Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken

1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0-0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied.2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (-log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions.3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.

[Bioassay for plasma cholecystokinin bioactivity]

A sensitive and specific bioassay for the measurement of plasma cholecystokinin (CCK) is reported. CCK was extracted from plasma by SEP-PAK cartridges and the extracts were measured for CCK levels based on their ability to stimulate amylase release from dispersed rat pancreatic acini. Plasma CCK levels as low as 0.86 pmol/L (CCK-8 equivalent) were detectable. Gastrin in physiological concentration did not affect the bioassay. The amylase release stimulated by plasma extracts was abolished by Bt2-cGMP, a specific CCK receptor antagonist, indicating that there might be no secretin or VIP in plasma extracts. With this bioassay, fasting and postprandial plasma CCK levels of 11 normal volunteers were determined. The fasting level of CCK was 0.95 +/- 0.22 pmol/L (mean +/- SE). It increased to 2.98 +/- 0.67 pmol/L 15 minutes after feeding and remained significantly higher than the fasting level during a 60-minute period.

[The study of GST mu gene deletion as the hereditary marker for susceptibility to lung cancer]

A total of 175 lung cancer patients and 104 controls were detected for GST mu gene using PCR technique. The results showed that the GST mu gene deletion rate in lung cancer patients was 71.4%, which was significantly higher than the controls, 51.9%. Analysis according to pathological classification of lung cancer indicated that the GST mu gene deletion rate in all three kinds of pathological types-squamous, adenocarcinoma and small cell carcinoma, were markedly higher than that of controls, especially for small cell carcinoma (the deletion sate is 77.5%). The frequency of GST mu gene was not associated with smoking in both groups, but the higher deficiency rate was found in the low age group of lung cancer patients, showed 85.3% compared to the high age group, 68.1%. All the results showed that GST mu gene deletion may be an important host hereditary marker for susceptibility to lung cancer.

[The relationship between the high inducibility genotype of CYP450IA1 and lung cancer susceptibility]

OBJECTIVE

To evaluate the role of polymorphism of CYP450IA1 gene in the susceptibility of lung cancer.

METHODS

The polymorphism of CYP450IA1 gene in 149 lung cancer patients and 208 healthy controls were investigated by PCR technique.

RESULTS

The high inducibility genotype (Val/Val type) of CYP450IA1 in lung cancer patients was 16.1%, which was significantly higher than that of controls, 8.7%. According to pathological classification of lung cancer, it was indicated that VAl/Val type in squamous carcinomas was the highest, 21.54%, which was significantly higher than that of controls (8.7%) and adenocarcinomas (8.00%). The Val/Val type in small cell carcinoma reached 17.6%. The relative risks were estimated according to smoking condition and CYP450IA1 genotype. Taking the risk of the category with non-smoking and non-high inducibility genotype (Val/ Val) to be at a baseline of 1.0, the odds ratio was 1.6 (P < 0.05) in non-smoking in non-smoking and Val/Val type 4.8 in smoking and Val/Val type (P < 0.001). The relative risk of Val/Val type was 2.2 times as non-Val/ Val type for smoking people.

CONCLUSIONS

Development of lung cancer was associated with the high inducibility genotype of CYP450IA1. And Val/Val genotype of CYP450IA1 gene might be an important host hereditary marker for susceptibility to lung cancer.

[Susceptibility gene location of simple congenital heart defect by transmission disequilibrium test]

OBJECTIVE

To locate the susceptibility gene of human simple congenital heart defect(CHD) and provide a sound basis for further gene cloning.

METHODS

Three short tandem repeats(STRs) in regions of chromosome 7p14-15, 17q21 where exist Hox gene family's A, B clusters which regulate the embryonic heart development were chosen. Genotypes of 112 members in 39 CHD families were analyzed by amplifying the STR fragments using fluorescence-PCR technique. Then transmission disequilibrium test(TDT) was used to test the data of genotypes.

RESULTS

Statistical chi(2) values of D7S1808, D7S673 and D17S791 were 31.3(P<0.005), 11.12(P<0.05) and 6.65 (P>0.05) respectively. These suggest that the former two are associated with CHD, while the latter is not.

CONCLUSION

Human simple CHD is associated with Hox gene A cluster. Hox A gene may be a candidate CHD's susceptive genes. The location of the CHD's susceptive genes is in chromosome 7p14-15.

[Effect of "yang wei kang liu" granula on expression of P53 and PCNA in mice bearing sarcoma 180]

OBJECTIVE

To study possible mechanism of "Yang Wei Kang Liu" (YWKL) granula in treating tumor.

METHODS

Mice bearing sarcoma180 and immunohisto-chemical method were adopted.

RESULTS

Both YWKL granula and its cooperated chemothrapy could restrain the expression of P53 and PCNA. Compared with the chemotherapy group and the cooperated chemotherapy, YWKL granula group was significantly different.

