High level expression of Acidothermus cellulolyticus β-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid

<p>Abstract</p> <p>Background</p> <p>Large-scale production of effective cellulose hydrolytic enzymes is the key to the bioconversion of agricultural residues to ethanol. The goal of this study was to develop a rice plant as a bioreactor for the large-scale production of cellulose hydrolytic enzymes via genetic transformation, and to simultaneously improve rice straw as an efficient biomass feedstock for conversion of cellulose to glucose.</p> <p>Results</p> <p>In this study, the cellulose hydrolytic enzyme β-1, 4-endoglucanase (<it>E1</it>) gene, from the thermophilic bacterium <it>Acidothermus cellulolyticus</it>, was overexpressed in rice through <it>Agrobacterium</it>-mediated transformation. The expression of the bacterial <it>E1 </it>gene in rice was driven by the constitutive Mac promoter, a hybrid promoter of Ti plasmid mannopine synthetase promoter and cauliflower mosaic virus 35S promoter enhancer, with the signal peptide of tobacco pathogenesis-related protein for targeting the E1 protein to the apoplastic compartment for storage. A total of 52 transgenic rice plants from six independent lines expressing the bacterial E1 enzyme were obtained that expressed the gene at high levels without severely impairing plant growth and development. However, some transgenic plants exhibited a shorter stature and flowered earlier than the wild type plants. The E1 specific activities in the leaves of the highest expressing transgenic rice lines were about 20-fold higher than those of various transgenic plants obtained in previous studies and the protein amounts accounted for up to 6.1% of the total leaf soluble protein. A zymogram and temperature-dependent activity analyses demonstrated the thermostability of the E1 enzyme and its substrate specificity against cellulose, and a simple heat treatment can be used to purify the protein. In addition, hydrolysis of transgenic rice straw with cultured cow gastric fluid for one hour at 39°C and another hour at 81°C yielded 43% more reducing sugars than wild type rice straw.</p> <p>Conclusion</p> <p>Taken together, these data suggest that transgenic rice can effectively serve as a bioreactor for the large-scale production of active, thermostable cellulose hydrolytic enzymes. As a feedstock, direct expression of large amount of cellulases in transgenic rice may also facilitate saccharification of cellulose in rice straw and significantly reduce the costs for hydrolytic enzymes.</p

Posterior Sampling for Competitive RL: Function Approximation and Partial Observation

This paper investigates posterior sampling algorithms for competitive reinforcement learning (RL) in the context of general function approximations. Focusing on zero-sum Markov games (MGs) under two critical settings, namely self-play and adversarial learning, we first propose the self-play and adversarial generalized eluder coefficient (GEC) as complexity measures for function approximation, capturing the exploration-exploitation trade-off in MGs. Based on self-play GEC, we propose a model-based self-play posterior sampling method to control both players to learn Nash equilibrium, which can successfully handle the partial observability of states. Furthermore, we identify a set of partially observable MG models fitting MG learning with the adversarial policies of the opponent. Incorporating the adversarial GEC, we propose a model-based posterior sampling method for learning adversarial MG with potential partial observability. We further provide low regret bounds for proposed algorithms that can scale sublinearly with the proposed GEC and the number of episodes $T$. To the best of our knowledge, we for the first time develop generic model-based posterior sampling algorithms for competitive RL that can be applied to a majority of tractable zero-sum MG classes in both fully observable and partially observable MGs with self-play and adversarial learning.Comment: NeurIPS 202

A molecular genetic toolbox for Yarrowia lipolytica

Background: Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. Results: We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. Conclusions: These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products

Hybrid-space reconstruction with add-on distortion correction for simultaneous multi-slab diffusion MRI

Purpose: This study aims to propose a model-based reconstruction algorithm for simultaneous multi-slab diffusion MRI acquired with blipped-CAIPI gradients (blipped-SMSlab), which can also incorporate distortion correction. Methods: We formulate blipped-SMSlab in a 4D k-space with kz gradients for the intra-slab slice encoding and km (blipped-CAIPI) gradients for the inter-slab encoding. Because kz and km gradients share the same physical axis, the blipped-CAIPI gradients introduce phase interference in the z-km domain while motion induces phase variations in the kz-m domain. Thus, our previous k-space-based reconstruction would need multiple steps to transform data back and forth between k-space and image space for phase correction. Here we propose a model-based hybrid-space reconstruction algorithm to correct the phase errors simultaneously. Moreover, the proposed algorithm is combined with distortion correction, and jointly reconstructs data acquired with the blip-up/down acquisition to reduce the g-factor penalty. Results: The blipped-CAIPI-induced phase interference is corrected by the hybrid-space reconstruction. Blipped-CAIPI can reduce the g-factor penalty compared to the non-blipped acquisition in the basic reconstruction. Additionally, the joint reconstruction simultaneously corrects the image distortions and improves the 1/g-factors by around 50%. Furthermore, through the joint reconstruction, SMSlab acquisitions without the blipped-CAIPI gradients also show comparable correction performance with blipped-SMSlab. Conclusion: The proposed model-based hybrid-space reconstruction can reconstruct blipped-SMSlab diffusion MRI successfully. Its extension to a joint reconstruction of the blip-up/down acquisition can correct EPI distortions and further reduce the g-factor penalty compared with the separate reconstruction.Comment: 10 figures+tables, 8 supplementary figure

