The value of hsa_circ_0058514 in plasma extracellular vesicles for breast cancer.

The aim of this study was to investigate the diagnostic value of hsa_circ_0058514 in plasma extracellular vesicles (EVs) in BC patients and its predictive value for neoadjuvant chemotherapy. The expression of hsa_circ_0058514 in a large sample of BC plasma and healthy subjects' plasma was detected by qPCR, and the ROC curve was drawn to verify its diagnostic value as a plasma tumor marker. Furthermore, the association between the expression of hsa_circ_0058514 and clinicopathological characteristics before and after treatment was detected in the plasma of 40 pairs of BC patients undergoing neoadjuvant therapy. The expression level of hsa_circ_0058514 in the plasma of BC patients was significantly higher than that of healthy subjects. The ROC curve showed that plasma hsa_circ_0058514 ROC in differentiating non-metastatic BC and healthy people had better diagnostic efficiency than conventional tumor markers CA153, CA125, and CEA. In patients with neoadjuvant therapy, the decrease in plasma hsa_circ_0058514 value before and after treatment correlated with pathological MP grade (r = 0.444, p = 0.004) and imaging tumor regression value (r = 0.43, p = 0.005) positive correlation. The detection of hsa_circ_0058514 in both extracellular vesicles of BC cell culture medium and human plasma was demonstrated. Hsa_circ_0058514 is detected in the plasma from BC cells secreted in the form of vesicles. Hsa_circ_0058514 can be used as an early plasma biological indicator for the diagnosis of BC in clinical applications, with a higher risk of recurrence and metastasis, and as a predictor of the effect of neoadjuvant therapy to guide the clinical use of neoadjuvant therapy.

Effects of Luteinizing Hormone Releasing Hormone A2 on Gonad Development in Juvenile Amur Sturgeon, Acipenser schrenckii, Revealed by Transcriptome Profiling Analysis.

Acipenser schrenckii is an economically important aquatic species whose gonads require particularly long times to reach sexual maturity. Luteinizing hormone plays important roles in gonad development, and luteinizing hormone releasing hormone A2 (LH-A2) is used as an oxytocin to promote ovulation in aquaculture of A. schrenckii. In this study, we aimed to determine the effects of LH-A2 on gonad development in juvenile A. schrenckii through transcriptome profiling analysis of the pituitary and gonads after LH-A2 treatment at a dose of 3 µg/kg. The 17ß-estradiol (E2) levels gradually increased with LH-A2 treatment time, and significantly differed from those of the control group on days 5 and 7 (p < 0.01). However, the content of testosterone (Testo) gradually decreased with LH-A2 treatment time and showed significant differences on day 3 (p < 0.05), and on days 5 and 7 (p < 0.01), compared to those in the control group. Thus, LH-A2 promotes the secretion of E2 and inhibits the secretion of Testo. Transcriptome profiling analysis revealed a total of 2,883 and 8,476 differentially expressed genes (DEGs) in the pituitary and gonads, respectively, thus indicating that LH-A2 has more regulatory effects on the gonads than the pituitary in A. schrenckii. Signal transduction, global and overview maps, immune system, endocrine system and lipid metabolism were the main enriched metabolic pathways in both the pituitary and gonads. Sixteen important genes were selected from these metabolic pathways. Seven genes were co-DEGs enriched in both signal transduction and endocrine system metabolic pathways. The other co-DEGs were selected from the immune system and lipid metabolism metabolic pathways, and showed mRNA expression changes of >7.0. The expression of five DEGs throughout LH-A2 treatment was verified to show the same patterns of change as those observed with RNA-seq, indicating the accuracy of the RNA-seq in this study. Our findings provide valuable evidence of the regulation of gonad development of juvenile A. schrenckii by LH-A2 and may enable the establishment of artificial techniques to regulate gonad development in this species.

Effects of replacing fishmeal with cottonseed protein concentrate on growth performance, blood metabolites, and the intestinal health of juvenile rainbow trout (Oncorhynchus mykiss).

