Expansion and evolution of insect GMC oxidoreductases

BackgroundThe GMC oxidoreductases comprise a large family of diverse FAD enzymes that share a homologous backbone. The relationship and origin of the GMC oxidoreductase genes, however, was unknown. Recent sequencing of entire genomes has allowed for the evolutionary analysis of the GMC oxidoreductase family. ResultsAlthough genes that encode enzyme families are rarely linked in higher eukaryotes, we discovered that the majority of the GMC oxidoreductase genes in the fruit fly (D. melanogaster), mosquito (A. gambiae), honeybee (A. mellifera), and flour beetle (T. castaneum) are located in a highly conserved cluster contained within a large intron of the flotillin-2 (Flo-2) gene. In contrast, the genomes of vertebrates and the nematode C. elegans contain few GMC genes and lack a GMC cluster, suggesting that the GMC cluster and the function of its resident genes are unique to insects or arthropods. We found that the development patterns of expression of the GMC cluster genes are highly complex. Among the GMC oxidoreductases located outside of the GMC gene cluster, the identities of two related enzymes, glucose dehydrogenase (GLD) and glucose oxidase (GOX), are known, and they play major roles in development and immunity. We have discovered that several additional GLD and GOX homologues exist in insects but are remotely similar to fungal GOX. ConclusionWe speculate that the GMC oxidoreductase cluster has been conserved to coordinately regulate these genes for a common developmental or physiological function related to ecdysteroid metabolism. Furthermore, we propose that the GMC gene cluster may be the birthplace of the insect GMC oxidoreductase genes. Through tandem duplication and divergence within the cluster, new GMC genes evolved. Some of the GMC genes have been retained in the cluster for hundreds of millions of years while others might have transposed to other regions of the genome. Consistent with this hypothesis, our analysis indicates that insect GOX and GLD arose from a different ancestral GMC gene than that of fungal GOX

Plasmon-phonon coupling in large-area graphene dot and antidot arrays

Nanostructured graphene on SiO2 substrates pave the way for enhanced light-matter interactions and explorations of strong plasmon-phonon hybridization in the mid-infrared regime. Unprecedented large-area graphene nanodot and antidot optical arrays are fabricated by nanosphere lithography, with structural control down to the sub-100 nanometer regime. The interaction between graphene plasmon modes and the substrate phonons is experimentally demonstrated and structural control is used to map out the hybridization of plasmons and phonons, showing coupling energies of the order 20 meV. Our findings are further supported by theoretical calculations and numerical simulations.Comment: 7 pages including 6 figures. Supporting information is available upon request to author

Effective electro-optical modulation with high extinction ratio by a graphene-silicon microring resonator

Graphene opens up for novel optoelectronic applications thanks to its high carrier mobility, ultra-large absorption bandwidth, and extremely fast material response. In particular, the opportunity to control optoelectronic properties through tuning of Fermi level enables electro-optical modulation, optical-optical switching, and other optoelectronics applications. However, achieving a high modulation depth remains a challenge because of the modest graphene-light interaction in the graphene-silicon devices, typically, utilizing only a monolayer or few layers of graphene. Here, we comprehensively study the interaction between graphene and a microring resonator, and its influence on the optical modulation depth. We demonstrate graphene-silicon microring devices showing a high modulation depth of 12.5 dB with a relatively low bias voltage of 8.8 V. On-off electro-optical switching with an extinction ratio of 3.8 dB is successfully demonstrated by applying a square-waveform with a 4 V peak-to-peak voltage.Comment: 12 pages, including 7 figure

Facile control of nanoporosity in Cellulose Acetate using Nickel(II) nitrate additive and water pressure treatment for highly efficient battery gel separators

We succeed in fabricating nearly straight nanopores in cellulose acetate (CA) polymers for use as battery gel separators by utilizing an inorganic hexahydrate (Ni(NO3)2??6H2O) complex and isostatic water pressure treatment. The continuous nanopores are generated when the polymer film is exposed to isostatic water pressure after complexing the nickel(II) nitrate hexahydrate (Ni(NO3)2??6H2O) with the CA. These results can be attributed to the manner in which the polymer chains are weakened because of the plasticization effect of the Ni(NO3)2??6H2O that is incorporated into the CA. Furthermore, we performed extensive molecular dynamics simulation for confirming the interaction between electrolyte and CA separator. The well controlled CA membrane after water pressure treatment enables fabrication of highly reliable cell by utilizing 2032-type coin cell structure. The resulting cell performance exhibits not only the effect of the physical morphology of CA separator, but also the chemical interaction of electrolyte with CA polymer which facilitates the Li-ion in the cell.ope

