Identification of Polymorphism in the MC1R Gene and Its Association with the Melanin Content in Feathers of Chinese Yellow Quails

MC1R plays a crucial role in controlling the type of melanin synthesized in the melanocytes, which greatly affects plumage color in birds. One g.16796362G/T SNP was found in the MC1R gene coding region, which caused a Met120Ile mutation in the amino acid sequence. The Met120Ile mutation was located in the third transmembrane domain of the MC1R protein and decreased protein stability. The g.16796362G/T locus achieved medium polymorphism and had significant association with feather melanin content in Chinese yellow quails. The contents of total melanin and pheomelanin with AA genotype were significant lower than those with AB or BB genotypes in skin tissues, while the expression levels of MC1R mRNA had no significant difference in feathers with different genotypes. This experiment indicated that the Met120Ile mutation could affect the function of the MC1R protein and change the biosynthesis of melanin in Chinese yellow quails.(AU)

Controlling nutritional status (CONUT) score-based nomogram to predict overall survival of patients with HBV-associated hepatocellular carcinoma after curative hepatectomy.

PURPOSE: As a novel immune-nutritional biomarker, the controlling nutritional status (CONUT) score has been reported to predict outcomes in cancer patients. We aimed to elucidate the prognostic value of preoperative CONUT score and construct a CONUT score-based nomogram to predict individual survival of patients with hepatitis B viral (HBV)-associated hepatocellular carcinoma (HCC) after curative hepatectomy. METHODS: Preoperative CONUT score was retrospectively calculated in 380 HBV-associated HCC patients undergoing radical resection between 2006 and 2012. Patients were assigned to two groups: CONUT-low ( < 2) and CONUT-high ( ≥ 2), according to the optimal cut-off value determined using receiver operating characteristic analysis. Associations of CONUT score with oncological outcomes were evaluated. The Cox proportional hazard model was used to identify predictors of survival and a new nomogram was developed based on the independent prognostic factors for overall survival (OS). RESULTS: The CONUT score exhibited a higher area under the curve value than the other immune-nutritional parameters. The CONUT-high group had significant poorer OS and recurrence-free survival compared with CONUT-low group (P < 0.001 and P = 0.016, respectively). Multivariate analyses identified CONUT score, liver cirrhosis, tumor size and differentiation as independent prognostic factors for OS. And the nomogram based on these four variables had superior discriminative ability to predict survival compared with other conventional staging systems. CONCLUSIONS: Preoperative CONUT score is an effective independent predictor of OS in patients with resected HBV-related HCC. This novel nomogram based on CONUT may provide accurate and individualized survival prediction for HCC patients undergoing surgical resection.

Development of two novel specific SCAR markers by cloning improved RAPD fragments from the medicinal mushroom Ganoderma lucidium (Leysser: Fr) Karst.

Development of sequence-characterized amplified region (SCAR) markers from random-amplified polymorphic DNA (RAPD) fragments is a valuable molecular approach for the genetic identification of different species. By using SCAR markers, molecular analysis is reduced to a simple polymerase chain reaction (PCR) analysis using primers designed from the amplicon sequence of RAPD. In this study, the DNA fragments from an improved RAPD amplification of Ganoderma species were cloned into a pGM-T vector; positive clones were identified by PCR amplification and enzymatic digestion, and finally, DNA fragments were sequenced using the Sanger sequencing method for developing the SCAR markers. Two SCAR markers, named LZ4-1 with 534 nucleotides, and LZ5-2 with 337 nucleotides were identified, which are specific to Ganoderma lucidium (Leysser: Fr) Karst species. BLAST of these two nucleotide sequences in the GenBank database showed no identity to other species. We deposited these sequences into the GenBank database (LZ4-1 accession No. KM391933, LZ5-2 accession No. KM391934). PCR assays confirmed them as novel molecular markers for G. lucidium (Leysser: Fr) Karst, which might be used for genetic authentication of adulterant samples. Thus, our study developed two specific SCAR markers for identifying and distinguishing the medicinal mushroom G. lucidium (Leysser: Fr) Karst from other Ganoderma species.

