Dual-Comb Gas Sensor Integrated with a Neural Network-Based Spectral Decoupling Algorithm of Overlapped Spectra for Gas Mixture Sensing.

Cross-interference among absorptions severely affects the ability to achieve accurate gas concentration retrieval through gas molecular specificity. In this study, a novel dual gas sensor was proposed to separate methane and water absorbance from the blended spectra of their mixture in the mid-infrared (MIR) band by employing a neural network algorithm. To address the scarcity of experimental data, the neural network was trained over a simulated data set constructed with the same distribution as the experimental ones. The system takes advantages of the broadband spectra to provide high-quality comb data and allows the neural network to establish an accurate spectral decoupling function. In addition, a feature absorption peak screening mechanism was proposed to achieve more accurate concentration retrieval, which avoids the prediction error introduced by interrogating the only peak of the separated spectra. The promising results of the systematic evaluation have demonstrated the feasibility of our methods in practical detections.

A Multi-Task Convolutional Neural Network for Lesion Region Segmentation and Classification of Non-Small Cell Lung Carcinoma.

Targeted therapy is an effective treatment for non-small cell lung cancer. Before treatment, pathologists need to confirm tumor morphology and type, which is time-consuming and highly repetitive. In this study, we propose a multi-task deep learning model based on a convolutional neural network for joint cancer lesion region segmentation and histological subtype classification, using magnified pathological tissue images. Firstly, we constructed a shared feature extraction channel to extract abstract information of visual space for joint segmentation and classification learning. Then, the weighted losses of segmentation and classification tasks were tuned to balance the computing bias of the multi-task model. We evaluated our model on a private in-house dataset of pathological tissue images collected from Qilu Hospital of Shandong University. The proposed approach achieved Dice similarity coefficients of 93.5% and 89.0% for segmenting squamous cell carcinoma (SCC) and adenocarcinoma (AD) specimens, respectively. In addition, the proposed method achieved an accuracy of 97.8% in classifying SCC vs. normal tissue and an accuracy of 100% in classifying AD vs. normal tissue. The experimental results demonstrated that our method outperforms other state-of-the-art methods and shows promising performance for both lesion region segmentation and subtype classification.

Variation in Growth, Colonization of Maize, and Metabolic Parameters of GFP- and DsRed-Labeled Fusarium verticillioides Strains.

Autofluorescent proteins are frequently applied as visual markers in the labeling of filamentous fungi. Genes gfp and DsRed were transformed into the genome of Fusarium verticillioides via the Agrobacterium tumefaciens-mediated transformation method. The selected transformants displayed a bright green or red fluorescence in all the organelles of the growing fungal mycelia and spores (except for the vacuoles) both in cultures and in the maize (Zea mays) roots they colonized. The results of gene-specific polymerase chain reaction (PCR) analysis and the thermal asymmetrical interlaced (TAIL)-PCR analysis demonstrated that gfp and DsRed were integrated on different chromosomes of the fungus. Reductions in the colony growth on the plates at pH 4.0 and 5.5 was observed for the green fluorescent protein (GFP)-transformant G3 and the DsRed-transformant R4, but transformants G4 and R1 grew as well as the wild-type strain at pH 4.0. The speed of growth of all the transformants was similar to the wild-type strain at pH ≥ 7. The insertion of gfp and DsRed did not alter the production of extracellular enzymes and fumonisin B by F. verticillioides. The transformants expressing GFP and DsRed proteins were able to colonize maize roots. However, the four transformants examined produced fewer CFU in the root samples than the wild-type strain during a sampling period of 7 to 28 days after inoculation.

[Vesicular transport protein VdSec22 is involved in secretion of extracellular protein and pathogenicity in Verticillium dahliae].

OBJECTIVE: The aim of this study was to characterize VdSec22 of Verticillium dahliae, which is an intracellular vesicle fusion protein involved in fungal secretory pathway, and to provide a potential gene target for controlling Verticillium wilt disease. METHODS: VdSec22 deletion mutant ΔQF and functional complementation strain CΔQF by reintroducing the VdSec22 intoAQF were constructed. Secretion ability of extracellular protein (including pectinase, cellulose, and phytotoxin protin) and pathogenicity of ΔQF and CΔQF were studied compared with that of wild type strain Vd991. Expression level of ER molecular chaperones by quantitative PCR was also performed to infer whether ER stress was induced in ΔQF. RESULTS: We successfully constructed VdSec22 deletion mutant strain ΔQF and functional complementation strain CΔQF. VdSec22 deficiencies did disturb secretion ability of extracellular protein such as pectinase, cellulose, and phytotoxin protin. Pathogenicity of ΔQF was dramatically reduce accordingly. We also found loss of VdSec22 resulted in ER stress in V. dahliae cells. Reintroducing functional VdSec22 into ΔQF can compensate for the deficiencies mentioned above. CONCLUSION: VdSec22 is an important secretion pathway protein involved in secretion of extracellular protein and pathogenicity in V. dahliae. VdSec22 provides a potential gene target for controlling the devastating disease.