CONCLUSION

YWKL granula could restrain the expression of P53 and PCNA, and increase the effect together with chemotherapy.

[Detection of aflatoxin-albumin adducts in human serum and its application]

Exposure to aflatoxin B1 (AFB1) is one of the major risk factors in the etiology of human hepatocellular carcinoma (HCC). The development of highly sensitive and specific methods for detecting AFB1 and its macromolecular biomarkers are critical for identifying individuals at risk for hepatocellular carcinoma. The detection of aflatoxin-albumin adducts (AFB-ALB) in serum has been used to investigate the relationship between aflatoxin exposure and HCC. A more sensitive and reliable method to detect AFB-ALB in serum was modified by separating serum albumin with Microcon-50 microconcentrators in stead of using precipitation. The method could separate serum albumin quickly and make protein digested in the same container. Thus, the step for transferring samples was reduced and recovery rate was improved. The AFB-ALB adducts were then determined by radioimmunoassay. The AFB-ALB adducts of human serum samples from Qidong, Jiangsu Province, and Fusui, Guangxi Zhuang Autonomous Region of the People's Republic of China were detected. The results indicated that the exposure of AFB1 is common and the positive rate for AFB-ALB adducts in serum of these populations is high.

[Community characteristics of benthonic animals and its relationship to environmental factors in the Nanhu Lake, Changchun]

There are only 21 species of benthonic animals in the Nanhu Lake, Changchun. The dominant species in the benthos community are obvious, and the individual quantity of Limnodrilus hoffmeisteri, Branchiura sowerbyi, and Tendipus plumosus accounts for 87% of the total individual quantity of all benthonic animals. It indicates that the water in the Nanhu Lake is suffering serious organic pollution, and belongs to an eutrophic lake. The peak values of benthos biomass and energy are found in July(48.23 g WW.m-2 and 241.16 kJ.m-2 respectively), while the maximum individual quantity is appeared in May(401 ind.m-2). The distribution of Oligochaeta and aquatic insects has a significant positive correlation to organic content in the sediment(alpha < 0.05). The community structure of benthonic animals reflects adequately the feature of the Nanhu Lake as an eutrophic lake in temperate zone.

[Effects of As2O3 on the BCR/ABL protein tyrosine phosphorylation in K562 cells]

OBJECTIVE

To explore the mechanisms of As2O3 inducing apoptosis and growth inhibition in K562 cells and provide theoretical basis for clinical application.

METHODS

The effects of As2O3 on BCR/ABL protein tyrosine phosphorylation(PTP) and its signal transduction as well as the expression of apoptosis-related genes were studied by means of immunoprecipitation, Western blot, biochemical method and immunofluorescence.

RESULTS

Tyrosine phosphorylation of several cellular proteins especially BCR/ABL protein was decreased by 1 mumol/L As2O3, but not by 0.1 mumol/L As2O3. As2O3 had no effect on PTP activity, downregulated the expression of JAK2 protein, but did not affect the expressions of STAT1 and STAT2 proteins and the STAT1 protein tyrosine phosphorylation. As2O3 had no effect on the expression of the apoptosis-related genes like Bcl-2, Bcl-xL/S, Bax, ICH-1L, p53, PARP, either, but downregulated PML protein expression in K562 cells.

CONCLUSION

As2O3 might induce K562 cell apoptosis and inhibit its growth by reducing tyrosine phosphorylation of cellular proteins especially BCR/ABL protein and/or by downregulating JAK2 protein expression to interfere with the BCR/ABL protein signal transduction.

[Expression of c-fos mRNA following moderate lateral fluid percussion brain injury in rats]

This experiment was designed to study the expression of c-fos mRNA in brain following moderate lateral fluid percussion brain injury in rats and to observe the temporal pattern of its expressions following percussion. Male Sprague-Dawley rats were divided into normal control, sham operation control and injury groups. The rats of the injury group were subjected to moderate lateral fluid percussion injury (0.2 MPa). The injury group was then subdivided into 5 min, 15 min, 30 min, 1 h, 2 h groups according to the time elapsed after injury. The expression of c-fos mRNA was studied with reverse transcription polymerase chain reaction(RT-PCR) semi-quantitatively. c-fos mRNA in cortex and brain stem was expressed weakly in control groups. After 5 min of percussion, the expression of c-fos mRNA increased progressively and remained elevated up to 2 h after brain injury. This result suggested that the induction and expression of the c-fos mRNA in cortex and brain stem after fluid percussion brain injury were increased rapidly. The temporal pattern of induction in cortex was similar to that in brain stem.

[Human blood stain identification using DNA amplification technique]

DNA was extracted from human's and 15 different species of mammals' dried blood stains as well as from camel hair roots. DNA amplification was carried out using primers of Alu 9.1 and Alu 9.2. The results have indicated that this method can be used for the identification of human's dried blood stain under general condition.

