Characterizing Long-range Correlation Properties in Nucleotide Sequences

Using continuous wavelet transform as the analytical tool, the fractal characteristic of nucleotide sequences was studied. The fractal dimension of the exon and intron sequences for different species was calculated. We use the Mexican hat wavelet function as the mother wavelet and Hurst exponent to describe the long-range correlation. It is found that the Hurst exponent of intron sequence is larger than that of exon sequence for the same gene.

Cloning and Sequence Analysis of Prophenoloxidase from Haemocytes of the Red Swamp Crayfish,Procambarus clarkii

The full-length cDNA sequence of prophenoloxidase was obtained through RACE technology. The complete cDNA sequence is 3 721-bp long, containing an open reading frame （ORF） of 1 881 bp, a 154-bp 5′-untranslated region, and a 1 686- bp 3′-untranslated region with three potential functional poly（A） signals （AATAAA）. The molecular mass of the deduced amino acid sequence （627 aa） was 72.3 kDa with an estimatedpI of 5.88. It contained putative copper-binding sites （copper A： 131, 135, 167 and copper B： 301,305, 341）, and a tentative complement-like motif （GCGWPDHL）. Eight potential N-linked glycosylation sites were predicted to be present in P. clarkii prophenoloxidase. Similar to those in other arthropod prophenoloxidases reported so far, no signal peptide was detected in the crayfish prophenoloxidase. The phylogenetic trees confirmed that P. clarkii prophenoloxidase was most closely related to that of freshwater crayfish P. leniusculus and more closely related to other crustacean prophenoloxidases from shrimp, prawn, and lobster than to the insect prophenoloxidases. Besides, two putative introns were found in this sequence of genomic DNA.

Cloning and sequence analysis of β-actin gene from Aedes albopictus (Diptera: Culicidae)

Objective： To obtain the complete β-actin gene from Aedes albopictus. Methods： Total RNA was extracted from C6/36 cells. Degenerate primers were designed based on the β-actin sequences of An. gambiae, Ae. aegypti, Cx. pipiens pallens and D. melanogaster. By RT-PCR, the product was amplified, purified, cloned into the pGT vector and sequenced. The β-actin sequence was aligned and phylogenetically analyzed by the BLAST program and the CLUSTAL W program. Results： A sequence of 1132 bp including an open reading frame of 1131 bp was obtained （GenBank DQ657949）. The deduced protein had 376 amino acids. Aligned to SWISS-PROT, it exhibited a high level of identity with β-actins from Anopheles, Drosophila and Culex at the amino acid sequence level. Phylogenetic analysis indicated that Ae. albopictus β-acfin was much more homologous with invertebrate β- actin than with vertebrate β-actin. Conclusion： The gene may be used as the internal control in the experiments of Ae. albopictus.

Association of Single Nucleotide Polymorphisms of ABCB1,OPRM1 and COMT with Pain Perception in Cancer Patients

Pain perception is influenced by multiple factors. The single nucleotide polymorphisms（SNPs） of some genes were found associated with pain perception. This study aimed to examine the association of the genotypes of ABCB1 C3435 T,OPRM1 A118 G and COMT V108/158M（valine 108/158 methionine） with pain perception in cancer patients. We genotyped 146 cancer pain patients and 139 cancer patients without pain for ABCB1 C3435T（rs1045642）,OPRM1 A118G（rs1799971） and COMT V108/158M（rs4680） by the fluorescent dye-terminator cycle sequencing method,and compared the genotype distribution between groups with different pain intensities by chi-square test and pain scores between groups with different genotypes by non-parametric test. The results showed that in these cancer patients,the frequency of variant T allele of ABCB1 C3435 T was 40.5%; that of G allele of OPRM1 A118 G was 38.5% and that of A allele of COMT V108/158 M was 23.3%. No significant difference in the genotype distribution of ABCB1 C3435T（rs1045642） and OPRM1 A118G（rs1799971） was observed between cancer pain group and control group（P=0.364 and 0.578）; however,significant difference occurred in the genotype distribution of COMT V108/158M（rs4680） between the two groups（P=0.001）. And the difference could not be explained by any other confounding factors. Moreover,we found that the genotypes of COMT V108/158 M and ABCB1 C3435 T were associated with the intensities of pain in cancer patients. In conclusion,our results indicate that the SNPs of COMT V108/158 M and ABCB1 C3435 T significantly influence the pain perception in Chinese cancer patients.

