Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species.

Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78-82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25-38 long repeats and 130-149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, and rpl32-trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.

Bioinformatic Analysis Reveals both Oversampled and Underexplored Biosynthetic Diversity in Nonribosomal Peptides.

The traditional natural product discovery approach has accessed only a fraction of the chemical diversity in nature. The use of bioinformatic tools to interpret the instructions encoded in microbial biosynthetic genes has the potential to circumvent the existing methodological bottlenecks and greatly expand the scope of discovery. Structural prediction algorithms for nonribosomal peptides (NRPs), the largest family of microbial natural products, lie at the heart of this new approach. To understand the scope and limitation of the existing prediction algorithms, we evaluated their performances on NRP synthetase biosynthetic gene clusters. Our systematic analysis shows that the NRP biosynthetic landscape is uneven. Phenylglycine and its derivatives as a group of NRP building blocks (BBs), for example, have been oversampled, reflecting an extensive historical interest in the glycopeptide antibiotics family. In contrast, the benzoyl BB, including 2,3-dihydroxybenzoate (DHB), has been the most underexplored, hinting at the possibility of a reservoir of as yet unknown DHB containing NRPs with functional roles other than a siderophore. Our results also suggest that there is still vast unexplored biosynthetic diversity in nature, and the analysis presented herein shall help guide and strategize future natural product discovery campaigns. We also discuss possible ways bioinformaticians and biochemists could work together to improve the existing prediction algorithms.

Improving MGMT methylation status prediction of glioblastoma through optimizing radiomics features using genetic algorithm-based machine learning approach.

O6-Methylguanine-DNA-methyltransferase (MGMT) promoter methylation was shown in many studies to be an important predictive biomarker for temozolomide (TMZ) resistance and poor progression-free survival in glioblastoma multiforme (GBM) patients. However, identifying the MGMT methylation status using molecular techniques remains challenging due to technical limitations, such as the inability to obtain tumor specimens, high prices for detection, and the high complexity of intralesional heterogeneity. To overcome these difficulties, we aimed to test the feasibility of using a novel radiomics-based machine learning (ML) model to preoperatively and noninvasively predict the MGMT methylation status. In this study, radiomics features extracted from multimodal images of GBM patients with annotated MGMT methylation status were downloaded from The Cancer Imaging Archive (TCIA) public database for retrospective analysis. The radiomics features extracted from multimodal images from magnetic resonance imaging (MRI) had undergone a two-stage feature selection method, including an eXtreme Gradient Boosting (XGBoost) feature selection model followed by a genetic algorithm (GA)-based wrapper model for extracting the most meaningful radiomics features for predictive purposes. The cross-validation results suggested that the GA-based wrapper model achieved the high performance with a sensitivity of 0.894, specificity of 0.966, and accuracy of 0.925 for predicting the MGMT methylation status in GBM. Application of the extracted GBM radiomics features on a low-grade glioma (LGG) dataset also achieved a sensitivity 0.780, specificity 0.620, and accuracy 0.750, indicating the potential of the selected radiomics features to be applied more widely on both low- and high-grade gliomas. The performance indicated that our model may potentially confer significant improvements in prognosis and treatment responses in GBM patients.

Characterization of the complete mitochondrial genome of Abscondita cerata (Olivier, 1911) (Coleoptera: Lampyridae) and its phylogenetic implications.

We sequenced and assembled the complete mitochondrial genome of Abscondita cerata from Nankang, Taipei City, Taiwan. The complete mitogenome of A. cerata is 16,964 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the A. cerata are A: 43.93%, T: 36.74%, C: 11.05%, and G: 8.28%. The AT and GC skewness of the mitogenome sequence are 0.0891 and -0.1434, showing the genome composition skewness toward adenine and cytosine. The clade including all Lampyridae species is well supported. The result indicates that Luciolinae is a monophyletic group but Lampyrinae is not a monophyletic group, as Lamprigera yunnana, which was originally classified into Lampyrinae, is sister to Luciolinae. The genus Lamprigera may share a unique phylogenetic position in Lampyridae. The genus Luciola is a polyphyletic group and the genus Abscondita is a monophyletic group. A. cerata is the sister species to A. chinensis in China. Mitogenomic data from this study will provide useful molecular markers for further studies on the population genetics, speciation, and conservation of endemic species A. cerata in Taiwan.

Artificial intelligence-assisted prediction of preeclampsia: Development and external validation of a nationwide health insurance dataset of the BPJS Kesehatan in Indonesia.

