Single cell sequencing revealed the mechanism of CRYAB in glioma and its diagnostic and prognostic value.

Background: We explored the characteristics of single-cell differentiation data in glioblastoma and established prognostic markers based on CRYAB to predict the prognosis of glioblastoma patients. Aberrant expression of CRYAB is associated with invasive behavior in various tumors, including glioblastoma. However, the specific role and mechanisms of CRYAB in glioblastoma are still unclear. Methods: We assessed RNA-seq and microarray data from TCGA and GEO databases, combined with scRNA-seq data on glioma patients from GEO. Utilizing the Seurat R package, we identified distinct survival-related gene clusters in the scRNA-seq data. Prognostic pivotal genes were discovered through single-factor Cox analysis, and a prognostic model was established using LASSO and stepwise regression algorithms. Moreover, we investigated the predictive potential of these genes in the immune microenvironment and their applicability in immunotherapy. Finally, in vitro experiments confirmed the functional significance of the high-risk gene CRYAB. Results: By analyzing the ScRNA-seq data, we identified 28 cell clusters representing seven cell types. After dimensionality reduction and clustering analysis, we obtained four subpopulations within the oligodendrocyte lineage based on their differentiation trajectory. Using CRYAB as a marker gene for the terminal-stage subpopulation, we found that its expression was associated with poor prognosis. In vitro experiments demonstrated that knocking out CRYAB in U87 and LN229 cells reduced cell viability, proliferation, and invasiveness. Conclusion: The risk model based on CRYAB holds promise in accurately predicting glioblastoma. A comprehensive study of the specific mechanisms of CRYAB in glioblastoma would contribute to understanding its response to immunotherapy. Targeting the CRYAB gene may be beneficial for glioblastoma patients.

Phylogenetic analysis of upland cotton MATE gene family reveals a conserved subfamily involved in transport of proanthocyanidins.

The multidrug and toxic compound extrusion (MATE) protein belongs to a secondary transporter family, which plays a role in transporting different kinds of substrates like phytohormones and secondary metabolites. In plant, MATE transporters related to the endogenous and exogenous mechanisms of detoxification for secondary metabolites such as alkaloids, flavonoids, anthocyanins and other secondary metabolites have been studied. However, a genome-wide analysis of the MATE family is rarely reported in upland cotton (Gossypium hirsutum L.). In the study, a total of 72 GhMATEs were identified from the genome of upland cotton, which were classified into four subfamilies with possible diverse functions such as transport of proanthocyanidins (PAs), accumulation of alkaloids, extrusion of xenobiotic compounds, regulation of disease resistance and response to abiotic stresses. Meanwhile, the gene structure, evolutionary relationship, physical location, conservative motifs, subcellular localization and gene expression pattern of GhMATEs have been further analysed. Three of these MATE genes (GhMATE12, GhMATE16 and GhMATE38) were identified as candidate genes due to their functions in transport of PA similar to GhTT12. These results provide a new perspective on upland cotton MATE gene family for their potential roles in transport of PA and a theoretical basis for further analyzing the function of MATE genes and improving the fiber quality of brown cotton.

Computer-assisted diagnosis of early esophageal squamous cell carcinoma using narrow-band imaging magnifying endoscopy.

