Molecular Biological Information Research Articles

Haplotype diversity of coastal horseshoe crab (Tachypleus gigas, Muller 1785) based on 16S rRNA gene markers as a basis for conservation

Abstract Tachypleus gigas is one of horseshoe crab species found in Indonesia, but does not have sufficient molecular biology information available. This study aims to predict the populations health of T. gigas from the waters of Langkat, Semarang, and Bintan; through analysis of haplotype diversity based on 16S rRNA gene markers. The observation was conducted from November 2022 until April 2023. Sample’s total DNA was isolated, extracted, amplified and then sequenced to obtain the nucleotide base sequence. The BLASTn results showed that the samples were validated as Tachypleus gigas and the genetic distance between locations showed a close kinship relationship between the three. The population health of the horseshoe crabs from Langkat and Semarang were indicated good with high haplotype diversity values, meanwhile the Bintan indicated poor health with low haplotype diversity values. This study of haplotype diversity provided the starting point to the conservation of horseshoe crab T. gigas

Correlation of glutamate dehydrogenase gene polymorphism and mRNA expression level with free glutamate content in the clam Meretrix petechialis

Free glutamate is a characteristic amino acid with a fresh taste. A high free glutamate content can increase the flavour of clams and better meet consumer demands. GDH is involved in the production of glutamate from a-ketoglutarate and determines the speed and direction of reaction in the glutamate metabolic pathway. In this study, we cloned a full-length cDNA of MpGDH homologues in the clam Meretrix petechialis and further investigated the relationship among MpGDH gene polymorphisms, gene expression levels, enzyme activity and glutamate content traits. A significant positive correlation of MpGDH gene expression with free glutamate content was observed (r = 0.62, p < 0.05). The relationship of variation in MpGDH gene expression with its SNP genotype and SNP haplotype was assessed. Five SNPs were found to be significantly associated with MpGDH gene expression (p < 0.05), from which we constructed two main haplotypes due to linkage disequilibrium. The results showed that haplotype H2 may be an effective haplotype associated with high MpGDH gene expression and high free glutamate content. The genetic effect of different haplotypes was validated by different family materials, which showed that MpGDH gene expression level of the H1H2 heterozygous genotype were significantly higher than those of the homozygous genotype H1H1 (p < 0.05). In summary, our findings revealed the potential influence of the MpGDH polymorphism on the free glutamate content and provided molecular biological information for the selective breeding of good-quality traits of M. petechialis.

PET/SPECT/spectral-CT/CBCT imaging in a small-animal radiation therapy platform: A Monte Carlo study-Part I: Quad-modal imaging.

In spite of the tremendous potential of game-changing biological image- and/or biologically guided radiation therapy (RT) and adaptive radiation therapy for cancer treatment, existing limited strategies for integrating molecular imaging and/or biological information with RT have impeded the translation of preclinical research findings to clinical applications. Additionally, there is an urgent need for a highly integrated small-animal radiation therapy (SART) platform that can seamlessly combine therapeutic and diagnostic capabilities to comprehensively enhance RT for cancer treatment. We investigated a highly integrated quad-modal on-board imaging configuration combining positron emission tomography (PET), single-photon emission computed tomography (SPECT), photon-counting spectral CT, and cone-beam computed tomography (CBCT) in a SART platform using a Monte Carlo model as a proof-of-concept. The quad-modal on-board imaging configuration of the SART platform was designed and evaluated by using the GATE Monte Carlo code. A partial-ring on-board PET imaging subsystem, utilizing advanced semiconductor thallium bromide detector technology, was designed to achieve high sensitivity and spatial resolution. On-board SPECT, photon-counting spectral-CT, and CBCT imaging were performed using a single cadmium zinc telluride flat detector panel. The absolute peak sensitivity and scatter fraction of the PET subsystem were estimated by using simulated phantoms described in the NEMA NU-4 standard. The spatial resolution of the PET image of the platform was evaluated by imaging a simulated micro-Derenzo hot-rod phantom. To evaluate the quantitative imaging capability of the system's spectral CT, the Bayesian eigentissue decomposition (ETD) method was utilized to quantitatively decompose the virtual noncontrast (VNC) electron densities and iodine contrast agent fractions in the Kidney1 inserts mixed with the iodine contrast agent within the simulated phantoms. The performance of the proposed quad-model imaging in the platform was validated by imaging a simulated phantom with multiple imaging probes, including an iodine contrast agent and radioisotopes of 18F and 99mTc. The PET subsystem demonstrated an absolute peak sensitivity of 18.5% at the scanner center, with an energy window of 175-560KeV, and a scatter fraction of only 3.5% for the mouse phantom, with a default energy window of 480-540KeV. The spatial resolution of PET on-board imaging exceeded 1.2mm. All imaging probes were identified clearly within the phantom. The PET and SPECT images agreed well with the actual spatial distributions of the tracers within the phantom. Average relative errors on electron density and iodine contrast agent fraction in the Kidney1 inserts were less than 3%. High-quality PET images, SPECT images, spectral-CT images (including iodine contrast agent fraction images and VNC electron density images), and CBCT images of the simulated phantom demonstrated the comprehensive multimodal imaging capability of the system. The results demonstrated the feasibility of the proposed quad-modal imaging configuration in a SART platform. The design incorporates anatomical, molecular, and functional information about tumors, thereby facilitating successful translation of preclinical studies into clinical practices.

