Deep learning-based hyperspectral technique identifies metastatic lymph nodes in oral squamous cell carcinoma-A pilot study.

AIMS: To establish a system based on hyperspectral imaging and deep learning for the detection of cancer cells in metastatic lymph nodes. MAIN METHODS: The continuous sections of metastatic lymph nodes from 45 oral squamous cell carcinoma (OSCC) patients were collected. An improved ResUNet algorithm was established for deep learning to analyze the spectral curve differences between cancer cells and lymphocytes, and that between tumor tissue and normal tissue. KEY FINDINGS: It was found that cancer cells, lymphocytes, and erythrocytes in the metastatic lymph nodes could be distinguished basing hyperspectral image, with overall accuracy (OA) as 87.30% and average accuracy (AA) as 85.46%. Cancerous area could be recognized by hyperspectral image and deep learning, and the average intersection over union (IOU) and accuracy were 0.6253 and 0.7692, respectively. SIGNIFICANCE: This study indicated that deep learning-based hyperspectral techniques can identify tumor tissue in OSCC metastatic lymph nodes, achieving high accuracy of pathological diagnosis, high work efficiency, and reducing work burden. But these are preliminary results limited to a small sample.

Enhanced Energy Density of Coaxial Fiber Asymmetric Supercapacitor Based on MoS2 @Fe2 O3 /Carbon Nanotube Paper and Ni(OH)2 @NiCo2 O4 /Carbon Nanotube Fiber Electrodes.

Fiber supercapacitors are promising energy storage devices for potential application in wearable and miniaturized portable electronics, which currently suffer from difficulties in achieving high capacitance and energy density synchronously owing to the limited specific surface area of the electrode materials and material incompatibility between the two electrodes. Herein, a strategy is developed for the manufacture of coaxial asymmetric fiber supercapacitors by wrapping a core of PVA-KOH gel electrolyte-coated Ni(OH)2 @NiCo2 O4 /CNT fibers with MoS2 @Fe2 O3 /CNT paper. The as-prepared coaxial fiber asymmetric supercapacitors exhibit a specific capacitance of 373 mF cm-2 (at a current density of 2 mA cm-2 ) and energy density of 0.13 mW h cm-2 (at a power density of 3.2 mW cm-2 ), and also show good rate capability, long cycle life, and excellent flexibility. This work provides the possibility for the practical application of fiber supercapacitors in wearable and portable energy storage equipment.

Plasma Treatment for Nitrogen-Doped 3D Graphene Framework by a Conductive Matrix with Sulfur for High-Performance Li-S Batteries.

Carbon materials have received considerable attention as host cathode materials for sulfur in lithium-sulfur batteries; N-doped carbon materials show particularly high electrocatalytic activity. Efforts are made to synthesize N-doped carbon materials by introducing nitrogen-rich sources followed by sintering or hydrothermal processes. In the present work, an in situ hollow cathode discharge plasma treatment method is used to prepare 3D porous frameworks based on N-doped graphene as a potential conductive matrix material. The resulting N-doped graphene is used to prepare a 3D porous framework with a S content of 90 wt% as a cathode in lithium-sulfur cells, which delivers a specific discharge capacity of 1186 mAh g-1 at 0.1 C, a coulombic efficiency of 96% after 200 cycles, and a capacity retention of 578 mAh g-1 at 1.0 C after 1000 cycles. The performance is attributed to the flexible 3D structure and clustering of pyridinic N-dopants in graphene. The N-doped graphene shows high electrochemical performance and the flexible 3D porous stable structure accommodates the considerable volume change of the active material during lithium insertion and extraction processes, improving the long-term electrochemical performance.

Characterization of genome-reduced Bacillus subtilis strains and their application for the production of guanosine and thymidine.