Cottonseed protein concentrate (CPC) is a potential non-food protein source for fishmeal replacement in fish feed. However, a high inclusion level of CPC in diets may have adverse effects on the metabolism and health of carnivorous fish. This study aimed to investigate CPC as a fishmeal alternative in the diet of rainbow trout Oncorhynchus mykiss based on growth performance, blood metabolites, and intestinal health. Five isonitrogenous (46% crude protein) and isolipidic (16% crude lipid) diets were formulated: a control diet (30% fishmeal) and four experimental diets with substitution of fishmeal by CPC at 25%, 50%, 75%, and 100%. A total of 600 fish (mean body weight 11.24g) were hand-fed the five formulated diets to apparent satiation for eight weeks. The results showed no adverse effects on growth performance when 75% dietary fishmeal was replaced by CPC. However, reduced growth and feed intake were observed in rainbow trout fed a fishmeal-free diet based on CPC (CPC100%). Changes in serum metabolites were also observed in CPC100% compared with the control group, including an increase in alanine aminotransferase (ALT), a decrease in alkaline phosphatase (ALP), alterations in free amino acids, and reductions in cholesterol metabolism. In addition, the CPC-based diet resulted in reduced intestinal trypsin, decreased villus height and width in the distal intestine, upregulated mRNA expression levels of inflammatory cytokines in the intestine, and impaired gut microbiota with reduced bacterial diversity and decreased abundance of Bacillaceae compared with the control group. The findings suggest that the optimum substitution rate of dietary fishmeal by CPC for rainbow trout should be less than 75%.

Factors affecting HPV infection in U.S. and Beijing females: A modeling study.

Background: Human papillomavirus (HPV) infection is an important carcinogenic infection highly prevalent among many populations. However, independent influencing factors and predictive models for HPV infection in both U.S. and Beijing females are rarely confirmed. In this study, our first objective was to explore the overlapping HPV infection-related factors in U.S. and Beijing females. Secondly, we aimed to develop an R package for identifying the top-performing prediction models and build the predictive models for HPV infection using this R package. Methods: This cross-sectional study used data from the 2009-2016 NHANES (a national population-based study) and the 2019 data on Beijing female union workers from various industries. Prevalence, potential influencing factors, and predictive models for HPV infection in both cohorts were explored. Results: There were 2,259 (NHANES cohort, age: 20-59 years) and 1,593 (Beijing female cohort, age: 20-70 years) participants included in analyses. The HPV infection rate of U.S. NHANES and Beijing females were, respectively 45.73 and 8.22%. The number of male sex partners, marital status, and history of HPV infection were the predominant factors that influenced HPV infection in both NHANES and Beijing female cohorts. However, condom application was not an independent influencing factor for HPV infection in both cohorts. R package Modelbest was established. The nomogram developed based on Modelbest package showed better performance than the nomogram which only included significant factors in multivariate regression analysis. Conclusion: Collectively, despite the widespread availability of HPV vaccines, HPV infection is still prevalent. Compared with condom promotion, avoidance of multiple sexual partners seems to be more effective for preventing HPV infection. Nomograms developed based on Modelbest can provide improved personalized risk assessment for HPV infection. Our R package Modelbest has potential to be a powerful tool for future predictive model studies.

Molecular characterization and expression patterns of two hormone-sensitive lipase genes in common carp Cyprinus carpio.

The hormone-sensitive lipase (HSL) gene plays an important role in mammals' lipid metabolism. Therefore, its function in fish is capturing increasing attention. In this study, two distinct cDNAs, designated HSL1 and HSL2, are firstly identified from common carp Cyprinus carpio. The full-length cDNA of HSL1 and HSL2 consists of 3379 bp and 2732 bp, encoding polypeptide of 693 and 847 amino acids, respectively, and shares 60.6% amino acid identity. Phylogenetic analysis suggests that HSL1 and HSL2 are derived from paralogous genes, which might have arisen during a teleost-specific genome duplication event. The two HSL mRNAs are differentially expressed, both in terms of distribution among tissues and in terms of abundance during embryogenesis. Moreover, both HSL mRNAs are expressed in various tissues, the highest in abdominal fat. Meanwhile, the two HSLs are detected at all stages of embryonic development, suggesting that they could be functional and involved in embryogenesis. In addition, the results show that the mRNA expression level of HSL2 in the high group of intramuscular fat content is significantly higher than that in the low group (P < 0.01). The research provides basic data for developing a further understanding of the function of HSL as well as molecular regulation mechanism in fat metabolism of common carp.

Factors associated with human papillomavirus infection - findings from a cervical cancer screening program for female employees in Beijing.

