hABCF3, a TPD52L2 interacting partner, enhances the proliferation of human liver cancer cell lines in vitro

In the present study, we characterized an evolutionarily conserved non-transmembrane ATP-binding cassette protein: hABCF3. Subcellular immunofluorescence staining demonstrated that hABCF3 localizes preferentially in cytoplasm, unlike its paralog protein hABCF1, which localizes in both cytoplasm and nucleus. Quantitative realtime PCR analysis revealed that hABCF3 is expressed in all tissues examined, with high expression level in heart, liver, and pancreas. Interestingly, ectopic hABCF3 promoted proliferation of human liver cancer cell lines. Moreover, knock down of hABCF3 protein expression by siRNA inhibited cell proliferation. In addition, we identified TPD52L2 (Tumor Protein D52-like 2) as a hABCF3 interacting protein via yeast two-hybrid. This interaction was further confirmed by in vivo co-immunoprecipitation and co-localization assays. Furthermore, we identified the interactional region of hABCF3 to be the first 200 amino acids uncharacterized region. Notably, the truncated version of hABCF3, which lacks the TPD52L2 binding region, remarkably impaired hABCF3-mediated cell proliferation. Taken together, these findings suggest that hABCF3 positively regulates cell proliferation, at least partially through the interaction with a tumor protein D52 protein family member: TPD52L2.     

Reproductive biology of Oxygymnocypris stewartii in the Yarlung Zangbo River in Tibet, China

We determined the gonadal histology, reproductive characteristics and implications for management of Oxygymnocypris stewartii from individuals collected in the Yarlung Zangbo River. Based on the analyses of gonad development and the size distribution of oocytes, O. stewartii spawns just once each year. Peak spawning occurred between late March and early April, when water temperature exceeded 5°C. The standard lengths and the ages at 50 % maturity for males and females were 273 mm and 357 mm, and 5.1 year and 7.3 years, respectively. The mean fecundity of 34211 and mean relative fecundity of 25.4 eggs per gram of fish body weight suggest that O. stewartii might be especially vulnerable to exploitation.     

66 Architectural role of HMO1 in bending,bridging, and compacting DNA

HMO1 proteins are abundant Saccharomyces cerevisiae (yeast) High Mobility Group Box (HMGB) protein (Kamau, Bauerla & Grove, 2004). HMGB proteins are nuclear proteins which are known to be architectural proteins (Travers, 2003). HMO1 possesses two HMGB box domains. It has been reported that double box HMGB proteins induce strong bends upon binding to DNA. It is also believed that they play an essential role in reorganizing chromatin and, therefore, are likely to be involved in gene activation. To characterize DNA binding we combine single molecule stretching experiments and AFM imaging of HMO1 proteins bound to DNA. By stretching DNA bound to HMO1, we determine the dissociation constant, measure protein induced average DNA bending angles, and determine the rate at which torsional constraint of the DNA is released by the protein. To further investigate the local nature of the binding, AFM images of HMO1-DNA complexes are imaged, and we probe the behavior of these complexes as a function of protein concentration. The results show that at lower concentrations, HMO1 preferentially binds to the ends of the double helix and links to the separate DNA strands. At higher concentrations HMO1 induces formation of a complex network that reorganizes DNA. Although HMG nuclear proteins are under intense investigation, little is known about HMO1. Our studies suggest that HMO1 proteins may facilitate interactions between multiple DNA molecules.     

ZmGA3ox2, a candidate gene for a major QTL,qPH3.1, for plant height in maize

Maize plant height is closely associated with biomass, lodging resistance and grain yield. Determining the genetic basis of plant height by characterizing and cloning plant height genes will guide the genetic improvement of crops. In this study, a quantitative trait locus (QTL) for plant height, qPH3.1, was identified on chromosome 3 using populations derived from a cross between Zong3 and its chromosome segment substitution line, SL15. The plant height of the two lines was obviously different, and application of exogenous gibberellin A₃ removed this difference. QTL mapping placed qPH3.1 within a 4.0 cM interval, explaining 32.3% of the phenotypic variance. Furthermore, eight homozygous segmental isolines (SILs) developed from two larger F₂ populations further narrowed down qPH3.1 to within a 12.6 kb interval. ZmGA3ox2, an ortholog of OsGA3ox2, which encodes a GA3 β‐hydroxylase, was positionally cloned. Association mapping identified two polymorphisms in ZmGA3ox2 that were significantly associated with plant height across two experiments. Quantitative RT‐PCR showed that SL15 had higher ZmGA3ox2 expression relative to Zong3. The resultant higher GA₁ accumulation led to longer internodes in SL15 because of increased cell lengths. Moreover, a large deletion in the coding region of ZmGA3ox2 is responsible for the dwarf mutant d1‐6016. The successfully isolated qPH3.1 enriches our knowledge on the genetic basis of plant height in maize, and provides an opportunity for improvement of plant architecture in maize breeding.     