First Report of Anthracnose Caused by Colletotrichum gloeosporioides on Cinnamomum camphora in Korea.

Cinnamomum camphora, known as the camphor tree, is an evergreen tree widely cultivated in Asia as an ornamental plant (Singh and Jawaid, 2012). In June 2023, several leaves on a total of 10 trees planted on a street in Suncheon, Jeonnam Province, Korea showed black spots. Disease incidence was observed in at least 15% of the 10 trees. The symptoms included circular spots with a light ash-colored center and dark brown borders. The size of lesions varied depending on the progress of the disease. The disease progressed by 30% on the tree leaves. To isolate the pathogen, we cut out the lesions on the leaf surface sterilized with 70% ethanol for one minute, washed three times with sterilized distilled water, dried, and placed on water agar. Then, it was incubated at 25°C for three days. Emerging hyphae from the samples were subcultured on potato dextrose agar (PDA), resulting in three independent isolates (SYP-F1226-1 to SYP-F1226-3) after single spore isolation from 3 independent trees. The isolates exhibited grayish fluffy mycelium in the center of the colony, while the edges were white on PDA. Conidia had rounded cylindrical shape and were 4.9 to 8.4 µm  1.4 to 3.1 µm (avg. 5.9  2.1 μm, n = 100) in size. Appressoria were round, dark gray, produced at the tip of the germ tube after a septum formed the conidium. The morphological characteristics matched those of Colletotrichum species complexes. (Damm et al., 2012; Weir et al., 2012). For molecular identification, ITS (OR647338 to 40), GAPDH (OR657042 to 44), CHS-1 (OR657045 to 47), ACT (OR657048 to 50), and CAL (OR657051 to 53) sequences from isolates SYP-F1226-1~3 showed a 99.65%, 98.56%, 99.00%, 99.28%, and 99.52% identity with that of type strain C. gloeosporioides ICMP 17821 (JX010152, JX010056, JX009818, JX009531, and JX010445, respectively). Using the MEGA X program (Kumar et al. 2018), maximum likelihood analysis based on the concatenated sequences placed the isolates within a clade comprising C. gloeosporioides. Pathogenicity of SYP-F1226-1 was tested using three leaves from a 1-year-old branch of three independent healthy C. camphora plants. The leaf surfaces were sterilized by rubbing a cotton pad soaked in 70% ethanol and then wiping them with a sterilized cotton pad. The leaves per plant were inoculated with 5 mL of a conidial suspension (1 × 105 conidia/mL), both with and without wounding. Another three control leaves were inoculated with sterile distilled water, both with and without wounding. The inoculated leaves were wrapped in a plastic bag for 48 hours under conditions of 100% relative humidity. Spot symptoms were observed on both wounded and non-wounded leaves 21 days after inoculation. No symptoms were observed in the control on either of the wounded leaves. Pathogenicity tests were performed three times. The pathogen was re-isolated from the lesion after treatment, and its identity was confirmed using the five genes and morphological characteristics. This confirms the fulfillment of Koch's postulates. C. fioriniae (Liu et al, 2022) and C. siamens (Liu et al, 2022; Khoo et al, 2023) have been reported as the causal pathogen of anthracnose in C. camphora, but C. gloeosporioides has not been reported as a pathogen in C. camphora. To our knowledge, this is the first report of anthracnose caused by C. gloeosporioides on C. camphora in Korea. This study will provide symptomatic, mycological, and molecular biological information for the early detection of anthracnose disease in C. camphora plants.

