Assigning alleles to different loci in amplifications of duplicated loci

Duplicated loci, for example those associated with major histocompatibility complex (MHC) genes, often have similar DNA sequences that can be coamplified with a pair of primers. This results in genotyping difficulties and inaccurate analyses. Here, we present a method to assign alleles to different loci in amplifications of duplicated loci. This method simultaneously considers several factors that may each affect correct allele assignment. These are the sharing of identical alleles among loci, null alleles, copy number variation, negative amplification, heterozygote excess or heterozygote deficiency, and linkage disequilibrium. The possible multilocus genotypes are extracted from the alleles for each individual and weighted to estimate the allele frequencies. The likelihood of an allele configuration is calculated and is optimized with a heuristic algorithm. Monte‐Carlo simulations and three empirical MHC data sets are used as examples to evaluate the efficacy of our method under different conditions. Our new software, mhc‐typer V1.1, is freely available at https://github.com/huangkang1987/mhc-typer .     

How the Sequence of a Gene Specifies Structural Symmetry in Proteins

Internal symmetry is commonly observed in the majority of fundamental protein folds. Meanwhile, sufficient evidence suggests that nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process allows mRNA to contain additional information on protein structure. In this paper, we study the relationship between gene sequences and protein structures from the viewpoint of symmetry to explore how gene sequences code for structural symmetry in proteins. We found that, for a set of two-fold symmetric proteins from left-handed beta-helix fold, intragenic symmetry always exists in their corresponding gene sequences. Meanwhile, codon usage bias and local mRNA structure might be involved in modulating translation speed for the formation of structural symmetry: a major decrease of local codon usage bias in the middle of the codon sequence can be identified as a common feature; and major or consecutive decreases in local mRNA folding energy near the boundaries of the symmetric substructures can also be observed. The results suggest that gene duplication and fusion may be an evolutionarily conserved process for this protein fold. In addition, the usage of rare codons and the formation of higher order of secondary structure near the boundaries of symmetric substructures might have coevolved as conserved mechanisms to slow down translation elongation and to facilitate effective folding of symmetric substructures. These findings provide valuable insights into our understanding of the mechanisms of translation and its evolution, as well as the design of proteins via symmetric modules.     

林业剩余物资源量评估方法

根据近十年来相关文献报道,分析了前人所建方法的合理性,结合中国林业生产实际,完善了林业剩余物资源潜力的计算方法。主要贡献包括:林业剩余物第二级分类的10个主要类型,即林木苗圃剩余物、林木修枝剩余物、木材采伐剩余物、木材造材剩余物、木材加工剩余物、竹材加工剩余物、薪材、废旧竹材、废旧木材、香蕉和菠萝残体;将经济林采伐和进口原木产生的剩余物计入相关木材剩余物计算范围;首次建立了包括木本水果在内的林木修枝剩余物的计算方法,以及多年生草本水果剩余物即香蕉和菠萝残体产量的计算方法;确定计算公式中参数所需要数据的来源;建议今后重点研究相关系数取值、林业剩余物资源量及其空间分布和相关行业标准等。     

Optimization of culture conditions for production of cis-epoxysuccinic acid hydrolase using response surface methodology

Response surface methodology, which allows for rapid identification of important factors and optimization of them to enhance enzyme production, was employed here to optimize culture conditions for the production of cis-epoxysuccinic acid hydrolase from Bordetella sp. strain 1–3. In the first step, a Plackett–Burman design was used to evaluate the effects of nine variables (yeast extract, cis-epoxysuccinic acid, KH₂PO₄, K₂HPO₄ · 3H₂O, MgSO₄ · 7H₂O, trace minerals solution, culture volume, initial pH and incubation time) on the enzyme production. Yeast extract, cis-epoxysuccinic acid and KH₂PO₄ had significant influences on cis-epoxysuccinic acid hydrolase production and their concentrations were further optimized using central composite design and response surface analysis. A combination of adjusting the concentration of yeast extract to 7.8 g/l, cis-epoxysuccinic acid to 9.8 g/l, and KH₂PO₄ to 1.12 g/l would favor maximum cis-epoxysuccinic acid hydrolase production. An enhancement of cis-epoxysuccinic acid hydrolase production from 5.6 U/ml to 9.27 U/ml was gained after optimization.     

