Mitochondrial genomes of four slug moths (Lepidoptera, Limacodidae): Genome description and phylogenetic implications.

The family Limacodidae belongs to the superfamily Zygaenoidea, which includes 1672 species commonly referred to as slug moths. Limacodidae larvae are major pests for many economically important plant species and can cause human dermatitis. At present, the structure of the mitochondrial genome (mitogenome), phylogenetic position, and adaptive evolution of slug moths are poorly understood. Herein, the mitogenomes of Parasa lepida, Phlossa conjuncta, Thosea sinensis, and Setora sinensis were sequenced and compared with other available mitogenome sequences to better characterize the mitogenomic diversity and evolution of this moth family. The mitogenomes of P. lepida, P. conjuncta, T. sinensis, and S. sinensis were confirmed to be circular in structure with lengths of 15,575 bp, 15,553 bp, 15,535 bp, and 15,529 bp, respectively. The Limacodidae mitogenomes exhibited similar nucleotide composition, codon usage, RNA structure, and control region patterns, indicating the conservation of the mitogenome in the family Limacodidae. A sliding window, Ka/Ks, and genetic distance analyses revealed that the atp8 and nad6 genes exhibited the highest levels of variability and the most rapid evolutionary rates among the 13 protein-coding genes (PCGs) encoded in these Limacodidae mitogenomes, suggesting that they may offer value as candidate DNA markers. The phylogenetic analysis recovered the overall relationship as Tortricoidea + (Sesiidae + (Zygaenoidea + (Cossoidea/+Choreutoidea + (others)))). Within Zygaenoidea, Limacodidae was recovered as monophyletic, and the phylogenetic relationships were recovered as (Phaudidae + Zyganidae) + Limacodidae in all six phylogenetic trees. The analysis indicated that P. lepida, P. conjuncta, T. sinensis, and S. sinensis are members of the Limacodidae.

Identification and prevalence investigation of cyathocotylid trematode (Trematoda: Digenea: Cyathocotylidae) in Carassius auratus in Wuhu, China.

The family Cyathocotylidae trematode is a world-widely distributed parasite whose adults are mainly found in fish, reptiles, birds, and mammals in both freshwater and marine environments. However, little is known of the prevalence of these trematode in China. For the first time, we found Cyathocotylidae trematode in the Wuhu area. Therefore, we investigated the prevalence of metacercariae in Carassius auratus from Zhang Lake, Kui Lake, Qingyi River, and Yangtze River (Wuhu Section) in Wuhu area. A total of 392 one-year-old C. auratus were tested in January, April, July, and October 2019, respectively. After the fish were euthanized, the back, chest, and tail muscles were used for preliminary screening for the presence of metacercariae by direct compression method. Metacercariae were isolated by the artificial digestion method and then morphologically and molecularly identified by cox1 (642 bp) and ITS2 (418 bp) sequences amplification by PCR. Based on morphological features and sequence analysis, they were identified as cyathocotylid metacercariae. The four water sources have different degrees of prevalence throughout the year, the prevalence ranges from 28.45% (29/102) in Yangtze River to 50.55% (46/91) in Zhang Lake, with an average prevalence of 40.56% (159/392). There were also differences in the prevalence in different months: The highest occurred in July, which was 81.63% (80/98), while the lowest occurred in January, which was 8.89% (8/90). This study can provide basic data for the prevention and control of cyathocotylid trematode in this area.

Identification of hub genes for early detection of bone metastasis in breast cancer.

Background: Globally, among all women, the most frequently detected and diagnosed and the most lethal type of cancer is breast cancer (BC). In particular, bone is one of the most frequent distant metastases 24in breast cancer patients and bone metastasis arises in approximately 80% of advanced patients. Thus, we need to identify and validate early detection markers that can differentiate metastasis from non-metastasis breast cancers. Methods: GSE55715, GSE103357, and GSE146661 gene expression profiling data were downloaded from the GEO database. There was 14 breast cancer with bone metastasis samples and 8 breast cancer tissue samples. GEO2R was used to screen for differentially expressed genes (DEGs). The volcano plots, Venn diagrams, and annular heatmap were generated by using the ggplot2 package. By using the cluster Profiler R package, KEGG and GO enrichment analyses of DEGs were conducted. Through PPI network construction using the STRING database, key hub genes were identified by cytoHubba. Finally, K-M survival and ROC curves were generated to validate hub gene expression. Results: By GO enrichment analysis, 143 DEGs were enriched in the following GO terms: extracellular structure organization, extracellular matrix organization, leukocyte migration class II protein complex, collagen tridermic protein complex, extracellular matrix structural constituent, growth factor binding, and platelet-derived growth factor binding. In the KEGG pathway enrichment analysis, DEGs were enriched in Staphylococcus aureus infection, Complement and coagulation cascades, and Asthma. By PPI network analysis, we selected the top 10 genes, including SLCO2B1, STAB1, SERPING1, HLA-DOA, AIF1, GIMAP4, C1orf162, HLA-DMB, ADAP2, and HAVCR2. By using TCGA and THPA databases, we validated 2 genes, SERPING1 and GIMAP4, that were related to the early detection of bone metastasis in BC. Conclusions: 2 abnormally expressed hub genes could play a pivotal role in the breast cancer with bone metastasis by affecting bone homeostasis imbalance in the bone microenvironment.

Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation.

Mauremys reevesii is an endangered freshwater turtle that symbolizes longevity in Chinese culture. Despite its importance, genetic studies of this species remain limited, with no genomic sequence reported to date. Here, we report a high-quality, chromosome-level genomic sequence of M. reevesii obtained using a combination of Nanopore and Hi-C sequencing technologies. The 2.37 Gb M. reevesii genome was assembled from a total of ~226.80 Gb of Nanopore sequencing data. The M. reevesii genome contig N50 is 34.73 Mb, the highest value in published turtle genomes. In total, 18,238 genes were functionally annotated. The contigs were clustered and ordered onto 27 pseudochromosomes covering ~96.55% of the genome assembled with Hi-C data. To explore genome evolution, synteny analysis was performed between M. reevesii (freshwater turtle) and Gopherus evgoodei (terrestrial turtle) genomes. In general, each chromosome of M. reevesii corresponded to one chromosome of Gopherus evgoodei, but some interchromosomal rearrangements occurred between the two species based on the assembled genomes. These interchromosomal rearrangements were further confirmed by mapping of the long-read nanopore data to the assembly. The reconstructed demographic history showed varied effective population size among freshwater, marine and terrestrial turtles. We also discovered expansion of genes related to the innate immune system in M. reevesii that may provide defence against freshwater pathogens. The high-quality genomic sequence provides a valuable genetic resource for further studies of genetics and genome evolution in turtles.

Comparison of Penile Appearance and Outcomes Between Prefabricated Urethra and Pre-implanted Urethral Plate for Treatment of Children With Severe Hypospadias: A Retrospective Study.

Objective: To compare the effect of prefabricated urethra and pre-implanted urethral plate in the treatment of severe hypospadias in children. Methods: We retrospectively analyzed the clinical data of 53 patients who diagnosed as severe hypospadias underwent staging urethroplasty from January 2015 to January 2018 in the Department of Pediatric Surgery, First People's Hospital, Zunyi City. The patients were divided into two groups: group A (n = 25) were treated with prefabricated urethra and group B (n = 28) were treated with pre-implanted urethral plate. After the second stage surgery, the ratios of complications such as urethral fistula, urethral stenosis, urethrocele, and recurrence chordee were compared. The penis was scored from meatus, glans, shaft skin, general appearance by the parents, blinded urologists according to The Pediatric Penile Perception Score, and the scores were compared too. Results: All patients were followed up after two stage operations for an average of 28 months. Glans dehiscence occurred in two patients (8%), urethral orifice stenosis occurred in one (4%) and urethral fistula occurred in three (12%) in group A. No urethral stenosis, urethrocele and recurrence chordee was observed. One patient presented urethral plate inactivation (3.6%), two patients presented urethral fistula (7.1%) and one patient presented urethral stenosis (3.6%) in group B. No urethrocele, glans dehiscence and recurrence chordee was observed. The total complication rate in group A was 24 and 14.3% in group B, respectively, and the difference was not statistically significant (P = 0.582). The differences between two groups scored by parents in glans (P = 0.030) was statistically significant. The differences between two groups scored by operators in meatus (P = 0.041), shaft skin (P = 0.000), glans (P = 0.001), and general appearance (P = 0.007) were statistically significant. The differences between two groups scored by counterparts in meatus (P = 0.006), shaft skin (P = 0.003), glans (P = 0.010), and general appearance (P = 0.014) were statistically significant. Conclusion: Both prefabricated urethra and pre-implanted urethral plate methods are suitable for correction of severe hypospadias as staging surgery in children. In general, pre-implanted urethral plate is more worthy of spread because it is much more applied in patients with small glans and achieve good appearance of penis.