Development and significance of SCAR marker QG12-5 for Canarium album (Lour.) Raeusch by molecular cloning from improved RAPD amplification.

Sequence-characterized amplified region (SCAR) is a valuable molecular marker for the genetic identification of any species. This marker is mainly derived from molecular cloning of random amplified polymorphic DNA (RAPD). We have previously reported the use of an improved RAPD technique for the genetic characterization of different samples of Canarium album (Lour.) Raeusch (C. album). In this study, DNA fragments were amplified using improved RAPD amplified from different samples of C. album. The amplified DNA fragment was excised, purified from an agarose gel and cloned into a pGM-T vector; subsequently, a positive clone, called QG12-5 was identified by PCR amplification and enzymatic digestion and sequenced by Sanger di-deoxy sequencing method. This clone was revealed consisting of 510 nucleotides of C. album. The SCAR marker QG12-5 was developed using specifically designed PCR primers and optimized PCR conditions. This SCAR marker expressed seven continuous "TATG" [(TATG)n] tandem repeats, which was found to characterize C. album. Subsequently, this novel SCAR marker was deposited in GenBank with accession No. KT359568. Therefore, we successfully developed a C. album-specific SCAR marker for the identification and authentication of different C. album species in this study.

Bioinformatic and expression analysis of the OMT gene family in Pyrus bretschneideri cv. Dangshan Su.

With high nutritional value in its fruits, Dangshan Su pear has been widely cultivated in China. The stone cell content in fruits is a key factor affecting fruit quality in pear, and the formation of stone cells has been associated with lignin biosynthesis. O-Methyltransferase (OMT) is a key enzyme involved in lignin metabolism within the phenylpropanoid pathway. Here, we screened 26 OMT genes from the Pyrus bretschneideri cv. Dangshan Su genome using the DNATOOLs software. To characterize the OMT gene family in pear, gene structure, chromosomal localization, and conserved motifs of PbOMTs were analyzed. PbOMTs were divided into two categories, type I (designated PbCCOMTs) and type II (designated PbCOMTs), indicating the differentiation of function during evolution. Based on the analysis of multiple sequence alignment, cis-element prediction, and phylogenetic relationships, two candidate genes, PbCCOMT1 and PbCCOMT3, were selected for the analysis of temporal and spatial gene expression in pear. The promoter regions of both PbCCOMT1 and PbCCOMT3 contain regulatory motifs for lignin synthesis. Moreover, the two genes show high similarity and close phylogenetic relationships with CCOMTs in other species. Expression analysis showed that transcript levels of two PbCCOMTs were positively associated with the contents of both stone cells and lignin during the development of pear fruit. These results suggest that PbCCOMT1 and PbCCOMT3 are closely associated with lignin biosynthesis. These findings will help clarify the function of PbOMTs in lignin metabolism and to elucidate the mechanisms underlying stone cell formation in pear.

An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers.

Random amplified polymorphic DNA (RAPD) is a widely used molecular marker technique. As traditional RAPD has poor reproducibility and productivity, we previously developed an improved RAPD method (termed RAMP-PCR), which increased the reproducibility, number of bands, and efficiency of studies on polymorphism. To further develop the efficiency of this method, we used high-GC content primers for improved RAMP-PCR with DNA samples from Lonicera japonica. Comparison of amplification profiles obtained by standard RAPD primers with those obtained by regular PCR and RAMP-PCR, and high-GC primers with regular PCR and RAMP-PCR showed that the average number of bands and polymorphisms per primer gradually and significantly increased (from 6.4 to 15.0 and from 4.6 to 10.2, respectively). Cluster dendrograms showed similar results, indicating that this new method is consistent and reproducible. A total of 22 samples from different species, including plants, animals, and humans, were used for RAMP-PCR with high-GC primers. Multiple bands were successfully amplified from all samples, demonstrating that this method is a reliable technique with consistent results and may be of general interest in studies on different genera and species. We developed highly effective DNA markers, which can provide a more effective and potentially valuable approach than traditional RAPD for the genetic identification of various organisms, particularly of medicinal plants.