Video Transmission Secrecy Improvement Based on Fractional Order Hyper Chaotic System

In the Digital World scenario,the confidentiality of information in video transmission plays an important role.Chaotic systems have been shown to be effective for video signal encryption.To improve video transmission secrecy,compressive encryption method is proposed to accomplish compression and encryption based on fractional order hyper chaotic system that incorporates Compressive Sensing(CS),pixel level,bit level scrambling and nucleotide Sequences operations.The measurement matrix generates by the fractional order hyper chaotic system strengthens the efficiency of the encryption process.To avoid plain text attack,the CS measurement is scrambled to its pixel level,bit level scrambling decreases the similarity between the adjacent measurements and the nucleotide sequence operations are done on the scrambled bits,increasing the encryption.Two stages are comprised in the reconstruction technique,the first stage uses the intra-frame similarity and offers robust preliminary retrieval for each frame,and the second stage iteratively improves the efficiency of reconstruction by integrating inter frame Multi Hypothesis(MH)estimation and weighted residual sparsity modeling.In each iteration,the residual coefficient weights are modified using a mathematical approach based on the MH predictions,and the Split Bregman iteration algorithm is defined to resolve weighted l1 regularization.Experimental findings show that the proposed algorithm provides good compression of video coupled with an efficient encryption method that is resistant to multiple attacks.

Molecular Phylogeny Supports the Validity of Polypedates impresus Yang 2008

The taxonomy of the Asian tree frogs of the Polypedates leucomystax complex, a group of widespread and morphologically similar species, is very controversial. To ascertain the taxonomic status of these species, we investi- gated the historical relationships among representative samples based on - 2 kb of nucleotide sequences from the mito- chondrial 12S rRNA, tRNAvalinc, and 16S rRNA genes. Our phylogeny resolved five well supported lineages （A, B, C, D and E） in the P leucomystax complex. Polypedates impresus from Yunnan, China, Polypedates cf. mutus and Polypedates cf. megacephalus from Guangxi and Yunnan, China, and Laos constructed Clade C, which is monophyletic. In order to recognize the unique position of this clade, we considered P impresus in Clade C as a valid species. Following our phy- logeny, Chinese Polypedates, corresponding to the other four clades, should include four species： P. mutus （Clade A）; P. braueri （Clade B）; P impresus （Clade C） and P. megacephalus （Clade D）. P Ieucomystax （Clade E） is mainly distributed in the Malaysia, Indonesia and Philippines.

Genetic Characterization of Fusion Protein of Human Respiratory Syncytial Virus: Beijing

Objective Fusion protein is a subunit of the human respiratory syncytial virus(HRSV)and a potential vaccine candidate.Thus,a study on the genetic characteristics of F protein was considered important for further investigations in this field.The aim of this study was to determine the prevalence and genetic diversity of the F gene of HRSV infections in hospitalized pediatric patients in Beijing with acute lower respiratory tract infections and to compare the circulating genotypes that are currently found worldwide.Methods HRSV particles were amplified by RT-PCR and the PCR products were purified for sequencing.Further analysis was carried out by Bioedit and MEGA 3.0 biological software programs.Results Seventy-six samples(23.1%)were positive for HRSV.The percentage of cases in patients younger than 1year was 84.21%.Among the six Beijing isolates,four belonged to subgroup A,whose respective F genes shared97.0%-97.4%nucleotide sequence identity and 92.1%-93.0%amino acid sequence identity.The other two isolates belonged to subgroup B.Here,97.3%and 98.2%sequence identity were found at nucleotide and amino acid levels,respectively.Conclusions Phylogenetic analysis of nucleotide sequences revealed that those four isolates within subgroup A were monophyletic and closely related to each other,but those two within subgroup B distributed in two distinct clusters.Subgroup A and B strains co-circulated,indicating that two different transmission chains occurred in Beijing from 2003-2004.

Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.

