameters can be strategically chosen to ensure monotonic convergence of the tracking error. Numerical and experimental results are presented to validate effectiveness of the proposed control scheme, which evaluate the tracking performance achieved by both the switching and the non-switching control methods.

In situ sonochemical synthesis of flower-like N-graphyne/BiOCl0.5Br0.5 microspheres for efficient removal of levofloxacin.

In this work, N-graphyne is in situ coupled with BiOCl0.5Br0.5via a facile one-step sonochemical method. To our knowledge, both the synthesis strategy for BiOCl0.5Br0.5 and the N-graphyne/BiOCl0.5Br0.5 photocatalytic system are new developments. A collection of characterization methods is adopted to detect the morphologies, structures, and electronic and optical properties. The results demonstrate that wrinkle-like N-graphyne nanosheets successfully enwind around or on flower-like BiOCl0.5Br0.5 microspheres, which are regularly assembled by BiOCl0.5Br0.5 nanosheets. Compared with pristine BiOCl0.5Br0.5, N-graphyne/BiOCl0.5Br0.5 composites exhibit superior adsorption capacity and visible-light-driven photocatalytic degradation of levofloxacin. In particular, the optimal N-graphyne amount for ameliorating the photocatalytic performance of BiOCl0.5Br0.5 is ascertained. In addition, the good stable performance for photocatalysis is confirmed by four cycling experiments. The dominant active species is confirmed to be O2˙- during photodegradation. The improved photocatalytic activity is attributed to the enhanced visible light response and the accelerated transfer/separation of photogenerated carriers by N-graphyne, which are verified using UV-vis absorption spectra, photocurrents, photopotentials, Nyquist plots, and Mott-Schottky curves. This study develops a new perspective for the synthesis and modification of BiOX solid solution, which can be used as an efficient photocatalyst.

In-situ sonochemical formation of N-graphyne modulated porous g-C3N4 for boosted photocatalysis degradation of pollutants and nitrogen fixation.

Herein, Nitrogen-doped graphyne/porous g-C3N4 composites are firstly in-situ synthesized via the ultrasound vibration of CaC2, triazine, and porous g-C3N4 in absolute ethanol. A variety of characterizations are performed to investigate the morphology, microstructure, composition, and electrical/optical features of the obtained composites, such as transmission electron microscopy, scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectra, X-ray photoelectron spectroscopy, and so forth. It is found that N-doped graphyne with flexible folds lamellar structure is intimately attached to flake g-C3N4 in the as-prepared composites. An enlargement of 1.68 and 1.44 folds for the photocatalytic degradation of levofloxacin, rhodamine B, Methylene blue, and Tetracycline is realized by N-doped graphyne/g-C3N4 in comparison with that of pristine g-C3N4, respectively. In addition, the highest NH3 production rate attains 1.71 mmol⋅gcat-1⋅h-1 for N-doped graphyne/g-C3N4, which is 5.89 times larger than that of g-C3N4 (0.29 mmol⋅gcat-1⋅h-1). The improved mechanism of photocatalysis including higher photo-response and carrier separation rate is verified by transient photo-current, transient photo-potential, Mott-Schottky plots, Tafel plots, electrochemical impedance spectroscopy, turn-over frequency, photoluminescence spectra, and UV-vis diffuse absorption spectra, etc. Overall, the current study shows that N-doped graphyne synthesized from CaC2 and triazine is a useful decoration to modulate the photocatalytic features of g-C3N4, which can also be widely extended for in-situ modification of other photocatalysts.

N-doped Ti3C2-reinforced porous g-C3N4 for photocatalytic contaminants degradation and nitrogen reduction.

Herein, a series of N-doped Ti3C2/porous g-C3N4 composites are ultrasonically prepared from N-doped Ti3C2 and porous g-C3N4 under N2 atmosphere. The structure, morphology, and optical characteristics of the as-prepared composites are characterized by X-ray diffraction, transmission electron microscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, UV-vis diffuse reflectance spectroscopy, etc. Moreover, photocatalytic measurements show that N-doped Ti3C2 is an excellent modifier for porous g-C3N4 to heighten its photocatalytic activity. Only 44.1% of rhodamine B can be degraded by the photocatalysis of pristine porous g-C3N4, while the photocatalytic degradation ratio of rhodamine B can reach up to 97.5% for the optimal N-doped Ti3C2 loading composites under visible light for 15 min. Moreover, the photocatalytic tests of N2 fixation confirm that the optimal composites show the highest production yield of NH4+ (11.8 µmol gcat-1 h-1), which is 2.11-folds more than that of porous g-C3N4 (5.6 µmol gcat-1 h-1). The reinforced photocatalytic properties are revealed to profit from the more photogenerated electrons and holes' separation, higher ability for light response, and more abundant active sites. This work develops the route for boosting the photocatalytic properties of porous g-C3N4 with N-doped Ti3C2.

In-situ assembling novel N-Ti3C2/BiOClxBr1-x composites with enhanced photocatalytic degradation and nitrogen reduction activity.

