Models of logistic regression analysis, support vector machine, and back-propagation neural network based on serum tumor markers in colorectal cancer diagnosis.

We evaluated the application of three machine learning algorithms, including logistic regression, support vector machine and back-propagation neural network, for diagnosing congenital heart disease and colorectal cancer. By inspecting related serum tumor marker levels in colorectal cancer patients and healthy subjects, early diagnosis models for colorectal cancer were built using three machine learning algorithms to assess their corresponding diagnostic values. Except for serum alpha-fetoprotein, the levels of 11 other serum markers of patients in the colorectal cancer group were higher than those in the benign colorectal cancer group (P < 0.05). The results of logistic regression analysis indicted that individual detection of serum carcinoembryonic antigens, CA199, CA242, CA125, and CA153 and their combined detection was effective for diagnosing colorectal cancer. Combined detection had a better diagnostic effect with a sensitivity of 94.2% and specificity of 97.7%; combining serum carcinoembryonic antigens, CA199, CA242, CA125, and CA153, with the support vector machine diagnosis model and back-propagation, a neural network diagnosis model was built with diagnostic accuracies of 82 and 75%, sensitivities of 85 and 80%, and specificities of 80 and 70%, respectively. Colorectal cancer diagnosis models based on the three machine learning algorithms showed high diagnostic value and can help obtain evidence for the early diagnosis of colorectal cancer.

Treatment Experience of Severe Abdominal Infection after Orthotopic Liver Transplantation.

This study aims to investigate the causes and treatment experience of severe abdominal infection after orthotopic liver transplantation. Clinical data were retrospectively analysed in perioperative severe abdominal infection of 186 orthotopic liver transplantation cases from March 2004 to November 2011. Among the 186 patients, 16 cases had severe abdominal infection: five cases had bile duct anastomotic leakage-inducing massive hydrops and infection under liver interstice, 10 cases had extensive bleeding of surgical wound leading to massive haematocele and infection around the liver, and one case had postoperative lower oesophageal fistula leakage causing massive hydrops and infection under the left diaphragm. After definite diagnosis, 12 cases underwent surgery within three days, with no death. Among the four cases that underwent surgery three days after diagnosis, one case died of multiple-organ failure five days after abdominal cavity exploration, which was performed 21 days after liver transplantation. Severe abdominal infections after liver transplantation were the most common causes of death in perioperative liver transplantation. Comprehensive treatment with efficacious antibiotics, multiple-organ support, controlled surgical removal of the lesion, and adequate drainage establishment was the key to the entire treatment.

3'-UTR polymorphism (rs10434) in the VEGF gene is associated with B-CLL in a Chinese population.

We investigated the relationship between a VEGF genetic polymorphism and B cell chronic lymphocytic leukemia (B-CLL). A total of 102 patients with B-CLL and 124 healthy subjects were included in this study. All individuals were typed for the rs10434 in the vascular endothelial growth factor (VEGF) gene using the TaqMan technique. We found that the A allele and the AA genotype of rs10434 were more frequent in B-CLL patients than in control subjects (0.54 vs 0.34; 27 vs 13%; respectively). VEGF alleles and genotypes segregated similarly in patients at different disease stages according to Rai classification. These results suggest a possible association between the VEGF polymorphism and high-risk B-CLL.

Cloning and characterization of peanut allene oxide cyclase gene involved in salt-stressed responses.

In this study, the full-length cDNA encoding allene oxide cyclase (AhAOC) was isolated from peanut (Arachis hypogaea L.). The deduced amino acid sequence of AhAOC showed high homology with other plant AOCs. The transcript of AhAOC was found to be abundantly expressed in roots. Expression analysis demonstrated that AhAOC was induced by abscisic acid, methyl-jasmonic acid, salicylic acid, salinity, polyethylene glycol, and cold stresses, particularly by high salinity. Overexpression of AhAOC in rice increased root elongation and plant height compared with expression in control plants and conferred tolerance against salinity. Thus, the AhAOC gene may play an important role in increasing the expression of transcription factors (MYB2 and OsONAC045) and functional genes (DREB1F and LEA3) in transgenic rice under salt stress as well as improve stress tolerance through the accumulation of compatible solutes (proline and soluble sugar). The AhAOC gene is a potential resource for enhancing salt tolerance in crop species.

Influence of sirolimus-induced TGF-ß secretion on mouse Treg cell proliferation.

We examined the effects of co-culturing CD4+ CD25+ Treg cells with sirolimus or cyclosporin A on Treg cell proliferation and differentiation and on transforming growth factor-ß (TGF-ß) and Foxp3 expression. CD4+ CD25+ Treg cells were harvested from mononuclear cells of spleens of C57BL/6 mice using immunomagnetic beads and divided into control, sirolimus, and cyclosporine groups. Following a 96-h co-culture, Treg cells were assayed by flow cytometry. FoxP3 and TGF-ß mRNA levels and secretion were assayed by reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. Smad protein of the TGF-ß signaling pathway was assayed by western blot and its effect on CD4+ CD25+ FoxP3+ Treg cell proliferation was determined. Sirolimus-promoted differentiation and proliferation was examined using a TGF-ß neutralizing antibody. Sirolimus-treated CD4+ T cell TGF-ß secretion increased 2.5X over control levels (P < 0.01), but that of the cyclosporine group decreased marginally (P > 0.05). The CD4+ cell proportion decreased significantly (41.25 vs 69.22%, P < 0.01) and slightly (65.21 vs 69.22, P > 0.05) in the cyclosporine and sirolimus groups, respectively. T cell Foxp3 mRNA expression was significantly higher in the sirolimus-treated than in the cyclosporine (53.7 vs 40.2%, P < 0.05) and control groups (P < 0.01), but was significantly lower in the cyclosporine group than in controls (23.6 vs 40.2%, P < 0.01). Overall, sirolimus promoted CD4+ CD25+ Treg cell proliferation and growth in vitro, whereas cyclosporin A inhibited proliferation. Sirolimus might promote CD4+ CD25+ FoxP3+ regulatory T cell proliferation by inducing TGF-ß secretion in vivo.

Mapping of quantitative trait loci for the bolting trait in Brassica rapa under vernalizing conditions.

Premature bolting can occur occasionally during spring cultivation of heading Chinese cabbage in East Asia when the plants encounter low temperatures (vernalization), leading to economic loss. Breeding bolting-resistant cultivars is the best choice for solving this problem. We looked for QTLs responsible for varietal differences in the bolting trait in Brassica rapa under environmental conditions that promote vernalization. To achieve this goal, we constructed a linkage map with 107 simple sequence repeats and 54 insertion/deletion markers based on a segregating population of 186 F2 individuals. The resulting map consisted of 10 linkage groups and covered a total length of 947.1 cM, with an average genetic distance of 5.84 cM between adjacent markers. QTL analysis of the bolting trait was performed by two phenotypic evaluations (bolting index and flowering time) based on the scores in an F2 population in the spring of 2010, and scores in F2:3 families in autumn 2010 and spring 2011, respectively. Twenty-six QTLs that controlled bolting were detected, accounting for 2.6 to 31.2% of the phenotypic variance. The detected QTLs with large effects co-localized mainly on linkage groups A02, A06, and A07. These QTLs may provide useful information for marker-assisted selection in a breeding program for late bolting or bolting-resistant cultivars in B. rapa crops.

Peroxiredoxin 3 is resistant to oxidation-induced apoptosis of Hep-3b cells.

OBJECTIVE: Although peroxiredoxin 3 (PRX3) was reported to be overexpressed in liver cancer, the precise function of PRX3 in the development and/or progression of liver cancer remained to be obscure. The present study was conducted to investigate the response of PRX3 to oxidative stress in hepatocellular carcinoma (HCC) cells. METHODS: After successful knockdown of PRX3 expression by small interfering RNA, we treated HCC cell lines Hep-3b and Hep-G2 with gradient concentrations of H2O2 and detected cell proliferation, apoptosis, and the level of reactive oxygen species (ROS) in the cells. RESULTS: After low-dose (5-20 µmol/l) H2O2 treatment, the ROS level was significantly higher in PRX3-knockdown Hep-3b cells than in controls. In addition, PRX3 down-regulation resulted in decreased proliferation, increased apoptosis, and increased caspase 3 activity of Hep-3b cells. We did not notice significant difference between PrxIII knockdown and control Hep-G2 cells in ROS level, cell viability or apoptosis. CONCLUSION: Our results suggest that PRX3 is an indispensable ROS scavenger that protects tumor cells against oxidative damage and subsequent apoptosis, which provides a clue that PRX3 may be involved in the chemotherapeutic resistance of liver cancer. The underlying mechanism for PRX3 function needs further investigation.

Isolation and characterization of polymorphic microsatellite markers from Coilia ectenes.

Coilia ectenes (Jordan and Seale 1905) is an important anadromous species that is an important resource at risk of extinction because of over-fishing, pollution, and coastal construction. To evaluate the genetic diversity of C. ectenes for use in breeding programs, elite microsatellite-enriched libraries were constructed and novel microsatellite markers were developed, and applied to genetically detect wild populations. Out of 92 randomly selected and sequenced clones, 89 contained a CA or GA repeat motif. Twenty-two pairs of primers were designed to investigate the polymorphism and genetic structure of a wild population collected from the Yellow River estuary, China. It was found that 2 loci were monomorphic and 20 loci were polymorphic. The number of alleles per polymorphic loci ranged from 3 to 13, with an average of 7.9. The expected heterozygosity per locus ranged from 0.05 to 0.89, with an average of 0.68. The isolated polymorphic markers are expected to be of use in future genetic breeding programs for C. ectenes, and in the assessment of genetic variation within this species.

