DriverDBv4: a multi-omics integration database for cancer driver gene research.

Advancements in high-throughput technology offer researchers an extensive range of multi-omics data that provide deep insights into the complex landscape of cancer biology. However, traditional statistical models and databases are inadequate to interpret these high-dimensional data within a multi-omics framework. To address this limitation, we introduce DriverDBv4, an updated iteration of the DriverDB cancer driver gene database (http://driverdb.bioinfomics.org/). This updated version offers several significant enhancements: (i) an increase in the number of cohorts from 33 to 70, encompassing approximately 24 000 samples; (ii) inclusion of proteomics data, augmenting the existing types of omics data and thus expanding the analytical scope; (iii) implementation of multiple multi-omics algorithms for identification of cancer drivers; (iv) new visualization features designed to succinctly summarize high-context data and redesigned existing sections to accommodate the increased volume of datasets and (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identification and subgroup expression analysis. DriverDBv4 facilitates comprehensive interpretation of multi-omics data across diverse cancer types, thereby enriching the understanding of cancer heterogeneity and aiding in the development of personalized clinical approaches. The database is designed to foster a more nuanced understanding of the multi-faceted nature of cancer.

Machine Learning and Radiomics of Bone Scintigraphy: Their Role in Predicting Recurrence of Localized or Locally Advanced Prostate Cancer.

BACKGROUND: Machine-learning (ML) and radiomics features have been utilized for survival outcome analysis in various cancers. This study aims to investigate the application of ML based on patients' clinical features and radiomics features derived from bone scintigraphy (BS) and to evaluate recurrence-free survival in local or locally advanced prostate cancer (PCa) patients after the initial treatment. METHODS: A total of 354 patients who met the eligibility criteria were analyzed and used to train the model. Clinical information and radiomics features of BS were obtained. Survival-related clinical features and radiomics features were included in the ML model training. Using the pyradiomics software, 128 radiomics features from each BS image's region of interest, validated by experts, were extracted. Four textural matrices were also calculated: GLCM, NGLDM, GLRLM, and GLSZM. Five training models (Logistic Regression, Naive Bayes, Random Forest, Support Vector Classification, and XGBoost) were applied using K-fold cross-validation. Recurrence was defined as either a rise in PSA levels, radiographic progression, or death. To assess the classifier's effectiveness, the ROC curve area and confusion matrix were employed. RESULTS: Of the 354 patients, 101 patients were categorized into the recurrence group with more advanced disease status compared to the non-recurrence group. Key clinical features including tumor stage, radical prostatectomy, initial PSA, Gleason Score primary pattern, and radiotherapy were used for model training. Random Forest (RF) was the best-performing model, with a sensitivity of 0.81, specificity of 0.87, and accuracy of 0.85. The ROC curve analysis showed that predictions from RF outperformed predictions from other ML models with a final AUC of 0.94 and a p-value of <0.001. The other models had accuracy ranges from 0.52 to 0.78 and AUC ranges from 0.67 to 0.84. CONCLUSIONS: The study showed that ML based on clinical features and radiomics features of BS improves the prediction of PCa recurrence after initial treatment. These findings highlight the added value of ML techniques for risk classification in PCa based on clinical features and radiomics features of BS.

Learning Curve of Transperineal MRI/US Fusion Prostate Biopsy: 4-Year Experience.

This study aimed to evaluate the learning curve of transperineal magnetic resonance imaging (MRI)/ultrasound (US) fusion biopsy in a team composed of a single surgeon, a single radiologist, and a single pathologist. We prospectively enrolled 206 patients undergoing MRI/US fusion prostate biopsy and divided them into four cohorts by the year of biopsy. We analyzed temporal changes in clinically significant prostate cancer (csPC) detection rate, percentage of positive cores on biopsy, and Gleason upgrading rate after radical prostatectomy. The csPC detection rate by MRI/US fusion targeted biopsy (TB) increased significantly (from 35.3% to 60.0%, p = 0.01). With increased experience, the csPC detection rates for small (≤1 cm) and anterior target lesions gradually increased (from 41.2% to 51.6%, p = 0.5; from 54.5% to 88.2%, p = 0.8, respectively). The percentage of positive cores on TB increased significantly (from 18.4% to 44.2%, p = 0.001). The Gleason upgrading rate gradually decreased (from 22.2% to 11.1%, p = 0.4). In conclusion, with accumulated experience and teamwork, the csPC detection rate by TB significantly increased. Multidisciplinary team meetings and a free-hand biopsy technique were the key factors for overcoming the learning curve.

Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn Macrobrachium rosenbergii.

Macrobrachium rosenbergii is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regulating life functions. In the present work, we applied PacBio RNA-seq to obtain and characterize the full-length transcriptomes of the brains and thoracic ganglia of female and male prawns, and we performed comparative transcriptome analysis of female and male prawns. A total of 159.1-Gb of subreads were obtained with an average length of 2175 bp and 93.2% completeness. A total of 84,627 high-quality unigenes were generated and annotated with functional databases. A total of 6367 transcript factors and 6287 LncRNAs were predicted. In total, 5287 and 6211 significantly differentially expressed genes (DEGs) were found in the brain and thoracic ganglion, respectively, and confirmed by qRT-PCR. Of the 435 genes associated with protein processing pathways in the endoplasmic reticula, 42 DEGs were detected, and 21/26 DEGs with upregulated expression in the male brain/thoracic ganglion. The DEGs in this pathway are regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our results provide novel theories and insights for studying the nervous system, sexual control, and growth dimorphism.

Pt/MoS2/Polyaniline Nanocomposite as a Highly Effective Room Temperature Flexible Gas Sensor for Ammonia Detection.

A Pt/MoS2/polyaniline (Pt/MoS2/PANI) nanocomposite is successfully synthesized by the hydrothermal process combined with the in situ polymerization method, and then Pt particles are decorated on its surface. The Pt/MoS2/PANI nanocomposite is deposited on a flexible Au-interdigitated electrode of a polyimide (PI) film. The flexible sensor exhibits a higher response value and fast response/recovery time to NH3 at room temperature (RT). It results in 2.32-fold and 1.13-fold improvement in the gas-sensing response toward 50 ppm NH3 compared to those of PANI and MoS2/PANI-based gas sensors. The detection limit is 250 ppb. The enhancement sensing mechanisms are attributed to the p-n heterojunction and the Schottky barrier between the three components, which has been confirmed by the current-voltage (I-V) curves. A satisfactory selectivity to NH3 against trimethylamine (TMA) and triethylamine (TEA) is obtained according to density functional theory (DFT), Bader's analysis, and differential charge density to illustrate the adsorption behavior and charge transfer of gas molecules on the surface of the sensing materials. The sensor retains the excellent sensing response value even under high relative humidity and sensing stability at higher bending angle/numbers to NH3 gas. Hence, Pt/MoS2/PANI can be regarded as a promising sensing material for high-performance NH3 detection at room temperature applied in flexible wearable electronics.

QSOFA and SOFA scores are valuable tools for predicting postoperative sepsis resulting from ureteroscopic lithotripsy (URSL).

The sequential organ failure assessment (SOFA) and quick sequential organ failure assessment (qSOFA) scores are new tools which are used to assess sepsis based on the Third International Consensus Definitions for Sepsis and Septic Shock Task Force. This study aimed to evaluate the feasibility of using the SOFA and qSOFA to predict post-ureteroscopic lithotripsy (URSL) sepsis. Patients who underwent URSL due to ureteral stone obstruction were retrospectively reviewed using SOFA and qSOFA scores. Patient characteristics including age, gender, comorbidities, American Society of Anesthesiologists Classification, stone burden, stone location, hydronephrosis status, infectious status, preoperative SOFA and qSOFA score were collected. Preoperative factors were analyzed to determine if they were correlated with postoperative sepsis. A total of 830 patients were included in this study, of whom 32 (3.9%) had postoperative sepsis. Multivariate analysis revealed that older age, proximal ureteral stones, severe hydronephrosis, and high preoperative qSOFA or SOFA score were significantly associated with postoperative sepsis. The areas under the curves of a qSOFA score ≥ 1 and SOFA score ≥ 2 for predicting postoperative sepsis were 0.754 and 0.823, respectively. Preoperative qSOFA and SOFA scores are convenient and effective for predicting post-URSL sepsis. Further preventive strategies should be performed in these high-risk patients.

Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish.

BACKGROUND: Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. RESULTS: We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. CONCLUSIONS: Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.

A comparative study of transperineal software-assisted magnetic resonance/ultrasound fusion biopsy and transrectal cognitive fusion biopsy of the prostate.

BACKGROUND: The advantages and disadvantages of transperineal and transrectal biopsies remain controversial in the era of prostate targeted biopsy. In this study, we compared the cancer detection and complication rates of transperineal magnetic resonance/ultrasound (MR/US) fusion biopsy and transrectal cognitive fusion biopsy of the prostate. METHODS: This was a comparative study of two prospectively collected cohorts. Men with clinically suspected prostate cancer and prostate imaging reporting and data system (PI-RADS) score ≥ 3 lesions on multi-parametric magnetic resonance imaging (mpMRI) were enrolled. They underwent either transperineal software fusion biopsy or transrectal cognitive fusion biopsy and systematic biopsy. The detection rates of any prostate cancer and clinically significant prostate cancer (csPC, defined as Gleason score ≥ 3 + 4) and the complication rates between both groups were analysed. RESULTS: Ninety-two and 85 patients underwent transperineal software fusion and transrectal cognitive fusion biopsies, respectively. The detection rate for any prostate cancer was similar between both groups (60.8% vs. 56.4%, p = 0.659). In terms of csPC detection, transperineal fusion biopsy outperformed transrectal fusion biopsy (52.2% vs. 36.5%, p = 0.036). In multivariate regression analysis, age, PI-RADS score > 3, and transperineal route were significant predictors of csPC. Meanwhile, transperineal biopsy resulted in a higher rate of urinary retention than transrectal biopsy (18.5% vs. 4.7%, p = 0.009). No serious infectious complications were noted, although a patient developed sepsis after transrectal biopsy. CONCLUSIONS: Transperineal software fusion biopsy provided a higher csPC detection rate than transrectal cognitive fusion biopsy and carried minimal risk for infectious complications in patients with MRI-visible prostate lesions.

Two New Types of Homodiploid Fish and Polyploid Hybrids Derived from the Distant Hybridization of Female Koi Carp and Male Bighead Carp.

Bighead carps  (Hypophthalmichthys nobilis) and silver carps (Hypophthalmichthys molitrix) represent an important component of freshwater ichthiofauna in its native range, though they might become mass propagation in other systems (North America) and the reason of concern for fisheries management. Therefore, understanding their reproductive traits and particularly in the context of hybridization with other cyprinids was of value to explain their rapid propagation as well as potential benefits for aquaculture due to their unique diet, behavior, growth potential, and tolerance to deteriorating environmental conditions in freshwater ecosystems. Distant hybridization is an effective tool to create different ploidy offspring with changed phenotypes and genotypes. In this study, we reported distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) × male bighead carp (Hypophthalmichthys nobilis, BIC, 2n = 48) and the spontaneous occurrence of two new "crucian" carp-like homodiploid fish (2nGCC-L; 2nCCC-L; 2n = 100), a new type of triploid hybrid (3nKB, 3n = 124), and a new type of tetraploid hybrid (4nKB, 4n = 148). The body color of 2nGCC-L and 2nCCC-L were gray and multicolor, respectively. Both phenotypes were similar to the crucian carp (Carassius auratus). The difference was that their heads were rounder than those of the crucian carp and they had higher backs. Compared with the KOC with two pairs of barbels and BIC without barbel, 2nGCC-L, 2nCCC-L, and 4nKB had no barbel, but 3nKB had one pair of barbels. Microsatellite patterns and 5S rDNA sequences confirmed that 2nGCC-L, 2nCCC-L, and 3nKB were of hybrid origin. In regard to feeding, KOC was omnivorous and BIC was a typical filter-feeder. However, the 2nGCC-L, 2nCCC-L, and 3nKB were omnivorous. The formation of four kinds of new offspring is a groundbreaking finding in fish genetic breeding and evolutionary biology.