BACKGROUND: We developed a computer-assisted diagnosis model to evaluate the feasibility of automated classification of intrapapillary capillary loops (IPCLs) to improve the detection of esophageal squamous cell carcinoma (ESCC). METHODS: We recruited patients who underwent magnifying endoscopy with narrow-band imaging for evaluation of a suspicious esophageal condition. Case images were evaluated to establish a gold standard IPCL classification according to the endoscopic diagnosis and histological findings. A double-labeling fully convolutional network (FCN) was developed for image segmentation. Diagnostic performance of the model was compared with that of endoscopists grouped according to years of experience (senior > 15 years; mid level 10 - 15 years; junior 5 - 10 years). RESULTS: Of the 1383 lesions in the study, the mean accuracies of IPCL classification were 92.0 %, 82.0 %, and 73.3 %, for the senior, mid level, and junior groups, respectively. The mean diagnostic accuracy of the model was 89.2 % and 93.0 % at the lesion and pixel levels, respectively. The interobserver agreement between the model and the gold standard was substantial (kappa value, 0.719). The accuracy of the model for inflammatory lesions (92.5 %) was superior to that of the mid level (88.1 %) and junior (86.3 %) groups (P < 0.001). For malignant lesions, the accuracy of the model (B1, 87.6 %; B2, 93.9 %) was significantly higher than that of the mid level (B1, 79.1 %; B2, 90.0 %) and junior (B1, 69.2 %; B2, 79.3 %) groups (P < 0.001). CONCLUSIONS: Double-labeling FCN automated IPCL recognition was feasible and could facilitate early detection of ESCC.

MALAT1 promotes angiogenesis of breast cancer.

Metastasis­associated lung adenocarcinoma transcript 1 (MALAT1) is a long non­coding RNA (lncRNA) that has an oncogenic role in some types of cancers, uncluding breast cancer (BC). To investigate the role of MALAT1 in human BC progression, we detected MALAT1 expression levels based on tissue samples from 20 BC cases and 20 healthy controls and found MALAT1 expression levels to be significantly high (P<0.05). Then, we knocked down endogenous MALAT1 in MCF­7 cells using MALAT1 short hairpin RNA (shRNA). The results revealed that MALAT1 knockdown could significantly inhibit proliferation, migration, and tube formation in vitro. In addition, miR­145 expression inversely changed in BC tissue cases. Furthermore, knockdown of endogenous MALAT1 significantly increased miR­145 levels in MCF­7 cells. This finding indicated an interaction between MALAT1 and miR­145. In addition, knockdown of MALAT1 significantly reduced the expression of vascular endothelial growth factor in MCF­7 cells. This outcome revealed that MALAT1 promoted angiogenesis in BC, which may be related to the expression of miR­145.

Genomic Comparison of the P-ATPase Gene Family in Four Cotton Species and Their Expression Patterns in Gossypium hirsutum.

Plant P-type H⁺-ATPase (P-ATPase) is a membrane protein existing in the plasma membrane that plays an important role in the transmembrane transport of plant cells. To understand the variety and quantity of P-ATPase proteins in different cotton species, we combined four databases from two diploid cotton species (Gossypium raimondii and G. arboreum) and two tetraploid cotton species (G. hirsutum and G. barbadense) to screen the P-ATPase gene family and resolved the evolutionary relationships between the former cotton species. We identified 53, 51, 99 and 98 P-ATPase genes from G. arboretum, G. raimondii, G. barbadense and G. hirsutum, respectively. The structural and phylogenetic analyses revealed that the gene structure was consistent between P-ATPase genes, with a close evolutionary relationship. The expression analysis of P-ATPase genes showed that many P-ATPase genes were highly expressed in various tissues and at different fiber developmental stages in G. hirsutum, suggesting that they have potential functions during growth and fiber development in cotton.

Genome-wide analysis of the GST gene family in Gossypium hirsutum L.