Morphological mechanism allowing a parasitic leech, Ozobranchus jantseanus (Rhynchobdellida: Ozobranchidae), to survive in ultra-low temperatures.

Ozobranchus jantseanus is the largest metazoan known to survive in liquid nitrogen without pretreatment to date; however, the mechanism underlying this tolerance remains unclear. In this study, the first analyses of histological and morphological changes in normal, frozen, and dehydrated states were performed. Adults survived after direct placement in liquid nitrogen for 96 h, with a survival rate of approximately 86.7%. The leech could withstand rapid desiccation and its survival rate after rehydration was 100% when its water loss was below about 84.8%. After freezing, desiccation, and ethanol dehydration, the leech immediately formed a hemispherical shape. Particularly during drying, an obvious transparent glass-like substance was observed on surface. Scanning electron microscopy revealed many pores on the surface of the posterior sucker, creating a sponge-like structure, which may help to rapidly expel water, and a hemispherical shape may protect the internal organs by contraction and folding reconstruction in the anterior-posterior direction. A substantial amount of mucopolysaccharides on the surface and acid cells and collagen fibers in the body, all of which contained substantial polysaccharides, may play a key protective role during freezing. Our results indicate that the resistance of leeches to ultra-low temperatures can be explained by cryoprotective dehydration/vitrification strategies. This article has an associated First Person interview with the first author of the paper.

Web-based calculator for biliary atresia screening in neonates and infants with cholestasis.

BACKGROUND: Distinguishing biliary atresia from non-biliary atresia in patients with cholestasis is challenging, as these conditions have a similar clinical presentation. We developed and externally validated a screening model for biliary atresia and devised a web-based calculator for use in clinical settings. METHODS: A screening model was developed based on data from 227 cholestatic infants (82 and 145 with and without biliary atresia, respectively) and validated in 234 infants (90 and 144 with and without biliary atresia, respectively) admitted to three hospitals. Variables were selected from routine examination results using the least absolute shrinkage and selection operator method and entered into a logistic regression model to construct a biliary-atresia-risk-predicting equation. Cutoff values for risk stratification were estimated using model sensitivity, derived from the receiver-operating characteristic curves. RESULTS: The final screening model included seven variables (i.e., weight at admission, clay-colored stools, γ-glutamyl transpeptidase and albumin levels at admission, abnormal gallbladder, triangular cord sign, and change in total bilirubin levels). The model generated an area under the curve of 0.94 with a sensitivity of 91.46 and specificity of 86.62 in the derivation cohort. This was confirmed in the validation cohort, as we found an area under the curve of 0.93 with a sensitivity of 93.1 and specificity of 80.15. Patients were stratified into three risk groups (low-, moderate-, and high-risk groups). Biliary atresia was excluded in the low-risk group. The high-risk group showed a higher detection rate of biliary atresia compared to the stool color screening method alone. This model was integrated into a user-friendly web-based system. CONCLUSIONS: The screening tool had a high predictive value and may help in decision-making by physicians at tertiary and community hospitals.

Comparison of Adult Testis and Ovary MicroRNA Expression Profiles in Reeves' Pond Turtles (Mauremys reevesii) With Temperature-Dependent Sex Determination.

Some differentially expressed genes (DEGs) that encode key enzymes involved in steroidogenic biosynthesis (CYP19A1) and key molecules related to gonadal functions (DMRT1, SOX9, AMH, FOXL2, WNT4, RSPO2, and GDF9) have been identified in adult gonadal RNA-seq studies of Reeves' pond turtle (Mauremys reevesii) with temperature-dependent sex determination (TSD). Gonadal functional maintenance and gametogenesis comprises a highly regulated and coordinated biological process, and increasing evidence indicates that microRNAs (miRNAs) may be involved in this dynamic program. However, it is not clear how the regulatory network comprising miRNAs changes the expression levels of these genes. In this study, miRNA sequencing of adult testis and ovary tissues from M. reevesii detected 25 known and 379 novel miRNAs, where 60 miRNAs were differentially expressed in the testis and ovary. A total of 1,477 target genes based on the differentially expressed miRNAs were predicted, where 221 target genes also exhibited differential expression. To verify the accuracy of the sequencing data, 10 differentially expressed miRNAs were validated by quantitative reverse transcription real-time PCR, and were found to be consistent with the transcriptome sequencing results. Moreover, several miRNA/target gene pairs, i.e., mre-let-7a-5p/mre-let-7e-5p and CYP19A1, mre-miR-200a-3p and DMRT1, mre-miR-101-3p and SOX9, and mre-miR-138-5p and AMH were identified. To explore the regulatory role of miRNAs, we conducted target gene enrichment analysis of the miRNAs and 221 target genes in the regulatory network. The signaling pathways related to gonadal functional maintenance and gametogenesis based on the DEGs and target genes were then compared. Our findings provide crucial information to facilitate further research into the regulatory mechanisms involving miRNAs in turtle species with TSD.

