Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe

An aptamer-molecular beacon (MB) multiple fluorescent probe for adenosine triphosphate (ATP) assay is proposed in this article. The ATP aptamer was used as a molecular recognition part, and an oligonucleotide (short strand, SS) partially complementary with the aptamer and an MB was used as the other part. In the presence of ATP, the aptamer bound with it, accompanied by the hybridization of MB and SS and the fluorescence recovering. Wherever there is only very weak fluorescence can be measured in the absence of ATP. Based on the relationship of recovering fluorescence and the concentration of ATP, a method for quantifying ATP has been developed. The fluorescence intensity was proportional to the concentration of ATP in the range of 10 to 500 nM with a detection limit of 0.1 nM. Moreover, this method was able to detect ATP with high selectivity in the presence of guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). This method is proved to be simple with high sensitivity, selectivity, and specificity.     

Regularized EM algorithm for sparse parameter estimation in nonlinear dynamic systems with application to gene regulatory network inference

Parameter estimation in dynamic systems finds applications in various disciplines, including system biology. The well-known expectation-maximization (EM) algorithm is a popular method and has been widely used to solve system identification and parameter estimation problems. However, the conventional EM algorithm cannot exploit the sparsity. On the other hand, in gene regulatory network inference problems, the parameters to be estimated often exhibit sparse structure. In this paper, a regularized expectation-maximization (rEM) algorithm for sparse parameter estimation in nonlinear dynamic systems is proposed that is based on the maximum a posteriori (MAP) estimation and can incorporate the sparse prior. The expectation step involves the forward Gaussian approximation filtering and the backward Gaussian approximation smoothing. The maximization step employs a re-weighted iterative thresholding method. The proposed algorithm is then applied to gene regulatory network inference. Results based on both synthetic and real data show the effectiveness of the proposed algorithm.     

无脊椎动物乙酰胆碱酯酶研究进展

乙酰胆碱酯酶(AChE)是生物体中一种十分重要的神经递质水解酶,也是有机磷和氨基甲酸酯类杀虫剂的作用靶标。AChE在不同生物中的性质显著不同,如编码基因个数、序列保守性、表达分布及生理功能等。作为杀虫剂的主要作用靶标之一,AChE不但可以通过单个点突变引起昆虫抗药性,还能够通过多个点突变联合作用、靶标表达量变化及基因复制等方式引起抗药性并且改变昆虫的适合度代价。本文主要从AChE的基因类型、分子进化、蛋白结构、生理功能、与昆虫的抗药性关系、同一物种中不同AChE的性质等6个方面对昆虫纲、蛛形纲和线虫等无脊椎动物AChE的研究进展作一综述。     

Facilitation among plants can accelerate density‐dependent mortality and steepen self‐thinning lines in stressful environments

The speed and slope of plant self‐thinning are all affected by plant–plant interactions across environmental gradients. Possible mechanisms driving the self‐thinning dynamics include the relative strength of root versus shoot competition, and the interplay between competition and facilitation. Although these mechanisms often act in concert, their relative importance has not yet been fully explored. We used both a one‐layer and a two‐layer zone‐of‐influence (ZOI) model to examine how competition and facilitation drive self‐thinning across stress gradients. As a development of the traditional ZOI model, the two‐layer version explicitly models shoot and root growth and neighbor interactions, and thus the overall size‐symmetry of competition is regulated by the relative strength of root versus shoot competition. One‐layer model simulations revealed that increasingly asymmetric competition accelerated thinning, and steepened (slope ranged from about –1 to –4/3) and lowered self‐thinning lines. Stress slowed down density‐dependent mortality considerably when competition was not completely symmetric. Stress significantly decreased the self‐thinning intercept, while facilitation simply counteracted stress effects. Both stress and facilitation showed little effect on the slope. In the two‐layer model, both stress and facilitation affected mortality in the same way as in the one‐layer version when competition was not completely symmetric. Different from the one‐layer model, the two‐layer version showed that the effects of stress and facilitation on the self‐thinning slope were mediated by the asymmetry of competition. As stress increased, the overall asymmetry of competition shifted from asymmetric to symmetric due to increased relative strength of root competition. High stress thus dramatically flattened self‐thinning lines, whereas the inclusion of facilitation counteracted stress and led to steeper self‐thinning lines. Our two‐layer model is based on the current knowledge of plant–plant interactions, and better represents ecological realities. It can help elaborate experiments for testing the role of competition and facilitation in driving plant population dynamics.     

