Serum immunoinflammation-related protein complexes discriminate between inflammatory bowel disease and colorectal cancer.

PURPOSE: Inflammatory bowel disease (IBD) is an important risk factor for colon cancer. Novel serum immunoinflammation-related protein complexes (IIRPCs) have shown associations with early cancer detection. Herein, we investigated the potential of serum IIRPCs for discriminating between IBD and colorectal cancer (CRC) patients. METHODS: Serum protein complexes of 65 healthy controls, 57 CRC, 69 (ulcerative colitis) UC, and 67 (Crohn's disease) CD patients were isolated by native-PAGE. The gray values of serum IIRPCs bands in the gel were quantified using Quantity One software. The receiver-operating characteristic (ROC) curves were constructed to assess the discriminating ability by calculating the area under the ROC curve. RESULTS: The serum IIRPCs levels in IBD and CRC patients were significantly elevated compared to healthy controls. ROC analysis indicated certain diagnostic ability of serum IIRPCs in differentiating IBD from CRC. Specifically, "a3" complex discriminated UC from CRC, with an AUC value of 0.722, sensitivity of 69.4% and specificity of 63.8%. Similarly, "b4" complex discriminated UC from CRC, with an AUC value of 0.709, sensitivity of 70.4%, and specificity of 60.0%. In addition, the "a3" complex also discriminated CD from CRC, with an AUC value of 0.785, sensitivity of 73.1%, and specificity of 74.1%, while the "b4" complex showed a tendency to discriminate CD from CRC, with an AUC value of 0.663, sensitivity of 67.9% and specificity of 50.0%. Thus, an equation based on multiple IIRPCs was built to further improve the discriminating power. CONCLUSIONS: Serum IIRPCs can be used to discriminate IBD from CRC and may also be associated with early screening of colitis-associated cancer.

Genome-wide analysis of TCP family in tobacco.

The TCP family is a transcription factor family, members of which are extensively involved in plant growth and development as well as in signal transduction in the response against many physiological and biochemical stimuli. In the present study, 61 TCP genes were identified in tobacco (Nicotiana tabacum) genome. Bioinformatic methods were employed for predicting and analyzing the gene structure, gene expression, phylogenetic analysis, and conserved domains of TCP proteins in tobacco. The 61 NtTCP genes were divided into three diverse groups, based on the division of TCP genes in tomato and Arabidopsis, and the results of the conserved domain and sequence analyses further confirmed the classification of the NtTCP genes. The expression pattern of NtTCP also demonstrated that majority of these genes play important roles in all the tissues, while some special genes exercise their functions only in specific tissues. In brief, the comprehensive and thorough study of the TCP family in other plants provides sufficient resources for studying the structure and functions of TCPs in tobacco.

Homology-based analysis of the GRAS gene family in tobacco.

Members of the GRAS gene family are important transcriptional regulators. In this study, 21 GRAS genes were identified from tobacco, and were classified into eight subgroups according to the classification of Arabidopsis thaliana. Here, we provide a preliminary overview of this gene family in tobacco, describing the gene structure, gene expression, protein motif organization, phylogenetic analysis, and comparative analysis in tobacco, Arabidopsis, and rice. Using the sequences of 21 GRAS genes in Arabidopsis to search against the American tobacco genome database, 21 homologous GRAS genes in tobacco were identified. Sequence analysis indicates that these GRAS proteins have five conserved domains, which is consistent with their counterparts in other plants. Phylogenetic analyses divided the GRAS gene family into eight subgroups, each of which has distinct conserved domains and biological functions. Furthermore, the expression pattern of these 21 GRAS genes reveals that most are expressed in all six tissues studied; however, some have tissue specificity. Taken together, this comprehensive analysis will provide a rich resource to assist in the study of GRAS protein functions in tobacco.

Transcriptional profiles of emasculated flowers of black locust (Robinia pseudoacacia) determined using the cDNA-AFLP technique.

Black locust (Robinia pseudoacacia) is a tree in the subfamily Faboideae, native to North America, that has been naturalized and widely planted in temperate Europe and Asia. Black locust has important ecological and economic value, but its quality needs improvement. Hybridization programs are important for black locust breeding, but the low rate of fruit set after controlled pollination limits both its breeding and that of other monoclinous plant species that share this problem. In this study, we investigated gene expression in emasculated black locust flowers using the cDNA-amplified fragment length polymorphism technique to determine why the rate of fruit set is low after controlled pollination. Flowers that were emasculated after being frozen in liquid nitrogen were used as controls. Changes in the flower transcriptome were more dramatic at 5 h after emasculation than at 48 h. Injury caused by emasculation decreased the expression levels of genes associated with metabolism, growth regulation, signal transduction, and photosynthesis, and it increased the expression of genes related to stress-response metabolism, signal transduction, and promotion of senescence. The changes in the expression levels of these genes had negative effects on sugar metabolism, protein metabolism, lipid metabolism, energy metabolism, matter transport, signal transduction, osmotic regulation, pH regulation, and photosynthesis. Thus, emasculation accelerated flower senescence, resulting in low fruit set.

