Translational selection on codon usage in the genus Aspergillus

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression.     

Simulating complex tumor dynamics from avascular to vascular growth using a general level-set method

A comprehensive continuum model of solid tumor evolution and development is investigated in detail numerically, both under the assumption of spherical symmetry and for arbitrary two-dimensional growth. The level set approach is used to obtain solutions for a recently developed multi-cell transport model formulated as a moving boundary problem for the evolution of the tumor. The model represents both the avascular and the vascular phase of growth, and is able to simulate when the transition occurs; progressive formation of a necrotic core and a rim structure in the tumor during the avascular phase are also captured. In terms of transport processes, the interaction of the tumor with the surrounding tissue is realistically incorporated. The two-dimensional simulation results are presented for different initial configurations. The computational framework, based on a Cartesian mesh/narrow band level-set method, can be applied to similar models that require the solution of coupled advection-diffusion equations with a moving boundary inside a fixed domain. The solution algorithm is designed so that extension to three-dimensional simulations is straightforward.     

Prediction of shape and internal structure of the proximal femur using a modified level set method for structural topology optimisation

A computational framework was developed to simulate the bone remodelling process as a structural topology optimisation problem. The mathematical formulation of the Level Set technique was extended and then implemented into a coronal plane model of the proximal femur to simulate the remodelling of internal structure and external geometry of bone into the optimal state. Results indicated that the proposed approach could reasonably mimic the major geometrical and material features of the natural bone. Simulation of the internal bone remodelling on the typical gross shape of the proximal femur, resulted in a density distribution pattern with good consistency with that of the natural bone. When both external and internal bone remodelling were simulated simultaneously, the initial rectangular design domain with a regularly distributed mass reduced gradually to an optimal state with external shape and internal structure similar to those of the natural proximal femur.     

Evaluation of statistical precision and design of efficient sampling for the population estimation based on frequency of occurrence

The binomial sampling to estimate population density of an organism based simply upon the frequency of its occurrence among sampled quadrats is a labour-saving technique which is potentially useful for small animals like insects and has actually been applied occasionally to studies of their populations. The present study provides a theoretical basis for this convenient technique, which makes it statistically reliable and tolerable for consistent use in intensive as well as preliminary population censuses. Firs, the magnitude of sampling error in relation to sample size is formulated mathematically for the estimate to be obtained by this indirect method of census, using either of the two popular models relating frequency of occurrence (p) to mean density (m), i.e. the negative binomial model, p=1−(1+m/k)^−k, and the empirical model, p=1−exp(−am^b). Then, the equations to calculate sample size and census cost that are necessary to attain a given desired level of precision in the estimation are derived for both models. A notable feature of the relationship of necessary sample size (or census cost) to mean density in the frequency method, in constrast to that in the ordinary census, is that it shows a concave curve which tends to rise sharply not only towards lower but also towards higher levels of density. These theoretical results make it also possible to design sequential estimation procedures based on this convenient census technique, which may enable us with the least necessary cost to get a series of population estimates with the desired precision level. Examples are presented to explain how to apply these programs to acutal censuses in the field.     

Detecting un-authorized genetically modified organisms (GMOs) and derived materials

Genetically modified plants, in the following referred to as genetically modified organisms or GMOs, have been commercially grown for almost two decades. In 2010 approximately 10% of the total global crop acreage was planted with GMOs (James, 2011). More than 30 countries have been growing commercial GMOs, and many more have performed field trials. Although the majority of commercial GMOs both in terms of acreage and specific events belong to the four species: soybean, maize, cotton and rapeseed, there are another 20 + species where GMOs are commercialized or in the pipeline for commercialization. The number of GMOs cultivated in field trials or for commercial production has constantly increased during this time period. So have the number of species, the number of countries involved, the diversity of novel (added) genetic elements and the global trade. All of these factors contribute to the increasing complexity of detecting and correctly identifying GMO derived material. Many jurisdictions, including the European Union (EU), legally distinguish between authorized (and therefore legal) and un-authorized (and therefore illegal) GMOs. Information about the developments, field trials, authorizations, cultivation, trade and observations made in the official GMO control laboratories in different countries around the world is often limited, despite several attempts such as the OECD BioTrack for voluntary dissemination of data. This lack of information inevitably makes it challenging to detect and identify GMOs, especially the un-authorized GMOs. The present paper reviews the state of the art technologies and approaches in light of coverage, practicability, sensitivity and limitations. Emphasis is put on exemplifying practical detection of un-authorized GMOs. Although this paper has a European (EU) bias when examples are given, the contents have global relevance.     