BACKGROUND: We developed and validated an artificial intelligence (AI)-assisted prediction of preeclampsia applied to a nationwide health insurance dataset in Indonesia. METHODS: The BPJS Kesehatan dataset have been preprocessed using a nested case-control design into preeclampsia/eclampsia (n = 3318) and normotensive pregnant women (n = 19,883) from all women with one pregnancy. The dataset provided 95 features consisting of demographic variables and medical histories started from 24 months to event and ended by delivery as the event. Six algorithms were compared by area under the receiver operating characteristics curve (AUROC) with a subgroup analysis by time to the event. We compared our model to similar prediction models from systematically reviewed studies. In addition, we conducted a text mining analysis based on natural language processing techniques to interpret our modeling results. FINDINGS: The best model consisted of 17 predictors extracted by a random forest algorithm. Nine∼12 months to the event was the period that had the best AUROC in external validation by either geographical (0.88, 95% confidence interval (CI) 0.88-0.89) or temporal split (0.86, 95% CI 0.85-0.86). We compared this model to prediction models in seven studies from 869 records in PUBMED, EMBASE, and SCOPUS. This model outperformed the previous models in terms of the precision, sensitivity, and specificity in all validation sets. INTERPRETATION: Our low-cost model improved preliminary prediction to decide pregnant women that will be predicted by the models with high specificity and advanced predictors. FUNDING: This work was supported by grant no. MOST108-2221-E-038-018 from the Ministry of Science and Technology of Taiwan.

Changes of Microbial Community in Treated Peri-implantitis Sites: An Experimental Study in Beagle Dogs.

OBJECTIVE: To investigate the changes of the bacterial community in the oral environment of beagle dogs to gain insights on the possible causes of failed therapy in peri-implantitis. METHODS: Beagles were used as models for experimental peri-implantitis. Samples from peri-implant soft tissue (supramargin and submargin), ligature and contaminated surface of peri-implantitis sites were collected and analysed by sequencing the bacterial 16S rRNA gene. RESULTS: The residual microbial community from the curettes-treated implant surface contained a variety of microorganisms, including periodontal pathogens, which showed no changes in their composition and structure. CONCLUSION: It is possible that the residual bacterial community remained unchanged and this was the cause of recurrent episodes of inflammation.

Flexible Cationic Nanoparticles with Photosensitizer Cores for Multifunctional Biomedical Applications.

One challenge for multimodal therapy is to develop appropriate multifunctional agents to meet the requirements of potential applications. Photodynamic therapy (PDT) is proven to be an effective way to treat cancers. Diverse polycations, such as ethylenediamine-functionalized poly(glycidyl methacrylate) (PGED) with plentiful primary amines, secondary amines, and hydroxyl groups, demonstrate good gene transfection performances. Herein, a series of multifunctional cationic nanoparticles (PRP) consisting of photosensitizer cores and PGED shells are readily developed through simple dopamine-involving processes for versatile bioapplications. A series of experiments demonstrates that PRP nanoparticles are able to effectively mediate gene delivery in different cell lines. PRP nanoparticles are further validated to possess remarkable capability of combined PDT and gene therapy for complementary tumor treatment. In addition, because of their high dispersities in biological matrix, the PRP nanoparticles can also be used for in vitro and in vivo imaging with minimal aggregation-caused quenching. Therefore, such flexible nanoplatforms with photosensitizer cores and polycationic shells are very promising for multimodal tumor therapy with high efficacy.

Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic-hydrocarbon-producing enzymes, and will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources, such as lignocellulosic biomass, rather than from petroleum.

Implication for second primary cancer from visible oral and oropharyngeal premalignant lesions in betel-nut chewing related oral cancer.

BACKGROUND: Visible oral and oropharyngeal premalignant lesions may be used to monitor for a second primary oral cancer. To control for bias, we focused on the visible oral and oropharyngeal premalignant lesions of patients with oral cancer with a positive betel-nut chewing habit. Visible oral and oropharyngeal premalignant lesions that can predict second primary oral cancers were studied. METHODS: Nine hundred ninety-seven patients with positive betel-nut chewing habits and oral cancer were enrolled in this retrospective cohort study. We analyzed the relevance of their visible oral and oropharyngeal premalignant lesion incidence and relative clinicopathological variables to the development of a second primary oral cancer. RESULTS: Second primary oral cancer risk was significantly higher in patients with positive visible oral and oropharyngeal premalignant lesions (P < .0001), especially in younger patients (P = .0023; ≤40 years: adjusted odds ratio [OR] 2.66; 40-60 years: adjusted OR 2.61). The heterogeneous leukoplakia was (adjusted OR 2.17) higher than homogeneous leukoplakia. CONCLUSION: The predictive value and practicality of visible oral and oropharyngeal premalignant lesions make it a potentially valuable marker in follow-ups of patients with a positive betel-nut chewing habit with oral cancer, especially young patients with heterogeneous leukoplakia.

Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.

The hydrocarbonoclastic bacterium Acinetobacter venetianus RAG-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. In this study, we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. Comparison of the transcriptional responses of RAG-1 grown on dodecane led to the identification of 1074 genes that were differentially expressed relative to sodium acetate. Of these, 622 genes were upregulated when grown in dodecane. The highly upregulated genes were involved in alkane catabolism, along with stress response. Our data suggest AlkMb to be primarily involved in dodecane oxidation. Transcriptional response of RAG-1 grown on dodecane relative to dodecanol also led to the identification of permease, outer membrane protein and thin fimbriae coding genes potentially involved in dodecane uptake. This study provides the first model for key genes involved in alkane uptake and metabolism in A. venetianus RAG-1.

Synovial TRPV1 is upregulated by 17-ß-estradiol and involved in allodynia of inflamed temporomandibular joints in female rats.

Women with reproductive capability are more likely to suffer from temporomandibular disorders (TMD), with orofacial pain as the most common complaint. In the past, we focused on the role of estradiol in TMD pain through the nervous system. In this study, we explored estradiol's influence on synoviocyte gene expressions involved in the allodynia of the inflamed TMJ. The influence of 17-ß-estradiol on NGF and TRPV1 expression in TMJ synovium was determined in vivo and in vitro and analyzed by Western blot and real-time PCR. Complete Freund's adjuvant (CFA) injection into the TMJ was used to induce TMJ arthritis. Capsazepine served as a TRPV1 antagonist. Head withdrawal threshold was examined using a von Frey Anesthesiometer. We observed that estradiol upregulated the expressions of TRPV1 and NGF in a dose-dependent manner. In the primary cultured synoviocytes, TRPV1 was upregulated by lipopolysaccharide (LPS), estradiol, and NGF, while NGF antibodies fully blocked LPS and estradiol-induced upregulation of TRPV1. Activation of TRPV1 in the primary synoviocytes with capsaicin, a TRPV1 agonist, dose-dependently enhanced COX-2 transcription. Moreover, intra-TMJ injection of TRPV1 antagonist, capsazepine, significantly attenuated allodynia of the inflamed TMJ induced by intra-TMJ injection of CFA in female rats. This article presents a possible local mechanism for estradiol that may be involved in TMJ inflammation or pain in the synovial membrane through the pain-related gene TRPV1. This finding could potentially help clinicians understand the sexual dimorphism of TMD pain.

Cell-based semiquantitative assay for sulfated glycosaminoglycans facilitating the identification of chondrogenesis.

Glycosaminoglycans (GAGs), in particular chondroitin sulfate, are an accepted marker of chondrogenic cells. In this study, a cell-based sulfated GAG assay for identifying the chondrogenesis of mesenchymal stem cells was developed. Based on fluorescent staining using safranin O and 4',6-diamidino-2-phenylindole (DAPI), this method was highly sensitive. The results were both qualitative and quantitative. The method is suitable for identifying the chondrogenic process and also for screening compounds. The method may be helpful for discovering novel bioactive compounds for cartilage regeneration.

An in vivo swine study for xeno-grafts of calcium sulfate-based bone grafts with human dental pulp stem cells (hDPSCs).

The purpose of this in vivo study was to evaluate the effect of human dental pulp stem cells (hDPSCs) on various resorbable calcium sulfate/calcium phosphate bone grafts in bone regeneration. Granular particles of calcium sulfate dehydrate (CSD), α-calcium sulfate hemihydrate/amorphous calcium phosphate (α-CSH/ACP), and CSD/ß-tricalcium phosphates (ß-TCP) were prepared for in vitro dissolution and implantation test. The chemical compositions of specimen residues after dissolution test were characterized by XRD. The ratios of new bone formation for implanted grafts/hDPSCs were evaluated using mandible bony defect model of Lanyu pig. All the graft systems exhibited a similar two-stage dissolution behavior and phase transformation of poor crystalline HAp. Eight weeks post-operation, the addition of hDPSCs to various graft systems showed statistically significant increasing in the ratio of new bone formation (p<0.05). Null hypothesis of hDPSCs showing no scaffold dependence in bone regeneration was rejected. The results suggest that the addition of hDPSCs to calcium sulfate based xenografts could enhance the bone regeneration in the bony defect.