Glutathione-S-transferase (GST) is a ubiquitous multi-functional protein superfamily that plays important roles in plant primary and secondary metabolism, stress and intercellular signal transduction. Concomitantly, it also functions as a ligand in the metabolism of plant hormones and substance transport. In order to understand the GST gene family in upland cotton (Gossypium hirsutum L.), herein we analyzed the species, evolutionary relationship, physical location, gene structure, conserved motifs and expression patterns. We identified 70 GST genes in the whole genome of upland cotton, and divided them into U, F, T, Z, EF1Bγ and TCHQD groups by phylogenetic tree and gene structure analyses. The gene mapping analysis indicated that the GST genes were on every chromosome except chromosome AD/At2, AD/At4, AD/At5, AD/Dt5 and AD/Dt10. Moreover, the GST gene cluster appeared on four chromosomes (AD/At9, AD/Dt7, AD/Dt12 and AD/Dt13). qRT-PCR assays showed that eight genes (GhGSTF2-9) were expressed in the root, stem, leave and fiber of different developmental stages while GhGSTF1 might be a pseudogene. Combining qRT-PCR and bioinformatic analysis, we speculated that GhGSTF8 might be involved in the transport and accumulation of proanthocyanidins/anthocyanins; GhGSTF4, 6 and 9 might play roles in regulating the growth and stress response of upland cotton; the function of GhGSTF2, 3, 5 and 7 remains to be further investigated. Our work provides a theoretical basis for further studies on the molecular evolution and function of the GST gene family in upland cotton.

A putative molybdate transporter LjMOT1 is required for molybdenum transport in Lotus japonicus.

Molybdenum (Mo) is an essential micronutrient that is required for plant growth and development, and it affects the formation of root nodules and nitrogen fixation in legumes. In this study, Lotus japonicus was grown on MS solid media containing 0 nmol l-1 (-Mo), 103 nmol l-1 (+Mo) and 1030 nmol l-1 (10 × Mo) of Mo. The phenotypes of plants growing on the three different media showed no obvious differences after 15 days, but the plants growing on -Mo for 45 days presented typical symptoms of Mo depletion, such as a short taproot, few lateral roots and yellowing leaves. A Mo transporter gene, LjMOT1, was isolated from L. japonicus. It encoded 468 amino acids, including two conserved motifs, and was predicted to locate to chromosome 3 of the L. japonicus genome. A homology comparison indicated that LjMOT1 had high similarities to other MOT1 proteins and was closely related to GmMOT1. Subcellular localization indicated that LjMOT1 is localized to the plasma membrane. qRT-PCR analyses showed that increasing Mo concentrations regulated the relative expression level of LjMOT1. Moreover, the Mo concentration in shoots was positively correlated to the expression of LjMOT1, but there was no such evident correlation in the roots. In addition, changes in the nitrate reductase activity were coincident with changes in the Mo concentration. These results suggest that LjMOT1 may be involved in the transport of Mo and provide a theoretical basis for further understanding of the mechanism of Mo transport in higher plants.

Molecular cloning, expression analysis and subcellular localization of a Transparent Testa 12 ortholog in brown cotton (Gossypium hirsutum L.).

Transparent Testa 12 (TT12) is a kind of transmembrane transporter of proanthocyanidins (PAs), which belongs to a membrane-localized multidrug and toxin efflux (MATE) family, but the molecular basis of PAs transport is still poorly understood. Here, we cloned a full-length TT12 cDNA from the fiber of brown cotton (Gossypium hirsutum), named GhTT12 (GenBank accession No. KF240564), which comprised 1733 bp with an open reading frame (ORF) of 1503 bp and encoded a putative protein containing 500 amino acid residues with a typical MATE conserved domain. The GhTT12 gene had 96.8% similarity to AA genome in Gossypium arboretum. Quantitative RT-PCR analysis denoted that the relative expression of GhTT12 in brown cotton was 1-5 folds higher than that in white cotton. The mRNA level was the highest at 5 days post anthesis (DPA) and reduced gradually during the fiber development. Expressing GhTT12-fused green fluorescent protein (GFP) in Nicotiana tabacum showed that GhTT12-GFP was localized in the vacuole membrane. The content of PAs increased firstly and decreased afterwards, and reached the maximum at 15 DPA in brown cotton. But for white cotton, the content of PAs remained at a low level during the fiber development. We speculate that GhTT12 may participate in the transportation of PAs from the cytoplasmic matrix to the vacuole. Taken together, our data revealed that GhTT12 was functional as a PAs transmembrane transporter.