Three-color risk stratification for improving the diagnostic accuracy for biliary atresia.

OBJECTIVES: It is challenging to early differentiate biliary atresia from other causes of cholestasis. We aimed to develop an algorithm with risk stratification to distinguish biliary atresia from infantile cholestasis. METHODS: In this study, we enrolled infants with cholestasis into 2 subgroups from January 2010 to April 2019. A prospective cohort (subgroup 2) of 187 patients (107 with biliary atresia and 80 without biliary atresia) underwent acoustic radiation force impulse elastography. Stepwise regression was used to identify significant predictors of biliary atresia. A sequential algorithm with risk stratification was constructed. RESULTS: Among 187 patients, shear wave speed > 1.35 m/s and presence of the triangular cord sign were considered high risk for biliary atresia (red), in which 73 of 78 patients (accuracy of 93.6%) with biliary atresia were identified. Afterwards, γ-GT, abnormal gallbladder, and clay stool were introduced into the algorithm and 55 intermediate-risk infants were identified (yellow) with a diagnostic accuracy of 60% for biliary atresia. Of the remaining 54 infants who were classified as low-risk patients (green), the accuracy for excluding biliary atresia was 98.1%. By applying a three-color risk stratification tool, 70.6% patients were identified as either high risk or low risk for biliary atresia (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%). We also estimated the risk of biliary atresia in different color groups, which was 94.7% (95%CI, 94.3-95.5%) in the red group and 7.2% (95%CI, 6.6-8.3%) in the green group. CONCLUSIONS: Our simple noninvasive approach was able to identify biliary atresia with high accuracy. KEY POINTS: • Five predictors, namely shear wave speed, triangle cord sign, γ-glutamyl transferase, abnormal gallbladder, and clay stool, were selected to identify biliary atresia in cholestasis. • Shear wave speed > 1.35 m/s and presence of the triangle cord sign were considered high-risk patients with a diagnostic accuracy of 93.6% for biliary atresia. • Risk for biliary atresia was high (red), intermediate (yellow), or low (green). In the red and green group, we achieved an extremely high diagnostic performance (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%).

Acoustic Radiation Force Impulse Imaging for Assessing Liver Fibrosis Preoperatively in Infants With Biliary Atresia: Comparison With Liver Fibrosis Biopsy Pathology.

OBJECTIVES: The purpose of this study was to investigate the diagnostic performance of acoustic radiation force impulse (ARFI) in assessing liver fibrosis preoperatively in infants with biliary atresia (BA). METHODS: A total of 50 consecutive infants with BA and 50 healthy infants who underwent ARFI examination were recruited. Siemens Acuson S2000 in Virtual Touch Quantification mode (Siemens Medical Solutions, Mountain View, CA) was used to measure shear wave speeds (SWSs). All infants with BA underwent a liver biopsy within 3 days after ARFI imaging. The liver fibrosis stages of specimens were defined according to the Batts-Ludwig scoring system. The correlation analysis was performed between SWSs and pathological findings. Cut-off values were determined using receiver operating characteristic (ROC) curves. RESULTS: The mean SWS in the BA group was significantly higher than controls (mean ± standard deviation): 1.89 ± 0.45 versus 1.12 ± 0.06 m/s; P < .001). A significant correlation was found between the SWSs and fibrosis stages (r = 0.719, P < .001). The cut-off value for predicting significant fibrosis (F ≥ 2), severe fibrosis (F ≥ 3), and cirrhosis (F = 4) was 1.53, 1.80 and 2.16 m/s, respectively, and the area under the ROC curve was 0.823, 0.884 and 0.917, respectively. CONCLUSIONS: Acoustic radiation force impulse imaging showed significant correlation with the severity of liver fibrosis by comparing it with liver fibrosis biopsy pathology. It may be an effective method for liver fibrosis assessment, prognosis prediction, and clinical management in infants with BA.

Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures.

