Application and prospect of cutting-edge information technology in biomedical big data.

In recent years, with the development of various high-throughput omics based biological technologies (BT), biomedical research began to enter the era of big data. In the face of high-dimensional, multi-domain and multi-modal biomedical big data, scientific research requires a new paradigm of data intensive scientific research. The vigorous development of cutting-edge information technologies (IT) such as cloud computing, blockchain and artificial intelligence provides technical means for the practice of this new research paradigm. Here,we describe the application of such cutting-edge information technologies in biomedical big data, and propose a forward-looking prospect for the construction of a new paradigm supporting environment for data intensive scientific research. We expect to establish a new research scheme and new scientific research paradigm integrating BT & IT technology, which can finally promote the great leap forward development of biomedical research.

Comparative transcriptome analysis of developmental stages of the Limonium bicolor leaf generates insights into salt gland differentiation.

With the expansion of saline land worldwide, it is essential to establish a model halophyte to study the salt-tolerance mechanism. The salt glands in the epidermis of Limonium bicolor (a recretohalophyte) play a pivotal role in salt tolerance by secreting excess salts from tissues. Despite the importance of salt secretion, nothing is known about the molecular mechanisms of salt gland development. In this study, we applied RNA sequencing to profile early leaf development using five distinct developmental stages, which were quantified by successive collections of the first true leaves of L. bicolor with precise spatial and temporal resolution. Specific gene expression patterns were identified for each developmental stage. In particular, we found that genes controlling salt gland differentiation in L. bicolor may evolve in a trichome formation, which was also confirmed by mutants with increased salt gland densities. Genes involved in the special ultrastructure of salt glands were also elucidated. Twenty-six genes were proposed to participate in salt gland differentiation. Our dataset sheds light on the molecular processes underpinning salt gland development and thus represents a first step towards the bioengineering of active salt-secretion capacity in crops.

Rig-I regulates NF-κB activity through binding to Nf-κb1 3'-UTR mRNA.

Retinoic acid inducible gene I (RIG-I) senses viral RNAs and triggers innate antiviral responses through induction of type I IFNs and inflammatory cytokines. However, whether RIG-I interacts with host cellular RNA remains undetermined. Here we report that Rig-I interacts with multiple cellular mRNAs, especially Nf-κb1. Rig-I is required for NF-κB activity via regulating Nf-κb1 expression at posttranscriptional levels. It interacts with the multiple binding sites within 3'-UTR of Nf-κb1 mRNA. Further analyses reveal that three distinct tandem motifs enriched in the 3'-UTR fragments can be recognized by Rig-I. The 3'-UTR binding with Rig-I plays a critical role in normal translation of Nf-κb1 by recruiting the ribosomal proteins [ribosomal protein L13 (Rpl13) and Rpl8] and rRNAs (18S and 28S). Down-regulation of Rig-I or Rpl13 significantly reduces Nf-κb1 and 3'-UTR-mediated luciferase expression levels. These findings indicate that Rig-I functions as a positive regulator for NF-κB signaling and is involved in multiple biological processes in addition to host antivirus immunity.

Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression.

Reversible phosphorylation of proteins is an important process modulating cellular activities from upstream, which mainly involves sequential phosphorylation of signaling molecules, to downstream where phosphorylation of transcription factors regulates gene expression. In this study, we combined quantitative labeling with multidimensional liquid chromatography-mass spectrometry to monitor the proteome and phosphoproteome changes in the initial period of adipocyte differentiation. The phosphorylation level of a specific protein may be regulated by a kinase or phosphatase without involvement of gene expression or as a phenomenon that accompanies the alteration of its gene expression. Concurrent quantification of phosphopeptides and non-phosphorylated peptides makes it possible to differentiate cellular phosphorylation changes at these two levels. Furthermore, on the system level, certain proteins were predicted as the targeted gene products regulated by identified transcription factors. Among them, several proteins showed significant expression changes along with the phosphorylation alteration of their transcription factors. This is to date the first work to concurrently quantify proteome and phosphoproteome changes during the initial period of adipocyte differentiation, providing an approach to reveal the system-wide association of protein phosphorylation and gene expression.

Association between alcohol, smoking and HLA-DQA1*0201 genotype in psoriasis.

