Biomedical subjects

Bo Liao

Publications and source records attributed to Bo Liao.

9 recordsLinked to original sources

PubMed2006

Coronavirus phylogeny based on 2D graphical representation of DNA sequence.

A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this aritcle, a new approach based on the 2D graphical representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the two-dimensional curves.

Animals↗

PubMed2005

Graphical approach to analyzing DNA sequences.

Recently, we proposed a 2D graphical representation of DNA sequence [J Comput Chem 25(2004) 1364-1368]. Based on this representation, we outline one approach to search optimal alignment. We also can judge the mutations between bases and an unknown sequence based on its graph and a known sequence's graph.

Algorithms↗

PubMed2005

On a six-dimensional representation of RNA secondary structures.

In this paper, we proposed a 6-D representation of RNA secondary structures. The use of the 6-D representation is illustrated by constructing structure invariants. Comparisons with the similarity/dissimilarity results based on 6-D representation for a set of RNA secondary structures, are considered to illustrate the use of our structure invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal.

Base Pairing↗

PubMed2005

[Studies of on-site night soil and kitchen garbage treatment].

The biological treatment technique of collection at source and disposition on-site of night soil and kitchen garbage were presented. By design project of overall technics, the lab-scale experiments were performed. It was revealed that water consumption of vacuum closestool was about 1 L/time. It consumed 0.4- 0.6L water to shred 1 kg kitchen garbage. Night soil covered 40%, kitchen garbage covered 60% in the influent. Water was controlled at about 93%, the C:N ratio was about 25:1, pH was between 6.2 and 7.3, the optical blend frequency was 6h/d and the overall solid retention time was 28 days in anaerobic digestion reactor. The COD removal rate of mixed supernatant was 91% in anaerobic baffled reactor. It was identified that these phosphorus strains and potassium strains were Bacillus. sp, and biological activated fertilizer was obtained by mixed these strains with digestion sludge which had been dehydrated and deodorized. These strains ability of forming phosphorus and potassium were determined, and the concentration of phosphorus increased 67.5%, potassium increased 33.4%.

Bacteria, Anaerobic↗

PubMed2004

New 2D graphical representation of DNA sequences.

We consider a 2D graphical representations of DNA sequences, which avoids loss of information associated with crossing and overlapping of the corresponding curve. We outline an approach, which is based on the construction of a three-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with DNA. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.

Algorithms↗

PubMed2004

General combinatorics of RNA secondary structure.

The total number of RNA secondary structures of a given length with minimal hairpin loop length m(m>0) and with minimal stack length l(l>0) is computed, under the assumption that all base pairs can occur. Asymptotics are derived from the determination of recurrence relations of decomposition properties.

Base Pairing↗

PubMed2003

[Construction and characterization of osteosarcoma 9901 cell cDNA library].

AIM: To construct human osteosarcoma 9901 cell cDNA expression library for screening osteosarcoma-specific antigens. METHODS: Total RNA was extracted from human osteosarcoma cell line 9901 and mRNA was purified. cDNA was synthesized by reverse transcription, and cDNA fragments larger than 400 bp were ligated with dephosphorylated arms of lambdagt11. The recombinants were packaged in-vitro, and a small portion of packaged phage was used to infect E.coli Y1090 for titration. The size of cDNA inserts and the diversity of library were detected by PCR. RESULTS: The osteosarcoma 9901 cell line cDNA library consisting of 1.5x10(6) recombinant bacteriophages was constructed. The average length of exogenous inserts in the recombinants was about 1.4 kb. CONCLUSION: The cDNA library reported herein is suitable for screening osteosarcoma-specific antigens.

Bone Neoplasms↗

PubMedDate not supplied

General combinatorics of RNA hairpins and cloverleaves.

For an abstract single-strand RNA, a combinatorial analysis is given for two important structures, hairpins and cloverleaves. The total number of hairpins and cloverleaves of a given length with minimal hairpin loop length m(m > 0) and with minimal stack length l(l > 0) is computed, under the assumption that all base pairs can occur.

Algorithms↗

PubMedDate not supplied

Analysis of similarity/dissimilarity of DNA sequences based on nonoverlapping triplets of nucleotide bases.

We consider a 6-D representation of triplets of nucleotide bases of DNA sequences. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the triplets derived from DNA sequences. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.

Animals↗