Evaluation of cyclooxygenase-2 fluctuation via a near-infrared fluorescent probe in idiopathic pulmonary fibrosis cell and mice models.

Idiopathic pulmonary fibrosis (IPF) is a devastating and fatal interstitial lung disease due to various challenges in diagnosis and treatment. Due to its complicated pathogenesis and difficulty in early diagnosis, there is no effective cure. Cyclooxygenase-2 (COX-2) is inextricably associated with pulmonary fibrosis. The abnormal level of COX-2 leads to extremely exacerbated pulmonary fibrosis. Therefore, we reported a near-infrared fluorescent probe Cy-COX to detect the fluctuation of COX-2 levels during pulmonary fibrosis and explain its important protective effect. The probe Cy-COX showed a significant enhancement of fluorescence signal to COX-2 with excellent selectivity and sensitivity. In order to clarify the relationship between COX-2 and pulmonary fibrosis, we used the probe Cy-COX to detect COX-2 fluctuation in organisms with pulmonary fibrosis. The results showed that the COX-2 level increased in the early stage and decreased in the late stage with the aggravation of pulmonary fibrosis. Furthermore, up-regulation of COX-2 levels can effectively alleviate the severity of pulmonary fibrosis. Therefore, Cy-COX is a fast and convenient imaging tool with great potential to predict the early stage of pulmonary fibrosis and evaluate the therapeutic effects.

Fluorescence 'turn-on' probe for Al3+ detection in water based on ZnS/ZnO quantum dots with excellent selectivity and stability.

In this work, an efficient and stable fluorescent probe for Al3+was established. The fluorescent probe based on the fluorescence 'turn-on' mode of zinc sulfide crystal composite zinc oxide quantum dots (ZnS/ZnO QDs). The ZnS/ZnO QDs were synthesized via two-step method using L-Cysteine (L-Cys) as a sulfur source and stabilizer. In the synthesis of ZnS/ZnO QDs, the fluorescence of zinc oxide quantum dots (ZnO QDs) decreased and its stability increased in aqueous solution after the addition of L-Cys. In addition, the as-synthesized ZnS/ZnO QDs shows fluorescent enhancement to Al3+. The ZnS/ZnO QDs based fluorescence 'turn-on' probe presented wide linear ranges (1 nM-8µM and 8-100µM). The availability of as-established sensing probe was also estimated by real water sample tests. Furthermore, the fluorescent enhancing mechanism was carried out by recording the fluorescent lifetime of samples, which might be related to the QDs dispersion and charge transfer weaken.

Excellent fluorescence detection of Cu2+in water system using N-acetyl-L-cysteines modified CdS quantum dots as fluorescence probe.

View of the negative influence of metal ions on natural environment and human health, fast and quantitative detection of metals ions in water systems is significant. Ultra-small grain size CdS quantum dots (QDs) modified with N-acetyl-L-cysteines (NALC) (NALC-CdS QDs) are successfully prepared via a facile hydrothermal route. Based on the changes of fluorescence intensity of NALC-CdS QDs solution after adding metal ions, the fluorescence probe made from the NALC-CdS QDs is developed to detect metal ions in water systems. Among various metal ions, the fluorescence of NALC-CdS QDs effectively quenched by the addition of Cu2+, the probe shows high sensitivity and selectivity for detecting Cu2+in other interferential metal ions coexisted system. Importantly, the fluorescence intensity of NALC-CdS QDs changes upon the concentration of Cu2+, the probe displays an excellent linear relationship between the fluorescence quenching rate and the concentration of Cu2+in ranging from 1 to 25µM. Besides, the detected limitation of the probe towards Cu2+as low as 0.48µM. The measurement of Cu2+in real water sample is also carried out using the probe. The results indicate that NALC-CdS QDs fluorescence probe may be a promising candidate for quantitative Cu2+detection in practical application.