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR-SSP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P<0.005). The HLA-DQA1*0201 allele was present at significantly higher frequency in the patients with psoriasis (OR=4.25, P<1.0 x 10(-6)). Association was found between smoking, alcohol and HLA-DQA1*0201 in male patients with psoriasis (OR>6.91, P<1.0 x 10(-4)).

[Effect of anti-human VEGF monoclonal antibody on VEGF level in serum of nude mice transplanted buccal carcinoma: a quantitative study].

OBJECTIVE: Quantitative study of the effect of anti-human VEGF mAb E11 to VEGF level in serum of nude mice transplanted buccal carcinoma. METHODS: E11 was administered into BALB/c nu/nu mice which were transplanted human buccal carcinoma. The saline was administrated as negative control. Mice were killed at 18 days. The VEGF level in serum of mice was determined by improved indirect ELISA. RESULTS: Compared with the VEGF level in serum of mice in saline group, it was dramatically decreased in E11 group. The VEGF level in serum of mice treated E11 by subcutaneous was lowest and only reached (1.17 +/- 0.13) microg/L. CONCLUSION: It demonstrated that the anti-human VEGF mAb could reduce the VEGF level in serum by binding VEGF, and block its biological activity. It indicates that VEGF in serum of malignant tumor patient is a new tumor marker.

[Detection of P-glycoprotein and glutathine S-transferase in mucoepidermoid carcinoma of salivary gland].

OBJECTIVE: The aim of this study was to investigate the mechanism(MDR) of multidrug resistance(MDR) of mucoepidermoid carcinoma in salivary gland. METHODS: 40 cases of mucoepidermoid carcinoma in salivary gland were examined the MDR gene product P-glycoprotein using a monoclonal antibody JSB-1. And 10 of them were also investigated by detecting the expression of GST-pi. All the cases had not been accepted any therapy before the samples were collected. RESULTS: 1. Positive expression of JSB-1 was observed in 27 of the 40 specimens. The positive expression was related not only with clinical stage, but also with differentiation degree. 2. The GST-pi positive expression was found in 9 of 10 cases. There was no significant different between the positive expression of JSB-1 and GST-pi. CONCLUSION: JSB-1 and GST-pi play an important role in MDR of mucoepidermoid carcinoma.

[Rhabdomysarcoma and combined treatment in oral and maxillofacial regions].

OBJECTIVE: To study the treatment outcome of rhabdomysarcoma(RMS). METHODS: 74 cases of RMS with definite pathologic diagnosis treated in our department during the past 20 years were investigated. The relationship between the therapy and prognosis was analyzed. RESULTS: 52 cases among the 74 patients received different surgical treatment and post-operative radiotherapy. 22 cases received radiotherapy or chemoradiotherapy without surgical treatment. The survival rates demonstrated great differences depending on the different clinical stages and therapy. CONCLUSION: The combined therapy including radiotherapy after surgical treatment may increase 5-year survival rate.

Mutation analysis of 20 SARS virus genome sequences: evidence for negative selection in replicase ORF1b and spike gene.

AIM: Recently, more SARS-CoV virus genome sequences are released to the GenBank database. The aim of this study is to reveal the evolution forces of SARS-CoV virus by analyzing the nucleotide mutations in these sequences. METHODS: We obtained 20 SARS-CoV virus genome sequences from NCBI database, and calculated the ratio of non-synonymous nucleotide substitution per non-synonymous site (Ka) and synonymous nucleotide substitution per synonymous site (Ks) for SARS-CoV virus genes. RESULTS: The Ka/Ks ratios for replicase polyprotein ORF1a, ORF1b, and spike protein gene are 1.09 (P=0.6501), 0.38 (P=0.0074), 0.65 (P=0.0685) respectively. CONCLUSION: SARS-CoV virus replicase polyprotein ORF1b is undergoing negative selection; negative selection force is also probably operating on spike protein gene. These results provide basis for future developing a new drug and vaccine against SARS.

[Construction of a proteomic map database].

The first proteomic map database of China will be published by Bioinformation Center and Research Center of Proteomics, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences.The database consists of physical layer, link layer and interfacial layer. As Java technique was introduced to construct the database system, the database does not depend on special working platform. With the search instruments users can easily look through the proteomic map and get concrete information of proteins they are interested in.