[Effect of CCK receptor antagonists on plasma CCK bioassay]

Fasting and postprandial plasma CCK levels of 102 normal subjects were measured by bioassay with dispersed rat pancreatic acini. The reference values ranged from 0 to 4.2 pmol/L (CCK-8 equivalents) for fasting and from 1.1 to 13.5 pmol/L for postprandial state. There was no significant difference between male and female, or in different age groups. The effects of CCK receptor antagonists of 3 different categories on CCK bioactivity in plasma measured by the bioassay were investigated. L 364,718 (5 nmol/L), proglumide (1.0 mmol/L), or Bt2-cGMP (0.1 mmol/L) was either extracted by SEP-PAK C18 cartridges together with human plasma containing 8 pmol/L of CCK-8, or added into the plasma extracts before the assay. The CCK bioactivity was inhibited by all of the 3 CCK antagonists. The action of L364,718 could be eliminated by the procedure of plasma extraction, but not of proglumide or Bt2-cGMP. It was suggested that CCK bioassay can be used even if L364,718 was administered. However, CCK cannot be measured accurately if there are proglumide or Bt2-cGMP in the plasma.

Optimising the performance of a lab-scale tidal flow reed bed system treating agricultural wastewater

A gravel-based tidal flow reed bed system was operated with three different strategies in order to investigate its optimal performance for the treatment of a high strength agricultural wastewater. According to the three strategies, individual reed beds were saturated and unsaturated with the wastewater for different periods while reasonably stable hydraulic and organic loadings were maintained. Experimental results demonstrated that the system produced the highest pollutant removal efficiencies with a relatively short saturated period and long unsaturated period, highlighting the importance of oxygen transfer into reed bed matrices during the treatment. Significant removals of some major organic and inorganic pollutants were achieved under all three operational conditions. Nitrification was not the major route of ammoniacal-nitrogen removal when the system was under high organic loading. Due to the filtration of suspended solids and the accumulation of biomass, gradual clogging of the reed bed matrices took place, which caused concerns over the long-term efficiency of the tidal flow system.

[Experimental comparison of two coxsackievirus B3 variants in murine myocardial cells]

There is lack of direct evidence whether the myocarditis can be induced by CVB3o. The two coxsackievirus B3 variants were used to infected murine myocardial cells. The results showed that: (1) In culture medium of murine myocardial cells infected with two variants, it did not show much differences in titers at 12 and 24 hours between CVB3o and CVB3m. (2) The two variants could all induce the death of myocardium, but with the elapse of time, the cell death rate of CVB3m infected cells was much higher than CVB3o. (3) CVB3o could not block the myocardial cells from infection by CVB3m. It is concluded that myocardial cells can be infected by CVB3o, but the degree of infection is lower than CVB3m.

Primary immunodeficiency in south China: clinical features and a genetic subanalysis of 138 children

OBJECTIVES

We analyzed the clinical features of 138 patients with primary immunodeficiency (PID) and performed genetic testing on a subset of patients in order to complete gaps in research on PID in South China and thus improve pediatricians' ability to recognize and diagnose PID.

METHODS

We performed a retrospective analysis based on the medical records of PID patients hospitalized in our institution between May 1999 and June 2012. Gene sequencing was performed in 59 cases.

RESULTS

Children with PID usually present with fever and repeated infections that generally affect the respiratory and digestive tracts. Growth retardation is observed in some cases. Of the 138 patients, 113 were boys, median age at onset was 5 months (range, 0-119 months), and age at diagnosis was 10 months (2-159 months). A family history of repeated infection or death of family members in infancy because of recurrent infections was recorded in 20 cases (14.49%). Antibody defects were detected in 48 cases (34.78%), combined immunodeficiency disease in 45 cases (32.61%), and other well-defined immunodeficiency syndromes in 45 cases (32.61%). Of the 59 patients from the genetic subanalysis, 24 (15.94%) had a genetic mutation (x-linked agammaglobulinemia, 8 cases; severe combined immunodeficiency, 8 cases; hyperimmunoglobulin M syndrome, 3 cases; hyperimmunoglobulin E syndrome, 3 cases; chronic granulomatous disease, 2 cases). We detected 4 novel mutations. No relevant mutations were found in the remaining 35 cases.After treatment with intravenous immunoglobulin and anti-infectious agents, 16 patients died in hospital, and 5 cases died after discontinuing treatment (mortality, 15.22%).

CONCLUSIONS

In recent years, the number of patients with PID has risen gradually in South China. Genetic testing can confirm diagnosis. Since PID seriously affects children's quality of life, it is important to diagnose, treat, and intervene early.We hope our clinical and genetic analyses of children with PID can provide diagnostic guidance for clinicians.