[Cloning and expression analysis of transcription factor gene DoWRKY1 in Dendrobium officinale].

WRKY transcription factors are novel transcriptional regulatory factors, which play an important role in regulating plant development, metabolism and other physiological processes. In this study, a new Dendrobium officinale WRKY transcription factor, designated as DoWRKY1 was cloned by using RT-PCR and RACE (GenBank Accession No. KF953910). Bioinformatic analysis demonstrated that, the full-length cDNA of DoWRKY1 was 1,704 bp. And DoWRKY1 contained a 1,629 bp open reading frame (ORF) that encoding a peptide of 542 amino acid residues. The putative DoWRKY1 protein contained two conserved WRKY domains and it belonged to the group I WRKY family protein. Yeast one-hybrid experiment showed that DoWRKY1 had transcriptional activation ability in yeast, and it could activate the expression of downstream report genes (His3 and Ade2). Semi-quantitative RT-PCR experiment showed that DoWRKY1 expressed in roots, stems, leaves and protocorm-like bodies. Real-time qRT-PCR proved that DoWRKY1 could be induced by methyl jasmonate (MeJA) and chitosan (Chitosan), and the expression level of this gene can reach the expression peak at 2 h and 1 h, respectively. These results are useful for further determination of the regulation function of this gene in secondary metabolism of D. officinale.

Microcystic/Reticular Schwannoma of the Mandible First Case Report and Review of the Literature.

Schwannoma comprises a group of nerve sheath tumors. Morphologic variants of schwannoma have no distinct relationship to clinical behavior, but unawareness of rare variants may lead to diagnostic pitfall and risk of mistreatment. Microcystic/reticular schwannoma is a recently described rare variant of schwannoma. We report a case of a 61-year-old female with a 5.0 cm × 3.5 cm × 3.0 cm mass in the right mandible, which has never been reported to date. Light microscopic evaluation showed that the mass was circumscribed with focal infiltration. Arranged in a prominent microcystic and reticular growth pattern, tumor cells were spindle-shaped with eosinophilic cytoplasm. No evidence of cytologic atypia, mitosis, or necrosis was observed. The stroma of the tumor mainly contained myxoid material with local infiltration of hyalinized collagen. Tumor cells showed diffuse and strong nuclear and cytoplasmic immunoreactivity for S100 protein. Tumor cells were also positive for CD34, CD99, and NSE, but negative for CK, EMA, CK5/6, P63, Calponin, CD10, SMA, Desmin, GFAP, NF, Syn, and CgA. The proliferation marker MIB-1 showed <1% nuclear reaction. Furthermore, we reviewed the clinical and pathological features of 24 previously reported cases of microcystic/reticular schwannoma. Unlike classic schwannoma, the reticular variant showed striking microcystic and reticular architecture microscopically. Recognition of these distinct entities is essential in avoiding misdiagnosis. Unlike classic schwannoma with a complete capsule, some masses were reported to lack encapsulation or contain focal infiltration. Further follow-up of tentative or identified cases is necessary to better understand this schwannoma.

[Genome-wide identification and analyses of 4CL gene families in Pyrus bretschneideri Rehd].

4-coumaric acid: coenzyme A ligase (4CL) gene is one of the key genes involved in the regulation of lignin metabolism and the synthesis of flavonoid and other secondary metabolites in plant, while the synthesized and polymerized lignin is deposited in cell walls and leads to thickening of secondary walls in some parenchyma cells and formation of stone cells. To better understand the variety and quantity of 4CL genes in Pyrus bretschneideri Rehd., we used the amino acid and cDNA databases of Pyrus bretschneideri Rehd. genome to screen 4CL gene family, and analyzed their classification, evolutionary relationships, physical location, gene structure and conserved motif. Our results showed that 29 4CL genes were identified and preliminarily characterized, and these 4CL genes were distributed in all chromosomes except chromosomes 4, 8, 11, 12 and clustered on chromosomes 9 and 17 through gene location analysis. The relationship between 4CL gene structure and evolution was further determined by comparing gene structure and phylogenetic tree. These findings provide a basis for further analysis of 4CL gene function in Pyrus bretschneideri Rehd.