Gas sensing materials roadmap.

Gas sensor technology is widely utilized in various areas ranging from home security, environment and air pollution, to industrial production. It also hold great promise in non-invasive exhaled breath detection and an essential device in future internet of things. The past decade has witnessed giant advance in both fundamental research and industrial development of gas sensors, yet current efforts are being explored to achieve better selectivity, higher sensitivity and lower power consumption. The sensing layer in gas sensors have attracted dominant attention in the past research. In addition to the conventional metal oxide semiconductors, emerging nanocomposites and graphene-like two-dimensional materials also have drawn considerable research interest. This inspires us to organize this comprehensive 2020 gas sensing materials roadmap to discuss the current status, state-of-the-art progress, and present and future challenges in various materials that is potentially useful for gas sensors.

Species and tissue specific analysis based on quantitative proteomics from allotetraploid and the parents.

Allotetraploids play central roles in the field of polyploid breeding of freshwater fishes. The molecular basis underlying distant hybridization and individual differences between allotetraploids and their parents is largely unknown. In this study, we performed quantitative proteomics profiling in gonad and liver tissues between allotetraploid and its parents Red Crucian Carp (♀) and Common Carp (♂) respectively. Thousands of proteins were identified and quantified. Species and tissue specific analysis revealed that a large number of causal proteins are specifically regulated in gonad or liver tissue in allotetraploid and its parents respectively. Subsequently, integrative bioinformatics analyses including functional enrichment, pathway and network analyses were conducted. The results suggested a series of gonad and liver specifically regulated proteins such as LSM3, LSM7, PABPC1B and ALDH3A1, EHHADHB, ACAT2 play crucial roles in reproduction-related and metabolism-related pathways including "DNA replication", "Spliceosome" and "Metabolic pathways", "Biosynthesis of antibiotics". Meanwhile, species specifically regulated proteins such as FMR1, MAO are involved in "RNA transport", "Glycine, serine and threonine metabolism". Herein, we established the first comprehensive proteomics knowledgebase for particular freshwater fishes. It may shed light on the molecular mechanisms underlying polyploidy breeding and individual differences and serve as an indispensable reference for further studies. SIGNIFICANCE: The molecular basis underlying distant hybridization and individual differences between allotetraploid and their parents Red Crucian Carp and Common Carp is largely unknown. Quantitative proteomics profiling integrated with multiple bioinformatics analysis revealed that a large number of causal proteins are specifically expressed in gonad or liver tissue in allotetraploid and its parents. Herein, we established the first comprehensive proteomics knowledgebase for particular freshwater fishes. It may shed light on the molecular mechanisms underlying polyploidy breeding and individual differences and serve as an indispensable reference for further associated studies.

External validation of the Simplified PADUA REnal (SPARE) nephrometry system in predicting surgical outcomes after partial nephrectomy.

