FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
MATERIAL AND METHODS: Differential gene expression was identified using the "limma" package in R. Prognosis-related LncRNAs were identified via univariate Cox regression analysis, while a prognostic model was crafted using multivariate Cox regression analysis. Survival analysis was conducted using Kaplan-Meier curves. The precision of the prognostic model was assessed through ROC analysis. Subsequently, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm were executed on the TCGA dataset via the TIDE database. Fractions of 24 types of immune cell infiltration were obtained from NCI Cancer Research Data Commons using deconvolution techniques. The protein expression levels encoded by specific genes were obtained through the TPCA database.
RESULTS: In this research, we have identified 85 LncRNAs associated with TP53 mutations and developed a corresponding signature referred to as TP53MLncSig. Kaplan-Meier analysis revealed a lower 3-year survival rate in high-risk patients (46.9%) compared to low-risk patients (74.2%). The accuracy of the prognostic TP53MLncSig was further evaluated by calculating the area under the ROC curve. The analysis yielded a 5-year ROC score of 0.793, confirming its effectiveness. Furthermore, a higher score for TP53MLncSig was found to be associated with an increased response rate to immune checkpoint blocker (ICB) therapy (p = .005). Patients possessing high-risk classification exhibited lower levels of P53 protein expression and higher levels of genomic instability.
CONCLUSION: The present study aimed to identify and validate LncRNAs associated with TP53 mutations. We constructed a prognostic model that can predict chemosensitivity and response to ICB therapy in HCC patients. This novel approach sheds light on the role of LncRNAs in TP53 mutation and provides valuable resources for analyzing patient prognosis and treatment selection.
NEW INFORMATION: Nine new species belonging to three genera of Cteninae are reported from Asia: Amauropelmakrabi sp. n. (female; Krabi, Thailand), Am.phangnga sp. n. (male; Phang Nga, Thailand), Am.saraburi sp. n. (male and female; Saraburi, Thailand); Anahitamedog sp. n. (male and female; Tibet, China); Bowieninhbinh sp. n. (male; Ninh Binh, Vietnam) and B.vinhphuc sp. n. (male and female; Vinh Phuc, Vietnam) from the robustus-species group; B.borneo sp. n. (male; Sabah, Malaysia) from the chinagirl-species group; B.engkilili sp. n. (female; Engkilili, Malaysia); B.sabah sp. n. (male and female; Sabah, Malaysia) from the scarymonsters-species group. The male of An.popa Jäger & Minn, 2015 and the female of B.fascination Jäger, 2022 (robustus-species group) are described for the first time. B.fascination Jäger, 2022 is reported from China for the first time. In addition, the DNA barcodes of all the species in this study were obtained, except for B.vinhphuc sp. n.
NEW INFORMATION: Three new species of ctenid spiders are described from Xishuangbanna Tropical Botanical Garden in Yunnan Province, China: Amauropelmayunnan sp. nov., Ctenusbanna sp. nov. and Ctenusyulin sp. nov. Amauropelma and Ctenusrobustus Thorell, 1897 are reported from China for the first time.
Methods: The dataset of visitors to 5 Asian countries with dengue were analyzed for 2016 and 2017, and in the Philippines, Thailand and Vietnam, imported cases of zika virus infection were also reported. For zika virus, a single imported case was reported from Brazil in 2016, and 2 imported cases reported from the Maldives in 2017. To understand the transmissibility in 5 Southeast Asian countries, the estimate of the force of infection, i.e., the hazard of infection per year and the average duration of travel has been extracted. Outbound travel numbers were retrieved from the World Tourism Organization, including business travelers.
Results: The incidence of imported dengue in 2016 was estimated at 7.46, 15.00, 2.14, 4.73 and 2.40 per 100,000 travelers visiting Philippines, Indonesia, Thailand, Malaysia and Vietnam, respectively. Similarly, 2.55, 1.65, 1.53, 1.86 and 1.70 per 100,000 travelers in 2017, respectively. It was estimated that there were 60.1 infections (range: from 16.8 to 150.7 infections) with zika virus in Brazil, 2016, and 345.6 infections (range: from 85.4 to 425.5 infections) with zika virus in the Maldives, 2017.
Conclusion: This study emphasizes that dengue and zika virus infections are mild in their nature, and a substantial number of infections may go undetected. An appropriate risk assessment of zika virus infection must use the estimated total size of infections.