The Genome Characteristics and Predicted Function of Methyl-Group Oxidation Pathway in the Obligate Aceticlastic Methanogens, Methanosaeta spp

In this work, we report the complete genome sequence of an obligate aceticlastic methanogen, Methanosaeta harundinacea 6Ac. Genome comparison indicated that the three cultured Methanosaeta spp., M. thermophila, M. concilii and M. harundinacea 6Ac, each carry an entire suite of genes encoding the proteins involved in the methyl-group oxidation pathway, a pathway whose function is not well documented in the obligately aceticlastic methanogens. Phylogenetic analysis showed that the methyl-group oxidation-involving proteins, Fwd, Mtd, Mch, and Mer from Methanosaeta strains cluster with the methylotrophic methanogens, and were not closely related to those from the hydrogenotrophic methanogens. Quantitative PCR detected the expression of all genes for this pathway, albeit ten times lower than the genes for aceticlastic methanogenesis in strain 6Ac. Western blots also revealed the expression of fwd and mch, genes involved in methyl-group oxidation. Moreover, 13C-labeling experiments suggested that the Methanosaeta strains might use the pathway as a methyl oxidation shunt during the aceticlastic metabolism. Because the mch mutants of Methanosarcina barkeri or M. acetivorans failed to grow on acetate, we suggest that Methanosaeta may use methyl-group oxidation pathway to generate reducing equivalents, possibly for biomass synthesis. An fpo operon, which encodes an electron transport complex for the reduction of CoM-CoB heterodisulfide, was found in the three genomes of the Methanosaeta strains. However, an incomplete protein complex lacking the FpoF subunit was predicted, as the gene for this protein was absent. Thus, F420H2 was predicted not to serve as the electron donor. In addition, two gene clusters encoding the two types of heterodisulfide reductase (Hdr), hdrABC, and hdrED, respectively, were found in the three Methanosaeta genomes. Quantitative PCR determined that the expression of hdrED was about ten times higher than hdrABC, suggesting that hdrED plays a major role in aceticlastic methanogenesis

Hemoglobin Bohr Effects: Atomic Origin of the Histidine Residue Contributions

The Bohr effect in hemoglobin, which refers to the dependence of the oxygen affinity on the pH, plays an important role in its cooperativity and physiological function. The dominant contribution to the Bohr effect arises from the difference in the p<i>K</i>_a values of His residues of the unliganded (deoxy) and liganded (carbonmonoxy) structures. Using recent high resolution structures, the residue p<i>K</i>_a values corresponding to the two structures are calculated. The method is based on determining the electrostatic interactions between residues in the protein, relative to those of the residue in solution, by use of the linearized finite difference Poisson–Boltzmann equation and Monte Carlo sampling of protonation states. Given that good agreement is obtained with the available experimental values for the contribution of His residues in HbA to the Bohr effect, the calculated results are used to determine the atomic origin of the p<i>K</i>_a shift between deoxy and carbonmonoxy HbA. The contributions to the p<i>K</i>_a shift calculated by means of the linear response approximation show that the salt bridge involving His146 plays an important role in the alkaline Bohr effect, as suggested by Perutz but that other interactions are significant as well. A corresponding analysis is made for the contribution of His143 to the acid Bohr effect for which there is no proposed explanation. The method used is summarized and the program by which it is implemented is described in the Appendix

Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson , Phys. Rev. Lett. 97, 123001 (2006); Phys. Rev. Lett. 100, 123004 (2008)] are analyzed. Because of the time-reversible propagation the dynamics of the extended electronic degrees of freedom is lossless with no dissipation of numerical errors. For long simulation times under ``noisy'' conditions, numerical errors may therefore accumulate to large fluctuations. We solve this problem by including a dissipative external electronic force that removes noise while keeping the energy stable. The approach corresponds to a Langevin-like dynamics for the electronic degrees of freedom with internal numerical error fluctuations and external, approximately energy conserving, dissipative forces. By tuning the dissipation to balance the numerical fluctuations the external perturbation can be kept to a minimum

Developing a Hybrid Algorithm Based on an Equilibrium Optimizer and an Improved Backpropagation Neural Network for Fault Warning