Identification of six type III effector genes with the PIP box in Xanthomonas campestris pv. campestris and five of them contribute individually to full pathogenicity.

Xanthomonas campestris pv. campestris is the pathogen of black rot of cruciferous plants. The pathogenicity of the pathogen depends on the type III secretion system (T3SS) that translocates directly effector proteins into plant cells, where they play important roles in the molecular interaction between the pathogen and its hosts. The T3SS of Xanthomonas spp. is encoded by a cluster of hypersensitive response and pathogenicity (hrp) genes. It has been demonstrated that the expression of hrp genes and some type III secreted (T3S)-effector genes is coactivated by the key hrp regulatory protein HrpX. The regulation by HrpX can be mediated by the binding of HrpX protein to a cis-regulatory element named the plant-inducible promoter (PIP) box present in the promoter region of HrpX-regulated genes. A genome screen revealed that X. campestris pv. campestris 8004 possesses 56 predicted genes with the PIP box. Nine of these genes have been shown to encode T3S effectors, Hrp, and Hrp-associated proteins. In this study, we employed an established T3S effector translocation assay with the hypersensitive-reaction-inducing domain of X. campestris pv. campestris AvrBs1 as a reporter to characterize the remaining 47 genes with the PIP box and showed that 6 of them, designated as XopXccE1, XopXccP, XopXccQ, XopXccR1, XopXccLR, and AvrXccB, harbor a functional translocation signal in their N-terminal regions, indicating that they are T3S effectors of X. campestris pv. campestris. We provided evidence to demonstrate that all these effectors are expressed in an HrpX-dependent manner and their translocation into plant cells relies on the translocon protein HrpF and the chaperone HpaB. Mutational analyses demonstrated that all these effectors, except AvrXccB, are individually required for full virulence and growth of X. campestris pv. campestris in the host plant Chinese radish.

AvrAC(Xcc8004), a type III effector with a leucine-rich repeat domain from Xanthomonas campestris pathovar campestris confers avirulence in vascular tissues of Arabidopsis thaliana ecotype Col-0.

Xanthomonas campestris pathovar campestris causes black rot, a vascular disease on cruciferous plants, including Arabidopsis thaliana. The gene XC1553 from X. campestris pv. campestris strain 8004 encodes a protein containing leucine-rich repeats (LRRs) and appears to be restricted to strains of X. campestris pv. campestris. LRRs are found in a number of type III-secreted effectors in plant and animal pathogens. These prompted us to investigate the role of the XC1553 gene in the interaction between X. campestris pv. campestris and A. thaliana. Translocation assays using the hypersensitive-reaction-inducing domain of X. campestris pv. campestris AvrBs1 as a reporter revealed that XC1553 is a type III effector. Infiltration of Arabidopsis leaf mesophyll with bacterial suspensions showed no differences between the wild-type strain and an XC1553 gene mutant; both strains induced disease symptoms on Kashmir and Col-0 ecotypes. However, a clear difference was observed when bacteria were introduced into the vascular system by piercing the central vein of leaves. In this case, the wild-type strain 8004 caused disease on the Kashmir ecotype, but not on ecotype Col-0; the XC1553 gene mutant became virulent on the Col-0 ecotype and still induced disease on the Kashmir ecotype. Altogether, these data show that the XC1553 gene, which was renamed avrAC(Xcc8004), functions as an avirulence gene whose product seems to be recognized in vascular tissues.

Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris.

BACKGROUND: Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS: We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated the genetic diversity and host specificity of Xcc by array-based comparative genome hybridization analyses of 18 virulent strains. The results demonstrate that a genetic core comprising 3,405 of the 4,186 coding sequences (CDSs) spotted on the array are conserved and a flexible gene pool with 730 CDSs is absent/highly divergent (AHD). The results also revealed that 258 of the 304 proved/presumed pathogenicity genes are conserved and 46 are AHD. The conserved pathogenicity genes include mainly the genes involved in type I, II and III secretion systems, the quorum sensing system, extracellular enzymes and polysaccharide production, as well as many other proved pathogenicity genes, while the AHD CDSs contain the genes encoding type IV secretion system (T4SS) and type III-effectors. A Xcc T4SS-deletion mutant displayed the same virulence as wild type. Furthermore, three avirulence genes (avrXccC, avrXccE1 and avrBs1) were identified. avrXccC and avrXccE1 conferred avirulence on the hosts mustard cultivar Guangtou and Chinese cabbage cultivar Zhongbai-83, respectively, and avrBs1 conferred hypersensitive response on the nonhost pepper ECW10R. CONCLUSION: About 80% of the Xcc CDSs, including 258 proved/presumed pathogenicity genes, is conserved in different strains. Xcc T4SS is not involved in pathogenicity. An efficient strategy to identify avr genes determining host specificity from the AHD genes was developed.