BACKGROUND: Genome streamlining has emerged as an effective strategy to boost the production efficiency of bio-based products. Many efforts have been made to construct desirable chassis cells by reducing the genome size of microbes. It has been reported that the genome-reduced Bacillus subtilis strain MBG874 showed clear advantages for the production of several heterologous enzymes including alkaline cellulase and protease. In addition to enzymes, B. subtilis is also used for the production of chemicals. To our best knowledge, it is still unknown whether genome reduction could be used to optimize the production of chemicals such as nucleoside products. RESULTS: In this study, we constructed a series of genome-reduced strains by deleting non-essential regions in the chromosome of B. subtilis 168. These strains with genome reductions ranging in size from 581.9 to 814.4 kb displayed markedly decreased growth rates, sporulation ratios, transformation efficiencies and maintenance coefficients, as well as increased cell yields. We re-engineered the genome-reduced strains to produce guanosine and thymidine, respectively. The strain BSK814G2, in which purA was knocked out, and prs, purF and guaB were co-overexpressed, produced 115.2 mg/L of guanosine, which was 4.4-fold higher compared to the control strain constructed by introducing the same gene modifications into the parental strain. We also constructed a thymidine producer by deleting the tdk gene and overexpressing the prs, ushA, thyA, dut, and ndk genes from Escherichia coli in strain BSK756, and the resulting strain BSK756T3 accumulated 151.2 mg/L thymidine, showing a 5.2-fold increase compared to the corresponding control strain. CONCLUSIONS: Genome-scale genetic manipulation has a variety of effects on the physiological characteristics and cell metabolism of B. subtilis. By introducing specific gene modifications related to guanosine and thymidine accumulation, respectively, we demonstrated that genome-reduced strains had greatly improved properties compared to the wild-type strain as chassis cells for the production of these two products. These strains also have great potential for the production of other nucleosides and similar derived chemicals.

Study on spatiotemporal dynamic characteristics of precipitation and causes of waterlogging based on a data-driven framework.

The discernible alterations in regional precipitation patterns, influenced by the intersecting factors of urbanization and climate change, exert a substantial impact on urban flood disasters. Based on multi-source precipitation data, a data-driven model fusion framework was constructed to analyze the spatial and temporal dynamic distribution characteristics of precipitation in Beijing. Wavelet analysis method was used to reveal the periodic variation characteristics and multi-scale effects of precipitation, and the machine learning method was used to characterize the spatiotemporal dynamic change pattern of precipitation. Finally, geographical detector was used to explore the causes of waterlogging in Beijing. The research outcomes reveal a disparate distribution of precipitation across the year, with 78 % of the total precipitation occurring during the flood season. The principal periodic cycles observed in annual cumulative precipitation (ACP) were identified at 21, 13, and 9-year intervals. Spatially, while a decreasing trend in precipitation was observed in most areas of Beijing, 63.4 % of the region exhibited an escalating concentration trend, thereby heightening the risk of urban waterlogging. Machine learning model clustering elucidated three predominant spatial dynamic distribution patterns of precipitation in Beijing. The utilization of web crawler technology to acquire water accumulation data addressed challenges in obtaining urban waterlogging data, and validation through Landsat8 images enhanced data reliability and authenticity. Factor detection shows that road network density, topography, and precipitation were the main factors affecting urban waterlogging. These findings hold significant implications for informing flood control strategies and emergency management protocols in urban areas across China.

miR-34b-5p suppresses the epithelial-mesenchymal transition and metastasis in endometrial cancer AN3CA cells by targeting ZEB1.

OBJECTIVES: Tumor metastasis is a primary cause of recurrence and mortality in endometrial cancer. miR-34b-5p is abnormally expressed in various cancers and participates in tumor cell progression and metastasis. The objective of this study was to elucidate the biological functions and molecular mechanisms of miR-34b-5p in regulating the epithelial-mesenchymal transition (EMT) and metastasis in AN3CA endometrial cancer cells. METHODS: The expression levels of miR-34b-5p and zinc finger E-box-binding homeobox 1 (ZEB1) in endometrial cancer cells were analyzed by qRT-PCR, and ZEB1 expression in endometrial cancer tissues was examined by immunohistochemistry. Proliferation, migration, and invasion of endometrial cancer AN3CA cells were evaluated using CCK8, scratch, and transwell assays, respectively. Bioinformatic analysis and dual-luciferase reporter gene assays were used to validate the targeting relationship between miR-34b-5p and ZEB1. Western blotting was performed to analyze the expression levels of ZEB1 and EMT-related proteins. RESULTS: miR-34b-5p was significantly downregulated in endometrial cancer AN3CA cells. Overexpression of miR-34b-5p significantly inhibited proliferation, invasion, migration, and the EMT of endometrial cancer AN3CA cells. ZEB1, which was identified as a direct target gene of miR-34b-5p, exhibited high expression in endometrial cancer cells and tissues. Additionally, ZEB1 upregulation partially reversed the inhibitory effects of miR-34b-5p on proliferation, migration, invasion, and the EMT of endometrial cancer AN3CA cells. CONCLUSIONS: miR-34b-5p suppresses the EMT and metastasis in endometrial cancer AN3CA cells by targeting ZEB1, indicating that the miR-34b-5p-ZEB1-EMT axis may be a therapeutic target for endometrial cancer.