Mycobacterium tuberculosis bacteremia in a human immunodeficiency virus-negative patient with liver cirrhosis:A case report

BACKGROUND With the increasing prevalence of human immunodeficiency virus(HIV),the incidence of Mycobacterium tuberculosis(M.tuberculosis)bacteremia has also increased.As a common affliction of acquired immunodeficiency syndrome patients,M.tuberculosis infection is associated in these patients with severe sepsis and high mortality.In contrast,M.tuberculosis bacteremia is rarely seen in HIVnegative patients,and M.tuberculosis has never been reported from the blood of patients with liver cirrhosis.CASE SUMMARY We evaluated a 55-year-old Chinese male patient who had been admitted to the hospital with abdominal distension of unknown cause of one-week duration,accompanied by diarrhea,shortness of breath,and occasional fever.Based on these indicators of abnormal inflammation and fever,we suspected the presence of an infection.Although evidence of microbial infection was not found in routine clinical tests and the patient did not show typical clinical symptoms of infection with M.tuberculosis,next-generation sequencing of blood samples nevertheless demonstrated the presence of M.tuberculosis,which was subsequently isolated from blood samples grown in conventional Bac T/ALERT FA blood culture bottles.CONCLUSION Our findings demonstrate that HIV-negative liver cirrhosis patients can also be infected with M.tuberculosis.

Sequence analysis of a soil-borne wheat mosaic virus isolate from Italy shows that it is the same virus as European wheat mosaic virus and Soil-borne rye mosaic virus

The complete sequence of the two RNAs of a furovirus isolate fromdurum wheat in Italy was determined. Sequence comparisons and phylogenetic analysis were done to compare the Italian virus with Soil-borne wheat mosaic virus (SBWMV) from the USA and with furovirus sequences recently published as European wheat mosaic virus (EWMV), from wheat in France, and Soil-borne rye mosaic virus (SBRMV), from rye and wheat in Germany. Over the entire genome, the Italian isolate RNA1 and RNA2 had respectively 97.5% and 98.6% nucleotide identity with EWMV, 95.5% and 85.8% with SBRMV-G and 70.6% and 64.5% with SBWMV. The Italian isolate was therefore clearly distinct from SBWMV. The European isolates all appear to belong to the same virus and the name Soil-borne cereal mosaic virus may resolve earlier ambiguities.

The complete genome of Enterovirus 71 China strain

Five overlapping clones covering the full genome of Enterovirus71 China strain SHZH98 were obtained and then the sequences were determined by the chain termination method. It showed that the full length of EV71 SHZH98 genome (not including Poly A tail) is 7408 bp. There are some diversities on the lengths and sequences of 5′ UTR and 3′ UTR between SHZH98 and the other EV71 strains. In P1 capsid region, which is closely associated with viral immunogenicity, EV71 strain SHZH98 shares the highest homology with Taiwan strains; but in P2 and P3 non-structural gene regions there are higher identities with Coxsakievirus A16 and EV71 strains MS, BrCr than with Taiwan strains. Phylogenetic tree constructed by structural gene region indicates that China strain SHZH98 has a closer relationship with Taiwan strains, however, in the non-coding region it has a closer relationship with Coxsakievirus A16, EV71 strains MS and BrCr. EV71 China strain was analyzed at the molecular level. The results will contribute to the basic study on enteroviruses and the EV71 prevention in China.

Clinical efficacy of a combination of Percoll continuous density gradient and swim-up techniques for semen processing in HIV-1 serodiscordant couples

To evaluate the clinical efficacy of a procedure comprising a combination of Percoll continuous density gradient and modified swim-up techniques for the removal of human immunodeficiency virus type 1 （HIV-1） from the semen of HIV-1 infected males, a total of 129 couples with an HIV-1 positive male partner and an HIV-1 negative female partner （serodiscordant couples） who were treated at Keio University Hospital between January 2002 and April 2012 were examined. A total of 183 ejaculates from 129 HIV-1 infected males were processed. After swim-up, we successfully collected motile sperms at a recovery rate as high as 100.0% in cases of normozoospermia （126/126 ejaculates）, oligozoospermia （6/6）, and asthenozoospermia （36/36）. The recovery rate of oligoasthenozoospermia was 86.7% （13/15）. In processed semen only four ejaculates （4/181：2.2%） showed viral nucleotide sequences consistent with those in the blood of the infected males. After using these sperms, no horizontal infections of the female patients and no vertical infections of the newborns were observed. Furthermore, no obvious adverse effects were observed in the offspring. This protocol allowed us to collect HIV-1 negative motile sperms at a high rate, even in male factor cases. We concluded that our protocol is clinically effective both for decreasing HIV-1 infections and for yielding a healthy child.