Characterization of ESTs from black locust for gene discovery and marker development.

Black locust (Robinia pseudoacacia L.) is an ecologically and economically important species. However, it has relatively underdeveloped genomic resources, and this limits gene discovery and marker-assisted selective breeding. In the present study, we obtained large-scale transcriptome data using a next-generation sequencing platform to compensate for the lack of black locust genomic information. Increasing the amount of transcriptome data for black locust will provide a valuable resource for multi-gene phylogenetic analyses and will facilitate research on the mechanisms whereby conserved genes and functions are maintained in the face of species divergence. We sequenced the black locust transcriptome from a cDNA library of multiple tissues and individuals on an Illumina platform, and this produced 108,229,352 clean sequence reads. The high-quality overlapping expressed sequence tags (ESTs) were assembled into 36,533 unigenes, and 4781 simple sequence repeats were characterized. A large collection of high-quality ESTs was obtained, de novo assembled, and characterized. Our results markedly expand the previous transcript catalogues of black locust and can gradually be applied to black locust breeding programs. Furthermore, our data will facilitate future research on the comparative genomics of black locust and related species.

Effects of microwave ablation or its combination with whole-body chemotherapy on serum vascular endothelial growth factor levels in patients with stage IIIB/IV NSCLC.

We aimed to analyze the changes of serum vascular endothelial growth factor (VEGF) before and after microwave ablation (MWA) in patients with stage IIIB-IV non-small cell lung cancer (NSCLC), and to observe the effects of MWA combined with chemotherapy on short-term therapeutic efficacy and long-term survival. Concentrations of serum VEGF in 20 healthy subjects were considered as controls. Changes of serum VEGF were detected by ELISA before and after MWA (1 and 7 days after treatment). Seven days after MWA, patients were divided into a combination chemotherapy group of 22 subjects and a MWA alone group of 18 subjects. Serum VEGF was measured 1 month after MWA and 4 cycles after chemotherapy (3 months) to evaluate term effects; and 1- and 2-year survival rates. Serum VEGF concentrations declined sharply 1 day after MWA, and were significantly different from the levels before treatment. Subsequently, VEGF rebounded 7 days after ablation, higher than that before treatment. At 1 and 3 months, serum VEGF levels in both treatment groups were remarkably lower than that before treatment; efficiency, or for the 1-year survival rate. However, the 2-year survival rates were significantly different between the two groups. We demonstrated that after MWA, the serum VEGF concentration undergoes a process of increasing, which might promote metastasis and recurrence of NSCLC. MWA combined with whole-body chemotherapy appears to be an effective method to increase the disease control rate, reduce the probability of metastasis and recurrence, and thus improve long-term survival.

Polymorphisms in a myostatin gene and associations with growth in a hybrid of Culter alburnus and Ancherythroculter nigrocauda.

Myostatin (MSTN) is a member of the transforming growth factor-ß superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of MSTN were screened for single nucleotide polymorphisms (SNPs) in a hybrid of Culter alburnus (♀) x Ancherythroculter nigro-cauda (♂) individuals from a commercial hatchery population, and two non-synonymous SNPs (c.6T>C and c.162G>A) and two synonymous SNPs (c.152G>A and c.155G>A) in exon 2 were identified. The two non-synonymous SNPs caused an amino acid change, from Ser to Pro and from Val to Ile, respectively. Genotyping by the direct sequencing of polymerase chain reaction products for these four SNPs was conducted in 190 individuals from the commercial hatchery population. Association analysis showed that one non-synonymous SNP (c.6T>C) in exon 2 was significantly associated with total length, body length, body height, head length, and body weight. Haplotype analyses revealed that the haplotype combination H1H3 exhibited the best growth performance. Our results demonstrate that some of the SNPs in MSTN may have positive effects on growth, and suggest that MSTN could be a candidate gene for marker-assisted selection in C. alburnus and A. nigrocauda.

Cloning and expression analysis of terpenoid metabolism-related gene NsyCMS in Nicotiana sylvestris.

