Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax).

A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.

A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken.

The biochemical pathway regulating the synthesis of yellow/red pheomelanin is less well characterized than the synthesis of black/brown eumelanin. Inhibitor of gold (IG phenotype) is a plumage colour variant in chicken that provides an opportunity to further explore this pathway since the recessive allele (IG) at this locus is associated with a defect in the production of pheomelanin. IG/IG homozygotes display a marked dilution of red pheomelanin pigmentation, whilst black pigmentation (eumelanin) is only slightly affected. Here we show that a 2-base pair insertion (frame-shift mutation) in the 5th exon of the Catechol-O-methyltransferase containing domain 1 gene (COMTD1), expected to cause a complete or partial loss-of-function of the COMTD1 enzyme, shows complete concordance with the IG phenotype within and across breeds. We show that the COMTD1 protein is localized to mitochondria in pigment cells. Knockout of Comtd1 in a mouse melanocytic cell line results in a reduction in pheomelanin metabolites and significant alterations in metabolites of glutamate/glutathione, riboflavin, and the tricarboxylic acid cycle. Furthermore, COMTD1 overexpression enhanced cellular proliferation following chemical-induced transfection, a potential inducer of oxidative stress. These observations suggest that COMTD1 plays a protective role for melanocytes against oxidative stress and that this supports their ability to produce pheomelanin.

A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway.

Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25-26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (FST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years.

Association of CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP with Clinicopathological Characteristics and Chemotherapeutic Outcomes of Lung Cancer.

OBJECTIVE: The aim of this study was to investigate the association of serum carcinoembryonic antigen (CEA), nerve-specific enolase (NSE), cytokeratin 19 fragment (CYFRA21-1), squamous cell carcinoma antigen (SCC-Ag), and pro-gastrin-releasing peptide (ProGRP) with the clinicopathological characteristics and chemotherapeutic outcomes of patients with lung cancer. METHODS: A total of 189 patients with lung cancer (lung cancer group) diagnosed at the Fourth Affiliated Hospital of Anhui Medical University from January 2020 to December 2021 were included. During the same period, 199 patients with benign lung disorders were included as the benign lung disease group and 75 healthy people were selected as the control group. The serum concentrations of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP in all the 3 groups were analyzed and compared in patients with different lung cancer tumor-node-metastasis (TNM) stages and pathological classifications. A total of 11 patients with small cell lung cancer (SCLC) and 18 patients with lung adenocarcinoma (LAC) were further evaluated for the dynamic changes of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP before chemotherapy and during the 6 courses of chemotherapy, and the outcome of chemotherapy was evaluated every 2 courses. RESULTS: The serum concentrations of CEA, NSE, CYFRA21-1, SCC-Ag, and ProGRP in the lung cancer group were significantly higher than those in the control group (P < .05). We found statistically significant differences in serum CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP among patients with different pathological types (LAC, squamous cell carcinoma, or SCLC) and different stages (I-IV). The ProGRP and NSE had the highest expression in SCLC, CEA showed the highest expression in LAC, whereas CYFRA21-1 and SCC-Ag showed the highest expression in lung squamous cell carcinoma (LSCC). The concentrations of all the markers were elevated in the advanced pathological stages. The receiver operating characteristic curve analysis showed that the diagnostic value of the combined detection of CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP for lung cancer was significantly higher than using a single biomarker (P < .05). Our dynamic monitoring results show that ProGRP progressively decreased in remission cases of SCLC and CEA progressively decreased in LAC remission cases. CONCLUSION: CEA, NSE, CYFRA 21-1, SCC-Ag, and ProGRP have good clinical value in the early diagnosis, differential diagnosis, and progression monitoring of lung cancer. The ProGRP and CEA concentrations are beneficial for evaluating the outcome of chemotherapy in SCLC and LAC. The combined detection of multiple biomarkers shows improved clinical value in the early diagnosis of lung cancer.

Differences in Power Acquisition Between Only and Non-only Children: The Effects of Cooperative Orientation, Competitive Orientation, and Dependency on Parents.

Drawing upon a developmental perspective, we investigated the differences in power acquisition (i.e., rank at work and leader role occupancy in university) between only and non-only children as well as the mediating role of cooperative and competitive orientations and the moderating role of dependency on parents. To test our hypotheses, we conducted two field studies in 155 part-time Master of Business Administration (MBA) students (Study 1) and 375 senior students (Study 2). Results showed that: (1) non-only children were more likely to achieve higher rank at work than only children; (2) only children were less likely than non-only children to acquire power in organizations because they scored lower in cooperative orientation; however, the mediating effect of competitive orientation was not significant; (3) the difference in cooperative orientation between only and non-only children was smaller when dependency on parents was high, whereas it became larger when dependency on parents was low. Our research contributes to the understanding of how family structure influences individual power acquisition.

A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation.

Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.

Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.

The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.

Genome-Wide Association Study of Muscle Glycogen in Jingxing Yellow Chicken.

Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 473 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs (p < 1/699341) and three INDELs (p < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 (CPNE4) on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci (p < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (NKD1). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals (p < 0.01). These mutations likely affecting two genes (CPNE4 and NKD1) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that CPNE4 and NKD1 may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.

Interleukin-8 promotes cell migration via CXCR1 and CXCR2 in liver cancer.