林业剩余物资源量评估所用系数的定义和取值

有机废弃物是重要的待开发利用的生物质资源,特别是发展生物炼制。文中针对林业剩余物第二级分类的全部10个类型,根据1993–2017年间报道的有关林业剩余物系数研究,首先在前人研究结果的基础上,完善了系数体系及其定义。然后,对以前的取值通过文献溯源甄别其合理性,对于没有明确依据的取值和迄今未取值的系数,通过相关研究获得数据并进行实地调研,确定了计算林木苗圃剩余物、林木修枝剩余物、木材采伐剩余物、木材造材剩余物、木材加工剩余物、竹材加工剩余物、薪材、废旧竹材和废旧木材、香蕉和菠萝残体所需系数的合理取值。     

Purification and characterization of a cis-epoxysuccinic acid hydrolase from Bordetella sp. strain 1–3

Purification of a cis-epoxysuccinic acid hydrolase was achieved by ammonium sulfate precipitation, ionic exchange chromatography, hydrophobic interaction chromatography followed by size-exclusion chromatography. The enzyme was purified 177-fold with a yield of 14.4%. The apparent molecular mass of the enzyme was determined to be 33 kDa under denaturing conditions. The optimum pH for enzyme activity was 7.0, and the enzyme exhibited maximum activity at about 45 °C in 50 mM sodium phosphate buffer (pH 7.5). EDTA and o-phenanthrolin inhibited the enzyme activity remarkably, suggesting that the enzyme needs some metal cation to maintain its activity. Results of inductively coupled plasma mass spectrometry analysis indicated that the cis-epoxysuccinic acid hydrolase needs Zn²⁺ as a cofactor. Eight amino acids sequenced from the N-terminal region of the cis-epoxysuccinic acid hydrolase showed the same sequence as the N-terminal region of the beta subunit of the cis-epoxysuccinic acid hydrolase obtained from Alcaligenes sp.     

Quantum Information Processing in the Wall of Cytoskeletal Microtubules

Microtubules (MT) are composed of 13 protofilaments, each of which is a series of two-state tubulin dimers. In the MT wall, these dimers can be pictured as “lattice” sites similar to crystal lattices. Based on the pseudo-spin model, two different location states of the mobile electron in each dimer are proposed. Accordingly, the MT wall is described as an anisotropic two-dimensional (2D) pseudo-spin system considering a periodic triangular “lattice”. Because three different “spin-spin” interactions in each cell exist periodically in the whole MT wall, the system may be shown to be an array of three types of two-pseudo-spin-state dimers. For the above-mentioned condition, the processing of quantum information is presented by using the scheme developed by Lloyd.     

Targeting Human Telomeric G-Quadruplex DNA and Inhibition of Telomerase Activity With [(dmb)2Ru(obip)Ru(dmb)2]4+

Inhibition of telomerase by inducing/stabilizing G-quadruplex formation is a promising strategy to design new anticancer drugs. We synthesized and characterized a new dinuclear complex [(dmb)₂Ru(obip)Ru(dmb)₂]⁴⁺ (dmb = 4,4’-dimethyl-2,2’-bipyridine, obip = (2-(2-pyridyl)imidazo[4,5-f][1,10]phenanthroline) with high affinity for both antiparallel and mixed parallel / antiparallel G-quadruplex DNA. This complex can promote the formation and stabilize G-quadruplex DNA. Dialysis and TRAP experiments indicated that [(dmb)₂Ru(obip)Ru(dmb)₂]⁴⁺ acted as an excellent telomerase inhibitor due to its obvious selectivity for G-quadruplex DNA rather than double stranded DNA. In vitro co-culture experiments implied that [(dmb)₂Ru(obip)Ru(dmb)₂]⁴⁺ inhibited telomerase activity and hindered cancer cell proliferation without side effects to normal fibroblast cells. TUNEL assay indicated that inhibition of telomerase activity induced DNA cleavage further apoptosis in cancer cells. Therefore, Ru^II complex represents an exciting opportunity for anticancer drug design by specifically targeting cancer cell G-quadruplexes DNA.