The 59-kDa polypeptide constituent of 8–10-nm cytoplasmic filaments in Neurospora crassa is a pyruvate decarboxylase

The fungus Neurospora crassa harbors large amounts of cytoplasmic filaments which are homopolymers of a 59-kDa polypeptide (P59Nc). We have used molecular cloning, sequencing and enzyme activity measurement strategies to demonstrate that these filaments are made of pyruvate decarboxylase (PDC, EC 4.1.1.1), which is the key enzyme in the glycolytic-fermentative pathway of ethanol production in fungi, and in certain plants and bacteria. Immunofluorescence analyses of 8–10-nm filaments, as well as quantitative Northern blot studies of P59Nc mRNA and measurements of PDC activity, showed that the presence and abundance of PDC filaments depends on the metabolic growth conditions of the cells. These findings may be of relevance to the biology of ethanol production by fungi, and may shed light on the nature and variable presence of filament bundles described in fungal cells.     

简并性还是多态性?——遗传密码子设定的进化特点的剖析(英文)

遗传密码子的设定表现出令人困惑的多态性特点 :不同氨基酸拥有的密码子的数目 ,除 5个外 ,从 1个到 6个都有 .这种特点显示出密码子无论在翻译行为还是进化轨迹上 ,都存在诸多的异质性 .因此 ,简并性一词的收敛含义 ,并不能表征这种多态性的进化内涵 .没有同义密码子的AUG(Met)和UGG (Trp)并无简并现象 .其余的密码子则可分为两大类 :一类是 ,4个同义密码子为 1组 ,具有相同的第 1、2位碱基 ,并遵循“3中读 2”的读出规则 .同组的 4个同义密码子 ,不过是来自同一个双字母原始密码子 (XYN)的孑遗物 ,从这个意义上讲 ,也不宜视为简并现象 ;另一类则主要是 ,2个同义密码子为一组 ,并遵循“3中读 3”读出规则 .它们是由编码 2个氨基酸的双义原始密码子 ,第 3位的未定碱基N进一步设定形成 .至于有 6个同义密码子的 ,特别令人困感不解的组别 ,实际上是 4 + 2个 ,这启示它们可能源于上述两大类 .遗传密码子多态性的起源 ,可能始于最初阶段 ,氨基酸同某类寡核苷酸的起始二联体的相互作用 ,而完成于所有的双义原始密码子的第 3位碱基的分化 .这种进化轨迹被传统的简并性一词所模糊 ,并导致鉴定各有关理论可信性的坚实依据和令不同观点取得共识的基础被掩盖起来 .这可能就是在遗传密码子起源领域里 ,长期存在着众     

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.     

Sequential Statistical Improvement of the Liquid Cultivation of Helicobacter pylori

Background: Colonization of the gastric mucosa by Helicobacter pylori is one of the most important causes of acute and chronic gastric pathologies in humans. Achieving the growth of H. pylori in liquid media is of great importance in the development of clinical studies. In this study, we developed a sequential optimization strategy based on statistical models to improve the conditions of liquid culture of H. pylori. Materials and Methods: Four statistical models were sequentially used. First, a Box‐Behnken design was used to select the best process conditions (shaking speed, inoculum concentration, and final volume of culture). Secondly, a general factorial design was used to evaluate the influence of adding gel blocks or gel beads (shape and composition). Then a D‐optimal reduce design was carried out to allow the selection of the most influential factors in increasing the cell concentration (culture media components). Finally, another Box‐Behnken design was used to optimize the concentration of the culture media components previously selected. Results: After 12 hours of liquid culture a concentration of 25 × 10⁸ cells per mL (9.4 log₁₀ cells per mL) of H. pylori was obtained, compared with a predicted 32 × 10⁸ (9.5 log₁₀ cells per mL), which means between 1 and 5 log₁₀ units higher than some previous reports. Conclusions: The sequential statistical approach increased the planktonic H. pylori cell culture. The final culture media and conditions were: Brain Heart Infusion, blood agarose (1.5% w/v), lamb’s blood (3.18% v/v), DENT (0.11% v/v), and Vitox (0.52% v/v) at 60 rpm and 37 °C with filtered CO₂ (5% v/v) bubbled directly into the culture media in a final volume of 76.22 mL.     

Patch time allocation in male parasitoids

Abstract 1. Patch time allocation has been mostly studied in female parasitoids exploiting patches of hosts. Different parameters such as oviposition, host encounters, patch quality, etc. have been repeatedly shown to modify the time females invest on hosts. 2. Male parasitoids are expected to maximise their lifetime fitness by maximising the number of females inseminated during their life. Because they can be sperm and/or time limited, they should optimise their time allocation on emergence patches. 3. Patch time allocation thus appears to be an important question for both male and female parasitoids. 4. In this study, we determined the parameters used by males of the egg parasitoid Trichogramma turkestanica to decide when to leave the emergence patch. Among the different patch‐leaving parameters tested, only contacts with parasitised hosts and presence of virgin females significantly influenced the patch‐leaving tendency. 5. Our results suggest that males express behaviours that could enable them to optimise their patch exploitation time, as females do, but using different strategies.     

The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage

Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.     

Consequences of adaptive foraging in diverse communities

1.  Selective pressures acting on foraging activities constrain the strength of interaction, hence the stability and energetic availability in food webs.
2.  Because such selective pressures are usually measured at the individual level and because most experimental and theoretical works focus on simple settings, linking adaptive foraging with community scale patterns is still a far stretch.
3.  Some recent models incorporate foraging adaptation in diverse communities. The models vary in the way they incorporate adaptation, via evolutionary or behavioural changes, and define individual fitness in various ways.
4.  In spite of these differences, some general results linking adaptation to community structure and functioning emerge. In the present article, I introduce these different models and highlight their common results.
5.  Adaptive foraging provides stability to large food web models and predicts successfully interaction patterns within food webs as well as other topological features such as food chain length.
6.  The relationships between adaptive foraging and other structuring factors particularly depend on how well connected the local community is with surrounding communities (metacommunity aspect).     

Effect of Chord Flexure on Aerodynamic Performance of a Flapping Wing

Inspired by the fact that a high flexible wing in nature generates high aerodynamic performance, we investigated the aerodynamic performance of the flapping wing with different chord flexures. The unsteady, incompressible, and viscous flow over airfoil NACA0012 in a plunge motion was analyzed by using Navier-Stokes equation. Grid deformation, in which finite element and interpolation ideas are mixed, was introduced for computing large grid deformation caused by the chord flexures. We explored the optimal phase angle for thrust force and propulsive efficiency by varying the chord flexure from 0.05 to 0.7 when reduced frequency and plunge amplitude were fixed. Throughout parametric study on the phase angle and chord flexure amplitude, the maximum thrust force is achieved near at 0° in all given conditions, meanwhile, it is found that the optimal phase angle has dependency of chord flexure amplitude, which achieves higher aerodynamic performance compared to previous studies. These findings will provide a useful guideline for determining wing flexibility in design of a bio-mimetic air vehicle.