Development of novel SCAR markers for genetic characterization of Lonicera japonica from high GC-RAMP-PCR and DNA cloning.

Sequence-characterized amplified region (SCAR) markers were further developed from high-GC primer RAMP-PCR-amplified fragments from Lonicera japonica DNA by molecular cloning. The four DNA fragments from three high-GC primers (FY-27, FY-28, and FY-29) were successfully cloned into a pGM-T vector. The positive clones were sequenced; their names, sizes, and GenBank numbers were JYHGC1-1, 345 bp, KJ620024; YJHGC2-1, 388 bp, KJ620025; JYHGC7-2, 1036 bp, KJ620026; and JYHGC6-2, 715 bp, KJ620027, respectively. Four novel SCAR markers were developed by designing specific primers, optimizing conditions, and PCR validation. The developed SCAR markers were used for the genetic authentication of L. japonica from its substitutes. This technique provides another means of developing DNA markers for the characterization and authentication of various organisms including medicinal plants and their substitutes.

Obesity leads to declines in motor skills across childhood.

BACKGROUND: Poor motor skills have been consistently linked with a higher body weight in childhood, but the causal direction of this association is not fully understood. This study investigated the temporal ordering between children's motor skills and weight status at 5 and 10 years. METHODS: Participants were 668 children (54% male) who were studied from infancy as part of an iron deficiency anaemia preventive trial and follow-up study in Santiago, Chile. All were healthy, full-term and weighing 3 kg or more at birth. Cross-lagged panel modelling was conducted to understand the temporal precedence between children's weight status and motor proficiency. Analyses also examined differences in gross and fine motor skills among healthy weight, overweight, and obese children. RESULTS: A higher BMI at 5 years contributed to declines in motor proficiency from 5 to 10 years. There was no support for the reverse, that is, poor motor skills at 5 years did not predict increases in relative weight from 5 to 10 years. Obesity at 5 years also predicted declines in motor proficiency. When compared with normal weight children, obese children had significantly poorer total and gross motor skills at both 5 and 10 years. Overweight children had poorer total and gross motor skills at 10 years only. The differences in total and gross motor skills among normal weight, overweight and obese children appear to increase with age. There were small differences in fine motor skill between obese and non-obese children at 5 years only. CONCLUSIONS: Obesity preceded declines in motor skills and not the reverse. Study findings suggest that early childhood obesity intervention efforts might help prevent declines in motor proficiency that, in turn, may positively impact children's physical activity and overall fitness levels.

Identification of the origin of marker chromosomes by two-color fluorescence in situ hybridization and polymerase chain reaction in azoospermic patients.

Y chromosomal microdeletions at the azoospermia factor locus and chromosome abnormalities have been implicated as the major causes of idiopathic male infertility. A marker chromosome is a structurally abnormal chromosome in which no part can be identified by cytogenetics. In this study, to identify the origin of the marker chromosomes and to perform a genetic diagnosis of patients with azoospermia, two-color fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques were carried out. The marker chromosomes for the two patients with azoospermia originated in the Y chromosome; it was ascertained that the karyotype of both patients was 46,X, ish del(Y)(q11)(DYZ3+, DXZ1-). The combination of two-color FISH and PCR techniques is an important method for the identification of the origin of marker chromosomes. Thus, genetic counseling and a clear genetic diagnosis of patients with azoospermia before intracytoplasmic sperm injection or other clinical managements are important.

Establishment and rapid detection of a heterozygous missense mutation in the CACNA1F gene by ARMS technique with double-base mismatched primers.

Retinitis pigmentosa (RP) is a retinal degenerative disorder that often causes complete blindness. Mutations of more than 50 genes have been identified as associated with RP, including the CACNA1F gene. In a recent study, by employing next-generation sequencing, we identified a novel mutation in the CACNA1F gene. In this study, we used the amplification refractory mutation system (ARMS) and identified a single nucleotide change c.1555C>T in exon 13 of the CACNA1F gene, leading to the substitution of arginine by tryptophan (p.R519W) in a Chinese individual affected by RP. This study actually confirms this novel mutation, and establishes the ARMS technique for the detection of mutations in RP.