Screening of flavonoids for effective osteoclastogenesis suppression.

Flavonoids are natural compounds derived from plants and some of them have been shown to inhibit osteoclast formation, implicating their potential use for the treatment of osteoporosis. Conventionally, the screening of antiosteoclastic agents is a tedious process that requires visual counting of the number of osteoclasts produced. The purpose of this study was to establish an easier and faster method for screening the antiosteoclastogenic flavonoids by using an enzyme assay. Tartrate-resistant acid phosphatase (TRAP) is a marker enzyme of the osteoclast. Results obtained demonstrated that cellular TRAP activity tended to correlate with the number of osteoclasts formed. However, the secreted TRAP activity was actually responsible for the resorption activities of the functional osteoclasts. Consequently, the effectiveness of antiosteoclastogenic agents was screened for by assessing their inhibition on receptor activator of NF-κB ligand (RANKL)-induced TRAP secretion. The half-inhibitory concentrations of flavonoids on TRAP secretion were employed as indices to compare the effectiveness of various flavonoids. The effective flavonoids also exhibited similar inhibitory potencies in the pit-formation analysis. This protocol provides a rapid analysis to screen for effective antiosteoclastogenic agents.

Hippocampal nerve growth factor potentiated by 17ß-estradiol and involved in allodynia of inflamed TMJ in rat.

UNLABELLED: The hippocampus is believed to play an important role in sex-based differences of pain perception. Whether estrogen potentiates allodynia in the inflamed temporomandibular joint (TMJ) through affecting the expressions of pain-related genes in the hippocampus remains largely unknown. Because the nerve growth factor (NGF) is an important gene related to inflammatory pain, we tested whether hippocampal NGF may be involved in TMJ inflammatory pain. Here we showed that the rat hippocampal NGF was upregulated by TMJ inflammation induced by complete Freund adjuvant. NGF upregulation was further potentiated by estradiol in a dose-dependent manner. In contrast, NGF transcription in the amygdala, prefrontal cortex, and thalamus was not affected by TMJ inflammation and estradiol. An intrahippocampal injection of NGF antibody or NGF receptor inhibitor K252a (inhibitor for tropomyosin receptor kinase A, TrkA) reduced the allodynia of inflamed TMJ in proestrous rats. Our data suggest that the hippocampal NGF is involved in estradiol-sensitized allodynia of inflammatory TMJ pain. PERSPECTIVE: We report that complete Freund adjuvant-induced temporomandibular joint (TMJ) inflammation upregulated hippocampal nerve growth factor (NGF) expression, and estradiol replacement potentiated this upregulation. These results propose that estradiol could modulate TMJ pain through the NGF signaling pathway in the hippocampus to exacerbate TMJ pain and offer a possible mechanism of sexual dimorphism of temporomandibular disorder pain.

17ß-estradiol aggravates temporomandibular joint inflammation through the NF-κB pathway in ovariectomized rats.

OBJECTIVE: Women of childbearing age are more likely than men to experience temporomandibular disorders, with pain as the main symptom. Temporomandibular joint (TMJ) inflammation is believed to be a major reason for TMJ pain. Whether sex hormones are involved in the sexual dimorphism of TMJ inflammation and pain remains to be elucidated. The aim of this study was to examine whether estrogen affects TMJ inflammation and pain via the NF-κB pathway. METHODS: Female rats were divided into 6 groups: the control group, the sham-ovariectomized group, and 4 groups of ovariectomized rats treated with 17ß-estradiol at a dosage of 0 µg/day, 20 µg/day, 80 µg/day, and 200 µg/day, respectively, for 10 days and then injected intraarticularly with Freund's complete adjuvant to induce TMJ inflammation. The behavior-related and histologic effects of 17ß-estradiol were evaluated 24 hours after the induction of TMJ inflammation. NF-κB activity in the synovial membrane was examined by electrophoretic mobility shift assay. The expression of the NF-κB target genes tumor necrosis factor α, interleukin-1ß (IL-1ß), IL-6, cyclooxygenase 2, and inducible nitric oxide synthase in the synovial membrane was examined by real-time polymerase chain reaction. RESULTS: Treatment with estradiol potentiated TMJ inflammation in a dose-dependent manner and also exacerbated the inflammation-induced decrease in food intake. Correspondingly, estradiol potentiated the DNA-binding activity of NF-κB and the transcription of its target genes in the synovial membrane. Furthermore, the estrogen receptor antagonist ICI 182780 or the NF-κB inhibitor pyrrolidine dithiocarbamate partially blocked the effects of estradiol on TMJ inflammation and pain and the NF-κB pathway. CONCLUSION: These results suggest that estradiol aggravates TMJ inflammation through the NF-κB pathway, leading to the induction of proinflammatory cytokines.