BACKGROUND: In 2018, the Beijing Federation of Trade Unions organized a cervical cancer screening program for female employees for the first time. This study aimed to investigate the screening results of this program and determine the factors associated with human papillomavirus (HPV) infection. METHODS: A total of 8297 female employees participating in the screening program between January 1, 2018, and December 31, 2018, were enrolled in this study. The methods for screening cervical cancer included ThinPrep cytology test (TCT) and HPV genotyping test. Single-factor analysis and multiple binary logistic regression analysis were used to identify the factors associated with HPV infection. RESULTS: Of the 8297 women (median age: 43.00 years), TCT was found to be abnormal in 116 patients (1.40%) and 1169 (14.09%) were positive for HPV genotyping test. Notably, HPV-52 was the most prevalent subtype (3.05%), followed by HPV-16 (2.82%), HPV-58 (2.01%), HPV-51 (1.58%) and HPV-56 (1.49%). Multivariate logistic regression analysis revealed that taxi drivers (OR =1.98; 95% CI =1.31-2.99) and single women with a history of sexual activity (OR =2.32; 95% CI =1.41-3.82) were significantly associated with an increased risk of HPV infection (P<0.05), whereas medical workers (OR =0.67; 95% CI =0.51-0.88) and factory workers (OR =0.36; 95% CI =0.17-0.77) were protective factors for HPV infection (P<0.05). CONCLUSION: HPV-52, HPV-16 and HPV-58 are the most common types of high-risk HPV among female employees in Beijing. Being taxi drivers and single women with a history of sexual activity are significantly associated with the risk of HPV infection.

Association of adiposity with thyroid nodules: a cross-sectional study of a healthy population in Beijing, China.

BACKGROUND: The relationship between thyroid nodules (TNs) and adiposity is controversial. This paper describes a cross-sectional investigation performed to determine the existence of any such relationship. To assess adiposity, body mass index (BMI) and visceral fat area (VFA) were utilized. METHODS: Between January 1, 2017 and March 3, 2019. Three thousand five hundred thirty four healthy people were examined using thyroid ultrasonography, visceral fat and anthropometric measurements, laboratory tests and questionnaire interview. Binary logistic regression analyses were used. RESULTS: Of the 3534 healthy subjects, 58.69% (2074/3534) of the subjects had TNs. A total of 55.91% (1976/3534) had BMI ≥ 25 kg/m2 and 39.67% (1402/3534) had VFA ≥ 100 cm2. After adjustment to address confounders, BMI-based overweight and obesity levels only correlated with higher risk TNs when used as a continuous variable (OR = 1.031, 95% CI: 1.008-1.055, P = 0.008), while VFA was both a continuous variable (OR = 1.003, 95% CI: 1.000-1.005, P = 0.034) and a categorical variable (OR = 1.198, 95% CI: 1.014-1.417, P = 0.034) associated with significantly elevated risk of TNs. Analyzing the subgroups, BMI ≥ 25 kg/m2 (OR = 1.500, 95% CI: 1.110-2.026, P = 0.008) was significantly correlated with TN risk in individuals with TG ≥ 1.7 mmol/L. VFA ≥ 100 cm2 correlated with the TN risk irrespective of age (< 50 years: OR = 1.374, 95% CI: 1.109-1.703, P = 0.004; ≥ 50 years: OR = 1.367, 95% CI: 1.063-1.759, P = 0.015) and in the following subgroups: women (OR = 4.575, 95% CI: 2.558-8.181, P = 0.000), FBG ≥ 6.1 mmol/L (OR = 1.522, 95% CI: 1.048-2.209, P = 0.027), and TG ≥ 1.7 mmol/L (OR = 1.414, 95% CI: 1.088-1.838, P = 0.010). CONCLUSIONS: Adiposity correlates with TNs. To assess TN risk in Chinese individuals, VFA is better than BMI.

An NLRP3 inflammasome-triggered cytokine storm contributes to Streptococcal toxic shock-like syndrome (STSLS).