Diversity of the intestinal microbiota in different patterns of feeding infants by Illumina high-throughput sequencing

The gastrointestinal microbiota plays a crucial role in the health and disease of the host through its impact on nutrition. Gut microbial composition is related to different diets, but an association of microbiota with different diets in infant has not yet been shown. In this work, we compared the fecal microbiota of breast-fed (BF) and formula-fed infants (FF). By using Illumina high-throughput sequencing and biochemical analyses, we found differences in gut microbiota between the two groups. BF infants showed a significant enrichment of Actinobacteria and Firmicutes and depletion of Proteobacteria (P < 0.05), the abundance of Bacteroidetes in the two groups was very low (P > 0.05). Enterobacteriaceae (Proteobacteria) were the dominant bacteria in FF infant fecal microbiota, and Veillonellaceae (Firmicutes) and Enterobacteriaceae (Proteobacteria) were the dominant bacteria in the BF infant fecal microbiota. The number of genera (percentage of sequences >0.1 %) in BF and FF infants was 17 and 15 respectively, and Streptococcus was the dominant bacterial genus in both groups.     

Patulin induces pro-survival functions via autophagy inhibition and p62 accumulation

Patulin (PAT) is one of the most common mycotoxins found in moldy fruits. Skin contact is one of the most likely exposure routes of PAT. Investigation of dermal toxicity of PAT is clearly needed and has been highlighted by WHO. In the present study, using human keratinocyte HaCaT cells as a model, we found that treatment with PAT caused an increased autophagosome accumulation. Measurements of autophagic flux demonstrated that the accumulation of autophagosomes by PAT was not directly due to enhanced autophagosome formation but due to inhibition of autophagosome degradation. Reductions in the activities of the lysosomal enzymes cathepsin B and cathepsin D by PAT might contribute to this inhibitory effect. Consistent with this, inhibition of autophagosome degradation by PAT resulted in accumulation of p62 that functioned as a pro-survival signal. The pro-survival function of p62 was found to be attributed to reactive oxygen species-mediated cytoprotective endoplasmic reticulum (ER) stress response. ER stress exerted cytoprotective effect via extracellular signal-regulated kinase1/2-dependent B-cell CLL/lymphoma 2-associated agonist of cell death inhibitory phosphorylation. Given the critical role of autophagy and its substrate p62 in carcinogenesis, our findings may have important implications in PAT-induced skin carcinogenesis.     

The Influence of Hepatitis B Viral Load and Pre-S Deletion Mutations on Post-Operative Recurrence of Hepatocellular Carcinoma and the Tertiary Preventive Effects by Anti-Viral Therapy

Background

Whether or not hepatitis B virus (HBV) genotypes, mutations, and viral loads determine outcomes for patients with HBV-induced hepatocellular carcinoma (HCC) remains controversial.

Aims

To study the influence of HBV viral factors on prognoses for patients with HBV-induced HCC after resection surgery and investigate if antiviral therapy could counteract the adverse effects of viral factors.

Methods

A total of 333 HBV-related HCC patients who underwent tumor resection were enrolled retrospectively. Serum HBV DNA levels, mutations, anti-viral therapy, and other clinical variables were analyzed for their association with post-operative recurrence.

Results

After a median follow-up of 45.9 months, 208 patients had HCC recurrence after resection. The 5-year overall survival and recurrence-free survival rates were 55.4% and 35.3%, respectively. Multivariate analysis showed indocyanine green retention rate at 15 minutes >10%, gamma-glutamyltransferase (GGT) level >60 U/L, macroscopic and microscopic venous invasion, and the absence of anti-viral therapy were significant risk factors for recurrence. Anti-viral therapy could decrease recurrence in patients with early stage HCC, but the effect was less apparent in those with the Barcelona-Clinic Liver Cancer stage C HCC. For patients without antiviral therapy after resection, serum HBV DNA levels >10⁶ copies/mL, GGT >60 U/L, and macroscopic and microscopic venous invasion were significant risk factors predicting recurrence. Among the 216 patients without anti-viral therapy but with complete HBV surface gene mapping data, 73 were with pre-S deletion mutants. Among patients with higher serum HBV DNA levels, those with pre-S deletion had significantly higher rates of recurrence. Moreover, multivariate analysis showed multi-nodularity, macroscopic venous invasion, cirrhosis, advanced tumor cell differentiation, and pre-S deletion were significant risk factors predictive of recurrence.

Conclusions

Ongoing HBV viral replication and pre-S deletion are crucial for determining post-operative tumor recurrence. Anti-viral therapy can help reduce recurrence and improve prognosis, especially for those with early stage HCC.     

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.