Identification of metabolism pathways directly regulated by sigma54 factor in Bacillus thuringiensis

Sigma54 (σ54) normally regulates nitrogen and carbon utilization in bacteria. Promoters that are σ54-dependent are highly conserved and contain short sequences located at the −24 and −12 positions upstream of the transcription initiation site. σ54 requires regulatory proteins known as bacterial enhancer-binding proteins (bEBPs) to activate gene transcription. We show that σ54 regulates the capacity to grow on various nitrogen sources using a Bacillus thuringiensis HD73 mutant lacking the sigL gene encoding σ54 (ΔsigL). A 2-fold-change cutoff and a false discovery rate cutoff of P < 0.05 were used to analyze the DNA microarray data, which revealed 255 genes that were downregulated and 121 that were upregulated in the ΔsigL mutant relative to the wild-type HD73 strain. The σ54 regulon (stationary phase) was characterized by DNA microarray, bioinformatics, and functional assay; 16 operons containing 47 genes were identified whose promoter regions contain the conserved −12/−24 element and whose transcriptional activities were abolished or reduced in the ΔsigL mutant. Eight σ54-dependent transcriptional bEBPs were found in the Bt HD73 genome, and they regulated night σ54-dependent promoters.The metabolic pathways activated by σ54 in this process have yet to be identified in Bacillus thuringiensis; nonetheless, the present analysis of the σ54 regulon provides a better understanding of the physiological roles of σ factors in bacteria

Integrated transcriptome analysis reveals miRNA-mRNA crosstalk in laryngeal squamous cell carcinoma.

Next generation sequencing (NGS) has proven to be a powerful tool in delineating myriads of molecular subtypes of cancer, as well as in revealing accumulation of genomic mutations throughout cancer progression. Whole genome microRNA (miRNA) and mRNA expression profiles were obtained from patients with laryngeal squamous cell carcinoma (LSCC) using deep sequencing technology, and were analyzed by utilizing integrative computational approaches. A large number of protein-coding and non-coding genes were detected to be differentially expressed, indicating a functional switch in LSCC cells. A total of 127 mutated genes were detected to be significantly associated with ectoderm and epidermis development. Eleven miRNAs were found to be differentially expressed, including a potential cancer suppressor miRNA, mir-34c, which was dramatically down-regulated. Integrated analysis of mRNA and miRNA transcriptomes further revealed correlated dynamics among 11 miRNAs and 138 targeted genes, forming a highly dynamical co-regulation network response to LSCC development

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes

Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database—LCGbase (a comprehensive database for lineage-based co-regulated genes)—hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene ontology (GO) annotation, promoter identification, gene expression (co-expression), and evolutionary analysis. This database not only provides a way to define lineage-specific and species-specific gene clusters but also facilitates future studies on gene co-regulation, epigenetic control of gene expression (DNA methylation and histone marks), and chromosomal structures in a context of gene clusters and species evolution. LCGbase is freely available at http://lcgbase.big.ac.cn/LCGbase

RealFlow: EM-based Realistic Optical Flow Dataset Generation from Videos

Obtaining the ground truth labels from a video is challenging since the manual annotation of pixel-wise flow labels is prohibitively expensive and laborious. Besides, existing approaches try to adapt the trained model on synthetic datasets to authentic videos, which inevitably suffers from domain discrepancy and hinders the performance for real-world applications. To solve these problems, we propose RealFlow, an Expectation-Maximization based framework that can create large-scale optical flow datasets directly from any unlabeled realistic videos. Specifically, we first estimate optical flow between a pair of video frames, and then synthesize a new image from this pair based on the predicted flow. Thus the new image pairs and their corresponding flows can be regarded as a new training set. Besides, we design a Realistic Image Pair Rendering (RIPR) module that adopts softmax splatting and bi-directional hole filling techniques to alleviate the artifacts of the image synthesis. In the E-step, RIPR renders new images to create a large quantity of training data. In the M-step, we utilize the generated training data to train an optical flow network, which can be used to estimate optical flows in the next E-step. During the iterative learning steps, the capability of the flow network is gradually improved, so is the accuracy of the flow, as well as the quality of the synthesized dataset. Experimental results show that RealFlow outperforms previous dataset generation methods by a considerably large margin. Moreover, based on the generated dataset, our approach achieves state-of-the-art performance on two standard benchmarks compared with both supervised and unsupervised optical flow methods. Our code and dataset are available at https://github.com/megvii-research/RealFlowComment: ECCV 2022 Ora

Seroprevalence of Bartonella in Eastern China and analysis of risk factors

<p>Abstract</p> <p>Background</p> <p><it>Bartonella </it>infections are emerging in the Zhejiang Province of China. However, there has been no effort to date to explore the epidemiology of these infections in this region, nor to identify risk factors associated with exposure to <it>Bartonella</it>. The aim of this study was to investigate the seroprevalence of <it>Bartonella </it>in both patients bitten by dogs and blood donors (for control) in Eastern China, and to identify risk factors associated with exposure to <it>Bartonella</it>. As no previous data for this region have been published, this study will provide baseline data useful for <it>Bartonella </it>infection surveillance, control, and prevention.</p> <p>Methods</p> <p>Blood samples were collected from industrial rabies clinic attendees and blood donors living in eight areas of the Zhejiang Province of China, between December 2005 and November 2006. An indirect immunofluorescent antibody test was used to determine the presence of <it>Bartonella </it>in these samples. Risk factors associated with <it>Bartonella </it>exposure were explored using Chi-square tests and logistic regression analysis of epidemiological data relating to the study's participants.</p> <p>Results</p> <p><it>Bartonella </it>antibodies were detected in 19.60% (109/556) of blood samples. Seroprevalence varied among the eight areas surveys, ranging from over 32% in Hangzhou to only 2% in Jiangshan (X²= 28.22, P < 0.001). We detected a significantly higher prevalence of <it>Bartonella </it>antibodies in people who had been bitten by dogs than in blood donors (X²= 13.86, P < 0.001). Seroprevalence of <it>Bartonella </it>was similar among males (18.61%, n = 317) and females (20.92%, n = 239).</p> <p>Conclusions</p> <p><it>Bartonella </it>antibodies were encountered in people living across Zhejiang Province and the seropositivity rate among those exposed to dog bites was significantly higher than that among blood donors, indicating that dog bites may be a risk factor for <it>Bartonella </it>infection.</p