Identification of a Classical Mutant in the Industrial Host <i>Aspergillus niger</i> by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites

The asexual filamentous fungus Aspergillus niger is an important industrial cell factory for citric acid production. In this study, we genetically characterized a UV-generated A. niger mutant that was originally isolated as a nonacidifying mutant, which is a desirable trait for industrial enzyme production. Physiological analysis showed that this mutant did not secrete large amounts of citric acid and oxalic acid, thus explaining the nonacidifying phenotype. As traditional complementation approaches to characterize the mutant genotype were unsuccessful, we used bulk segregant analysis in combination with high-throughput genome sequencing to identify the mutation responsible for the nonacidifying phenotype. Since A. niger has no sexual cycle, parasexual genetics was used to generate haploid segregants derived from diploids by loss of whole chromosomes. We found that the nonacidifying phenotype was caused by a point mutation in the laeA gene. LaeA encodes a putative methyltransferase-domain protein, which we show here to be required for citric acid production in an A. niger lab strain (N402) and in other citric acid production strains. The unexpected link between LaeA and citric acid production could provide new insights into the transcriptional control mechanisms related to citric acid production in A. niger. Interestingly, the secondary metabolite profile of a ΔlaeA strain differed from the wild-type strain, showing both decreased and increased metabolite levels, indicating that LaeA is also involved in regulating the production of secondary metabolites. Finally, we show that our systems genetics approach is a powerful tool to identify trait mutations

The chemical profiling of Salvia plebeia during different growth periods and the biosynthesis of its main flavonoids ingredients

Salvia plebeia (Lamiaceae) is a valuable medicinal plant widely distributed across Asia and Oceania. However, the composition and accumulation patterns of its active ingredients in different organs during the growth and their biosynthetic mechanism remain unknown. Therefore, we conducted metabolite profiling, transcriptomic analysis, and biological functional verification to explore the distribution, accumulation, and biosynthesis mechanisms of flavonoids in S. plebeia. We identified 70 metabolites including 46 flavonoids, 16 phenolic acids, seven terpenoids, and one organic acid, of which 21 were previously unreported in S. plebeia. Combining metabolomic-transcriptomic analysis and biological functional verification, we identified the key genes involved in biosynthesis of its main active ingredients, hispidulin and homoplantaginin, including SpPAL, SpC4H, Sp4CL2, Sp4CL5, SpCHS1, SpCHI, SpFNS, SpF6H1, SpF6OMT1, SpF6OMT2, SpUGT1, SpUGT2, and SpUGT3. Using the identified genes, we reconstructed the hispidulin and homoplantaginin biosynthesis pathways in Escherichia coli, and obtained a yield of 5.33 and 3.86 mg/L for hispidulin and homoplantaginin, respectively. Our findings provide valuable insights into the changes in chemical components in different organs of S. plebeia during different growth and harvest stages and establishes a foundation for identifying and synthesizing its active components

The association of serum total bile acid with non-alcoholic fatty liver disease in Chinese adults: a cross sectional study

Background Non-alcoholic fatty liver disease (NAFLD) is currently the major cause of chronic liver disease globally. Bile acids (BAs) have emerged as relevant signaling molecules that are associated with NAFLD development. This study was aimed to examine the association of serum total bile acids (TBAs) with NAFLD in a large population of Chinese subjects. Methods This cross sectional study recruited 152,336 participants from the Second Xiangya Hospital, China. NAFLD was diagnosed based on the presence of hepatic steatosis on ultrasonography, without significant alcohol consumption and other known causes for chronic liver disease. A multivariate logistic regression model was used to test for the association of serum TBAs with NAFLD, adjusting for conventional risk factors of NAFLD. Results A total of 27.4% of the participants had NAFLD. Patients with NAFLD had slightly higher TBA levels than those without, 3.4 vs. 3.0 μmol/L (p < 0.001). However, TBA levels were not associated with NAFLD in the multivariate logistic regression model, which adjusted for age, gender and other acknowledged risk factors for NAFLD (OR = 1.00. 95% CI: 1.00–1.00, p = 0.797). Conclusions We found that the serum TBA levels were not associated with NAFLD. Future studies in a large population, focusing on serum BA composition may improve the understating of the role of BAs in NAFLD

Giant magnetic quantum oscillations in the thermal conductivity of TaAs: Indications of chiral zero sound

Charge transport of topological semimetals has been in the focus of intensive investigations because of their non-trivial band topology. Heat transport of these materials, on the other hand, is largely unexplored and remains elusive. Here we report on an observation of unprecedented, giant magnetic quantum oscillations of thermal conductivity in the prototypical Weyl semimetal TaAs. The oscillations are antiphase with the quantum oscillating electronic density of states of a Weyl pocket, and their amplitudes amount to two orders of magnitude of the estimation based on the Wiedemann-Franz law. Our analyses show that all the conventional heat-transport mechanisms through diffusions of propagating electrons, phonons and electron-hole bipolar excitations, are far inadequate to account for these phenomena. Taking further experimental facts that the parallel field configuration favors much higher magneto-thermal conductivity, we propose that the newly proposed chiral zero sound provides a reasonable explanation to these exotic phenomena. More work focusing on other topological semimetals along the same line is badly called for.Comment: 15 pages, 5 figure