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

Association between TNFSF4 tagSNPs and myocardial infarction in a Chinese Han population.

Tumor necrosis factor superfamily member 4 (TNFSF4) plays an important role in atherosclerosis development. However, the biological significance of TNFSF4 variants on myocardial infarction (MI) pathogenesis remains poorly understood. We investigated the influence of 5 TNFSF4 tagging single nucleotide polymorphisms (rs3861950, rs17346501, rs7518045, rs1234313, and rs3850641) on individual susceptibility to MI in a Chinese population of 285 MI patients and 645 controls. Genotyping was performed using the polymerase chain reaction-ligase detection reaction method. In multivariate logistic regression analysis, only the TNFSF4 tagging single nucleotide polymorphism rs7518045 exhibited a significant effect on MI risk; A allele (odds ratio = 0.68, 95% confidence interval = 0.46-1.00, P = 0.048) and AA genotype (odds ratio = 0.64, 95% confidence interval = 0.42-0.97, P = 0.036) were associated with a decreased risk of MI compared with the G allele and the combined AG/GG genotype, respectively. Moreover, the haplotype rs3861950C-rs17346501C-rs7518045A-rs1234313G containing the rs7518045 A allele also exhibited a significant association with a decreased risk for MI (odds ratio = 0.42, 95% confidence interval = 0.21-0.84, P = 0.011). Our study showed that the A allele of the rs7518045 and haplotype rs3861950C-rs17346501C-rs7518045A-rs1234313G in the TNFSF4 gene were associated with decreased MI risk in a Chinese Han population. Further studies using larger sample sizes and in diverse ethnic populations are needed to confirm the general validity of our findings.

Osteoprotegerin polymorphisms in Chinese Han patients with rheumatoid arthritis.

In order to investigate the association between osteoprotegerin (OPG) gene polymorphisms and rheumatoid arthritis (RA), we studied OPG rs3102735 T/C and rs2073618 G/C polymorphisms in a Chinese Han population comprising 574 patients with RA and 804 controls. Genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was conducted. Our data indicated that OPG rs3102735 T/C and rs2073618 G/C polymorphisms were not associated with the risk of RA. However, among older patients (≥55 years), patients with the OPG rs3102735 TC (TC vs TT: OR = 0.68, 95%CI = 0.49­0.96, P = 0.029) and TC/CC (TC+CC vs TT: OR = 0.69, 95%CI = 0.49­0.96, P = 0.026) genotypes showed a significantly lower risk of RA than patients with the TT genotype, while patients with the OPG rs2073618 GC (GC vs GG: OR = 1.53, 95%CI = 1.13­2.07, P = 0.006) and GC/CC (GC+CC vs GG: OR = 1.43, 95%CI = 1.07­1.92, P = 0.015) genotypes showed a significantly higher risk of RA than patients with the GG genotype. We also found a significantly increased risk of RA associated with the OPG rs2073618 GC (GC vs GG: OR = 1.44, 95%CI = 1.07­1.93, P = 0.018) and GC/CC (GC+CC vs GG: OR = 1.39, 95%CI = 1.04­1.86, P = 0.024) genotypes among functional class III+IV patients. Our results were obtained from only a moderate-sized sample and, thus, a larger study with a more diverse ethnic population is needed to confirm these results.

Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species.

Persimmon (Diospyros L.) is an economically important fruit in the world, and it has been recognized as a healthy nutrient supply for human consumption. In this study, 14 microsatellite markers were developed from an AG/TC and AC/TG-enriched genomic library of Chinese persimmon Mopanshi. Twelve polymorphic markers were selected in 4 related species; these markers showed transferability to the 4 related persimmon species. In addition, 10 simple sequence repeat (SSR) markers were used to detect the genetic diversity among 51 persimmon accessions from China, Japan, and Korea. A total of 57 polymorphic bands with an average of 5.7 bands per primer pair were observed. According to cluster analysis and principal coordinate analysis, all persimmon accessions could be divided into 4 groups. A close relationship existed between D. kaki and D. oleifera, and D. glaucifolia and D. lotus. Jinzaoshi could be considered a separate species of persimmon. These new SSR markers provide tools for evaluating genetic relatedness among different persimmon species.