Poly(2,5-dihydroxy-1,4-benzoquinonyl sulfide) (PDBS) as a cathode material for lithium ion batteries

An organic cathode material, poly(2,5-dihydroxyl-1,4-benzoquinonyl sulfide) (PDBS), has been synthesized and assessed as a cathode material for lithium ion batteries. The prepared polymer material is characterized by (13)C solid state NMR, FTIR, XPS and elemental analysis techniques. The (13)C solid state NMR, FTIR and XPS results indicate that the chlorine of chloranilic acid (CLA) is successfully substituted by sulfur after a sulfurization reaction. Elemental analysis shows that the prepared polymer is mainly composed of dimer and trimer. The electrochemical measurements show that the initial discharge capacity of PDBS is up to 350 mAh g(-1), and 184 mAh g(-1) still remains after 100 cycles at the current density of 15 mA g(-1) in the voltage range of 1.5-3.6 V. The PDBS also shows high cycling stability, good rate capability and discharge/ charge coulombic efficiency of higher than 98%, except for in the initial cycles. The good cycling stabilities and the high coulombic efficiency of the material are ascribed to the stable thioether bonds for stabilizing the framework of the polymer and the highly reversible carbonyl groups for energy storage.National Natural Science Foundation of China[20873115]; National Basic Research Program of China (973 program)[2007CB209702

Quantitatively analyzing the failure processes of rechargeable Li metal batteries.

Practical use of lithium (Li) metal for high–energy density lithium metal batteries has been prevented by the continuous formation of Li dendrites, electrochemically isolated Li metal, and the irreversible formation of solid electrolyte interphases (SEIs). Differentiating and quantifying these inactive Li species are key to understand the failure mode. Here, using operando nuclear magnetic resonance (NMR) spectroscopy together with ex situ titration gas chromatography (TGC) and mass spectrometry titration (MST) techniques, we established a solid foundation for quantifying the evolution of dead Li metal and SEI separately. The existence of LiH is identified, which causes deviation in the quantification results of dead Li metal obtained by these three techniques. The formation of inactive Li under various operating conditions has been studied quantitatively, which revealed a general “two-stage” failure process for the Li metal. The combined techniques presented here establish a benchmark to unravel the complex failure mechanism of Li metal

Study on wound healing effect of low-carbon topical dressings with new green packaging

In order to verify the effect of the new green and low-carbon hydrogel dressing on promoting wound healing, this project applied a sodium alginate hydrogel dressing product containing Escherichia coli and taro toxin analgesic polypeptide (The specific ingredients of the dressing) to skin wounds in common rats. Effects of the hydrogel dressing on promoting skin wound healing was evaluated by observing the occurrence and frequency of behavioral changes in rats, observing wwhistological sections under a high-power microscope, changes in serum cytokine indicators, and Image J analysis of collagen fiber reconstruction ratios in tissue sections. Through comprehensive evaluation, it can be found that hydrogel dressing has analgesic, anti-inflammatory and anti-infection effects on rat wound surface, and acts on promoting wound healing, promoting the formation of new blood vessels in the damaged skin tissue area, promoting the growth of granulation tissue, and promoting the reconstruction of collagen fibers in wound tissue

Evaluation of resistance of banana genotypes with AAB genome to Fusarium Wilt Tropical Race 4 in China

Banana cultivars with the AAB genome group comprise diverse subgroups, such as Plantain, Silk, Iholena, and Pisang Raja, among others, which play an important role in food security in many developing countries. Some of these cultivars are susceptible to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), the most destructive pathogen threatening banana production worldwide, and some of them are still largely unknown. We evaluated the resistance of 37 banana genotypes, including Plantain, Silk, Iholena, Maia Maoli/Popoulu, Pisang Raja, Pome, and Mysore, to Foc TR4 under both greenhouse and field conditions. Genotypes from the Silk and Iholena subgroups were highly susceptible to Foc TR4. Pome and Mysore showed resistance and intermediate resistance, respectively. However, Pisang Raja ranged from susceptible to intermediate resistance. One cultivar from the Maia Maoli/Popoulu subgroup was highly susceptible, while the other displayed significant resistance. Most Plantain cultivars exhibited high resistance to Foc TR4, except two French types of cultivar, 'Uganda Plantain' and 'Njombe N°2', which were susceptible. The susceptibility to Foc TR4 of some of the AAB genotypes evaluated, especially Plantain and other cooking bananas, indicates that growers dependent on these varieties need to be included as part of the prevention and integrated Foc TR4 management strategies, as these genotypes play a crucial role in food security and livelihoods