Liver cancer (LC), which is one of the most common types of cancer worldwide, is notorious for its high morbidity and mortality rates. Interleukin-8 (IL-8), an important member of the CXC chemokine family that was originally classified as a potent neutrophil chemoattractant, has been shown to serve an important role in inflammation, tumor growth, invasion and metastasis through interactions with its receptors. However, the expression and functional roles of IL-8 and its receptors, CXC chemokine receptor (CXCR) 1 and CXCR2 in the progression of liver cancer remain to be fully elucidated. In the present study, it was shown that the mRNA levels of IL-8, CXCR1 and CXCR2 were increased in peripheral blood mononuclear cells from patients with liver cancer compared with those from patients with cirrhosis or normal controls (P<0.05). Higher levels of CXCR1, CXCR2 and IL-8 were associated with advanced tumor stage and increased risk of lymph node or distant metastasis. Immunohistochemistry showed that the IL-8, CXCR1 and CXCR2 proteins were expressed in the cytoplasm of hepatoma cells at higher intensities than those of normal controls (P<0.05). The semi-quantitative analysis revealed that the relative mean density of hepatic IL-8, CXCR1 and CXCR2 staining in liver cancer was significantly increased compared with that in normal liver tissues (P<0.05). The analysis revealed that the mRNA expression of IL-8 was positively associated with that of CXCR1 (r=0.618; P<0.05) and CXCR2 (r=0.569; P<0.05). The mRNA levels of CXCR1 and CXCR2 gradually increased with elevated expression of IL-8 in liver cancer. Experiments were performed using human Huh-7 and HepG2 cell lines, incubating cells with IL-8 and conducting in vitro migration and invasion assays. The results showed that the wound healing activity and migration of Huh-7 and HepG2 cells were increased by IL-8. Pretreatment of the cells with anti-CXCR1 or anti-CXCR2 (5 µM) for 30 min markedly inhibited IL-8-directed cell migration. Taken together, these results indicated that IL-8 promotes liver cancer cell migration via CXCR1 and CXCR2 and that targeting the CXCR1/2 may be a potential strategy for liver cancer treatment.

Brown eggshell fading with layer ageing: dynamic change in the content of protoporphyrin IX.

The dynamic change in brown eggshell color as hens age has been observed, but much uncertainty still exists. We aimed to analyze the depth of eggshell color and quantity of protoporphyrin ΙΧ throughout the laying period to explore the reasons for color variation. In this study, 120 Rhode Island Red hens were used, and two eggs were collected from each individual at 26, 34, 42, 50, 60, and 70 wk of age. The eggshell color (L*, a*, b*), egg weight, eggshell dry weight, and protoporphyrin ΙΧ quantity in eggshell were measured for individual eggs. Our results showed that the intensity of brown eggshell color weaken as hens aged from 26 to 60 wk of age (L* gradually increased from 61.43 to 68.07), while eggshell lightness recovered slightly at 70 wk (L* = 64.77). The correlation analysis indicated that the content of protoporphyrin ΙΧ deposited in the eggshell was an important factor for lightness fading with the ageing process (the average r was 0.66, P < 0.01), while the egg weight had little impact on the eggshell color (the average r was 0.07, P > 0.05). The shade of the eggshell color (L* and a*) at the early laying period (26 or 34 wk) had a low correlation with the other age points (42, 50, 60, and 70 wk). However, high correlations between the shell color at 42 wk of age and subsequent ages (50, 60, and 70 wk) were found, suggesting that the intensity of eggshell color is more stable after egg-laying peaks (such as 42 wk of age). In conclusion, the intensity of brown eggshell color varies greatly among the whole laying cycle and breeders can choose the proper age for eggshell color measurements to ensure the degree of shell color in the late laying period.

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq.

Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.

[Influence of IFN on expression of chemokine receptor CXCR1, CXCR2 and their ligand IL-8 in the patients with chronic hepatitis B].

AIM: To study the mRNA levels of chemokine receptor CXCR1, CXCR2 and IL-8 in the patients with chronic hepatitis B and their association with IFN therapy. METHODS: The mRNA levels of CXCR1, CXCR2 and IL-8 in peripheral blood mononuclear cells(PBMC)of chronic hepatitis B patients were determined by real-time RT-PCR before and during the IFN-α therapy. RESULTS: The mRNA levels of CXCR1(0.4474 ± 0.0386)and IL-8(1.1897 ± 0.1028)in peripheral blood of the patients with chronic hepatitis B were significantly higher than those in healthy donors(P<0.01). The mRNA level of CXCR2(0.4720 ± 0.0458)was higher than those in healthy donors, but there was no significant differences between the two groups. During the treatment, the mRNA levels of CXCR1, CXCR2 and IL-8 obviously decreased. After treatment for six month, the mRNA level of CXCR1(0.4129 ± 0.0395), CXCR2(0.4461 ± 0.0477) and IL-8(0.8660 ± 0.1307)were significantly lower than those before treatment(P<0.01 or P<0.05). Additionally, the expressive levels of CXCR1, CXCR2 and IL-8 in the high HBV loading group(HBV-DNA>10(6);)were much higher than those in the low HBV loading group(HBV-DNA<10(6);). CONCLUSION: CXCR1 and IL-8 may contribute to hepatic inflammation. Among them, CXCR1, CXCR2 and IL-8 decrease after IFN treatment, which illustrates that IFN-α plays an important role in down-regulating inflammation response, controlling the development of the patients' condition.