Differential gene expression profiling of gastric intraepithelial neoplasia and early-stage adenocarcinoma

AIM: To investigate the differentiated whole genome expression profiling of gastric high- and low-grade intraepithelial neoplasia and early-stage adenocarcinoma.

Genes encoding heat shock proteins in the endoparasitoid wasp,Cotesia chilonis,and their expression in response to temperatures

Five genes encoding heat shock proteins（HSPs）, Cchsp40, Cchsp60, Cchsp70, Cchsc70 and Cchsp90, were cloned and sequenced from Cotesia chilonis using RT-PCR and RACE. The c DNA sequences of Cchsp40, Cchsp60, Cchsp70, Cchsc70 and Cchsp90 were 1 265, 2 551, 2 094, 2 297 and 2 635 bp in length, respectively, with a molecular weight（MW） of 39.1, 60.6, 71.45, 70.19 and 82.92 k Da, respectively. The predicted amino acid sequences of these proteins showed high similarities with published HSPs of other insects in Hymenoptera. Analysis of genomic DNAs indicated that Cchsp40, Cchsp60, Cchsp70 and Cchsp90 lacked introns, but Cchsc70 contained an intron. The results also suggested that CcH SP40 in C. chilonis was the Type II HSP40, Cc HSP60 was a member of the mitochondrial HSP60 family, and Cc HSP90 was a part of cytoplasmic HSP90 A family. Expression patterns varied in the five Cchsps in response to temperature. Expression of Cchsp40 and Cchsp60 was induced significantly by cold but not heat stress. Cchsp70 and Cchsc70 showed similar response to the thermal stress and could be induced by both cold and heat, but their expression levels were consistently lower than that of Cchsp40 and Cchsp60. Cchsp90 could be induced by heat stress and mild cold, but not cold stress. In addition, the results demonstrated Cchsc70 might be constitutive and inducible protein that was expressed during normal cell functioning and also up-regulated in response to stressful stimuli while Cchsp70 was solely inducible protein induced by temperature changes. Overall, results generated from this study could significantly advance the understanding of Cchsps in response to temperature and provide important biological information for C. chilonis insects that reared under different temperatures.

Association of TCR-signaling pathway with the development of lacrimal gland benign lymphoepithelial lesions

·AIM: To identify the association of the T cell receptor(TCR) signaling with the development of benign lymphoepithelial lesions(BLEL) of the lacrimal gland.· METHODS: We collected affected lacrimal gland tissues from 9 patients who underwent dacryoadenectomy in the Capital Medical University Beijing Tongren Hospital Eye Center between August2010 and March 2013 and were confirmed to have lacrimal gland BLEL by histopathological analysis. Tumor tissues from 9 patients with orbital cavernous hemangioma were also collected and used as control.Whole genome gene expression microarray was used to compare gene expression profiles of affected lacrimal gland tissues from patients with lacrimal gland BLEL to those from of orbital cavernous hemangiomas.Differential expression of TCR pathway genes between these tissues was confirmed by polymerase chain reaction(PCR) and immunohistochemistry.·RESULTS: Microarray analysis showed that in lacrimal glands with BLEL, 32 signaling pathways were enriched in the upregulated genes, while 25 signaling pathways were enriched in the downregulated genes. In-depth analysis of the microarray data showed that the expression of 27 genes of the TCR signaling pathway increased significantly. To verify the differential expression of three of these genes, CD3, CD4, and interleukin(IL)-10, reverse transcription-PCR(RT-PCR)and immunohistochemistry assays were performed. RT-PCR analysis showed that CD3 and CD4 were expressed in the lacrimal glands with BLEL, but IL-10 was not expressed. Immunohistochemistry confirmed that CD3 and CD4 proteins were also present, but IL-10 protein was not. CD3, CD4, or IL-10 expression was not found in the orbital cavernous hemangiomas with either RT-PCR or immunohistochemistry.· CONCLUSION: TCR signaling pathway might be involved in the pathogenesis of lacrimal gland BLEL.

Genome wide expression analysis of the effect of Socheongryong Tang in asthma model of mice

OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal instillation of ovalbumin in mouse.After administration of SCRT on asthma-induced mouse,the expression of genes in lung tissue was measured using whole genome microarray.The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed.RESULTS:Treatment of SCRT restored expression level of many up- or down-regulated genes in asthma model,and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites.CONCLUSION:In this study,we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.