Circulating-free DNA Mutation Associated with Response of Targeted Therapy in Human Epidermal Growth Factor Receptor 2-positive Metastatic Breast Cancer

Background： The addition of anti-human epidermal growth factor receptor 2 （HER2）-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine （T-DM1）, to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations ofbiopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-tiER2 therapeutic response through circulating-free DNA （ctDNA）. Methods： From March 6, 2014 to December 10, 2014, 24 plasma samples from 20 patients with HER2-positive metastatic breast cancer who received systemic therapy were eligible. We used a panel for detection of hot-spot mutations from 50 oncogenes and tumor suppressor genes, and then used targeted next-generation sequencing （NGS） to identify somatic mutation of these samples in those 50 genes. Samples taken before their first trastuzumab administration and subsequently proven with clinical benefit were grouped into sensitive group. The others were collected after disease progression of the trastuzumab-based therapy and were grouped into the resistant group. Results： A total of 486 single-nucleotide variants from 46 genes were detected. Of these 46 genes, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha （PIK3C）I）, proto-oncogene c-Kit （KIT）, and tumor protein p53 （TP53） were the most common mntated genes. Seven genes, including epidermal growth factor receptor （EGFR）, G protein subunit alpha S （GNAS）, HRas proto-oncogene （HRAS）, mutL homolog I （MLHI）, cadherin 1 （CDHI）, neuroblastoma RAS viral oncogene homolog （NRAS）, and NOTCttl, that only occurred mutations in the resistant group were associated with the resistance of targeted therapy. In addition, we detected a HER2 S8551 mutation in two patients who had persistent benefits from anti-HER2 therapy. Conclusion： Targeted NGS of cfDNA has potential clinical utility to detect biomarkers from HER2-targeted therapies.

Curative efficacy of extract from Ganjiangdazao recipe on functional dyspepsia in rats

OBJECTIVE:To evaluate the efficacy of the extract from Ganjiangdazao recipe(EGR)on functional dyspepsia in rats with spleen-stomach deficiency cold pattern(SSDCP)in terms of Traditional Chinese Medicine,and to investigate its pharmacodynamics.METHODS:Sixty Sprague-Dawley rats were randomly divided into the control group,SSDCP group,low-EGR SSDCP group,high-EGR SSDCP group,probiotics group,EGR group.SSDCP model was induced by gavage with the 0℃edible vinegar.The symptoms and manifestations were scored by method from the relative literature,the ecological changes in cecal microflora was analyzed by 16SrRNA high-throughput sequencing technology,gastric tissues were treated by immunohistochemistry,the levels of related biochemical components related to the gastrointestinal functions were detected by enzyme-linked immunosorbent assay and colorimetry,gastric juice was measured by pH meter,blood pressure measurement by trapping tail method,surface temperature measured by infrared thermal imaging,and the content of 6-gingerol in the serum was determined by liquid-mass chromatography before and after EGR was given.RESULTS:It was found that EGR could effectively relieve the symptoms and manifestations of the SSDCP rats(P<0.05);the value of the relative abundance of Lactobacillus,Streptococcus,Enterococcus and Coprobacillus increased,while the value of the relative abundance of Clostridium decreased(P<0.05)in the cecal microflora in the SSDCP rats after high-EGR administration;It was also found that EGR had no substantial effect on the related biochemical components related to the gastrointestinal functions of in the SSDCP rats;and a certain amount of 6-gingerol was detected in the serum of EGR group.CONCLUSION:The pharmacodynamic site of EGR is the intestinal tract,and the mechanism behind the effect of EGR on SSDCP rats,involves increasing the beneficial bacteria and decreasing the proinflammatory bacteria in the intestinal tract.The blood pharmacodynamics of EGR remains to be further studied in the future.

Analysis of Allele Specific Expression——A Survey

Allele specific expression is essential for cellular programming and development and the diversity of cellular phenotypes. Traditional analysis methods utilize RNA and depend on single nucleotide polymorphisms,thus to suffer from limited amount of materials for analysis. The rapid development of next-generation sequencing technologies provides more comprehensive and powerful approaches to analyze the genomic, epigenetic, and transcriptomic data, and further to detect and measure allele specific expressions. It will potentially enhance the understanding of the allele specific expressions, their complexities, and the effect on biological processes. In this paper, we extensively review the state-of-art enabling technologies and tools to analyze, detect, and measure allele specific expressions, compare their features, and point out the future trend of the methods.