Genetic analysis of the ELOVL6 gene polymorphism associated with type 2 diabetes mellitus.

Recent animal studies have indicated that overexpression of the elongation of long-chain fatty acids family member 6 (Elovl6) gene can cause insulin resistance and ß-cell dysfunction. These are the major factors involved in the development of type 2 diabetes mellitus (T2DM). To identify the relationship between single nucleotide polymorphisms (SNP) of ELOVL6 and T2DM pathogenesis, we conducted a case-control study of 610 Han Chinese individuals (328 newly diagnosed T2DM and 282 healthy subjects). Insulin resistance and islet first-phase secretion function were evaluated by assessment of insulin resistance in a homeostasis model (HOMA-IR) and an arginine stimulation test. Three SNPs of the ELOVL6 gene were genotyped with polymerase chain reaction-restriction fragment length polymorphism, with DNA sequencing used to confirm the results. Only genotypes TT and CT of the ELOVL6 SNP rs12504538 were detected in the samples. Genotype CC was not observed. The T2DM group had a higher frequency of the C allele and the CT genotype than the control group. Subjects with the CT genotype had higher HOMA-IR values than those with the TT genotype. In addition, no statistical significance was observed between the genotype and allele frequencies of the control and T2DM groups for SNPs rs17041272 and rs6824447. The study indicated that the ELOVL6 gene polymorphism rs12504538 is associated with an increased risk of T2DM, because it causes an increase in insulin resistance.

Inactivation of putative PKS genes can double geldanamycin yield in Streptomyces hygroscopicus 17997.

The putative polyketide biosynthesis (PKS) genes cos10 and pg10 were inactivated by insertion of a kanamycin-resistance gene into the genome of the geldanamycin-producing strain, Streptomyces hygroscopicus 17997. The resultant inactivation were confirmed by PCR analysis. The abilities of the PKS gene inactivation strains to produce geldanamycin were compared with the natural geldanamycin- producing strain, S. hygroscopicus 17997. The cos10-inactivated strain exhibited an unchanged ability to produce geldanamycin, but the pg10- inactivated strain can produce twice the yield of the natural strain when grown under the same conditions. We propose that there is a sub-PKS pathway in the geldanamycin-producing strain, S. hygroscopicus 17997.

Genetic analysis of the ELOVL6 gene polymorphism associated with type 2 diabetes mellitus

Recent animal studies have indicated that overexpression of the elongation of long-chain fatty acids family member 6 (Elovl6) gene can cause insulin resistance and β-cell dysfunction. These are the major factors involved in the development of type 2 diabetes mellitus (T2DM). To identify the relationship between single nucleotide polymorphisms (SNP) of ELOVL6 and T2DM pathogenesis, we conducted a case-control study of 610 Han Chinese individuals (328 newly diagnosed T2DM and 282 healthy subjects). Insulin resistance and islet first-phase secretion function were evaluated by assessment of insulin resistance in a homeostasis model (HOMA-IR) and an arginine stimulation test. Three SNPs of the ELOVL6 gene were genotyped with polymerase chain reaction-restriction fragment length polymorphism, with DNA sequencing used to confirm the results. Only genotypes TT and CT of the ELOVL6 SNP rs12504538 were detected in the samples. Genotype CC was not observed. The T2DM group had a higher frequency of the C allele and the CT genotype than the control group. Subjects with the CT genotype had higher HOMA-IR values than those with the TT genotype. In addition, no statistical significance was observed between the genotype and allele frequencies of the control and T2DM groups for SNPs rs17041272 and rs6824447. The study indicated that the ELOVL6 gene polymorphism rs12504538 is associated with an increased risk of T2DM, because it causes an increase in insulin resistance.

Isolation of novel microsatellite markers from Paralichthys lethostigma (Paralichthyidae) and their cross-species application in Pleuronectiformes.

We investigated the genetic diversity of the southern flounder Paralichthys lethostigma. Microsatellite-enriched libraries were constructed and novel microsatellite markers were developed and applied for genetic detection of wild populations. Cross-species amplification was also conducted in five pleuronectiforme species. Of 45 randomly selected and sequenced clones, 43 contained a CA or GA repeat motif. Fourteen pairs of primers were designed to investigate the polymorphism and genetic structure of a wild population collected from North Carolina State coastal waters. Two loci were monomorphic and 12 loci were polymorphic. The number of alleles per polymorphic locus ranged from 2 to 16, with an average of 7.3, and the expected heterozygosity per locus ranged from 0.10 to 0.92, with an average of 0.58. Cross-species amplification showed that most of the markers could successfully amplify Paralichthys olivaceus DNAs, few markers amplified in Verasper variegatus and Verasper moseri, and none of them could amplify Scophthatmus maximus and Cynoglossus semilaevis DNAs. The isolated polymorphic markers would be useful for the genetic breeding and assessment of genetic variation within the genus Paralichthys.