Distribution patterns and influential factors of pathogenic bacteria in freshwater aquaculture sediments.

Pathogenic bacteria, the major causative agents of aquaculture diseases, are a serious impediment to the aquaculture industry. However, the bioinformatics of pathogenic bacteria and virulence factors (VFs) in sediments, an important component of freshwater aquaculture ecosystems, are not well characterized. In this study, 20 sediment samples were collected from fish pond sediments (FPS), shrimp field sediments (SFS), fish pond sediment control (FPSC), and shrimp field sediment control (SFSC). Molecular biological information was obtained on a total of 173 pathogenic bacteria, 1093 virulence factors (VFs), and 8475 mobile genetic elements (MGEs) from these samples. The results indicated that (1) aquaculture patterns and sediment characteristics can affect the distribution of pathogenic bacteria. According to the results of the Kruskal-Wallis H test, except for Mycobacterium gilvum, there were significant differences (P < 0.05) among the four sediment types in the average abundance of major pathogenic bacteria (top 30 in abundance), and the average abundance of major pathogenic bacteria in the four sediment types followed the following pattern: FPS > SFS > FPSC > SFSC. (2) Pathogenic bacteria are able to implement a variety of complex pathogenic mechanisms such as adhesion, invasion, immune evasion, and metabolic regulation in the host because they carry a variety of VFs such as type IV pili, HSI-I, Alginate, Colibactin, and Capsule. According to the primary classification of the Virulence Factor Database (VFDB), the abundance of VFs in all four types of sediments showed the following pattern: offensive VFs > non-specific VFs > defensive VFs > regulation of virulence-related genes. (3) Total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), nitrite, and nitrate were mostly only weakly positively correlated with the major pathogenic bacteria and could promote the growth of pathogenic bacteria to some extent, whereas ammonia was significantly positively correlated with most of the major pathogenic bacteria and could play an important role in promoting the growth and reproduction of pathogenic bacteria. (4) Meanwhile, there was also a significant positive correlation between CAZyme genes and major pathogenic bacteria (0.62 ≤ R ≤ 0.89, P < 0.05). This suggests that these pathogenic bacteria could be the main carriers of CAZyme genes and, to some extent, gained a higher level of metabolic activity by degrading organic matter in the sediments to maintain their competitive advantage. (5) Worryingly, the results of correlation analyses indicated that MGEs in aquaculture sediments could play an important role in the spread of VFs (R = 0.82, P < 0.01), and in particular, plasmids (R = 0.75, P < 0.01) and integrative and conjugative elements (ICEs, R = 0.65, P < 0.05) could be these major vectors of VFs. The results of this study contribute to a comprehensive understanding of the health of freshwater aquaculture sediments and provide a scientific basis for aquaculture management and conservation.

Review on NMR as a tool to analyse natural products extract directly: Molecular structure elucidation and biological activity analysis.

Natural products, the small organic molecules produced by plants, microbes and invertebrates, often present in the form of a mixture, this leads to the structural characterisation of natural extracts often requiring time-consuming multistep purification procedures. Nuclear magnetic resonance (NMR) technology is traditionally utilised as a tool for the structural elucidation of pure compounds. Contemporarily, an up-to-date trend in the application of NMR in natural product research is shifting to the direct NMR analysis of crude mixtures, to obtain molecular structure and biological activity information without performing cumbersome separation. To review works of literature on the evolution, principle and progress of NMR technologies for analysing mixtures, we focus on the successful application of NMR technologies in direct analysis of natural product extracts. Based on our research experience, academic tracking and extensive literature search, which involved, but not limited to, the use of various databases, like Web of Knowledge and PubMed. The keywords used, in various combinations, to retrieve recent literature on the successful application of NMR technologies to sheer natural product extracts, and excluded artificially natural product mixture and biofluid. NMR technologies for direct natural extracts analysis, including two-dimensional J-resolved spectroscopy (2D-JRES), pure shift NMR, diffusion-ordered NMR spectroscopy (DOSY), statistical correlation spectroscopy (STOCSY), concentration-ordered NMR spectroscopy (CORDY), saturation transfer difference (STD) and water-ligand observed via gradient spectroscopy (WaterLOGSY) were illustrated. By these methods, molecular structure and biological activity information will be directly obtained from NMR analysis of natural products extract, aiming to save experimental time and expenses.