Certified data-driven physics-informed greedy auto-encoder simulator

A parametric adaptive greedy Latent Space Dynamics Identification (gLaSDI) framework is developed for accurate, efficient, and certified data-driven physics-informed greedy auto-encoder simulators of high-dimensional nonlinear dynamical systems. In the proposed framework, an auto-encoder and dynamics identification models are trained interactively to discover intrinsic and simple latent-space dynamics. To effectively explore the parameter space for optimal model performance, an adaptive greedy sampling algorithm integrated with a physics-informed error indicator is introduced to search for optimal training samples on the fly, outperforming the conventional predefined uniform sampling. Further, an efficient k-nearest neighbor convex interpolation scheme is employed to exploit local latent-space dynamics for improved predictability. Numerical results demonstrate that the proposed method achieves 121 to 2,658x speed-up with 1 to 5% relative errors for radial advection and 2D Burgers dynamical problems.Comment: arXiv admin note: substantial text overlap with arXiv:2204.1200

Anisotropy-mediated reentrant localization

We consider a 2d dipolar system, $d=2$, with the generalized dipole-dipole interaction $\sim r^{-a}$, with the power $a$ controlled experimentally in trapped-ion or Rydberg-atom systems via their interaction with cavity modes. We focus on the dilute dipolar excitation case when the problem can be effectively considered as single-particle with the interaction providing long-range dipolar-like hopping. % We show that the spatially homogeneous tilt $\beta$ of the dipoles giving rise to the anisotropic dipole exchange leads to the non-trivial reentrant localization beyond the locator expansion, $a<d$, unlike the models with random dipole orientation. The Anderson transitions are found to occur at the finite values of the tilt parameter $\beta = a$, $0<a<d$, and $\beta = a/(a-d/2)$, $d/2<a<d$, showing the robustness of the localization at small and large anisotropy values. % Both extensive numerical calculations and analytical methods show power-law localized eigenstates in the bulk of the spectrum, obeying recently discovered duality $a\leftrightarrow 2d-a$ of their spatial decay rate, on the localized side of the transition, $a>a_{AT}$. This localization emerges due to the presence of the ergodic extended states at either spectral edge, which constitute a zero fraction of states in the thermodynamic limit, decaying though extremely slowly with the system size.Comment: 11 pages, 5 figures, 80 references (in 6 pages) + 14 pages, 11 figures in Appendice

Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon

Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate–carrier protein complex from the translocon is the energy-requiring step in T9SS transport

The Development of Biophotovoltaic Systems for Power Generation and Biological Analysis.

Biophotovoltaic systems (BPVs) resemble microbial fuel cells, but utilise oxygenic photosynthetic microorganisms associated with an anode to generate an extracellular electrical current, which is stimulated by illumination. Study and exploitation of BPVs have come a long way over the last few decades, having benefited from several generations of electrode development and improvements in wiring schemes. Power densities of up to 0.5 W m-2 and the powering of small electrical devices such as a digital clock have been reported. Improvements in standardisation have meant that this biophotoelectrochemical phenomenon can be further exploited to address biological questions relating to the organisms. Here, we aim to provide both biologists and electrochemists with a review of the progress of BPV development with a focus on biological materials, electrode design and interfacial wiring considerations, and propose steps for driving the field forward

Comparative phylogenomics and multi-gene cluster analyses of the Citrus Huanglongbing (HLB)-associated bacterium Candidatus Liberibacter

<p>Abstract</p> <p>Background</p> <p>Huanglongbing (HLB, previously known as citrus greening), is associated with <it>Candidatus </it>Liberibacter species and is a serious threat to citrus production world-wide. The pathogen is a Gram negative, unculturable, phloem-limited bacterium with limited known genomic information. Expanding the genetic knowledge of this organism may provide better understanding of the pathogen and possibly develop effective strategies for control and management of HLB.</p> <p>Results</p> <p>Here, we report cloning and characterization of an additional 14.7 Kb of new genomic sequences from three different genomic regions of the <it>Candidatus </it>Liberibacter asiaticus (Las). Sequence variation analyses among the available <it>Ca</it>. Liberibacter species sequences as well as the newly cloned 1.5 Kb of <it>rpo</it>B gene from different <it>Ca</it>. Liberibacter strains have identified INDELs and SNPs. Phylogenetic analysis of the deduced protein sequences from the cloned regions characterizes the HLB-associated <it>Candidatus </it>Liberibacter as a new clade in the sub-division of the α-proteobacteria.</p> <p>Conclusion</p> <p>Comparative analyses of the cloned gene regions of <it>Candidatus </it>Liberibacter with members of the order Rhizobiales suggest overall gene structure and order conservation, albeit with minor variations including gene decay due to the identified pseudogenes. The newly cloned gene regions contribute to our understanding of the molecular aspects of genomic evolution of <it>Ca</it>. Liberibacter.</p