FD-Net: Feature Distillation Network for Oral Squamous Cell Carcinoma Lymph Node Segmentation in Hyperspectral Imagery.

Oral squamous cell carcinoma (OSCC) has the characteristics of early regional lymph node metastasis. OSCC patients often have poor prognoses and low survival rates due to cervical lymph metastases. Therefore, it is necessary to rely on a reasonable screening method to quickly judge the cervical lymph metastastic condition of OSCC patients and develop appropriate treatment plans. In this study, the widely used pathological sections with hematoxylin-eosin (H&E) staining are taken as the target, and combined with the advantages of hyperspectral imaging technology, a novel diagnostic method for identifying OSCC lymph node metastases is proposed. The method consists of a learning stage and a decision-making stage, focusing on cancer and non-cancer nuclei, gradually completing the lesions' segmentation from coarse to fine, and achieving high accuracy. In the learning stage, the proposed feature distillation-Net (FD-Net) network is developed to segment the cancerous and non-cancerous nuclei. In the decision-making stage, the segmentation results are post-processed, and the lesions are effectively distinguished based on the prior. Experimental results demonstrate that the proposed FD-Net is very competitive in the OSCC hyperspectral medical image segmentation task. The proposed FD-Net method performs best on the seven segmentation evaluation indicators: MIoU, OA, AA, SE, CSI, GDR, and DICE. Among these seven evaluation indicators, the proposed FD-Net method is 1.75%, 1.27%, 0.35%, 1.9%, 0.88%, 4.45%, and 1.98% higher than the DeepLab V3 method, which ranks second in performance, respectively. In addition, the proposed diagnosis method of OSCC lymph node metastasis can effectively assist pathologists in disease screening and reduce the workload of pathologists.

Multi-omics analysis of small RNA, transcriptome, and degradome to identify putative miRNAs linked to MeJA regulated and oridonin biosynthesis in Isodon rubescens.

Isodon rubescens has garnered much attention due to its anti-tumor or anti-cancer properties. However, little is known about the molecular mechanism of oridonin biosynthesis leveraging the regulatory network between small RNAs and mRNAs. In this study, the regulatory networks of miRNAs and targets were examined by combining mRNA, miRNA, and degradome. A total of 348 miRNAs, including 287 known miRNAs and 61 novel miRNAs, were identified. Among them, 51 miRNAs were significantly expressed, and 36 miRNAs responded to MeJA. A total of 3066 target genes were associated with 228 miRNAs via degradome sequencing. Multi-omics analysis demonstrated that 27 miRNA-mRNA pairs were speculated to be involved in MeJA regulation, and 36 miRNA-mRNA pairs were hypothesized to be involved in the genotype-dependence of I. rubescens. Furthermore, 151 and 7 miRNA-mRNA modules were likely engaged in oridonin biosynthesis as identified by psRNATarget and degradome sequencing, respectively. Some miRNA-mRNA modules were confirmed via RT-qPCR. Moreover, miRNAs targeting plant hormone signal transduction pathway genes were identified, such as miR156, miR167, miR393, and PC-3p-19822_242. Collectively, our results demonstrate for the first time that miRNAs are identified in I. rubescens, and laid a solid foundation for further research on the molecular mechanism of oridonin biosynthesis mediated by miRNA.

Analysis of cellular response to drugs with a microfluidic single-cell platform based on hyperspectral imaging.

BACKGROUND: Cellular response to pharmacological action of drugs is significant for drug development. Traditional detection method for cellular response to drugs normally rely on cell proliferation assay and metabolomics examination. In principle, these analytical methods often required cell labeling, invasion analysis, and hours of co-culture with drugs, which are relatively complex and time-consuming. Moreover, these methods can only indicate the drug effectiveness on cell colony rather than single cells. Thus, to meet the requirements of personal precision medicine, the development of drug response analysis on the high resolution of single cell is demanded. RESULTS: To provide precise result for drug response on single-cell level, a microfluidic platform coupled with the label-free hyperspectral imaging was developed. With the help of horizontal single-cell trapping sieves, hundreds of single cells were trapped independently in microfluidic channels for the purposes of real-time drug delivery and single-cell hyperspectral image recording. To significantly identify the cellular hyperspectral change after drug stimulation, the differenced single-cell spectrum was proposed. Compared with the deep learning classification method based on hyperspectral images, an optimal performance can be achieved by the classification strategy based on differenced spectra. And the cellular response to different reagents, for example, K+, Epidermal Growth Factor (EGF), and Gefitinib at different concentrations can be accurately characterized by the differenced single-cell spectra analysis. SIGNIFICANCE AND NOVELTY: The high-throughput, rapid analysis of cellular response to drugs at the single-cell level can be accurately performed by our platform. After systematically analyzing the materials and the structures of the single-cell microfluidic chip, the optimal single-cell trapping method was proposed to contribute to the further application of hyperspectral imaging on microfluidic single-cell analysis. And the hyperspectral characterization of single-cell with cancer drug stimulation proved the application potential of our method in personal cancer medication.