Novel SNPs of the Caprine Growth Hormone Secretagogue Receptor (GHSR) Gene and Their Association with Growth Traits in Goats

Growth hormone secretagogue receptor (GHSR), a G protein-coupled receptor that binds ghrelin, plays an important role in the central regulation of pituitary growth hormone secretion, food intake, and energy homeostasis. This study analyzed polymorphism of the caprine GHSR gene as a genetic marker candidate for growth traits in goats. Two single nucleotide polymorphisms (GU014697:g.165G→A and GU014697:g.548T→C) were identified in exon 2 of the caprine GHSR gene by PCR-single-strand conformation polymorphism and DNA sequencing methods. Their associations with growth traits were analyzed in 313 Xuhuai goats. The results indicated that GU014697:g.548T→C had significant effects on growth traits. Body length and body length index were significantly higher in individuals with genotype TT than CC and CT in (P < 0.05). TT individuals also tended to have better performance in other traits, such as body height and chest circumference, although there were no statistical differences (P > 0.05). This suggests that GHSR is a strong candidate gene that affects growth traits in goats.     

Phylogenetic conservatism and climate factors shape flowering phenology in alpine meadows

The study of phylogenetic conservatism in alpine plant phenology is critical for predicting climate change impacts; currently we have a poor understanding of how phylogeny and climate factors interactively influence plant phenology. Therefore, we explored the influence of phylogeny and climate factors on flowering phenology in alpine meadows. For two different types of alpine plant communities, we recorded phenological data, including flowering peak, first flower budding, first flowering, first fruiting and the flowering end for 62 species over the course of 5 years (2008–2012). From sequences in two plastid regions, we constructed phylogenetic trees. We used Blomberg’s K and Pagel’s lambda to assess the phylogenetic signal in phenological traits and species’ phenological responses to climate factors. We found a significant phylogenetic signal in the date of all reproductive phenological events and in species’ phenological responses to weekly day length and temperature. The number of species in flower was strongly associated with the weekly day lengths and followed by the weekly temperature prior to phenological activity. Based on phylogenetic eigenvector regression (PVR) analysis, we found a highly shared influence of phylogeny and climate factors on alpine species flowering phenology. Our results suggest the phylogenetic conservatism in both flowering and fruiting phenology may depend on the similarity of responses to external environmental cues among close relatives.     

枇杷种子的脱水敏感性与膜脂过氧化作用

枇杷种子不耐贮藏,属于脱水敏感的种子。在干燥脱水过程中,子叶和胚轴的超氧物歧化酶（ＳＯＤ） 和过氧化物酶（ＰＯＤ） 活性不断下降,而丙二醛（ ＭＤＡ） 含量及种子浸泡液的电导率不断增加,种子活力逐渐降低。外源０ ．０５ ～０ ．２５ ｍｍｏｌ／Ｌ 的抗坏血酸（ＡＳＡ） ,０ ．０５ ～５ ．０ ｍｍｏｌ／Ｌ 的还原性谷胱甘肽（ＧＳＨ）和０ ．０５ ～０ ．５ ｍｍｏｌ／Ｌ 的Ｃａ２ ＋ 处理能有效地增强种胚防御过氧化的能力,缓解氧自由基对种胚的伤害,提高脱水劣变的种子活力。     

The Mitochondrial Genome of Paramphistomum cervi (Digenea), the First Representative for the Family Paramphistomidae

We determined the complete mitochondrial DNA (mtDNA) sequence of a fluke, Paramphistomum cervi (Digenea: Paramphistomidae). This genome (14,014 bp) is slightly larger than that of Clonorchis sinensis (13,875 bp), but smaller than those of other digenean species. The mt genome of P. cervi contains 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (NCRs), a complement consistent with those of other digeneans. The arrangement of protein-coding and ribosomal RNA genes in the P. cervi mitochondrial genome is identical to that of other digeneans except for a group of Schistosoma species that exhibit a derived arrangement. The positions of some transfer RNA genes differ. Bayesian phylogenetic analyses, based on concatenated nucleotide sequences and amino-acid sequences of the 12 protein-coding genes, placed P. cervi within the Order Plagiorchiida, but relationships depicted within that order were not quite as expected from previous studies. The complete mtDNA sequence of P. cervi provides important genetic markers for diagnostics, ecological and evolutionary studies of digeneans.