Expression and characterization of keratinase from Deinococcus gobiensis I-0

Keratin is a nonnutritious hard protein widely distributed in feather, wool, animal hoof, horn, and toenail. The disulfide bond interacts to form a dense structure of keratin, which is difficult to be degraded and utilized. Keratinase is a kind of enzymes that can destroy the dense structure of keratin to achieve the degradation, and has a good application prospect. In order to further tap the important gene resources of keratinase, improve its hydrolytic activity，and provide theoretical basis for industrial production, this experiment cloned a gene encoding keratinase from Deinococcus gobiensis I-0 isolated from Gobi desert of Xinjiang and named it as Kerdg. Prokaryotic expression vector pET-22B-Kerdg was constructed and then induced, expressed and purified in vitro, the optimal temperature and pH of the crude enzyme solution were determined through the hydrolysis activity to feathers. Results showed that the first 50 amino acids of N terminal had a great influence on the expression and purification of protein Kerdg. The crude enzyme solution of recombinant strain completely decomposed feathers in three days. The transparent circle on milk powder plate appeared more notable in crude enzyme solution of recombinant strain than that of empty strain. Kerdg adapted to a wide range of temperatures and pH，among which the optimal temperature was 60℃ and the optimal pH was 5.0. The Kerdg can degrade feathers and thus will have great application space in the future industrial production and treatment of waste feathers. Please click Additional Files below to see the full abstract

The phytotoxin coronatine is a multifunctional component of the virulence armament of Pseudomonas syringae

Plant pathogens deploy an array of virulence factors to suppress host defense and promote pathogenicity. Numerous strains of Pseudomonas syringae produce the phytotoxin coronatine (COR). A major aspect of COR function is its ability to mimic a bioactive jasmonic acid (JA) conjugate and thus target the JA-receptor COR-insensitive 1 (COI1). Biological activities of COR include stimulation of JA-signaling and consequent suppression of SA-dependent defense through antagonistic crosstalk, antagonism of stomatal closure to allow bacterial entry into the interior of plant leaves, contribution to chlorotic symptoms in infected plants, and suppression of plant cell wall defense through perturbation of secondary metabolism. Here, we review the virulence function of COR, including updates on these established activities as well as more recent findings revealing COI1-independent activity of COR and shedding light on cooperative or redundant defense suppression between COR and type III effector proteins

Efficient Joint Optimization of Layer-Adaptive Weight Pruning in Deep Neural Networks

In this paper, we propose a novel layer-adaptive weight-pruning approach for Deep Neural Networks (DNNs) that addresses the challenge of optimizing the output distortion minimization while adhering to a target pruning ratio constraint. Our approach takes into account the collective influence of all layers to design a layer-adaptive pruning scheme. We discover and utilize a very important additivity property of output distortion caused by pruning weights on multiple layers. This property enables us to formulate the pruning as a combinatorial optimization problem and efficiently solve it through dynamic programming. By decomposing the problem into sub-problems, we achieve linear time complexity, making our optimization algorithm fast and feasible to run on CPUs. Our extensive experiments demonstrate the superiority of our approach over existing methods on the ImageNet and CIFAR-10 datasets. On CIFAR-10, our method achieves remarkable improvements, outperforming others by up to 1.0% for ResNet-32, 0.5% for VGG-16, and 0.7% for DenseNet-121 in terms of top-1 accuracy. On ImageNet, we achieve up to 4.7% and 4.6% higher top-1 accuracy compared to other methods for VGG-16 and ResNet-50, respectively. These results highlight the effectiveness and practicality of our approach for enhancing DNN performance through layer-adaptive weight pruning. Code will be available on https://github.com/Akimoto-Cris/RD_VIT_PRUNE

Genome-wide investigation and functional characterization of the β-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501

<p>Abstract</p> <p>Background</p> <p>Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs.</p> <p>Results</p> <p>In this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of <it>Pseudomonas stutzeri </it>A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The <it>P. stutzeri </it>A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (<it>ben</it>) and 4-hydroxybenzoate (<it>pob</it>), and in the catechol (<it>cat</it>) and protocatechuate (<it>pca</it>) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the <it>catR </it>and <it>pcaK </it>genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the <it>ben </it>operon, while transcription from the <it>catBC </it>promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate.</p> <p>Conclusions</p> <p>The expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.</p

HLA-matched sibling transplantation with G-CSF mobilized PBSCs and BM decreases GVHD in adult patients with severe aplastic anemia

<p>Abstract</p> <p>Background</p> <p>Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an effective treatment for severe aplastic anemia (SAA). However, graft failure and graft-versus-host disease (GVHD) are major causes of the early morbidity in Allo-HSCT.</p> <p>Methods</p> <p>To reduce graft failure and GVHD, we treated fifteen patients with SAA using high- dose of HSCT with both G-CSF mobilized PB and BMSCs from HLA-identical siblings to treat patients with SAA.</p> <p>Results</p> <p>All patients had successful bone marrow engraftment. Only one patient had late rejection. Median time to ANC greater than 0.5 × 10⁹/L and platelet counts greater than 20 × 10⁹/L was 12 and 16.5 days, respectively. No acute GVHD was observed. The incidence of chronic GVHD was 6.67%. The total three-year probability of disease-free survival was 79.8%.</p> <p>Conclusion</p> <p>HSCT with both G-CSF mobilized PB and BMSCs is a promising approach for heavily transfused and/or allo-immunized patients with SAA.</p