Misdiagnosis analysis of 2291 cases of haematolymphoid neoplasms.

To retrospectively analyze the reasons for misdiagnosis of haematolymphoid neoplasms and provide experience for improving the diagnostic level in China. A retrospective analysis was performed on 2291 cases of haematolymphoid diseases evaluated by the Department of Pathology of our hospital from 1 July 2019 to 30 June 2021. All 2291 cases were reviewed by two hematopathologist experts and classified according to the 2017 revised WHO classification criteria, supplemented immunohistochemistry (IHC), molecular biology and genetic information as needed. The diagnostic discordance between primary and expert review was evaluated. The possible causes of the diagnostic discrepancies were analyzed for each step involved in the procedure of diagnosis. In total, 912 cases did not conform to the expert diagnoses among all the 2291 cases, with a total misdiagnosis rate of 39.8%. Among them, misdiagnosis between benign and malignant lesions accounted for 24.3% (222/912), misdiagnosis between haematolymphoid neoplasms and non-haematolymphoid neoplasms accounted for 3.3% (30/912), misdiagnosis among lineages accounted for 9.3% (85/912), misclassification in lymphoma subtypes accounted for 60.8% (554/912), and other misdiagnoses among benign lesions accounted for 2.3% (21/912) of cases, among which misclassification of lymphoma subtypes was the most common. The accurate diagnosis of haematolymphoid neoplasms is challenging, involving various types of misdiagnosis and complicated causes, however, it is important for precise treatment. Through this analysis, we aimed to highlight the importance of accurate diagnosis, avoid diagnostic pitfalls and to improve the diagnostic level in our country.

Novel device for dividing core needle biopsy specimens to provide paired mirror image-like tissues for genetic and pathological tests

In a world that seeks precision medicine, genetic testing is gaining importance in clinical decision making. We previously reported the utility of a novel tool for longitudinally dividing core needle biopsy (CNB) tissues into two filamentous tissues that can provide paired mirror image-like tissues (mirror-tissues) that spatially match each other. In this study, we investigated its application in gene panel testing in patients who underwent prostate CNB. Four hundred and forty-three biopsy cores were obtained from 40 patients. Of them, 361 biopsy cores (81.5%) were judged by a physician to be appropriate for dividing into two pieces using the new device, of which a histopathological diagnosis was successfully reached in 358 biopsy cores (99.2%). Among them, the quality and quantity of nucleic acid in 16 appropriately divided cores were assessed and found to be sufficient for gene panel testing, and histopathological diagnosis was successfully obtained from the remaining divided cores. The novel device for longitudinally-dividing CNB tissue provided mirror image-like paired-tissues for gene panel and pathology testing. The device might be a promising tool for obtaining genetic and molecular biological information, in addition to histopathological diagnosis, helping to advance personalized medicine.

Non-invasive imaging in the diagnosis of combined hepatocellular carcinoma and cholangiocarcinoma.

Combined hepatocellular-cholangiocarcinoma (cHCC-CC) is a rare type of primary liver cancer. It is a complex "biphenotypic" tumor type consisting of bipotential hepatic progenitor cells that can differentiate into cholangiocytes subtype and hepatocytes subtype. The prognosis of patients with cHCC-CC is quite poor with its specific and more aggressive nature. Furthermore, there are no definite demographic or clinical features of cHCC-CC, thus a clear preoperative identification and accurate non-invasive imaging diagnostic analysis of cHCC-CC are of great value. In this review, we first summarized the epidemiological features, pathological findings, molecular biological information and serological indicators of cHCC-CC disease. Then we reviewed the important applications of non-invasive imaging modalities-particularly ultrasound (US)-in cHCC-CC, covering both diagnostic and prognostic assessment of patients with cHCC-CC. Finally, we presented the shortcomings and potential outlooks for imaging studies in cHCC-CC.

Recent development of machine learning models for the prediction of drug-drug interactions.

