A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides

Abstract

A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem.     

Optimization of human umbilical cord mesenchymal stem cell isolation and culture methods

Human umbilical cord mesenchymal stem cells (hUCMSCs) are considered to be an ideal replacement for bone marrow MSCs. However, up to date, there is no convenient and efficient method for hUCMSC isolation and culture. The present study was carried out to explore the modified enzyme digestion for hUCMSC in vitro. Conventional enzyme digestion, modified enzyme digestion, and tissue explant were used on hUCMSCs to compare their efficiencies of isolation and culture, to observe primary cell growth and cell subculture. The results show that the cells cultured using the tissue explant method had a longer culture cycle (P < 0.01) and lower yield of primary cells per centimetre of umbilical cord (P < 0.01) compared with the two enzyme digestion methods. Subculture adherence and cell doubling took significantly less time with the tissue explant method (P < 0.05) than with the conventional enzyme digestion method; however, there was no significant difference between the tissue explant method and the modified enzyme digestion method (P > 0.05). Comparing two enzyme digestion methods, the modified method yielded more cells than did the conventional method (P < 0.01), and primary cell adherence took significantly less time with the modified method than with the conventional method (P < 0.05). Cell cycle analysis of the third-generation hUCMSCs cultured by modified enzyme digestion method indicated that most cells were quiescent. Immunofluorescence staining showed that these cells expressed MSC markers CD44 and CD90. And Von Kossa and oil red O staining detection showed that they could be differentiated into osteoblasts and adipocytes with induction medium in vitro. This study suggests that hUCMSC isolation and culture using 0.2 % collagenase II at 37 °C for digestion of 16–20 h is an effective and simple modified enzyme digestion method.     

Impact of GC content on gene expression pattern in chicken

Background

GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution.

Methods

Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5^′ untranslated region sequences (5^′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1.

Results

In chicken, the GC content of 5^′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression.

Conclusions

GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.     

滤泡树突细胞肉瘤二例报道并文献复习

目的探讨滤泡树突细胞肉瘤（FDCS）的临床表现、病理形态、免疫组化、生物学行为和预后,提高对该病的认识。方法对2例滤泡树突细胞肉瘤进行报道,并结合临床资料、肿瘤大体及镜下特征、免疫组化标记结果及预后和国内外文献进行分析。结果2例FDCS,1例发生于颈部淋巴结,另1例发生于肠系膜,镜检肿瘤由梭形及卵圆形细胞组成,呈束状、漩涡状、编织状排列;免疫组化显示肿瘤细胞CD21、CD23和CD35阳性;患者预后不良。结论滤泡树突细胞肉瘤是一种罕见且容易误诊的低度恶性肿瘤,组织化学和免疫组化染色有助于该肿瘤的诊断及鉴别诊断,减少误诊。     

Localization of QTLs for seed color using recombinant inbred lines of Brassica napus in different environments.

Yellow seed is one of the most important traits of Brassica napus L. Efficient selection of the yellow-seed trait is one of the most important objectives in oilseed rape breeding. Two recombinant inbred line (RIL) populations (RIL-1 and RIL-2) were analyzed for 2 years at 2 locations. Four hundred and twenty SSR, RAPD, and SRAP marker loci covering 1744 cM were mapped in 26 linkage groups of RIL-1, while 265 loci covering 1135 cM were mapped in 20 linkage groups of RIL-2. A total of 19 QTLs were detected in the 2 populations. A major QTL was detected adjacent to the same marker (EM11ME20/200) in both maps in both years. This major QTL could explain 53.71%, 39.34%, 42.42%, 30.18%, 24.86%, and 15.08% of phenotypic variation in 6 combinations (location x year x population). BLASTn analysis of the sequences of the markers flanking the major QTL revealed that the homologous region corresponding to this major QTL was anchored between genes At5g44440 and At5g49640 of Arabidopsis thaliana chromosome 5 (At C5). Based on comparative genomic analysis, the bifunctional gene TT10 is nearest to the homologue of EM11ME20/200 on At C5 and can be considered an important candidate gene for the major QTL identified here. Besides providing an effective strategy for marker-assisted selection of the yellow-seed trait in B. napus, our results also provide important clues for cloning of the candidate gene corresponding to this major QTL.     

PCR-DGGE detection of the bacterial community structure in the Inner Mongolia steppe with two different DNA extraction methods

Compared with conventional methods, molecular biological technique, such as PCR-DGGE (denaturing gradient gel electrophoresis), is informative in examining the structure of the soil bacterial community through the extraction of microbial DNA from soil and generation of bacterial community profiles by PCR amplification of 16S rRNA genes. Extraction efficiency of soil microbial DNA is the most important step in these methods. At present, the frozen-thawing method and bead-beating method are most widely used in genomic extraction. Nevertheless, comparison of these two methods has not been conducted in different soil types, especially in humus-rich soil. In this study, extraction efficiencies of the two methods were compared in humus-rich steppe soil in Inner Mongolia based on the PCR-DGGE analysis of bacterial community structure. The results indicated that the bead-beating method is better than the frozen-thawing method in genomic DNA extraction efficiency. In addition, 21 bands in the DGGE pattern with the bead-beating method were further selected, cloned and sequenced. Based on similarity matching, all the sequences formed five major clusters: Actinobacteria; α-, β-, γ-, Proteobacteria ; Bacteriodetes ; Gemmatimonadetes and Acidobacteria . Of the 21 clones obtained from DGGE patterns, YC4 showed 99.7% similarity to Pseudomonas sp. (DQ339153); YC5, YC18 and YC19 showed 99.9 % similarity to Gram-positive bacterium (AB008510), Virgisporangium ochraceum (AB006162) and Micromonospora chalcea (X92613), respectively.     

Cytological Studies of Deoxyribonucleic Acid Replication in Escherichia coli 15T−: Replication at Slow Growth Rates and After a Shift-Up into Rich Medium

We examined the gross nuclear morphology of Escherichia coli 15T⁻ grown in different media with doubling times ranging from 22 to 270 min. In slowly growing cells, deoxyribonucleic acid synthesis was measured by autoradiography and shown to occur with greatest probability during the first two-thirds of the division cycle. In such cells, segregation occurred later, at the end of the division cycle rather than at the end of deoxyribonucleic acid replication. Nuclear regions in L-broth cells (22-min doubling time) cannot correspond to separate chromosomes but probably represent regions of replication activity. Segregation of template nucleotide strands was measured after a shift-up from proline M9 or glucose M9 media into L broth. A model is presented to account for the pattern of segregation observed.     

Calculation of an Adequate Intake (AI) Value and Safe Range of Selenium (Se) for Chinese Infants 0–3 Months Old Based on Se Concentration in the Milk of Lactating Chinese Women with Optimal Se Intake

Biological Trace Element Research - The required selenium intake for optimal health in Chinese residents was published in 2014. However, the adequate intake (AI) value for Chinese infants...