Natural mortality at different population densities of a pine shoot moth,Evetria cristata

A field population of Evetria cristata was studied in 10 plots in 1962 and in 6 plots in 1963. These plots were divided into 2 or 3 groups of different population levels of the shoot moth in respective years. The survival of the insect was then analysed in these different groups of plots. The survival rate of E. cristata from eggs to adults in the first generation was found always higher in the group with low population density, which indicates the existence of some factors that affect the population more severely when the insect is more abundant. Lissonota evetriae and Pediobius sp. seemed to have killed more proportion of the hosts where the shoot moth density was high. However, the total effect of the all natural enemies was not always great in the plots with high density of the moth. The survival of the second generation of the moth in 1963 was observed to be much higher at any population level than in the other generations.     

A new method of sequential sampling to obtain the population estimates with a fixed level of precision

A simple method of sequential sampling is developed which would make it automatically possible to secure, without excess sampling, a predetermined level of precision for a series of population estimates being required. It appears to have wide application to sampling field populations under various situations since it is simply based upon the relationship of variance to mean for which a comprehensive formula deduced for biological populations from the linearity in the regression of mean crowding on mean density could be adopted. Some problems that may arise in practical application of the method are also discussed.     

Spinal loads and trunk muscles forces during level walking – A combined in vivo and in silico study on six subjects

During level walking, lumbar spine is subjected to cyclic movements and intricate loading of the spinal discs and trunk musculature. This study aimed to estimate the spinal loads (T12–S1) and trunk muscles forces during a complete gait cycle.Six men, 24–33 years walk barefoot at self-selected speed (4–5 km/h). 3D kinematics and ground reaction forces were recorded using a motion capturing system and two force plates, implemented in an inverse dynamic musculoskeletal model to predict the spinal loads and trunk muscles forces. Additionally, the sensitivity of the intra-abdominal pressure and lumbar segment rotational stiffness was investigated.Peak spinal loads and trunk muscle forces were between the gait instances of heel strike and toe off. In L4–L5 segment, sensitivity analysis showed that average peak compressive, antero-posterior and medio-lateral shear forces were 130–179%, 2–15% and 1–6%, with max standard deviation (±STD) of 40%, 6% and 3% of the body weight. Average peak global muscles forces were 24–55% (longissimus thoracis), 11–23% (iliocostalis thoracis), 12–16% (external oblique), 17–25% (internal oblique) and 0–8% (rectus abdominus) of body weight whereas, the average peak local muscles forces were 11–19% (longissimus lumborum), 14–31% (iliocostalis lumborum) and 12–17% (multifidus). Maximum ± STD of the global and local muscles forces were 13% and 8% of the body weight.Large inter-individual differences were found in peak compressive and trunk muscles forces whereas the sensitivity analysis also showed a substantial variation.     

昆明山海棠对中国仓鼠V79细胞二酰基甘油含量的影响

本研究以昆明山海棠根部水抽提物(Tripterygium Hypoglaucum(Level)Hutch,THH)处理中国仓鼠V79细胞,通过检测V79细胞C-M细胞频率以及二酰基甘油(1,2-diacylgcerol,DAG)的含量测定,分析了THH诱发非整倍体与细胞醇磷酯信号通路的关系.结果指出THH能在1mg/ml、2mg/ml两个剂量上使V79细胞的DAG含量显著升高(P＜0.001),并明显的提高C-M细胞频率(P＜0.05),提示肌醇酯信号通路是介导THH诱发非整倍体的途径之一.