Polypharmacy, the co-administration of multiple drugs, has become an area of concern as the elderly population grows and an unexpected infection, such as COVID-19 pandemic, keeps emerging. However, it is very costly and time-consuming to experimentally examine the pharmacological effects of polypharmacy. To address this challenge, machine learning models that predict drug-drug interactions (DDIs) have actively been developed in recent years. In particular, the growing volume of drug datasets and the advances in machine learning have facilitated the model development. In this regard, this review discusses the DDI-predicting machine learning models that have been developed since 2018. Our discussion focuses on dataset sources used to develop the models, featurization approaches of molecular structures and biological information, and types of DDI prediction outcomes from the models. Finally, we make suggestions for research opportunities in this field.

Radiogenomic analysis of prediction HER2 status in breast cancer by linking ultrasound radiomic feature module with biological functions

BackgroundHuman epidermal growth factor receptor 2 (HER2) overexpressed associated with poor prognosis in breast cancer and HER2 has been defined as a therapeutic target for breast cancer treatment. We aimed to explore the molecular biological information in ultrasound radiomic features (URFs) of HER2-positive breast cancer using radiogenomic analysis. Moreover, a radiomics model was developed to predict the status of HER2 in breast cancer.MethodsThis retrospective study included 489 patients who were diagnosed with breast cancer. URFs were extracted from a radiomics analysis set using PyRadiomics. The correlations between differential URFs and HER2-related genes were calculated using Pearson correlation analysis. Functional enrichment of the identified URFs-correlated HER2 positive-specific genes was performed. Lastly, the radiomics model was developed based on the URF-module mined from auxiliary differential URFs to assess the HER2 status of breast cancer.ResultsEight differential URFs (p < 0.05) were identified among the 86 URFs extracted by Pyradiomics. 25 genes that were found to be the most closely associated with URFs. Then, the relevant biological functions of each differential URF were obtained through functional enrichment analysis. Among them, Zone Entropy is related to immune cell activity, which regulate the generation of calcification in breast cancer. The radiomics model based on the Logistic classifier and URF-module showed good discriminative ability (AUC = 0.80, 95% CI).ConclusionWe searched for the URFs of HER2-positive breast cancer, and explored the underlying genes and biological functions of these URFs. Furthermore, the radiomics model based on the Logistic classifier and URF-module relatively accurately predicted the HER2 status in breast cancer.

The Impact of Tissue Preparation on Salivary Gland Tumors Investigated by Fourier-Transform Infrared Microspectroscopy.

Due to the wide variety of benign and malignant salivary gland tumors, classification and malignant behavior determination based on histomorphological criteria can be difficult and sometimes impossible. Spectroscopical procedures can acquire molecular biological information without destroying the tissue within the measurement processes. Since several tissue preparation procedures exist, our study investigated the impact of these preparations on the chemical composition of healthy and tumorous salivary gland tissue by Fourier-transform infrared (FTIR) microspectroscopy. Sequential tissue cross-sections were prepared from native, formalin-fixed and formalin-fixed paraffin-embedded (FFPE) tissue and analyzed. The FFPE cross-sections were dewaxed and remeasured. By using principal component analysis (PCA) combined with a discriminant analysis (DA), robust models for the distinction of sample preparations were built individually for each parotid tissue type. As a result, the PCA-DA model evaluation showed a high similarity between native and formalin-fixed tissues based on their chemical composition. Thus, formalin-fixed tissues are highly representative of the native samples and facilitate a transfer from scientific laboratory analysis into the clinical routine due to their robust nature. Furthermore, the dewaxing of the cross-sections entails the loss of molecular information. Our study successfully demonstrated how FTIR microspectroscopy can be used as a powerful tool within existing clinical workflows.

Exploring novel disease-disease associations based on multi-view fusion network

Established taxonomy system based on disease symptom and tissue characteristics have provided an important basis for physicians to correctly identify diseases and treat them successfully. However, these classifications tend to be based on phenotypic observations, lacking a molecular biological foundation. Therefore, there is an urgent to integrate multi-dimensional molecular biological information or multi-omics data to redefine disease classification in order to provide a powerful perspective for understanding the molecular structure of diseases. Therefore, we offer a flexible disease classification that integrates the biological process, gene expression, and symptom phenotype of diseases, and propose a disease-disease association network based on multi-view fusion. We applied the fusion approach to 223 diseases and divided them into 24 disease clusters. The contribution of internal and external edges of disease clusters were analyzed. The results of the fusion model were compared with Medical Subject Headings, a traditional and commonly used disease taxonomy. Then, experimental results of model performance comparison show that our approach performs better than other integration methods. As it was observed, the obtained clusters provided more interesting and novel disease-disease associations. This multi-view human disease association network describes relationships between diseases based on multiple molecular levels, thus breaking through the limitation of the disease classification system based on tissues and organs. This approach which motivates clinicians and researchers to reposition the understanding of diseases and explore diagnosis and therapy strategies, extends the existing disease taxonomy. Availability of data and materialsThe preprocessed dataset and source code supporting the conclusions of this article are available at GitHub repository https://github.com/yangxiaoxi89/mvHDN.