Isolation and analysis of cell-free fetal DNA from maternal peripheral blood in Chinese women.

Non-invasive prenatal diagnosis is used to detect the genetic material of the fetus by isolating the cell-free fetal DNA (cffDNA) from maternal peripheral blood. In order to establish an isolation method for cffDNA from maternal peripheral blood in Chinese women, the cffDNA was acquired with a two-step centrifugation using a QlAamp DNA Blood mini kit. The SRY gene of plasma DNA was amplified by polymerase chain reaction (PCR). Real-time quantitative PCR was used to measure the concentration of cffDNA in maternal peripheral blood in different pregnant women. The results of the SRY gene amplification of plasma DNA from pregnant women was the same as that of the amniocyte DNA. The average concentration of cffDNA in maternal peripheral blood of pregnant women in different gestational stages was 0.98 ng/mL (0.26-1.49 ng/mL), 1.43 ng/mL (0.46- 2.34 ng/mL), and 1.95 ng/mL (0.65-6.81 ng/mL) from early, middle, and late gestational stages, respectively. The mean of cffDNA from total DNA in plasma in different stages of gestation was 22.28% (9.86-27.81%). The lowest concentration of DNA amplified by nested-PCR in our research was 10-4-10-3 ng/µL. The isolation method for cffDNA from maternal peripheral blood was successfully established and further research into its applications will be conducted.

Analysis of key genes and modules during the courses of traumatic brain injury with microarray technology.

Gene expression data acquired at different times after traumatic brain injury (TBI) were analyzed to identify differentially expressed genes (DEGs). Interaction network analysis and functional enrichment analysis were performed to extract valuable information, which may benefit diagnosis and treatment of TBI. Microarray data were downloaded from Gene Expression Omnibus and pre-treated with MATLAB. DEGs were screened out with the SAM method. Interaction networks of the DEGs were established, followed by module analysis and functional enrichment analysis to obtain insight into the molecular mechanisms. A total of 39 samples at six time points (30 min, 4, 8, 24 , 72 h, and 21 days) were analyzed and generated 377 DEGs. Eight modules were identified from the networks and network ontology analysis revealed that cell surface receptor-linked signaling pathway, response to wounding and signaling pathway were significantly overrepresented. Altered risk genes and modules in TBI were uncovered through comparing the gene expression data acquired at various time points. These genes or modules could be potential biomarkers for diagnosis and treatment of TBI.

MTA1 promotes cell proliferation via DNA damage repair in epithelial ovarian cancer.

We examined whether metastasis-associated gene 1 (MTA1) promotes cell proliferation via DNA damage repair in ovarian cancer. MTA1 was successfully down-regulated using small interfering RNA in the epithelial ovarian cancer cell lines SKOV-3 and OVCAR-3. Cell growth was evaluated through MTT and colony formation assays. Fluorescence-activated cell sorting analysis was used to evaluate the distribution of cells in the cell cycle, and cytotoxicity assays were performed to study cell sensitivity to cisplatin. A neutral comet assay was used to measure levels of ionizing radiation-induced DNA damage in SKOV-3 cells, and Western blot analyses were carried out to examine the expression of key proteins involved in DNA damage repair pathways. MTA1 knockdown markedly inhibited cell growth and led to S phase cell cycle arrest. In addition, MTA1 depletion conferred sensitivity of ovarian cancer cells to cisplatin. Moreover, MTA1 depletion increased the level of ionizing radiation-induced DNA damage and caused irreparable damage, which was illustrated by a remarkable increase and persistent existence of a comet tail as well as protein expression levels of γH2AX, pRPA, and pChk1, all of which play critical roles in DNA repair. Thus, MTA1 promotes the proliferation of epithelial ovarian cancer cells by enhancing DNA repair.