BACKGROUND: A key challenge in thyroid carcinoma is preoperatively diagnosing malignant thyroid nodules. A novel diagnostic test that measures the expression of a 3-gene signature (DPP4, SCG5 and CA12) has demonstrated promise in thyroid carcinoma assessment. However, more reliable prediction methods combining clinical features with genomic signatures with high accuracy, good stability and low cost are needed. METHODOLOGY/PRINCIPAL FINDINGS: 25 clinical information were recorded in 771 patients. Feature selection and validation were conducted using random forest. Thyroid samples and clinical data were obtained from 142 patients at two different hospitals, and expression of the 3-gene signature was measured using quantitative PCR. The predictive abilities of three models (based on the selected clinical variables, the gene expression profile, and integrated gene expression and clinical information) were compared. Seven clinical characteristics were selected based on a training set (539 patients) and tested in three test sets, yielding predictive accuracies of 82.3% (n = 232), 81.4% (n = 70), and 81.9% (n = 72). The predictive sensitivity, specificity, and accuracy were 72.3%, 80.5% and 76.8% for the model based on the gene expression signature, 66.2%, 81.8% and 74.6% for the model based on the clinical data, and 83.1%, 84.4% and 83.8% for the combined model in a 10-fold cross-validation (n = 142). CONCLUSIONS: These findings reveal that the integrated model, which combines clinical data with the 3-gene signature, is superior to models based on gene expression or clinical data alone. The integrated model appears to be a reliable tool for the preoperative diagnosis of thyroid tumors.

[Metorchis orientalis founded in basin of Wuhu City, Anhui Province].

OBJECTIVE: To investigate the epidemic situation of Metorchis orientalis in Wuhu City, Anhui Province. METHODS: Three lakes (Fengming, Longwo and Kui lakes) were selected in Wuhu City, and the poultries around the lakes and freshwater fishes in the lakes were captured to test the infection of M. orientalis, and the infection rates were calculated. RESULTS: The adult worms of M. orientalis were found in gall bladder and hepatic duct of domestic ducks with infection rate of 16.7%. The metacercariae of M. orientalis were discovered in the muscle of Pseudorasbora parva and Pseudogobio rivularis with infection rates of 7.13% and 3.38% respectively. CONCLUSION: M. orientalis is endemic in Wuhu City, which should be paid enough attention to the animal husbandry, aquaculture and medicine.

Analysis on the sequence of the whole genome of an isolated enterovirus 71 strain.

An enterovirus 71 (EV71) strain Query was isolated from a patient specimen in 2015. In order to known about its genetic evolution, this study amplified gene fragment of the isolated stain by RT-PCT and carried out sequencing of the total genome. The homology and genetic evolution of the gene sequence of the virus strain in the study were analyzed. The results showed that the isolated EV71 strain in this study had higher homology of nucleotide sequence and amino acid sequence with other virus strains, which was 80%-97% and 88% to 92%, respectively, but it had lower homology with Cox.A16 (homology of nucleotide sequence and amino acid sequence of Cox.A16 was 81% and 79%, respectively). Compare of homologous sequence at the encoding region VP1 demonstrated that the experimental isolated strain EV71 had higher homology of amino acid sequence at VP1 region with other virus strains. Genetic evolution of nucleotide sequence at VP1 region of the identified strain and other EV71 strains was analyzed, and the results demonstrated gene sequence at VP1 region and 5'UTR region of the isolated strain and SDLY017 strain was at the same branch, both of which belonged to C4a, a subtype of type C4.

[Koyanagi technique for repairing proximal hypospadias with penoscrotal transposition].

OBJECTIVE: To investigate the application of Koyanagi technique for repairing proximal hypospadias with penoscrotal transposition. METHODS: Koyanagi procedure was used for repairing proximal hypospadias with penoscrotal transposition in 26 boys (mean age 4.2 years) between July 2005 and June 2010. RESULTS: Primary healing was achieved in 22 cases. Three patients suffered from urinary fistula and the external urethral orifice in one patient was retracted to penis coronary sulcus, who were re-operated successfully. Two cases showed slight penile ventral curvature. Slight stricture of the urethral external orifice was noted in one case, which relieved after one to two times of urethral sounding every week for eight months. 20 patients were followed up for 6-36 months (mean 10.5 months) with good cosmetic result and normal urethra function. The penoscrotal transposition was also corrected. CONCLUSIONS: The original Koyanagi procedure might be one of the simple and effective method for repairing proximal hypospadias with penoscrotal transposition.