Herein, a collection of novel N-Ti3C2/BiOClxBr1-x composites are fabricated via a simple in-situ sonochemical process. Not only the preparation method for N-Ti3C2 but also the photocatalytic system of N-Ti3C2/BiOClxBr1-x are firstly developed. Multiple characterizations jointly demonstrate the successful fabrication of the composites. Compared to that of BiOClxBr1-x, the maximum improvements of 1.16, 1.25 and 1.26 folds are severally confirmed for the photocatalytic degradation of levofloxacin, Rhodamine B, and methylene blue over N-Ti3C2/BiOClxBr1-x composites. In addition, through radicals trapping tests, the primary active species in photocatalytic degradation process are verified to be O2-. Moreover, N-Ti3C2/BiOClxBr1-x composites also exhibit 1.18 and 1.14 times enhancements for NH3 production compared with that of BiOClxBr1-x with or without the presence of methanol, respectively. In addition, the maximum improvements of photo-current and photo-potential for BiOClxBr1-x are 1.29 and 1.86 folds with the introduction of N-Ti3C2, respectively. The enhanced photocatalytic activity of N-Ti3C2/BiOClxBr1-x composites is owing to the heightened light absorption, increased specific surface area, and accelerated separation of photoinduced carriers. Additionally, the stable photocatalytic properties of N-Ti3C2/BiOClxBr1-x are confirmed by three photocatalytic recycle tests on pollutant degradation and nitrogen reduction combined with X-ray diffraction patterns before and after three recycles. This study suggests that N-Ti3C2 is an efficient ornamentation for boosting photocatalytic activity ofBiOClxBr1-x, which can also be expanded as a promising modifier for other semiconductors.

Adaptive Learning Control Algorithms for Infinite-Duration Tracking.

Learning control is applicable to systems that operate periodically or over finite time intervals. Currently, there is a lack of research results about learning control approaches to infinite-duration tracking, without requiring periodicity or repeatability. This article addresses the problem of adaptive learning control (ALC) for systems performing infinite-duration tasks. Instead of using integral adaptation, incremental adaptive mechanisms are exploited, by which the numerical integration for implementation can be avoided. The comparison with the conventional integral adaptive mechanisms indicates that the suggested methodology can be an alternative to the adaptive system designs. Using an error-tracking approach, the approximation-based backstepping design is carried out for systems in the strict-feedback form, where a novel integral Lyapunov function is shown to be efficient in the treatment of state-dependent control gain. Theoretical results for the performance analysis are presented in detail. In particular, the robust convergence of the tracking error is established, while the boundedness of the variables of the closed-loop system is characterized, with the aid of a key technical lemma. It is shown that the proposed control method can provide satisfactory tracking performance and simplify the controller designs. Numerical results are presented to demonstrate effectiveness of the learning control schemes.

On convergence of extended state observers for nonlinear systems with non-differentiable uncertainties.

The analysis of convergence of extended state observers (ESOs) requires the total disturbance to be differentiable. However, this requirement is not satisfied in many control engineering practices. In this paper, we attempt to analyze the convergence of ESOs for nonlinear systems with non-differentiable uncertainties. A decomposition method is first presented to divide the non-differentiable total disturbance into a differentiable signal and a bounded but non-differentiable signal. Based on this decomposition, we give out the convergence of both nonlinear and linear ESOs (NLESO/LESO), low- and high-power ESOs (LPESO/HPESO), and fixed-time ESO (FxESO). We also derive the explicit formulas for the estimation errors of these ESOs. Simulations and experiments demonstrate the correctness of the analysis results.

On a Finitely Activated Terminal RNN Approach to Time-Variant Problem Solving.

This article concerns with terminal recurrent neural network (RNN) models for time-variant computing, featuring finite-valued activation functions (AFs), and finite-time convergence of error variables. Terminal RNNs stand for specific models that admit terminal attractors, and the dynamics of each neuron retains finite-time convergence. The might-existing imperfection in solving time-variant problems, through theoretically examining the asymptotically convergent RNNs, is pointed out for which the finite-time-convergent models are most desirable. The existing AFs are summarized, and it is found that there is a lack of the AFs that take only finite values. A finitely valued terminal RNN, among others, is taken into account, which involves only basic algebraic operations and taking roots. The proposed terminal RNN model is used to solve the time-variant problems undertaken, including the time-variant quadratic programming and motion planning of redundant manipulators. The numerical results are presented to demonstrate effectiveness of the proposed neural network, by which the convergence rate is comparable with that of the existing power-rate RNN.

Practical fixed-time trajectory tracking control of constrained wheeled mobile robots with kinematic disturbances.

This paper addresses the problem of practical fixed-time trajectory tracking for wheeled mobile robots (WMRs) subject to kinematic disturbances and input saturation. Firstly, considering the under-actuated characteristics of the WMR systems, the WMR model under kinematic disturbances is transformed into a two-input two-output interference system by using a set of output equations. Then, the tracking error state equation with lumped disturbances in the acceleration-level pseudo-dynamic control (ALPDC) structure is established. The lumped disturbances are estimated by a designed fixed-time extended state observer (FESO) without requiring the differentiability of the first-time derivatives of the kinematic disturbances. Meanwhile, a practical fixed-time output feedback control law is developed for trajectory tracking. By resorting to the Lyapunov stability theorem, the fixed-time stability analysis of the closed-loop WMR system in the presence of input saturation is conducted. Finally, simulation results are presented to show the effectiveness of the proposed approach.

Micromechanics of human mitotic chromosomes.

Eukaryote cells dramatically reorganize their long chromosomal DNAs to facilitate their physical segregation during mitosis. The internal organization of folded mitotic chromosomes remains a basic mystery of cell biology; its understanding would likely shed light on how chromosomes are separated from one another as well as into chromosome structure between cell divisions. We report biophysical experiments on single mitotic chromosomes from human cells, where we combine micromanipulation, nano-Newton-scale force measurement and biochemical treatments to study chromosome connectivity and topology. Results are in accord with previous experiments on amphibian chromosomes and support the 'chromatin network' model of mitotic chromosome structure. Prospects for studies of chromosome-organizing proteins using siRNA expression knockdowns, as well as for differential studies of chromosomes with and without mutations associated with genetic diseases, are also discussed.