Functional assessment of hydrophilic domains of lea proteins from distant organisms

Late embryogenesis abundant (LEA) proteins play a protective role during desiccation and oxidation stresses. LEA3 proteins are a major group characterized by a hydrophilic domain (HD) with a highly conserved repeating 11-amino acid motif. We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into a-helical structures with the addition of glycerol or trifluoroethanol. Heterologous HD expression conferred enhanced desiccation and oxidation tolerance to Escherichia coli. These four HDs protected the enzymatic activities of lactate dehydrogenase (LDH) by preventing its aggregation under desiccation stress. The HDs also interacted with LDH, which was intensified by the addition of hydrogen peroxide (H2O2), suggesting a protective role in a chaperone-like manner. Based on these results, the HDs of LEA3 proteins show promise as protectants for desiccation and oxidation stresses, especially DrHD, which is a potential ideal stress-response element that can be applied in synthetic biology due to its extraordinary protection and stress resistance ability. Please click Additional Files below to see the full abstract

Effect of dry-wet cycles on dynamic properties and microstructures of sandstone: Experiments and modelling

Underground pumped storage power plant (UPSP) is an innovative concept for space recycling of abandoned mines. Its realization requires better understanding of the dynamic performance and durability of reservoir rock. This paper conducted ultrasonic detection, split Hopkinson pressure bar (SHPB) impact, mercury intrusion porosimetry (MIP), and backscatter electron observation (BSE) tests to investigate the dynamical behaviour and microstructure of sandstone with cyclical dry-wet damage. A coupling FEM-DEM model was constructed for reappearing mesoscopic structure damage. The results show that dry-wet cycles decrease the dynamic compressive strength (DCS) with a maximum reduction of 39.40%, the elastic limit strength is reduced from 41.75 to 25.62 MPa. The sieved fragments obtain the highest crack growth rate during the 23rd dry-wet cycle with a predictable life of 25 cycles for each rock particle. The pore fractal features of the macropores and micro-meso pores show great differences between the early and late cycles, which verifies the computational statistics analysis of particle deterioration. The numerical results show that the failure patterns are governed by the strain in pre-peak stage and the shear cracks are dominant. The dry-wet cycles reduce the energy transfer efficiency and lead to the discretization of force chain and crack fields

A SVM-based method for identifying fracture modes of rock using WVD spectrogram features of AE signals

In order to achieve the highly efficient and accurate identification of fracture modes including tension or shear fractures during rock failure, an intelligent identification method based on Wigner-Ville distribution (WVD) spectrogram features of acoustic emission (AE) signals was proposed. This method was mainly constructed by the following steps: Firstly, AE hits corre-sponding to tension and shear fractures were obtained through conducting the Brazilian disc test (tension fracture) and direct shear test (shear fracture) of limestone. Secondly, the WVD spectro-grams of these tensile-type and shear-type AE hits were respectively extracted and then trans-formed into the image features of relatively low-dimension as the sample set based on the gray-level cooccurrence matrix (GLCM) and histogram of oriented gradient (HOG). Finally, on the basis of the processed and classified sample set of the WVD spectrogram features, an identifica-tion model of rock fracture modes was established by a support vector machine (SVM) learning algorithm. To verify this method, the fracture modes of limestone subjected to biaxial compres-sion were identified by the method. The results showed that the method not only can greatly re-veal the fracture modes change from tension-dominated to shear-dominated fractures, but also has advantages over the RA-AF value method, such as applicability, accuracy and practicality

Rational Reprogramming of Fungal Polyketide First Ring Cyclization

Resorcylic acid lactones (RAL) and dihydroxyphenylacetic acid lactones (DAL) represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS (hrPKS) whose product is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates towards defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the DAL dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal versus the bacterial folding mode difference is portable upon creating hybrid enzymes, and structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations, and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first ring cyclizations will facilitate efforts towards the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides

Evaluation of InSAR and TomoSAR for monitoring deformations caused by mining in a mountainous area with high resolution satellite-based SAR

Interferometric Synthetic Aperture Radar (InSAR) and Differential Interferometric Synthetic Aperture Radar (DInSAR) have shown numerous applications for subsidence monitoring. In the past 10 years, the Persistent Scatterer InSAR (PSI) and Small BAseline Subset (SBAS) approaches were developed to overcome the problem of decorrelation and atmospheric effects, which are common in interferograms. However, DInSAR or PSI applications in rural areas, especially in mountainous regions, can be extremely challenging. In this study we have employed a combined technique, i.e., SBAS-DInSAR, to a mountainous area that is severely affected by mining activities. In addition, L-band (ALOS) and C-band (ENVISAT) data sets, 21 TerraSAR-X images provided by German Aerospace Center (DLR) with a high resolution have been used. In order to evaluate the ability of TerraSAR-X for mining monitoring, we present a case study of TerraSAR-X SAR images for Subsidence Hazard Boundary (SHB) extraction. The resulting data analysis gives an initial evaluation of InSAR applications within a mountainous region where fast movements and big phase gradients are common. Moreover, the experiment of four-dimension (4-D) Tomography SAR (TomoSAR) for structure monitoring inside the mining area indicates a potential near all-wave monitoring, which is an extension of conventional InSAR

Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zhang, M., Guo, Z., Xu, S., Barry, P. H., Sano, Y., Zhang, L., Halldorsson, S. A., Chen, A.-T., Cheng, Z., Liu, C.-Q., Li, S.-L., Lang, Y.-C., Zheng, G., Li, Z., Li, L., & Li, Y. Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau. Nature Communications, 12(1), (2021): 4157, https://doi.org/10.1038/s41467-021-24415-y.The episodic growth of high-elevation orogenic plateaux is controlled by a series of geodynamic processes. However, determining the underlying mechanisms that drive plateau growth dynamics over geological history and constraining the depths at which growth originates, remains challenging. Here we present He-CO2-N2 systematics of hydrothermal fluids that reveal the existence of a lithospheric-scale fault system in the southeastern Tibetan Plateau, whereby multi-stage plateau growth occurred in the geological past and continues to the present. He isotopes provide unambiguous evidence for the involvement of mantle-scale dynamics in lateral expansion and localized surface uplift of the Tibetan Plateau. The excellent correlation between 3He/4He values and strain rates, along the strike of Indian indentation into Asia, suggests non-uniform distribution of stresses between the plateau boundary and interior, which modulate southeastward growth of the Tibetan Plateau within the context of India-Asia convergence. Our results demonstrate that deeply-sourced volatile geochemistry can be used to constrain deep dynamic processes involved in orogenic plateau growth.This work was supported by China Seismic Experimental Site (CSES) (2019CSES0104), the Strategic Priority Research Program (B) of Chinese Academy of Sciences (XDB26000000), the National Key Research and Development Program of China (2020YFA0607700), the National Natural Science Foundation of China (41930642, 41602341, 41772355, and 41702361), the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) (2019QZKK0702), and the United Laboratory of High-Pressure Physics and Earthquake Science (2019HPPES02). P.H.B. was supported by the US National Science Foundation EAR Grant 1144559 during a portion of this work

Insights into Adaptations to a Near- Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora

Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle