Severe obesity prior to diagnosis limits survival in colorectal cancer patients evaluated at a large cancer centre

Background:

In contrast to the consistent evidence for obesity and colorectal cancer (CRC) risk, the impact of obesity in CRC patients is less clear. In a well-characterised cohort of CRC patients, we prospectively evaluated class I and class II obesity with survival outcomes.

Methods:

The CRC patients (N=634) were followed from the date of diagnosis until disease progression/first recurrence (progression-free survival (PFS)) or death (overall survival (OS)). Body mass index (BMI) was calculated from reported usual weight prior to diagnosis. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated in models adjusted for clinicopathologic, treatment, and lifestyle factors.

Results:

Over a median follow-up of 4 years, 208 (33%) patients died and 235 (37%) recurred or progressed. Class II obesity, as compared with either overweight or normal weight, was associated with an increased risk of death (HR and 95% CI: 1.55 (0.97–2.48) and 1.65 (1.02–2.68), respectively), but no clear association was observed with PFS. In analyses restricted to patients who presented as stages I–III, who reported stable weight, or who were aged <50 years, obesity was associated with a significant two- to five-fold increased risk of death.

Conclusions:

In CRC patients evaluated at a large cancer centre, severely obese patients experienced worse survival outcomes independent of many other factors.

Characterization and comparative profiling of the small RNA transcriptomes in two phases of flowering in Cymbidium ensifolium

Background

Cymbidium ensifolium is one of the most important ornamental flowers in China, with an elegant shape, beautiful appearance, and a fragrant aroma. Its unique flower shape has long attracted scientists. MicroRNAs (miRNAs) are critical regulators in plant development and physiology, including floral development. However, to date, few studies have examined miRNAs in C. ensifolium.

Results

In this study, we employed Solexa technology to sequence four small RNA libraries from two flowering phases to identify miRNAs related to floral development. We identified 48 mature conserved miRNA and 71 precursors. These conserved miRNA belonged to 20 families. We also identified 45 novel miRNA which includes 21 putative novel miRNAs*, and 28 hairpin forming precursors. Two trans-acting small interfering RNAs (ta-siRNAs) were identified, one of which was homologous to TAS3a1. TAS3a1 belongs to the TAS3 family, which has been previously reported to target auxin response factors (ARF) and be involved in plant growth and floral development. Moreover, we built a C. ensifolium transctriptome database to identify genes targeted by miRNA, which resulted in 790 transcriptomic target unigenes. The target unigenes were annotated with information from the non-redundant (Nr), gene ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto encyclopedia of genes and genomes (KEGG) database. The unigenes included MADS-box transcription factors targeted by miR156, miR172 and miR5179, and various hormone responding factors targeted by miR159. The MADS-box transcription factors are well known to determine the identity of flower organs and hormone responding factors involved in floral development. In expression analysis, three novel and four conserved miRNA were differentially expressed between two phases of flowering. The results were confirmed by RNA-seq and qRT-PCR. The differential expression of two miRNA, miR160 and miR396, targeted ARFs and growth regulating factor (GRF), respectively. However, most of these small RNA were clustered in the uncharacterized group, which suggests there may be many novel small non-coding RNAs yet to be discovered.

Conclusion

Our study provides a diverse set of miRNAs related to cymbidium floral development and serves as a useful resource for investigating miRNA-mediated regulatory mechanisms of floral development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1764-1) contains supplementary material, which is available to authorized users.

Adult patients with respiratory syncytial virus infection: impact of solid organ and hematopoietic stem cell transplantation on outcomes

BACKGROUND

Respiratory syncytial virus (RSV) is a common community-acquired pathogen responsible for a substantial disease burden in adults. We investigated the outcomes after RSV infection in hospitalized adults over a 3-year period.

METHODS

This single-center, retrospective study identified 174 patients hospitalized with RSV upper or lower respiratory tract infection (LRTI) between January 1, 2009 and June 30, 2012. Clinical data were extracted from medical records. The primary outcome analyzed was all-cause mortality, defined as death during the index hospital admission. Subjects were divided into 3 groups for comparison: hematopoietic stem cell transplant (HSCT) patients, solid organ transplant (SOT) patients, and non-transplant patients.

RESULTS

In our study, 41/174 (23.6%) were HSCT recipients and 28/174 (16.1%) were SOT recipients. Twelve of 174 (6.9%) died. Death occurred in 2/41 (4.9%) HSCT and 3/28 (10.7%) SOT recipients, compared to 7/106 (6.6%) non-transplant patients. When compared to the non-transplant cohort, HSCT and SOT were not found to be significant risk factors for mortality (P = 0.685 and 0.645, respectively). In multivariate logistic regression, age >60 was associated with mortality (P = 0.019), while lymphopenia on admission trended toward an association with death (P = 0.054). HSCT patients were less likely to be admitted to an intensive care unit (odds ratio [OR] 0.26, P = 0.04), but were significantly more likely to receive ribavirin therapy (OR 11.62, P < 0.0001).

CONCLUSION

Adults hospitalized with RSV LRTI are at significant risk of mortality, and this risk may be increased in patients age >60 or with lymphopenia on admission. This study did not identify any significant increased mortality or morbidity associated with RSV infection in immune suppressed transplant recipients vs. patients who had not received a transplant.

[Tight junction protein expression of gastric mucosa and its significance in children with Helicobacter pylori infection]

OBJECTIVE

To understand the junction protein expression of gastric mucosa including occlusal proteins (occludin), closed protein-4 (claudin-4), zonula occluden-1(ZO-1), epithelial cadherin (E-cadherin), and β ring protein (β-catenin) and the clinical significance in children with Helicobacter pylori (Hp) infection.

METHOD

Seventy patients in whom gastric endoscopy was performed because of nausea, vomiting, abdominal pain, bloating, acid reflux, melena, and other gastrointestinal symptoms were enrolled in this study from Dec. 2010 to Apr. 2013 in our hospital. Informed consent was signed by their parents, and the study was in accordance with the principles of medical ethics. Hp positivity was confirmed if both respiratory urea test (RUT) and Hp were positive by gastric mucosal pathology. Gastric mucosal samples from 70 patients were enrolled in this study, 23 of them were Hp negative, 47 of them were Hp positive (24 cases without peptic ulcer, 23 cases with peptic ulcer). The mRNA levels and protein expression of tight junction protein of gastric mucosa were measured by RT-PCR and Western blot respectively. The location and semi quantitative content of E-cadherin and β-catenin in gastric mucosa were detected by immunohistochemical staining method.

RESULT

The mRNA level of E-cadherin, β-catenin, ZO-1 in the Hp positive group regardless of peptic ulcer was significantly lower than that in the Hp negative group. Hp positive without peptic ulcer group were 0.0008, 0.0040, 0.0014, respectively; Hp positive with peptic ulcer group were 0.0010, 0.0090, 0.0013, respectively; Hp negative group were 0.0137, 0.0423, 0.0198, respectively (F values were 36.956, 39.893, 38.962, respectively, all P<0.05). The expression of claudin-4 mRNA in Hp positive group with peptic ulcer increased significantly, the difference among Hp positive group with peptic ulcer, Hp positive group without peptic ulcer and Hp negative group was statistically significant (0.1438 vs. 0.0926 vs. 0.0789) (F value was 11.964, P<0.05), while the difference of occludin mRNA levels among the three groups was not statistically significant.Immunohistochemistry results showed that the score of E-cadherin, β-catenin positive cell in the Hp positive patients were also significantly lower than that in the Hp negative group (t values were 3.981 and 2.340, all P<0.05, respectively). Western blot results showed that the protein levels of β-catenin in Hp positive group with peptic ulcer were significantly lower than that in Hp negative group, while the protein levels of E-cadherin in Hp positive patients regardless of peptic ulcer were decreased significantly in Hp negative group.

CONCLUSION

Our results revealed that the tight junction protein E-cadherin, β-catenin, ZO-1 expression of gastric mucosa were decreased in children with Hp infection, while claudin-4 expression was increased in Hp positive patients with peptic ulcer, suggesting that damage to gastric epithelial barrier function may be the main pathogenesis of Hp associated gastric diseases in children.

Endoplasmic reticulum stress and oxidative stress are involved in ZnO nanoparticle-induced hepatotoxicity

Zinc oxide nanoparticles (Nano-ZnO) are widely used in sunscreens, clothes, medicine and electronic devices. However, the potential risks of human exposure and the potential for adverse health impacts are not well understood. Previous studies have demonstrated that exposure to Nano-ZnO caused liver damage and hepatocyte apoptosis through oxidative stress, but the molecular mechanisms that are involved in Nano-ZnO-induced hepatotoxicity are still unclear. Endoplasmic reticulum (ER) is sensitive to oxidative stress, and also plays a crucial role in oxidative stress-induced damage. Previous studies showed that ER stress was involved in many chemical-induced liver injuries. We hypothesized that exposure to Nano-ZnO caused oxidative stress and ER stress that were involved in Nano-ZnO-induced liver injury. To test our hypothesis, mice were gavaged with 200 mg/kg or 400 mg/kg of Nano-ZnO once a day for a period of 90 days, and blood and liver tissues were obtained for study. Our results showed that exposure to Nano-ZnO caused liver injury that was reflected by focal hepatocellular necrosis, congestive dilation of central veins, and significantly increased alanine transaminase (ALT) and aspartate transaminase (AST) levels. Exposure to Nano-ZnO also caused depletion of glutathione (GSH) in the liver tissues. In addition, our electron microscope results showed that ER swelling and ribosomal degranulation were observed in the liver tissues from mice treated with Nano-ZnO. The mRNA expression levels of ER stress-associated genes (grp78, grp94, pdi-3, xbp-1) were also up-regulated in Nano-ZnO-treated mice. Nano-ZnO caused increased phosphorylation of RNA-dependent protein kinase-like ER kinase (PERK) and eukaryotic initiation factor 2α (eIF2α). Finally, we found that exposure to Nano-ZnO caused increased ER stress-associated apoptotic protein levels, such as caspase-3, caspase-9, caspase-12, phosphorylation of JNK, and CHOP/GADD153, and up-regulation of pro-apoptotic genes (chop and bax). These results suggest that oxidative stress and ER stress-induced apoptosis are involved in Nano-ZnO-induced hepatotoxicity in mice.

Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums

Background

Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assisting parental selection and breeding strategy design, however, in plants such as cymbidiums limited genomic resources exist. In order to obtain efficient markers, we deep sequenced the C. ensifolium transcriptome to identify simple sequence repeats derived from gene regions (genic-SSR).

Result

The 7,936 genic-SSR markers were identified. A total of 80 genic-SSRs were selected, and primers were designed according to their flanking sequences. Of the 80 genic-SSR primer sets, 62 were amplified in C. ensifolium successfully, and 55 showed polymorphism when cross-tested among 9 Cymbidium species comprising 59 accessions. Unigenes containing the 62 genic-SSRs were searched against Non-redundant (Nr), Gene Ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The search resulted in 53 matching Nr sequences, of which 39 had GO terms, 18 were assigned to KOGs, and 15 were annotated with KEGG. Genetic diversity and population structure were analyzed based on 55 polymorphic genic-SSR data among 59 accessions. The genetic distance averaged 0.3911, ranging from 0.016 to 0.618. The polymorphic index content (PIC) of 55 polymorphic markers averaged 0.407, ranging from 0.033 to 0.863. A model-based clustering analysis revealed that five genetic groups existed in the collection. Accessions from the same species were typically grouped together; however, C. goeringii accessions did not always form a separate cluster, suggesting that C. goeringii accessions were polyphyletic.

Conclusion

The genic-SSR identified in this study constitute a set of markers that can be applied across multiple Cymbidium species and used for the evaluation of genetic relationships as well as qualitative and quantitative trait mapping studies. Genic-SSR’s coupled with the functional annotations provided by the unigenes will aid in mapping candidate genes of specific function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0124-5) contains supplementary material, which is available to authorized users.

Enhanced formation and impaired degradation of neutrophil extracellular traps in dermatomyositis and polymyositis: a potential contributor to interstitial lung disease complications

Dermatomyositis (DM) and polymyosits (PM) are systemic autoimmune diseases whose pathogeneses remain unclear. Neutrophil extracellular traps (NETs) are reputed to play an important role in the pathogenesis of autoimmune diseases. This study tests the hypothesis that NETs may be pathogenic in DM/PM. Plasma samples from 97 DM/PM patients (72 DM, 25 PM) and 54 healthy controls were tested for the capacities to induce and degrade NETs. Plasma DNase I activity was tested to further explore possible reasons for the incomplete degradation of NETs. Results from 35 DM patients and seven PM patients with interstitial lung disease (ILD) were compared with results from DM/PM patients without ILD. Compared with control subjects, DM/PM patients exhibited a significantly enhanced capacity for inducing NETs, which was supported by elevated levels of plasma LL-37 and circulating cell-free DNA (cfDNA) in DM/PM. NETs degradation and DNase I activity were also decreased significantly in DM/PM patients and were correlated positively. Moreover, DM/PM patients with ILD exhibited the lowest NETs degradation in vitro due to the decrease in DNase I activity. DNase I activity in patients with anti-Jo-1 antibodies was significantly lower than in patients without. Glucocorticoid therapy seems to improve DNase I activity. Our findings demonstrate that excessively formed NETs cannot be degraded completely because of decreased DNase I activity in DM/PM patients, especially in patients with ILD, suggesting that abnormal regulation of NETs may be involved in the pathogenesis of DM/PM and could be one of the factors that initiate and aggravate ILD.

Effects of grain development on formation of resistant starch in rice

Three rice mutants with different contents of resistant starch (RS) were selected to investigate the effects of grain filling process on the formation of resistant starch. During grain development, the content of RS was increased with grain maturation and showed negative correlations with the grain weight and the starch molecular weight (Mn, Mw) and a positive correlation with the distribution of molecular mass (polydispersity, Pd). The morphologies of starch granules in high-RS rice were almost uniform in single starch granules and exhibited different proliferation modes from common rice. The lower activities of ADP-glucose pyrophosphorylase and starch branching enzyme and the higher activity of starch synthase and starch de-branching enzyme observed in high-RS rice might be responsible for the formation of small irregular starch granules with large spaces between them. In addition, the lower molecular weight and the broad distribution of molecular weights lead to differences in the physiochemical properties of starch.

Atopic conditions and brain tumor risk in children and adolescents--an international case-control study (CEFALO)

BACKGROUND

A number of epidemiological studies indicate an inverse association between atopy and brain tumors in adults, particularly gliomas. We investigated the association between atopic disorders and intracranial brain tumors in children and adolescents, using international collaborative CEFALO data.

PATIENTS AND METHODS

CEFALO is a population-based case-control study conducted in Denmark, Norway, Sweden, and Switzerland, including all children and adolescents in the age range 7-19 years diagnosed with a primary brain tumor between 2004 and 2008. Two controls per case were randomly selected from population registers matched on age, sex, and geographic region. Information about atopic conditions and potential confounders was collected through personal interviews.

RESULTS

In total, 352 cases (83%) and 646 controls (71%) participated in the study. For all brain tumors combined, there was no association between ever having had an atopic disorder and brain tumor risk [odds ratio 1.03; 95% confidence interval (CI) 0.70-1.34]. The OR was 0.76 (95% CI 0.53-1.11) for a current atopic condition (in the year before diagnosis) and 1.22 (95% CI 0.86-1.74) for an atopic condition in the past. Similar results were observed for glioma.

CONCLUSIONS

There was no association between atopic conditions and risk of all brain tumors combined or of glioma in particular. Stratification on current or past atopic conditions suggested the possibility of reverse causality, but may also the result of random variation because of small numbers in subgroups. In addition, an ongoing tumor treatment may affect the manifestation of atopic conditions, which could possibly affect recall when reporting about a history of atopic diseases. Only a few studies on atopic conditions and pediatric brain tumors are currently available, and the evidence is conflicting.

Aggregate human health risk assessment from dust of daily life in the urban environment of Beijing

Because of the high emissions of polycyclic aromatic hydrocarbons (PAHs) into the environment by the increasing number of vehicles in Beijing and the absorption of these PAHs onto particulates, the performance of a preliminary health risk assessment of the aggregate exposure to PAHs of urban citizens in daily life is very important. Urban dust can be used to examine the aggregation of atmospheric particulates from local pollution sources over a long time period and the direct exposure of the urban human population. The environment's correlative with clothing, dining, residing, and traveling in urban daily life was assessed using exposure-receptor-oriented analysis. The multipathway exposure model was used to simulate the lifetime exposure of a female citizen to PAHs in dust. All of the PAH concentrations in dust for each behavior and its correlative environment in Beijing were acceptable because all of the carcinogenic risks of PAHs in the dust were approximately 1.0 × 10(-6). The dominant induced carcinogenic risks in the dust were Benzo(a)pyrene and Dibenzo(a,h)anthracene. The main carcinogenic risk routes for humans were dermal contact and oral intake, which contributed on average 99.78% of the risk. Indoor risk is especially important, as the decoration and height within the building were important impact factors for carcinogenic risk induced by indoor PAHs. For people living in an urban area, a healthy lifestyle includes less decoration per room, living on a low floor, wearing a respirator, and reducing exposed skin area when traveling.

Sequence variation and haplotypes of lipoxygenase gene LOX-1 in the Australian barley varieties

Background

Lipoxygenases are a family of enzymes which catalyse the hydroperoxidation of polyunsaturated fatty acids with a cis, cis-1,4-pentadiene to form conjugated hydroperoxydienes. Lipoxygenase-1 (LOX-1) in barley worsens the flavour and foam stability of beer. It has become a major selection criteria for malting quality in the last few years.

Results

Lipoxygenase activity was investigated in 41 Australian barley cultivars and advanced breeding lines released since the 1950s; the cultivars differed markedly, ranging from 22.3 to 46.5 U/g. The structural gene and its promoter of lipoxygenase-1 were sequenced from the barley varieties representing different levels of LOX. Based on the analysis of nucleotide and deduced amino acid sequences, two major haplotypes were identified. Barley varieties with lower LOX were classified into three categories based on their pedigrees and sequence variations in the structural gene: (1) barley varieties derived from Canadian varieties with the pre-harvest sprouting susceptible allele, (2) Skiff and Hindmarsh with unique haplotype in the structural gene, and (3) Gairdner and Onslow with an unknown mechanism.

Conclusion

Lipoxygenase activity has been reduced in the malting barley cultivars in the last 60 years although it is only recognized as a malting quality trait recently. There are clear haplotypes of the lipoxygenase structual gene. The polymorphisms detected in the structural gene can be used to design molecular markers for selection of low LOX haplotype. Other mechanisms also existed for controlling lipoxygenase activity. The results suggest that it is possible to develop barley varieties with lower LOX by combination of low LOX-1 haplotype and other trans-regulation factors.

Quantification of amylose, amylopectin, and β-glucan in search for genes controlling the three major quality traits in barley by genome-wide association studies

Genome-wide association studies (GWAS) for amylose, amylopectin and β-glucan concentration in a collection of 254 European spring barley varieties allowed to identify 20, 17, and 21 single nucleotide polymorphic (SNP) markers, respectively, associated with these important grain quality traits. Negative correlations between the content of amylose and β-glucan (R = -0.62, P < 0.01) and amylopectin and β-glucan (R = -0.487, P < 0.01) were found in this large collection of spring barley varieties. Besides HvCslF6, amo1 and AGPL2, sex6, and waxy were identified among the major genes responsible for β-glucan, amylose and amylopectin content, respectively. Several minor genes like HvGSL4, HvGSL3, and HvCesA6, PWD were also detected by GWAS for the first time. Furthermore, the gene encoding β-fructofuranosidase, located on the short arm of chromosome 7H at 1.49 cM, and SRF6, encoding "leucine-rich repeat receptor kinase protein" on chromosome 2 H, are proposed to be new candidate genes for amylopectin formation in barley endosperm. Several of the associated SNPs on chromosome 1, 5, 6, and 7H mapped to overlapping regions containing QTLs and genes controlling the three grain constituents. In particular chromosomes 5 and 7H carry many QTLs controlling barley grain quality. Amylose, amylopectin and β-glucan were interacted among each other through a metabolic network connected by UDP showing pleiotropic effects. Taken together, these results showed that cereal quality traits related each other and regulated through an interaction network, the identified major genes and genetic regions for amylose, amylopectin and β-glucan is a helpful for further research on carbohydrates and barley breeding.

Protein kinase B phosphorylation correlates with vascular endothelial growth factor A and microvessel density in gastric adenocarcinoma

OBJECTIVE

The signalling molecule protein kinase B (Akt) modulates many cellular processes. Phosphatidylinositol 3-kinase (PI3K)/Akt signalling pathways play important roles in tumour angiogenesis. The aim of this study was to determine the role of phosphorylated Akt (pAkt) in angiogenesis and its correlation with vascular endothelial growth factor (VEGF)-A in gastric adenocarcinoma.

METHODS

Tumour tissue and matched healthy gastric mucosa were obtained from patients undergoing surgical resection of gastric adenocarcinoma. Akt and pAkt were detected via Western blotting. VEGF-A, pAkt and CD34 were examined by immunohistochemistry.

RESULTS

Akt and pAkt protein levels were significantly higher in gastric cancer tissue than in normal tissue (n = 48 patients). Positive VEGF-A immunostaining was significantly associated with pAkt immunostaining. Microvessel density was correlated with both VEGF-A and pAkt positivity.

CONCLUSIONS

Phosphorylated Akt and VEGF-A are involved in angiogenesis of gastric adenocarcinoma, and Akt activation may contribute to angiogenesis via VEGF-A upregulation. The PI3K/Akt/VEGF signalling pathway may be involved in gastric adeno carcinoma.