A new endoscopic classification system of early-stage esophageal carcinoma and its usefulness in assessing the infiltration depth of esophageal carcinoma.

The growth pattern, height, and depth of early esophageal carcinoma were observed under gastroscopy and endoscopic ultrasonography. The infiltration depth of carcinomas was determined pathologically. Early esophageal carcinomas were classified into five types by endoscopy: surface propagating growth, intraluminal growth, intramural growth, bilateral growth, and mixed growth. Intramucosal and submucosal carcinomas were differentiated on the basis of the different types, height of intraluminal growth and bilateral growth, and depth of intramural growth type. The accuracy of differentiate diagnosis was 87.2%. Our results indicate that this new endoscopic classification system can accurately differentiate intramucosal and submucosal infiltration of early-stage esophageal carcinomas.

17-Beta-estradiol enhanced allodynia of inflammatory temporomandibular joint through upregulation of hippocampal TRPV1 in ovariectomized rats.

Temporomandibular disorders (TMDs) predominantly affect reproductive female patients, with pain the most frequent complaint. Although estrogens are believed to play important roles in TMD pain, the mechanism underlying modulation of TMD pain by estrogens remains largely unknown. Accumulating evidence implies that the hippocampus is involved in sexual dimorphism of pain sensitivity. In this study, we investigated the hippocampal TRPV1 (transient receptor potential vanilloid 1) expression in ovariectomized rats that received 17-beta-estradiol substitution and found that 17-beta-estradiol enhanced the mechanical allodynia of inflamed temporomandibular joint (TMJ) induced by complete Freund's adjuvant. Real-time PCR and immunoblotting demonstrated that TMJ inflammation significantly induced hippocampal TRPV1 expression compared with the control group but failed to induce it in the ovariectomized rats that received no estradiol replacement. In addition, estradiol potentiated TMJ inflammation-induced hippocampal TRPV1 expression in a dose-dependent manner in the ovariectomized rats. In contrast, TRPV1 transcription in amygdala, prefrontal cortex, and thalamus was not affected by TMJ inflammation and estradiol. Immunostaining showed TRPV1 localized in the processes and cytoplasm of pyramidal neurons in CA1-CA3 regions of the hippocampus. Moreover, intrahippocampal injection of TRPV1 antagonists capsazepine and 5'-iodo-resiniferatoxin into the CA1 region of the hippocampus significantly attenuated allodynia of inflamed TMJ in both nonovariectomized and ovariectomized rats that received estradiol replacement. Our results suggested that hippocampal TRPV1 can modulate central pain processing and estradiol may contribute to the sexual dimorphism of TMD pain sensitivity through upregulation of TRPV1 expression in the hippocampus.

Effects of radiation on the expression of nerve growth factor in rat submandibular gland.

OBJECTIVE: to investigate the correlation between the expression of nerve growth factor (NGF) and tissue injury in irradiated rat submandibular gland. METHODS: the salivary gland regions of the rats were irradiated with a single dose of 15 Gy X-ray. The histopathological changes in the submandibular gland were observed, while the expression of NGF was determined by immunohistochemistry and real-time PCR. RESULTS: the weight of the body and submandibular gland decreased in the irradiated rats 30 days after irradiation, compared with the control group. There were also significant histopathological changes in the submandibular gland of the irradiated rats compared with the non-irradiated rats. The acinar cells and ducts were degenerated obviously. Fibrosis appeared around the ducts. The mRNA and protein expression of NGF in the submandibular gland decreased in the irradiated rats compared with the control group. Protein expression of NGF was even observed in the striated duct in the irradiated rats. conclusion: NGF may play an important role in protection of the submandibular glands of rats from radiation.