Proteomics analysis of immune response-related proteins in Guillain-Barré Syndrome (GBS) and Chronic Inflammatory Demyelinating Polyneuropathy (CIDP).

The objective is to characterize differentially expressed proteins (DEPs) in Guillain-Barré Syndrome (GBS) and Chronic Inflammatory Demyelinating Polyneuropathy (CIDP) through high-throughput analysis. Sera from 11 healthy controls (HCs), 21 GBS and 19 CIDP patients were subjected to Olink Proteomics Analysis. In the comparison between CIDP and GBS groups, up-regulation of ITM2A and down-regulation of NTF4 were observed. Comparing GBS with HCs revealed 18 up-regulated and 4 down-regulated proteins. Comparing CIDP with the HCs identified 15 up-regulated and 4 down-regulated proteins. Additionally, the correlation between clinical characteristics and DEPs were uncovered. In conclusion, the DEPs have significant potential to advance our understanding of the pathogenesis in these debilitating neurological disorders.

Interferon-induced transmembrane protein-1 competitively blocks Ephrin receptor A2-mediated Epstein-Barr virus entry into epithelial cells.

Epstein-Barr virus (EBV) can infect both B cells and epithelial cells (ECs), causing diseases such as mononucleosis and cancer. It enters ECs via Ephrin receptor A2 (EphA2). The function of interferon-induced transmembrane protein-1 (IFITM1) in EBV infection of ECs remains elusive. Here we report that IFITM1 inhibits EphA2-mediated EBV entry into ECs. RNA-sequencing and clinical sample analysis show reduced IFITM1 in EBV-positive ECs and a negative correlation between IFITM1 level and EBV copy number. IFITM1 depletion increases EBV infection and vice versa. Exogenous soluble IFITM1 effectively prevents EBV infection in vitro and in vivo. Furthermore, three-dimensional structure prediction and site-directed mutagenesis demonstrate that IFITM1 interacts with EphA2 via its two specific residues, competitively blocking EphA2 binding to EBV glycoproteins. Finally, YTHDF3, an m6A reader, suppresses IFITM1 via degradation-related DEAD-box protein 5 (DDX5). Thus, this study underscores IFITM1's crucial role in blocking EphA2-mediated EBV entry into ECs, indicating its potential in preventing EBV infection.

Analysis of the genetic effects of prolactin gene polymorphisms on chicken egg production.

Chicken prolactin (PRL) is a physiological candidate gene for egg production. Variations of T8052C and G8113C in exon 5 of PRL gene may associate with chicken egg production. The objective of the study was to investigate the association of these two single nucleotide polymorphisms in PRL gene with egg production of Recessive White chickens and Qingyuan Partridge chickens. Genotyping was performed by polymerase chain reaction-ligase detection reaction (PCR-LDR) method. The T8052C and G8113C of PRL were significantly associated with age at first egg (AFE) and total egg number at 300 days of age (EN 300). A significant association was also found between T8052C-G8113C haplotypes and AFE as well as EN300, the H2H3 was the most advantageous diplotype for egg production. We putatively drew the conclusion that these two SNPs in PRL gene as well as their haplotypes could be used as the potential molecular markers for egg production traits in chicken.

Microarray analysis of genes involved with shell strength in layer shell gland at the early stage of active calcification.