In today’s rapidly evolving manufacturing landscape with the advent of intelligent technologies, ensuring smooth equipment operation and fostering stable business growth rely heavily on accurate early fault detection and timely maintenance. Machine learning techniques have proven to be effective in detecting faults in modern production processes. Among various machine learning algorithms, the Backpropagation (BP) neural network is a commonly used model for fault detection. However, due to the intricacies of the BP neural network training process and the challenges posed by local minima, it has certain limitations in practical applications, which hinder its ability to meet efficiency and accuracy requirements in real-world scenarios. This paper aims to optimize BP networks and develop more effective fault warning methods. The primary contribution of this research is the proposal of a novel hybrid algorithm that combines a random wandering strategy within the main loop of an equilibrium optimizer (EO), a local search operator inspired by simulated annealing, and an adaptive learning strategy within the BP neural network. Through analysis and comparison of multiple sets of experimental data, the algorithm demonstrates exceptional accuracy and stability in fault warning tasks, effectively predicting the future operation of equipment and systems. This innovative approach not only overcomes the limitations of traditional BP neural networks, but also provides an efficient and reliable solution for fault detection and early warning in practical applications

Large-Size Suspended Mono-Layer Graphene Film Transfer Based on the Inverted Floating Method

Suspended graphene can perfectly present the excellent material properties of graphene, which has a good application prospect in graphene sensors. The existing suspended graphene pressure sensor has several problems that need to be solved, one of which is the fabrication of a suspended sample. It is still very difficult to obtain large-size suspended graphene films with a high integrity that are defect-free. Based on the simulation and analysis of the kinetic process of the traditional suspended graphene release process, a novel setup for large-size suspended graphene release was designed based on the inverted floating method (IFM). The success rate of the single-layer suspended graphene with a diameter of 200 μm transferred on a stainless-steel substrate was close to 50%, which is greatly improved compared with the traditional impregnation method. The effects of the defects and burrs around the substrate cavity on the stress concentration of graphene transfer explain why the transfer success rate of large-size suspended graphene is not high. This research lays the foundation for providing large-size suspended graphene films in the area of graphene high-precision sensors

Acute Ethanol-Induced Changes in Edema and Metabolite Concentrations in Rat Brain

The aim of this study is to describe the acute effects of EtOH on brain edema and cerebral metabolites, using diffusion weight imaging (DWI) and proton magnetic resonance spectroscopy (1H-MRS) at a 7.0T MR and to define changes in apparent diffusion coefficient (ADC) values and the concentration of metabolites in the rat brain after acute EtOH intoxication. ADC values in each ROI decreased significantly at 1 h and 3 h after ethanol administration. ADC values in frontal lobe were decreased significantly compared with other regions at 3 h. For EtOH/Cr+PCr and cerebral metabolites (Cho, Tau, and Glu) differing over time, no significant differences for Ins, NAA, and Cr were observed in frontal lobes. Regression analysis revealed a significant association between TSEtOH/Cr+PCr and TSCho, TSTau, TSGlu, and TSADC. The changes of ADC values in different brain regions reflect the process of the cytotoxic edema in vivo. The characterization of frontal lobes metabolites changes and the correlations between TSEtOH/Cr+PCr and TSCho, TSTau, and TSGlu provide a better understanding for the biological mechanisms in neurotoxic effects of EtOH on the brain. In addition, the correlations between TSEtOH/Cr+PCr and TSADC will help us to understand development of the ethanol-induced brain cytotoxic edema

Gene organizations of formylmethanofuran dehydrogenase (<i>fmd</i> or <i>fwd</i>) in the genomes of <i>M. harundinacea</i> (A), <i>M. concilii</i> (B), and <i>M. theromphila</i> (C) compared with those in the genomes of <i>Msr. mazei</i> (D), <i>Msr. barkeri</i> (E) and <i>Msr. acetivorans</i> (F).

<p>Gene organizations of formylmethanofuran dehydrogenase (<i>fmd</i> or <i>fwd</i>) in the genomes of <i>M. harundinacea</i> (A), <i>M. concilii</i> (B), and <i>M. theromphila</i> (C) compared with those in the genomes of <i>Msr. mazei</i> (D), <i>Msr. barkeri</i> (E) and <i>Msr. acetivorans</i> (F).</p

Transcript abundance of the genes for methyl-group oxidation pathway in <i>M. harundinacea</i> 6Ac estimated by QPCR.

*<p>, copy number of gene/copies of 16S rRNA gene×10⁵.</p