Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential

The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop structure and other selective pressures on genomes. In the present study, we evaluated the reliability of FORS-D analysis by comparing it with statistically significant stem-loop potential, another robust method developed by Le and Maizel for examining stem-loop structure. We found that FORS-M values calculated using 10 randomized sequences are as reliable as those calculated using 100 randomized sequences. The resulting FORS-D values have a similar trend and distribution as statistically significant stem-loop potential, implying that FORS-D analysis is as reliable as the latter in measuring the distribution of base order-dependent stem-loop potential. Since the calculation of the FORS-M values is time consuming, the integrated program Bodslp developed by us will become a convenient tool for large-scale FORS-D analysis. The results also suggest that for some purposes the online program SigStb developed by Le and Maizel may be used as an alternative tool for FORS-D analysis. C. Y. Zhang and J. F. Wei contributed equally to this paper.     

Did natural selection make the Dutch taller? A cautionary note on the importance of quantification in understanding evolution

One of the main achievements of the modern synthesis is a rigorous mathematical theory for evolution by natural selection. Combining this theory with statistical models makes it possible to estimate the relevant parameters so as to quantify selection and evolution in nature. Although quantification is a sign of a mature science, statistical models are unfortunately often interpreted independently of the motivating mathematical theory. Without a link to theory, numerical results do not represent proper quantifications, because they lack the connections that designate their biological meaning. Here, we want to raise awareness and exemplify this problem by examining a recent study on natural selection in a contemporary human population. Stulp et al. (2015) concluded that natural selection may partly explain the increasing stature of the Dutch population. This conclusion was based on a qualitative assessment of the presence of selection on height. Here, we provide a quantitative interpretation of these results using standard evolutionary theory to show that natural selection has had a minuscule effect.     

生态系统关键种理论的研究进展

１９６９年,由Ｐａｉｎｅ提出的“关键种”概念,迅速成为国际生态学的研究热点。关键种理论从系统调控的水平,揭示了生态系统稳定性和物种多样性的一种维持机制,并对保护生物学具有指导意义。但是关键种的确定标准、普适性及研究方法等方面仍存在局限性。关键种理论还需要通过大量观察和实验加以补充、论证与完善。     

Generalization and simplification of the Moore-Goodman test for significance of alignment homologies

Summary A test given by Moore and Goodman (1977) that checks the significance of a homology between protein sequences is generalized to any type of distance measure and to any classification of codon pairs or amino acids according to this measure. A normal distribution is shown to approximate satisfactorily the probability distribution underlying this test for the examples chosen, and supposedly for any distance measure. The test accordingly reduces to a simple standard procedure.     

Pinocytose und Bewegung von Amöben

Zusammenfassung Die Mucoidschicht von Amoeba proteus enthält saure Mucopolysaccharide und ist funktionell einem Kationenaustauscher vergleichbar. Schwermetallpartikel und Proteine werden in Abhängigkeit vom pH-Wert des Kulturmediums in unterschiedlich starken Mengen an die Mucoidfilamente gebunden. Die dem Plasmalemm unmittelbar aufliegende globuläre Grundschicht besitzt dagegen für die untersuchten Substanzen keine Adsorptionsfunktion und unterscheidet sich demnach sowohl physiologisch als auch chemisch von der filamentartigen Zone.Quantitative Messungen über die pH-abhängige Anlagerung von Ferritin haben ergeben, daß die Mucoidfilamente in der Lage sind, Kationen aus dem Kulturmedium bis zu einer um das 17fache höheren Konzentration anzureichern.Die Ergebnisse der vorliegenden Untersuchung sprechen dafür, daß die Anreicherung derartiger Substanzen an der Zelloberfläche eine notwendige und physiologisch sinnvolle Voraussetzung für die Auslösung einer induzierten Endocytose darstellt.