Terpenoids constitute the main class of secondary metabolites produced in plants with industrial, pharmacological, and agricultural interests. Nicotiana sylvestris has been widely adopted as a diploid model system in plant biology for studies of terpenoid biosynthesis. In this paper, we report the isolation and analysis of the 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (CMS) gene of the MEP (methylerythritol 4-phosphate) pathway from N. sylvestris. We used homologous-based cloning with a RACE method to obtain the full-length coding sequence of the NsCMS. Then, the physical and chemical properties, function, and three-dimensional structure of the NsyCMS protein were predicted. Fluorogenic quantitative PCR was used to conduct an expression analysis at different developmental stages of various tissues of the NsyCMS. The sequence of the NsyCMS consists of a 954-bp open reading frame and encodes a predicted protein of 317 amino acids, with a molecular weight of approximately 49.6 kDa and pi of 6.92. The in vivo localization of the encoded protein was cytoplasmic with no signal peptide, whereas 2 transmembrane regions were found in NsyCMS. The conserved domains of typical 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase, aminotransferase, and pyridoxal phosphate-dependent transferase were found in NsyCMS. Differential expression patterns of the NsyCMS were observed throughout the different developmental stages and tissues. NsyCMS messenger RNA was expressed in all tissues, with the highest level of expression in the seedling leaves. NsyMK was expressed at a higher level in the resettling roots. The results from our study set the foundation for exploring the terpenoid biosynthetic pathways in N. sylvestris.

Computed tomography-guided percutaneous microwave ablation therapy for lung cancer.

This study evaluated the clinical efficacy and value of computed tomography (CT)-guided percutaneous microwave ablation therapy (PMAT) for lung cancer without surgical treatment. A total of 39 lesions in 29 patients with peripheral lung cancer were treated by CT-guided PMAT under local anesthesia. The microwave energy was 50-70 W at a frequency of 2450 MHz. The treatment was performed by using 1 or 2 points of ablation emission according to the size and shape of the tumor. Operations were completed in 29 patients. The average operating time was 8 min (range: 5-12 min). After PMAT, lower density in the ablated area was observed by CT. Pre- and post-treatment CT values were 52.60 and 26.12 Hu, respectively. Eight, 14, 4, and 3 patients achieved complete remission, partial remission, stable status, and progression, respectively, for an effectiveness rate of 75.86%. Complications included 5, 2, and 15 cases of pneumothorax, pleural effusion, and fever, respectively. No needle track implantation was observed. Mean progression-free survival was 14.6 months. The 1- and 2-year survival rates were 91.3 and 82.6%, respectively. Thus, PMAT is a minimally invasive, safe, and effective treatment for lung cancer. It can improve quality of life, prolong survival, and improve the survival rate.

Genetic characterization of red-colored heartwood genotypes of Chinese fir using simple sequence repeat (SSR) markers.

The present study investigated the genetic characterization of red-colored heartwood Chinese fir [Cunninghamia lanceolata (Lamb.) Hook.] in Guangxi using 21 simple sequence repeat (SSR) markers and analyzes of the genetic variation (N = 149) in samples obtained from five sites in Guangxi Province, China. The number of different alleles and the Shannon's information index per locus ranged from 3 to 12 and from 0.398 to 2.258 with average values of 6 and 1.211, respectively, indicating moderate levels of genetic diversity within this germplasm collection. The observed and expected heterozygosity ranged from 0.199 to 0.827 and from 0.198 to 0.878 with an average of 0.562 and 0.584, respectively. Although, the mean fixation index was 0.044, indicative of a low level of genetic differentiation among germplasms, analysis of molecular variance revealed considerable differentiation (99%) within the samples. The neighbor-joining dendrogram revealed that the majority of red-colored Chinese fir genotypes were apparently not associated with their geographic origins. Further analysis by STRUCTURE showed that this Guangxi germplasm collection could be divided into three genetic groups comprising 76, 37, and 36 members, respectively; these were classified into mixed groups with no obvious population structure. These results were consistent with those of the cluster analysis. On the whole, our data provide a starting point for the management and conservation of the current Guangxi germplasm collection as well as for their efficient use in Chinese fir-breeding programs.

Independent and joint effects of the IL-6 and IL-10 gene polymorphisms in pulmonary tuberculosis among the Chinese Han population.

We investigated the association between interleukin (IL)-6 and IL-10 gene polymorphisms and the susceptibility to pulmonary tuberculosis (PTB). DNA samples were obtained from 191 Han Chinese patients with PTB and 191 healthy control subjects. IL-6 (-572, -174, -597) and IL-10 (-1082, -819) polymorphisms were analyzed using polymerase chain reaction-restriction fragment length polymorphism. The IL-6 -572 C/C and IL-10 -819 T/T genotypes were observed less frequently in the case group than in the control group, with crude odds ratios of 0.591 [95% confidence interval (CI) = 0.381-0.917] and 0.401 (95%CI = 0.257-0.627), respectively. A significant association remained after adjusting for environmental factors in multivariate logistic analysis. The homozygote genotypes of IL-6 -572 and IL-10 -819 had an adjusted OR of 0.565 (95%CI = 0.356-0.898) and 0.341 (95%CI = 0.210-0.553), respectively. These results indicate that the mutant heterozygote IL-10 -1082 A/ G+G/G genotype and the homozygote IL-10 -819 T/T genotype have a combined effect on PTB. These results suggest that the IL-6 -572 C/C and IL-10 -819 T/T genotype polymorphisms are protective factors against PTB.