Structural and Expressional Variation Analyses of Mitochondrial Genomes Reveal Candidate Transcripts for the S^V Cytoplasmic Male Sterility in Wheat(Triticum aestivum L.)

Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.

The allopolyploid B. juncea genome uncovered differential homoeolog gene expression influencing selection

With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at Zhejiang University,assembled an allopolyploid B.juncea genome and uncovered differential homoeolog gene expression influencing selection,which was published in Nature

Safety profile of two-dimensional Pd nanosheets for photothermal therapy and photoacoustic imaging

Two-dimensional （2D） nanosheets have emerged as an important class of nanomaterial with great potential in the field of biomedicines, particularly in cancer theranostics. However, owing to the lack of effective methods that synthesize uniform 2D nanomaterials with controlled size, systematic evaluation of size-dependent bio-behaviors of 2D nanomaterials is rarely reported. To the best of our knowledge, we are the first to report a systematic evaluation of the influence of size of 2D nanomaterials on their bio-behaviors. 2D Pd nanosheets with diameters ranging from 5 to 80 nm were synthesized and tested in cell and animal models to assess their size-dependent bioapplication, biodistribution, elimination, toxicity, and genomic gene expression profiles. Our results showed size significantly influences the biological behaviors of Pd nanosheets, including their photothermal and photoacoustic effects, pharmacokinetics, and toxicity. Compared to larger-sized Pd nanosheets, smaller-sized Pd nanosheets exhibited more advanced photoacoustic imaging and photothermal effects upon ultralow laser irradiation. Moreover, in vivo results indicated that 5-nm Pd nanosheets escape from the reticuloendothelial system with a longer blood half-life and can be cleared by renal excretion, while Pd nanosheets with larger sizes mainly accumulate in the liver and spleen. The 30-nm Pd nanosheets exhibited the highest tumor accumulation. Although Pd nanosheets did not cause any appreciable toxicity at the cellular level, we observed slight lipid accumulation in the liver and inflammation in the spleen. Genomic gene expression analysis showed that 80-nm Pd nanosheets interacted with more cellular components and affected more biological processes in the liver, as compared to 5-nm Pd nanosheets. We believe this work will provide valuable information and insights into the clinical application of 2D Pd nanosheets as nanomedicines.

CRISPR/Cas9 and TALE： beyond cut and paste

Nuclease-based genome editing has proven to be a powerful and promising tool for disease modeling and gene therapy. Recent advances in CRISPR/Cas and TALE indicate that they could also be used as a targeted regulator of gene expression, as well as being utilized for illuminating specific chromosomal structures or genomic regions.

Genomic structure and evolution of beta-defensin genes in the golden pheasant and hwamei

Defensins play a vital role in the early stage of infection before adaptive immune responses are generated. Thus far, only limited detailed genomic data for avian defensin genes have been described. Here, using bacterial ar- tificial chromosome libraries, we found that a 95 kb and 177 kb sequences in the golden pheasant （Chrysolophus pictus, Galliformes） and hwamei （Garrulax canorus, Passeriformes） corresponds to 16 and 30 defensin genes, respectively. Fluorescence in situ hybridization assigned defensin gene clusters in the golden pheasant and hwamei to chromosomes 2q and 3q, respectively. In combination with the previous chicken （Gallus gallus, Galliformes） and zebra finch （Taeniopygia guttata, Passeriformes） defensin clusters, the comparative genomic analysis revealed that lineage- specific duplications and deletions have given rise to clearly different genomic structures. On the basis of genomic char- acteristics, we further found that transposable elements act as agents of evolution, causing direct and indirect copy number variations in defensin genes via duplications. Tissue ex- pression analysis showed that the Passeriformes-specific duplicated AvBD1 and AvBD3 genes are mainly expressed in the upper and lower respiratory tract, tongue, and spleen. Our analyses indicate that the duplication-and-deletion of defensin genes conformed to the birth-and-death evolutionary process and that transposable elements induced theduplication of defensin genes. Moreover, the respiratory system-specific expression pattern of Passeriformes-specific expanded AvBD1 and AvBD3 genes suggests their important role in maintaining the singing trait of songbirds. The understanding of the genomic structure, expression, and evolution of defensin genes can provide a crucial immunological foundation to study and prevent avian diseases.