Isolation and molecular characterization of an ethylene response factor NtERF1-1 in Nicotiana tabacum cv. Xanthi.

Apetala2/Ethylene Response Factors (AP2/ERF) play important roles in regulating gene expression under abiotic and biotic stress in the plant kingdom. Here, we isolated a member of the AP2/ERF transcription factors, NtERF1-1, from Nicotiana tabcum cv. Xanthi NN carrying the N gene, which is resistant to Tobacco mosaic virus (TMV). NtERF1-1 encoded a putative protein of 229 amino acids with a predicted molecular mass of 24.58 kDa. Nucleotide sequence analysis showed that NtERF1-1 contained a conserved DNA-binding domain at the N-terminal. Comparison of amino acid sequences revealed that NtERF1-1 possessed high similarities to ERFs from diverse plants. Semi-quantitative and real-time quantitative RT-PCR analyses indicated that NtERF1-1 was up-regulated following TMV infection. In addition, we speculated that NtERF1-1 might participate in the signal transduction pathway of defence response inducted by the interaction between the N gene and TMV.

[Studies on genetic diversity of medicinal Dendrobium by SRAP].

OBJECTIVE: To study the genetic diversity of medicinal Dendrobium by SRAP. METHOD: The genetic diversity of 9 spices Dendrobium was studied by using the optimized SRAP reaction system. The NTSYS software was used to analyze the markers. RESULT: Forty primer pairs were selected from 88 amplified 1 782 polymorphic bands with an average of 44.55 polymorphic bands per primer pair. Cluster analysis using UPGMA method based on the data of SRAP amplified bands by 40 primer pairs showed that 9 spices of could be distinguished into two main groups. Jaccard's similarity coefficient ranged from 0.330 2-0.789 2. CONCLUSION: The results of this research indicate that SRAP molecular marker is efficient to study the medical Dendrobium genetic diversity.

[Comparison on growth, physiology and medicinal components of Dendrobium huoshanense hybrid and its parents].

OBJECTIVE: To compare the hybrid between species of Dendrobium huoshanense and its parents on growing, physiologic indexes and content of medicinal components, and provide theoretical basis for species quality improvement. METHOD: The chlorophyll content, the photosynthesis rate, the polysaccharides content and the alkaloids content were measured by anhydrous ethanol method, Cl-310 photosynthesis determination system, colorimetry of concentrated sulphuric acid-phenol and acid dyes colorimetry respectively. RESULT: The growth of hybrid was close to D. moniliforme, and apparently higher than D. huoshanense. The chlorophyll content and the photosynthesis rate of one-year-hybrid were markedly higher than its parents. The content of polysaccharides and alkaloids in two-year-stem and three-year-stem of hybrid were close to that of D. huoshanense. CONCLUSION: The hybrid integrates superiority of parents on growth and accumulation of medicinal components opens vast vistas for development and utilization.

[Studies on the growth, chemical components and physiological characteristics of F1 generation of Dendrobium huoshanense].

OBJECTIVE: Through a comparison between F1 and its' parents on the growth, chemical components and physiology, this study aims to find the possibility of selecting new dendrobium hybrids with high yield and good quality. METHOD: To determinate the growth, chemical components, photosynthesis, hormones and isoenzyme in the plants. RESULT: Photosynthetic area, content of chlorophyll, net photosynthesis and yield of F1 generation are higher than those of the parents; chla/b rate is lower; growth is almost the same as in Dendrobium moniliforme; content of chemical components are the same as in D. huoshanense. F1 is approaching of advantages of parents. CONCLUSION: Physiological characters, yield and quality of F1 are greatly improved by hybridization.