Bioautomation

Volume 17, Issue 2
Editorial
New books
Bioinformatics
SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence	65-72
Zhou Yuan Wu, Ray P. S. Han [ +/- abstract ][ full text ]
In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids) as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database) without considering homologous, and Q3 accuracy is ~74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.
The Expression Analysis of Genes in Fatty Acid Biosynthesis Pathway during the Seed Development of Tung Tree	73-82
Guixiong Jiang, Hao Chen, Xiaofeng Tan [ +/- abstract ][ full text ]
Tung tree (Vernicia fordii) is one of the important oil plants in China. The current researches on tung tree are mainly focused on the cultivation and breeding while the molecular mechanisms hidden in the back of tung tree's phenotypes are still uncovered. This research compared the transcriptome of three different stages during tung tree's seed development using RNA-Seq and obtained a lot of differentially expressed Unigenes. Through GO classification and pathway enrichment analysis, all of these differentially expressed Unigenes were classified into 128 signaling pathways including fatty acid biosynthesis. Fourteen homologous proteins were obtained when the sequences of 54 Unigenes within fatty acid biosynthesis pathway were aligned against KEGG database and the expression profiles of the genes encoding these proteins during seed development were analyzed. This research provides necessary data platform to elucidate the molecular mechanism underlies fatty acid biosynthesis of tung tree's seeds and theoretical guidance of tung tree varieties' improvement to increase output of tung oil.
Bioprocess systems
Lysine Content Determination in Xianyu 335 Corn and Its Uncertainty Assessment	83-90
Chen Ying, Zhang Min [ +/- abstract ][ full text ]
[Objective] To establish a mathematical model of uncertainty assessment for lysine content in Xianyu 335 corn by the amino acid assay, completely concerning the sources of uncertainty in the measurement process. [Methods] Analyze and measure the main source of uncertainty, and evaluate and calculate the each component of uncertainty. [Results] For 0.1055 g sample, the lysine determination in Xianyu 335 showed a good linear relationship. [Conclusion] This method is suitable for the Uncertainty Evaluation of lysine measurement in Xianyu 335 by amino acid assay.
Biomedical systems
Effect of Local Temperature on the Detecting for Pulse Wave of Local Blood Volume	91-96
Tingting Yan, Song Zhang, Lin Yang, Yimin Yang, Xuwen Li [ +/- abstract ][ full text ]
[Objective] Temperature of a subject's external body parts is an interference condition in pulse wave of local blood volume measurement. It is necessary to rule it out. By changing the influence factors, an experiment to research the effect of temperature of subjected part in pulse wave of local blood volume measurement was carried out. [Methods] When the 32 experimenters' left middle finger temperature fall below to 20°C, pulse wave of local blood volume would be recorded detected in real-time until the temperature returned to the measured values before the experiment [Results] While the temperature of subjected part ranged from 26°C to 31°C, the parameters of K', K₁', K₂' and the amplitude of pulse wave remain basically unchanged. [Conclusion] As a result of the research data, it is stipulated that the pulse wave of local blood volume can be measured only if the finger temperature is in the range of 26-31°C.
Comparison of the Polysaccharide Content of Cultivated Dioscorea nipponica Makino and Research on Pharmacologic Activity of Polysaccharide	97-106
Guangqing Xia, Junyi Zhu, Wei Liu, Lihong Dong, Huimin Yao, Jinzhi Song [ +/- abstract ][ full text ]
Dioscorea nipponica Makino, a perennial herb growing in mountainous areas of the Chinese Changbai mountains and Korean peninsula, has long been used as a folk medicine for bronchitis, asthma, and rheumatoid arthritis. Due to these therapeutic properties, wild Dioscorea nipponica Makino resources become less and less, some wild species have been tamed to be cultivated ones. In this paper, we compared the content of polysaccharide in stem root between biennial and three-year old cultivated Dioscorea nipponica Makino. The results indicated there is no significant difference between these samples, while in different harvest stages (from the early of June to the late of September), the polysaccharide content displayed significant difference (p < 0.01). The polysaccharide content in the Epigean leaves also showed the same change rule in the growth stages (from the late of June to the late of July). Moreover, the pharmacologic activity analysis implied that the polysaccharide of cultivated Dioscorea nipponica Makino could reduce the hyperlipidemia mice serum cholesterol (TC), triglyceride (TG) low density lipoprotein cholesterol (LDL-C) level, while increase high density lipoprotein cholesterol (HDL-C) level. These results demonstrated that the polysaccharide accumulation in biennial cultivated Dioscorea nipponica Makino almost get the same standard as three-year old ones, and the polysaccharide from epigean leaves also have some therapeutic properties as the stem root.
Immunomodulation and Antitumor Activities of Degraded Polysaccharide from Marine Microalgae Sarcinochrysis marina Geitler	107-116
Liqin Sun, Ling Wang, Jing Li, Honghui Liu [ +/- abstract ][ full text ]
The polysaccharide (SMP) from Sarcinochrysis marina Geitler were degraded using ascorbate and hydrogen peroxide in combination by ultrasonic assistant, and the degraded fractions were purified by gelchromatography. Then three different uniform fragments (SMP1, SMP2 and SMP3) were obtained with molecular weight of 452.79, 168.66 and 8.69 kDa. Their effects on peritoneal macrophage and spleen lymphocyte activation in vitro and the growth of mouse transplantable tumor S180 were measured. The results showed that the degraded fragments could evidently increased phagocytosis and proliferation of macrophage, stimulate NO emission to different extents, and promote propagate of lymphocytes. The immunocompetence had a direct proportion to molecular weight of the samples. The low molecular weight fraction (SMP3) had the strongest immunity activity. Different doses of samples could significantly inhibit the growth of S180 solid tumors, increase the thymus index and spleen index, and promote splenocyte proliferation of tumor-bearing mice. The effect is dose-dependent in a linear fashion. SMP2 had the strongest antitumor activity, and the tumor inhibition index of 200 mg/kg/day dose was 58.51%. All of above results indicated that the antitumor activity of SMP might be achieved by improving body immune response.