The objective of this study was to get a comprehensive understanding of how genes in chicken shell gland modulate eggshell strength at the early stage of active calcification. Four 32-week old of purebred Xianju hens with consistent high or low shell breakage strength were grouped into two pairs. Using Affymetrix Chicken Array, a whole-transcriptome analysis was performed on hen's shell gland at 9 h post oviposition. Gene ontology enrichment analysis for differentially expressed (DE) transcripts was performed using the web-based GOEAST, and the validation of DE-transcripts was tested by qRT-PCR. 1,195 DE-transcripts, corresponding to 941 unique genes were identified in hens with strong eggshell compared to weak shell hens. According to gene ontology annotations, there are 77 DE-transcripts encoding ion transporters and secreted extracellular matrix proteins, and at least 26 DE-transcripts related to carbohydrate metabolism or post-translation glycosylation modification; furthermore, there are 88 signaling DE-transcripts. GO term enrichment analysis suggests that some DE-transcripts mediate reproductive hormones or neurotransmitters to affect eggshell quality through a complex suite of biophysical processes. These results reveal some candidate genes involved with eggshell strength at the early stage of active calcification which may facilitate our understanding of regulating mechanisms of eggshell quality.

Functional lightweight polystyrene@polydopamine nanoparticle for high-performance ELISA.

Nanoparticles are usually used as carrier to load more antibody and enzyme to improve the sensitivity of enzyme-linked immunosorbent assay (ELISA). However, limited by high density and complicated modification procedure, the traditional nanoparticles such as Au nanoparticles (AuNPs) usually induce large background signal and poor reproducibility in ELISA. In this work, functional lightweigh nanoparticle polystyrene@polydopamine (PS@PDA) was prepared and induced as the carrier of detection antibody and horseradish peroxidase (HRP) to form PS@PDA@Ab2/HRP biojungates. The appropriate density (close to water) and good hydropilicity ensure the good dispersion of PS@PDA@Ab2/HRP in solution, preventing the physical sedimention and decreasing the background signal even though the bioconjugate's size is close to 200 nm. The large surface area and abundant active group from PDA facilitate the loading of detection antibody and HRP, improving the loading efficiency and stability of biojungates. Based on it, taking interleukin-17A (IL-17A, a biomarker of psoriasis) as the detection target, we developed a PS@PDA-based sandwich ELISA, achieving a sensitive dynamic range from 0.3 to 80 pg/mL and a detection limit of 0.2 pg/mL. Furthermore, the contents of IL-17A were assayed successfully in 10-fold diluted serum samples from psoriasis patients. Compared with those commercial or AuNP-based ELISA, our PS@PDA-based ELISA method exhibits higher sensitivity, lower background interference, and higher stability, which will significantly improve the application of ELISA in the low-abundant biomolecule assays.

A Diamond/Graphene/Diamond Electrode for Waste Water Treatment.

Boron-doped diamond (BDD) thin film electrodes have great application potential in water treatment. However, the high electrode energy consumption due to high resistance directly limits the application range of existing BDD electrodes. In this paper, the BDD/graphene/BDD (DGD) sandwich structure electrode was prepared, which effectively improved the conductivity of the electrode. Meanwhile, the sandwich electrode can effectively avoid the degradation of electrode performance caused by the large amount of non-diamond carbon introduced by heavy doping, such as the reduction of the electrochemical window and the decrease of physical and chemical stability. The microstructure and composition of the film were characterized by scanning electron microscope (SEM), atomic force microscopy (AFM), Raman spectroscopy, and transmission electron microscopy (TEM). Then, the degradation performance of citric acid (CA), catechol, and tetracycline hydrochloride (TCH) by DGD electrodes was systematically studied by total organic carbon (TOC) and Energy consumption per unit TOC removal (ECTOC). Compared with the single BDD electrode, the new DGD electrode improves the mobility of the electrode and reduces the mass transfer resistance by 1/3, showing better water treatment performance. In the process of dealing with Citric acid, the step current of the DGD electrode was 1.35 times that of the BDD electrode, and the energy utilization ratio of the DGD electrode was 2.4 times that of the BDD electrode. The energy consumption per unit TOC removal (ECTOC) of the DGD electrode was lower than that of BDD, especially Catechol, which was reduced to 66.9% of BDD. The DGD sandwich electrode, as a new electrode material, has good electrochemical degradation performance and can be used for high-efficiency electrocatalytic degradation of organic pollutants.

Genome resequencing reveals the evolutionary history of garlic reproduction traits.

The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.

Metabolic engineering of Bacillus subtilis for enhanced production of acetoin.

Acetoin is widely used in food and other industries. A bdhA and acoA double-knockout strain of Bacillus subtilis produced acetoin at 0.72 mol/mol, a 16.4 % increased compared to the wild type. Subsequent overexpression of the alsSD operon enhanced the acetolactate synthase activity by 52 and 66 % in growth and stationary phases, respectively. However, deletion of pta gene caused little increase of acetoin production. For acetoin production by the final engineered strain, BSUW06, acetoin productivity was improved from 0.087 g/l h, using M9 medium plus 30 g glucose/l under micro-aerobic conditions, to 0.273 g/h l using LB medium plus 50 g glucose/l under aerobic conditions. In fermentor culture, BSUW06 produced acetoin up to 20 g/l.