PPDP: A Data Portal of Paris polyphylla for Polyphyllin Biosynthesis and Germplasm Resource Exploration

Paris polyphylla Smith is a perennial medicinal herb with records from around 2000 years ago. Polyphyllins are the main bioactive compounds of this herb, which are found to have remarkable effects on bacteriostatic, antiphlogistic, sedative, and antitumor. However, the market demand for P. polyphylla is sharply increasing, and the wild resources are threatened by plundering exploitation. Integrating molecular data of P. polyphylla can benefit the sustainable resource exploitation. Here, we constructed PPDP (Paris polyphylla Data Portal) to provide a data platform for polyphyllin biosynthesis and germplasm resource research. PPDP integrates related molecular data resources, functional genomics analysis, and morphological identification. The database provides abundant data (transcriptome, CDS, lncRNA, alternative splicing, gene family, SSR, and chloroplast genome) and practical analytical tools (network construction, heatmap of expression profiles, enrichment, and pathway search) with a user-friendly interface. So far, PPDP is the first biomolecular database for the genus Paris plants. In the future, we will gradually add genomic data and other necessary molecular biological information to improve the database.

Piperidine-based natural products targeting Type IV pili antivirulence: A computational approach

Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dynamic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.

The LIM Protein AJUBA is a Potential Oncogenic Target and Prognostic Marker in Human Cancer via Pan-Cancer Analysis.

Purpose : The LIM (Lin-11, Isl1, MEC-3) domain protein AJUBA is involved in multiple biological functions, and its aberrant expression is related to the occurrence and progression of various cancers. However, there are no analytical studies on AJUBA in pan-cancer. Methods: We performed a comprehensive pan-cancer analysis and explored the potential oncogenic roles of AJUBA, including gene expression, genetic mutation, protein phosphorylation, clinical diagnostic biomarker, prognosis, and AJUBA-related immune infiltration based on The Cancer Genome Atlas and Genotype-Tissue Expression databases. Results: The results revealed that the expression of AJUBA highly correlated with poor clinical outcomes in patients with different types of cancer. Meanwhile, AJUBA expression was positively correlated with cancer-associated fibroblasts in many human cancers, such as breast invasive carcinoma, colon adenocarcinoma, brain lower-grade glioma, lung adenocarcinoma (LUAD), and ovarian serous cystadenocarcinoma (OV). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that AJUBA is mainly involved in protein serine/threonine kinase activity, cell–cell junction, covalent chromatin modification, and Hippo signaling pathway. Conclusion: The pan-cancer study reveals the oncogenic roles of AJUBA and provides a comprehensive understanding of the molecular biological genetic information of AJUBA in various tumors.

Comparative Analysis of the Chloroplast Genome for Aconitum Species: Genome Structure and Phylogenetic Relationships.

Aconitum is an important medicinal group of the Ranunculaceae family and has been used as conventional medicine in Bai, Yi, and other ethnic groups of China. There are about 350 Aconitum species globally and about 170 species in China. It is challenging to identify the species in morphology, and the lack of molecular biology information hinders the identification and rational utilization of the germplasm of this genus. Therefore, it is necessary to increase the molecular data of Aconitum species. This paper acquired the complete chloroplast (CP) genome sequence of ten medicinal plants of Aconitum species from Yunnan by Illumina paired-end (PE) sequencing technology and compared it with other species in the same family and genus. These CP genomes exhibited typical circular quadripartite structure, and their sizes ranged from 155,475 (A. stylosum) to 155,921 bp (A. vilmoinianum), including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs). Their gene content, order, and GC content (38.1%) were similar. Moreover, their number of genes ranged from 129 (A. vilmoinianum) to 132 (A. ramulosum), including 83 to 85 protein-coding genes (PCGs), 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and two pseudogenes. In addition, we performed repeated sequence analysis, genomic structure, and comparative analysis using 42 Aconitum chloroplast genomes, including ten Aconitum chloroplast genomes and other sequenced Aconitum species. A total of 48–79 simple sequence repeats (SSRs) and 17 to 77 long repeat sequences were identified. IR regions showed higher variability than the SSC region and LSC region. Seven mutational hotspots were screened out, including trnK-UUU-trnQ-UGG, psbD, ndhJ-ndhK, clpP, psbH-petB, ycf1, and trnA-UGC-trnI-GAU, respectively. The phylogenetic trees of ten Aconitum species and other Aconitum species revealed that the complete CP genome was beneficial in determining the complex phylogenetic relationships among Aconitum species. This study provides a potential molecular marker and genomic resource for phylogeny and species identification of Aconitum species and an important reference and basis for Ranunculaceae species identification and phylogeny.