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Pinocytosis and locomotion of amoebaeX. The significance of the mucous layer for the initial phase of the induced endocytosis in Amoeba proteus

Summary The mucoid layer of Amoeba proteus contains acid mucopolysaccharides, which are involved in the exchange of cations. Depending on the pH of the external medium, different amounts of heavy metal particles and proteins are bound to the mucoid filaments. The globular ground layer, which is directly apposed to the plasma membrane does not bind any of the substances studied and, therefore, differs from the mucoid filaments in function as well as chemical nature. Measurements of the pH-dependent adsorption of ferritin demonstrate that the mucoid filaments are able to accumulate cations in concentrations 17 times that of the external medium. These results suggest that the accumulation of substances at the cell surface is a prerequisite for the initiation of induced endocytosis.

     

Estimation of Variances at Different Significance Levels

Variance components and their ratios broad-sense heritability and constancy were estimated for some quantitative traits in northwestern Spain populations of maize. Estimations were carried out at the significance levels of 5% and 25% and without significance limits. It can be concluded that estimation without significance limits is more efficient than the estimations at the usual levels in the method of analysis of experimental data from fields experiments.     

Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network

Mammalian phospholipase D (PLD) enzyme family consists of six members. Among them, PLD1/2/6 catalyzes phosphatidic acid (PA) production, while PLD3/4/5 has no catalytic activities. Deregulation of the PLD-PA lipid signaling has been associated with various human diseases including cancer. However, a comprehensive analysis of the regulators and effectors for this crucial lipid metabolic pathway has not been fully achieved. Using a proteomic approach, we defined the protein interaction network for the human PLD family of enzymes and PA and revealed diverse cellular signaling events involving them. Through it, we identified PJA2 as a novel E3 ubiquitin ligase for PLD1 involved in control of the PLD1-mediated mammalian target of rapamycin signaling. Additionally, we showed that PA interacted with and positively regulated sphingosine kinase 1. Taken together, our study not only generates a rich interactome resource for further characterizing the human PLD-PA lipid signaling but also connects this important metabolic pathway with numerous biological processes.     

Recognition of phylogenetic relationships from polypeptide chain fold similarities

Summary Structural similarities between proteins with no amino acid sequence homology either indicate a phylogenetic relationship, or they are merely the expression of a physically preferred way of folding a polypeptide chain. It is shown that one can distinguish between these alternatives by evaluating the significance of the similarity. Such significances have been derived for comparison between chain folds containing-pleated sheets (Schulz and Schirmer, 1974; Richardson et al., 1976; Sternberg and Thornton, 1976). An extension of this method to comparisons between any two chain folds is outlined here.     

Mitochondrial-related gene expression profiles suggest an important role of PGC-1alpha in the compensatory mechanism of endemic dilated cardiomyopathy

Keshan disease (KD) is an endemic dilated cardiomyopathy with unclear etiology. In this study, we compared mitochondrial-related gene expression profiles of peripheral blood mononuclear cells (PBMCs) derived from 16 KD patients and 16 normal controls in KD areas. Total RNA was isolated, amplified, labeled and hybridized to Agilent human 4×44k whole genome microarrays. Mitochondrial-related genes were screened out by the Third-Generation Human Mitochondria-Focused cDNA Microarray (hMitChip3). Quantitative real-time PCR, immunohistochemical and biochemical parameters related mitochondrial metabolism were conducted to validate our microarray results. In KD samples, 34 up-regulated genes (ratios≥2.0) were detected by significance analysis of microarrays and ingenuity systems pathway analysis (IPA). The highest ranked molecular and cellular functions of the differentially regulated genes were closely related to amino acid metabolism, free radical scavenging, carbohydrate metabolism, and energy production. Using IPA, 40 significant pathways and four significant networks, involved mainly in apoptosis, mitochondrion dysfunction, and nuclear receptor signaling were identified. Based on our results, we suggest that PGC-1alpha regulated energy metabolism and anti-apoptosis might play an important role in the compensatory mechanism of KD. Our results may lead to the identification of potential diagnostic biomarkers for KD in PBMCs, and may help to understand the pathogenesis of KD.