Homology-based cloning and expression analysis of Rf genes encoding PPR-containing proteins in tobacco.

As a model plant, mechanisms of the cytoplasmic male sterility/restoration of fertility (CMS/Rf) system in tobacco are seldom studied. Using Rf gene sequences from other Solanaceae plants and the draft genome of Nicotiana benthamiana, degenerate primers were designed to amplify the cDNA pool of N. tomentosiformis. In total, six possible Rf sequences were identified, two of which contained base-deletion mutations. The other four were intact open reading frames, of which NtomPPR5 harbored a 3-pentatricopeptide repeat (PPR) motif deletion. Structure analysis revealed that they all encoded a PPR-containing protein with putative mitochondrial targeting signals at their N-terminus, and they all belong to the P subfamily. Phylogenetic analysis showed that all of the Rf-coding PPRs clustered together, and recent duplication events might have occurred in tobacco after the divergence of the species. Quantitative reverse transcription polymerase chain reaction analysis demonstrated that the NtomRfs were expressed in all tissues of N. tomentosiformis and (CMS) K326, although the expression levels varied with gene, organ, and developmental stage. Furthermore, the expression levels of Rf sequences in K326 were lower than those in CMS K326. The molecular basis of the CMS/Rf system in tobacco requires further investigation.

Evidence for inbreeding depression in the tree Robinia pseudoacacia L. (Fabaceae).

The magnitude of inbreeding depression within populations is important for the evolution and maintenance of mixed mating systems. However, data are sparse on the magnitude of inbreeding depression in Robinia pseudoacacia. In this study, we compared differences in the mature seed set per fruit, seed mass, germination success, and seedling growth between self- and cross-pollination treatments and estimated the inbreeding depression at 3 stages: seed maturation, seedling emergence, and seedling growth at 10 and 20 weeks. We found that progenies resulting from cross-pollination treatments showed significantly higher fitness than progenies resulting from self-pollination, causing high levels of inbreeding depression. Inbreeding depression was not uniformly manifested, however, over the 3 stages. Inbreeding depression was the greatest between fertilization and seed maturation stage (δ = 0.5419), and the seedling emergence (0.3654) stage was second. No significant differences in seedling growth were observed between selfed and crossed progenies. The cumulative inbreeding depression (δ) across all 3 stages averaged 0.7452. Inbreeding depression may promote outcrossing in R. pseudoacacia by acting as a post-pollination barrier to selfing. The large difference in the seed set between self- and cross-pollination that we detected indicated that inbreeding depression would probably be a reasonable explanation for the high abortion and low seed set in R. pseudoacacia.

Assessment of genetic diversity and variation of Robinia pseudoacacia seeds induced by short-term spaceflight based on two molecular marker systems and morphological traits.

The black locust (Robinia pseudoacacia) is a forest legume that is highly valued as a honey plant and for its wood. We explored the effect of short-term spaceflight on development of R. pseudoacacia seedlings derived from seeds that endured a 15-day flight; the genetic diversity and variation of plants sampled from space-mutagenized seeds were compared to plants from parallel ground-based control seeds using molecular markers and morphological traits. In the morphology analysis, the space-mutagenized group had apparent variation compared with the control group in morphological traits, including plant height, basal diameter, number of branches, branch stipular thorn length, branch stipular thorn middle width, leaflet vertex angle, and tippy leaf vertex angle. Simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker analyses showed a slightly higher levels of genetic diversity in the space-mutagenized group compared to the control group. In the SRAP analysis, the space-mutagenized group had 115 polymorphic bands vs 98 in the controls; 91.27% polymorphic loci vs 77.78% in the controls; 1.9127 ± 0.2834 alleles vs 1.7778 ± 0.4174 in the controls; Nei's genetic diversity (h) was 0.2930 ± 0.1631 vs 0.2688 ± 0.1862 in the controls, and the Shannon's information index (I) was 0.4452 ± 0.2177 vs 0.4031 ± 0.2596 in the controls. The number of alleles was significantly higher in the space-mutagenized group. In the SSR analysis, the space-mutagenized group also had more polymorphic bands (51 vs 46), a greater percentage of polymorphic loci (89.47% vs 80.70%); h was also higher (0.2534 ± 0.1533 vs 0.2240 ± 0.1743), as was I (0.3980 ± 0.2069 vs 0.3501 ± 0.2412). These results demonstrated that the range of genetic variation in the populations of R. pseudoacacia increased after spaceflight. It also suggested that the SSR and SRAP markers are effective markers for studying mutations and genetic diversity in R. pseudoacacia. The data provide valuable molecular evidence for the effects of the space environment on R. pseudoacacia and may contribute to future space-breeding programs involving forest trees.