Analysis of treatment failure phenotype and prognostic factors of stage Ⅰ non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is one of the most severe malignant tumors worldwide. Lobectomy and systematic nodal dissection remain the standard treatment for stageⅠNSCLC. Stereotactic body radiotherapy (SBRT) has become the standard treatment for medically inoperable patients. Though the prognosis of stage Ⅰ NSCLC patients is generally good, there are still about 20% of patients with local recurrence and distant metastasis. There is significant heterogeneity in the prognosis and failure phenotype of patients, which cannot be precisely distinguished by the pathological TNM classification system. Identification of the risk factors for the prognosis of patients with stage Ⅰ NSCLC is a key step to realize the treatment from experience to precision. Screening the high-risk patients will facilitate to individually develop the adjuvant therapy strategy after surgery or SBRT and improve the overall curative effect. There are many factors that are significantly related to the prognosis of stage Ⅰ NSCLC including individual factors such as gender, age, and systemic inflammatory biomarkers; treatment-related factors such as the extent of surgical resection of the primary tumor and lymph nodes, the choice of different radiation rays, and different dose fractionation; and tumor-related factors such as imaging information, pathology information; and molecular biology information. This review will analyze the treatment failure phenotype and prognostic factors of stageⅠ NSCLC in various perspectives such as individual-, tumor- and treatment-related factors.

The Development of Single-Cell Metabolism and Its Role in Studying Cancer Emergent Properties.

Metabolic reprogramming is one of the hallmarks of malignant tumors, which provides energy and material basis for tumor rapid proliferation, immune escape, as well as extensive invasion and metastasis. Blocking the energy and material supply of tumor cells is one of the strategies to treat tumor, however tumor cell metabolic heterogeneity prevents metabolic-based anti-cancer treatment. Therefore, searching for the key metabolic factors that regulate cell cancerous change and tumor recurrence has become a major challenge. Emerging technology––single-cell metabolomics is different from the traditional metabolomics that obtains average information of a group of cells. Single-cell metabolomics identifies the metabolites of single cells in different states by mass spectrometry, and captures the molecular biological information of the energy and substances synthesized in single cells, which provides more detailed information for tumor treatment metabolic target screening. This review will combine the current research status of tumor cell metabolism with the advantages of single-cell metabolomics technology, and explore the role of single-cell sequencing technology in searching key factors regulating tumor metabolism. The addition of single-cell technology will accelerate the development of metabolism-based anti-cancer strategies, which may greatly improve the prognostic survival rate of cancer patients.

Precision Medicine for Ependymoma

Herein we discuss precision medicine for ependymoma. We reviewed the new molecular classifications of ependymoma, studies on the molecular mechanisms involved in carcinogenesis and proliferation, and the various studies exploring new therapeutic strategies. Of the nine molecular classifications of ependymoma, supratentorial ependymomas with ZFTA fusion, posterior fossa PFA group, and spinal ependymomas with MYCN amplification are treatment-resistant, and candidates for precision medicine. Precision medicine is considered to select a treatment method based on molecular biological information, but its application is thought to be difficult for ependymomas with few somatic mutations. Recent studies have shown that epigenetic mechanisms are involved in the development and growth of PFA ependymomas without recurrent somatic mutations. It has been found that ZFTA forms fusion genes with various genes other than the typical ZFTA-RELA fusion, and a common therapeutic target has been suggested for the genes downstream of it. Unfortunately, these findings have not yet been clinically applied to precision medicine for ependymoma, but newer discoveries are gradually accumulating. Further development of research is warranted.