Genome-wide Identification and Characterization of the GRAS Transcription Factors in Garlic (Allium sativum L.).

GRAS transcription factors play crucial roles in plant growth and development and have been widely explored in many plant species. Garlic (Allium sativum L.) is an important crop owing to its edible and medicinal properties. However, no GRAS transcription factors have been identified in this crop. In this study, 46 garlic GRAS genes were identified and assigned to 16 subfamilies using the GRAS members of Arabidopsis thaliana, Oryza sativa, and Amborella trichopoda as reference queries. Expression analysis revealed that garlic GRAS genes showed distinct differences in various garlic tissues, as well as during different growth stages of the bulbs. Five of these 46 genes were identified as DELLA-like protein-encoding genes and three of which, Asa2G00237.1/Asa2G00240.1 and Asa4G02090.1, responded to exogenous GA3 treatment, and showed a significant association between their transcription abundance and bulb traits in 102 garlic accessions, thereby indicating their role in regulating the growth of garlic bulbs. These results will lay a useful foundation for further investigation of the biological functions of GRAS genes and guiding the genetic breeding of garlic in the future.

Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens.

Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases and conditions such as inflammation, respiratory and gastrointestinal bacterial infections, and malignant tumors. However, the contents of the main active components of I. rubescens from different origins differ significantly, which greatly affected its quality. Therefore, a molecular method to identify and classify I. rubescens is needed. Here, we report the DNA sequence of the chloroplast genome of I. rubescens collected from Lushan, Henan province. The genome is 152,642 bp in length and has a conserved structure that includes a pair of IR regions (25,726 bp), a LSC region (83,527 bp) and a SSC region (17,663 bp). The chloroplast genome contains 113 unique genes, four rRNA genes, 30 tRNA genes, and 79 protein-coding genes, 23 of which contain introns. The protein-coding genes account for a total of 24,412 codons, and most of them are A/T biased usage. We identified 32 simple sequence repeats (SSRs) and 48 long repeats. Furthermore, we developed valuable chloroplast molecular resources by comparing chloroplast genomes from three Isodon species, and both mVISTA and DnaSP analyses showed that rps16-trnQ, trnS-trnG, and ndhC-trnM are candidate regions that will allow the identification of intraspecific differences within I. rubescens. Also 14 candidate fragments can be used to identify interspecific differences between species in Isodon. A phylogenetic analysis of the complete chloroplast genomes of 24 species in subfamily Nepetoideae was performed using the maximum likelihood method, and shows that I. rubescens clustered closer to I. serra than I. lophanthoides. Interestingly, our analysis showed that I. rubescens (MW018469.1) from Xianyang, Shaanxi Province (IR-X), is closer to I. serra than to the other two I. rubescens accessions. These results strongly indicate that intraspecific diversity is present in I. rubescens. Therefore, our results provide further insight into the phylogenetic relationships and interspecific diversity of species in the genus Isodon.

Novel serological biomarker panel using protein microarray can distinguish active TB from latent TB infection.

BACKGROUND: Rapid laboratory technologies which can effectively distinguish active tuberculosis (ATB) from controls and latent tuberculosis infection (LTBI) are lacked.The objective of this study is to explore MTB biomarkers in serum that can distinguish ATB from LTBI. METHODS: We constructed a tuberculosis protein microarray containing 64 MTB associated antigens. We then used this microarray to screen 180 serum samples, from patients with ATB and LTBI, and healthy volunteer controls. Both SAM (Significance analysis of microarrays) and ROC curve analysis were used to identify the differentially recognized biomarkers between groups. Extra 300 serum samples from patients with ATB and LTBI, and healthy volunteer controls were employed to validate the identified biomarkers using ELISA-based method. RESULTS: According to the results, the best biomarker combinations of 4 proteins (Rv1860, RV3881c, Rv2031c and Rv3803c) were selected. The biomarker panel containing these 4 proteins has reached a sensitivity of 93.3% and specificity of 97.7% for distinguishing ATB from LTBI, and a sensitivity of 86% and specificity of 97.6% for distinguishing ATB from HC. CONCLUSION: The biomarker combination in this study has high sensitivity and specificity in distinguishing ATB from LTBI, suggesting it is worthy for further validation in more clinical samples.