BACKGROUND: Pentafecta is a major goal in the era of partial nephrectomy (PN). Simplified PADUA REnal (SPARE) nephrometry system was developed to evaluate the complexity of tumor. However, the predictive ability in pentafecta of SPARE system is yet to be determined. The aim of this study was to externally validate the applicability of SPARE nephrometry system in predicting pentafecta achievement after partial nephrectomy, and to examine inter-observer concordance. METHODS: We retrospectively reviewed data of 207 consecutive patients who underwent PN between January 2012 and August 2018 at a tertiary referral center. We obtained SPARE, R.E.N.A.L., and PADUA scores and evaluated correlations among the nephrometries and surgical outcomes including pentafecta by Spearman test. Logistic regression analysis was used to identify independent predictors of pentafecta outcomes. We compared the nephrometries to determine the predictive ability of achieving pentafecta using receiver operating characteristic curve analysis. Fleiss' generalized kappa was used to assessed interobserver variation in the SPARE system. RESULTS: Based on the SPARE system, 120, 74, and 13 patients were stratified into low-risk, intermediate-risk, and high-risk groups, respectively. Regarding the individual components of pentafecta, there were significant differences in the complication rate (p = 0.03), ischemia time (p < 0.001), and percent change of eGFR (p < 0.001) among the three risk groups. In addition, higher tumor complexity was significantly associated with a lower achievement rate of pentafecta (p = 0.01). In Spearman correlation tests, SPARE nephrometry was correlated with ischemia time (ρ:0.37, p < 0.001), operative time (ρ:0.28, p < 0.001), complication rate (ρ:0.34, p < 0.001), percent change of eGFR (ρ:0.34, p < 0.001), and progression of chronic kidney disease stage (ρ:0.17, p = 0.02). Multivariate analysis revealed that SPARE significantly affected pentafecta (OR: 0.67, p < 0.001). In ROC curve analysis, SPARE showed fair predictive ability in the achievement pentafecta (AUC: 0.71). The predictive ability of pentafecta was similar between nephrometries (SPARE vs. R.E.N.A.L., p = 0.78; SPARE vs. PADUA, p = 0.66). The interobserver concordance of SPARE was excellent (Kappa: 0.82, p = 0.03). CONCLUSIONS: SPARE system was a predictive factor of surgical outcomes after PN. This refined nephrometry had similar predictive abilities for pentafecta achievement compared with R.E.N.A.L. and PADUA.

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish.

A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates to ~15 million years ago. Comprehensive analyses identify changes in subgenomic evolution from asymmetrical oscillation in goldfish and common carp to diverse stabilization and balanced gene expression during continuous rediploidization. The homoeologs are coexpressed in most pathways, and their expression dominance shifts temporally during embryogenesis. Homoeolog expression correlates negatively with alternation of DNA methylation. The results show that allotetraploid cyprinids have a unique strategy for balancing subgenomic stabilization and diversification. Rediploidization process in these fishes provides intriguing insights into genome evolution and function in allopolyploid vertebrates.

Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus.

The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.

Hox genes reveal variations in the genomic DNA of allotetraploid hybrids derived from Carassius auratus red var. (female) × Cyprinus carpio L. (male).

BACKGROUND: Hox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, thus potentially serving as species-specific molecular markers. Here, we systematically studied the evolution of genomic sequences of Hox loci in an artificial allotetraploid lineage (4nAT, 4n = 200) derived from a red crucian carp (♀, RCC, 2n = 100) × common carp (♂, CC, 2n = 100) cross and its parents (RCC and CC). RESULTS: PCR amplification yielded 23 distinct Hox gene fragments from 160 clones in 4nAT, 22 fragments from 90 clones in RCC, and 19 fragments from 90 clones in CC. Sequence alignment of the HoxA3a and HoxC10a genes indicated both the inheritance and loss of paternal genomic DNA in 4nAT. The HoxA5a gene from 4nAT consisted of two subtypes from RCC and two subtypes from CC, indicating that homologous recombination occurred in the 4nAT hybrid genome. Moreover, 4nAT carried genomic pseudogenization in the HoxA10b and HoxC13a loci. Interestingly, a new type of HoxC9a gene was found in 4nAT as a hybrid sequence of CC and RCC by recombination in the intronic region. CONCLUSION: The results revealed the influence of Hox genes during polyploidization in hybrid fish. The data provided insight into the evolution of vertebrate genomes and might be benefit for artificial breeding programs.

Comparative analyses of the Sox9a-Amh-Cyp19a1a regulatory Cascade in Autotetraploid fish and its diploid parent.