Infection with the Streptococcus suis (S. suis) epidemic strain can cause Streptococcal toxic shock-like syndrome (STSLS), which is characterized by a cytokine storm, dysfunction of multiple organs and a high incidence of mortality despite adequate treatment. Despite some progress concerning the contribution of the inflammatory response to STSLS, the precise mechanism underlying STSLS development remains elusive. Here, we use a murine model to demonstrate that caspase-1 activity is critical for STSLS development. Furthermore, we show that inflammasome activation by S. suis is mainly dependent on NLRP3 but not on NLRP1, AIM2 or NLRC4. The important role of NLRP3 activation in STSLS is further confirmed in vivo with the NLRP3 inhibitor MCC950 and nlrp3-knockout mice. By comparison of WT strain with isogenic strains with mutation of various virulence genes for inflammasome activation, Suilysin is essential for inflammasome activation, which is dependent on the membrane perforation activity to cause cytosolic K+ efflux. Moreover, the mutant strain msly (P353L) expressing mutagenic SLY without hemolytic activity was unable to activate the inflammasome and does not cause STSLS. In summary, we demonstrate that the high membrane perforation activity of the epidemic strain induces a high level of NLRP3 inflammasome activation, which is essential for the development of the cytokine storm and multi-organ dysfunction in STSLS and suggests NLRP3 inflammasome as an attractive target for the treatment of STSLS.

Quantitative trait loci for morphometric traits in multiple families of common carp (Cyprinus carpio).

Quantitative trait locus (QTL) mapping is frequently used to understand the genetic architecture of quantitative traits. Herein, we performed a genome scan for QTL affecting the morphometric characters in eight full-sib families containing 522 individuals using different statistical methods (Sib-pair and half-sib model). A total of 194 QTLs were detected in 25 different regions on 10 linkage groups (LGs). Among them, 37 QTLs on five LGs (eight, 13, 24, 40 and 45) were significant (5% genome-wide level), while the remaining 40 (1% chromosome-wide level) and 117 (5% chromosome-wide level) indicated suggestive effect on those traits. Heritabilities for most morphometric traits were moderate to high, ranging from 0.21 to 0.66, with generally strong phenotypic and genetic correlations between the traits. A large number of QTLs for morphometric traits were co-located, consistent with their high correlations, and may reflect pleiotropic effect on the same genes. Biological pathways were mapped for possible candidate genes on QTL regions. One significantly enriched pathway was identified on LG45, which had a P-value of 0.04 and corresponded to the "regulation of actin cytoskeleton pathway". The results are expected to be useful in marker-assisted selection (MAS) and provide valuable information for the study of gene pathway for morphometric and growth traits of the common carp.

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio).

Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.

A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

BACKGROUND: Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. RESULTS: We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. CONCLUSION: A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

The complete mitochondrial genome sequence of Silver Gudgeon (Gnathopogon argentatus).

The complete mitochondrial genome of Gnathopogon argentatus was determined to be 16,607 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. The complete mitochondrial genome of G. argentatus is 16,607 bp in length with 56.02% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The complete mitochondrial genome of G. argentatus was obtained for the first time and would play an important role in population structure and conservation genetic studies.

The complete mitochondrial genome sequence of Sarcochellichthys lacustris (Dybowski).

The complete mitochondrial genome of Sarcochellichthys lacustris was determined to be 16,683 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. The circular genome consists of 37 typical animal mitochondrial genes (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes) and 1 control region (D-loop).

The complete mitochondrial genome sequence of Khanka spiny bitterling (Acanthorhodeus chankaensis).

The genus Acanthorhodeus chankaensis belongs to the family Cyprindea, subfamily Acheilognathinae. The complete mitochondrial genome of A. chankaensis is 16,774 bp in length with 57.65% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The mitogenome sequence of Acanthorhodeus chankaensis would play an important role in population structure and conservation genetic studies.

Genome sequence and genetic diversity of the common carp, Cyprinus carpio.

The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

A consensus linkage map of common carp (Cyprinus carpio L.) to compare the distribution and variation of QTLs associated with growth traits.

The ability to detect and identify quantitative trait loci (QTLs) in a single population is often limited. Analyzing multiple populations in QTL analysis improves the power of detecting QTLs and provides a better understanding of their functional allelic variation and distribution. In this study, a consensus map of the common carp was constructed, based on four populations, to compare the distribution and variation of QTLs. The consensus map spans 2371.6 cM across the 42 linkage groups and comprises 257 microsatellites and 421 SNPs, with a mean marker interval of 3.7 cM/marker. Sixty-seven QTLs affecting four growth traits from the four populations were mapped to the consensus map. Only one QTL was common to three populations, and nine QTLs were detected in two populations. However, no QTL was common to all four populations. The results of the QTL comparison suggest that the QTLs are responsible for the phenotypic variability observed for these traits in a broad array of common carp germplasms. The study also reveals the different genetic performances between major and minor genes in different populations.