Quantitative analysis of P16 gene CpG methylation in Uyghur patients with cervical squamous cell carcinoma and its relationship with HPV16 infection.

The methylation of CpG sites in the promoter region of the P16 gene in Uyghur patients with cervical squamous cell carcinoma (CSCC) was quantitatively analyzed and its relationship with human papillomavirus 16 (HPV16) infection was explored. Cervical samples were collected from 20 Uyghur patients with CSCC and 20 Uyghur controls. Matrix-assisted laser desorption ionization-time of flight mass spectrometry was applied to detect methylation of CpG sites in the promoter region of the P16 gene; polymerase chain reaction was performed to assess HPV16 infection in the 2 groups. Among the 16 CpG sites in the P16 gene promoter region, the methylation level of the CpG1-2 and CpG 6 sites, as well as the HPV16 infection rate, was higher in the CSCC group than in the control group (P<0.05). There was no significant correlation between P16 CpG methylation and HPV16 infection in Uyghur patients with CSCC. The P16 gene CpG1-2 and CpG 6 hypermethylation and HPV16 infection, which are independent of each other, play an important role in cervical squamous cell carcinogenesis in Uyghur patients.

Effect of mitochondrial ATP-sensitive potassium channel opening on the translocation of protein kinase C epsilon in adult rat ventricular myocytes.

This study aimed to investigate the effects of mitochondrial ATP-sensitive potassium (MitoKATP) channel opening on the translocation of protein kinase C epsilon (PKCε). In addition, we aimed to determine the relationship between PKCε translocation and the production of reactive oxygen species (ROS). PKCε protein expression in cultured adult rat ventricular myocytes was investigated by immunofluorescence and Western blotting. Diazoxide (DZ), a selective MitoKATP channel activator, caused a significant translocation to myofibrillar-like structures in cultured adult rat ventricular myocytes. N-2-Mercaptopropionylglycine, a free radical scavenger, could partially inhibit the translocation of PKCε induced by DZ. By contrast, chelerythrine, a selective PKC inhibitor, could completely block the translocation of PKCε induced by DZ. The opening of MitoKATP channels might activate and cause PKCε to translocate into myofibrillar-like structures. PKCε activation occurred downstream of the MitoKATP channel, possibly as a result of ROS production that occurred after the MitoKATP channels opened.

Serum thyroid hormone reference intervals in the apparently healthy individuals of Zhengzhou area of China.

This study aimed to establish reference intervals for serum thyroid hormones [serum thyroid-stimulating hormone (TSH), triiodothyronine (TT3), thyroxine (TT4), free triiodothyronine (FT3), and free thyroxine (FT4)] in apparently healthy individuals living in Zhengzhou. According to the requirement for laboratory support for the diagnosis and monitoring of thyroid diseases in the National Academy of Clinical Biochemistry (NACB) laboratory medicine practice guidelines, a total of 211 apparently healthy individuals were enrolled (94 men, 117 women, 23-77 years old) from Zhengzhou for measurement of serum levels of TSH, TT3, TT4, FT3, and FT4 by using the Siemens ADVIA Centaur XP analyzer. All markers were analyzed across gender- and age-specific groups by using the t-test and ANOVA. The reference intervals of all markers were determined by P2.5-P97.5. We detected gender-associated statistical significances for TT3, TT4, FT3, and FT4 (t=3.299, 2.141, 5.868, 5.358; P<0.05), but not for TSH (t=-1.776, P>0.05). Correlation analysis showed that all markers were negatively correlated with age (P>0.05). The new reference intervals for TT3, TT4, FT3, FT4, and TSH were established: 0.76-1.38 ng/mL, 5.96-11.27 µg/dL, 3.88-5.59 pM, 11.69-18.84 pM, 0.89-5.93 µIU/mL, respectively. In conclusion, we added a new database of reference intervals of the serum thyroid hormones for the Chinese adult population.