BACKGROUND: Autotetraploid Carassius auratus (4nRCC, 4n = 200, RRRR) was derived from the whole genome duplication of diploid red crucian carp (Carassius auratus red var.) (2nRCC, 2n = 100, RR). To investigate the genetic effects of tetraploidization, we analyzed DNA variation, epigenetic modification and gene expression changes in the Sox9a-Amh-Cyp19a1a regulatory cascade between 4nRCC and 2nRCC. RESULTS: We found that the Sox9a gene contained two variants in 2nRCC and four variants in 4nRCC. Compared with that in 2nRCC, DNA methylation in the promoter regions of the Amh and Cyp19a1a genes in 4nRCC was altered by single nucleotide polymorphism (SNP) mutations, which resulted in the insertions and deletions of CpG sites, and the methylation levels of the Sox9a, Amh and Cyp19a1a genes increased after tetraploidization. The gene expression level of the Sox9a-Amh-Cyp19a1a regulatory cascade was downregulated in 4nRCC compared with that in 2nRCC. CONCLUSION: The above results demonstrate that tetraploidization leads to significant changes in the genome, epigenetic modification and gene expression in the Sox9a-Amh-Cyp19a1a regulatory cascade; these findings increase the extant knowledge regarding the effects of polyploidization.

The role of RENAL, PADUA, C-index, CSA nephrometry systems in predicting ipsilateral renal function after partial nephrectomy.

BACKGROUND: Functional outcome is an important issue in nephron-sparing surgery. Various nephrometries have been developed to predict renal function preservation. The aim of this study was to examine the applicability of R.E.N.A.L., PADUA, C-index, and mathematical tumor contact surface area (CSA) in predicting ipsilateral renal function after partial nephrectomy using radio-isotope scans. METHODS: We performed this retrospective study in patients who underwent partial nephrectomy between May 2013 and April 2017, and used abdominopelvic computerized tomography or magnetic resonance imaging to obtain R.E.N.A.L., C-index, and CSA. Renal function was measured by 99mTc mercaptoacetyltriglycine (MAG3). We evaluated correlations between nephrometries and perioperative parameters, and comparatively analyzed different nephrometries to determine the predictive ability in the percent change of effective renal plasma flow of the affected kidney. RESULTS: Three, two, and 35 patients received partial nephrectomy in open, laparoscopic, and robotic approaches, respectively. The median (IQR) tumor size was 3.13 (2.4) cm. The median (IQR) R.E.N.A.L., PADUA, C-index, and CSA scores were 7 (3), 8 (2), 2.01 (1.87), and 14.14 (19.25) cm2, respectively. Spearman correlation analysis showed that four nephrometries were correlated with each other. The strongest correlations were between CSA and C-index (coefficient: - 0.885, p < 0.001), followed by R.E.N.A.L. and PADUA (coefficient: 0.778, p < 0.001). Ischemia time was significantly correlated with R.EN.A.L. (coefficient: 0.35, p = 0.025), PADUA (coefficient: 0.42, p = 0.007), C-index (coefficient: - 0.45, p = 0.004), and CSA (coefficient: 0.41, p = 0.009). In multivariate analysis, PADUA significantly affected ischemia time (p = 0.04). The percent change in effective renal plasma flow (PCE) of the operated kidney was correlated with PADUA (coefficient: 0.48 p = 0.002), C-index (coefficient: - 0.74, p < 0.001), and CSA (coefficient: 0.75, p < 0.001). Only CSA and C-index independently affected PCE (both p < 0.05) in multivariate analysis. In ROC curve analysis, both C-index and CSA could predict 20% change in effective renal plasma flow (AUC: 0.91 vs 0.86, p = 0.2) of the affected kidney. CONCLUSIONS: We suggest using PADUA to evaluate surgical complexity and ischemia time. Regarding the accuracy of the prediction of post-operative ipsilateral renal function, both CSA and C-index outperformed R.E.N.A.L. and PADUA nephrometries.