Predicting Statistical Properties of Open Reading Frames in Bacterial Genomes

An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.     

Statistical Mechanical Approach for Predicting the Transition to Non-B DNA Structures in Supercoiled DNA

Abstract

Supercoiling causes global twist of DNA structure and the supercoiled state has wide influence on conformational transition. A statistical mechanical approach was made for prediction of the transition probability to non-B DNA structures under torsional stress. A conditional partition function was defined as the sum over all possible states of the DNA sequence with basepair 1 and basepair n being in B-form helix and a recurrence formula was developed which expressed the partition function for basepair n with those for less number of pairs. This new definition permits a quick enumeration of every configuration of secondary structures. Energetic parameters of all conformations concerned, involving B-form, interior loop, cruciform and Z-form, were included in the equation. The probability of transition to each non-B conformation could be derived from these conditional partition functions. For treatment of effects of superhelicity, supercoiling energy was considered, and a twist of each conformation was determined to minimize the supercoiling energy. As the twist itself affects the transition probability, the whole scheme of equations was solved by renormalization technique. The present method permits a simultaneous treatment of serveral types of conformations under a common torsional stress.

A set of energetic parameters of DNA secondary structures has been chosen for calculation. Some DNA sequences were submitted to the calculation, and all the sequences that we submitted gave stable convergence. Some of them have been investigated the critical supercoil density for the transition to non-B DNA structures. Even though the reliability of the set of parameters was not enough, the prediction of secondary structure transition showed good agreement with reported observation. Hence, the present algorithm can estimate the probability of local conformational change of DNA under a given supercoil density, and also be employed to predict some specific sequences in which conformational change is sensitive to superhelicity.     

果实风味的代谢基础及其调控机制研究进展

果实风味是重要农艺性状,基因组、代谢组、转录组等多组学联用技术的发展和应用,已相对系统地揭示了风味物质基础。这些物质代谢具有明显的器官、发育以及环境特异性调控的特点,其代谢机制的阐述是果品调控的重要研究热点问题。乙烯是植物生长发育过程中重要的信号分子,对果实风味物质的合成和代谢具有独特的调节作用。在近年来国内外果实风味物质研究的基础上,本文总结了果实风味的代谢基础、调控机制、风味物质对乙烯信号的响应以及生物信息学在果实风味研究中的应用。最后,对该方向未来的发展提出展望,以期为果实风味营养的提高和调控提供理论参考。     

Basis for vaccine recommendations

Once a new vaccine has been granted its licensing, a public health expertise is needed in order to support the decision regarding its possible inclusion within the national immunisation schedule. This analysis, based on an assessment of the benefits/risks balance and costs/effectiveness ratio, is a multidisciplinary exercise. Largely based on epidemiological and immunological expertises, it also requires bio-mathematical and economical inputs, if the long term consequences of the vaccination are to be taken into account. Indeed, the main drivers of the decision are the burden of the disease, the characteristics of the vaccine in term of effectiveness and safety, the cost of the vaccination, the feasibility of the adjunction of the vaccine in the schedule, the social demand for this vaccination and the positive or negative indirect effects of a large vaccination on the epidemiology of the disease, in addition to the direct protective effect for vaccinated individuals. New vaccines are generally characterised by a more limited epidemiological impact than older vaccines, in a context of growing requirements from our society regarding drugs, and especially vaccines, safety. Both the real and perceived benefits/risks balances for the more recent vaccines appear questionable. The possibility of detrimental epidemiological consequences of either insufficient vaccination coverage or serotype (or serogroup) replacement is another factor that makes the decision regarding vaccination strategies increasingly complex.     

木质纤维生产燃料乙醇工艺的研究进展

利用丰富而廉价的木质纤维原料代替粮食生产燃料乙醇,对经济和社会的可持续发展有着重要的意义。以木质纤维为原料发酵生产燃料乙醇可分为4种工艺:分步糖水解化发酵法、同步糖化发酵法、同步糖化共发酵法和直接微生物转化法。介绍了以上4种工艺的研究进展,并对今后进一步研究提出了建议。     

Drivers of Inequality in Millennium Development Goal Progress: A Statistical Analysis

Background

Many low- and middle-income countries are not on track to reach the public health targets set out in the Millennium Development Goals (MDGs). We evaluated whether differential progress towards health MDGs was associated with economic development, public health funding (both overall and as percentage of available domestic funds), or health system infrastructure. We also examined the impact of joint epidemics of HIV/AIDS and noncommunicable diseases (NCDs), which may limit the ability of households to address child mortality and increase risks of infectious diseases.

Methods and Findings

We calculated each country''s distance from its MDG goals for HIV/AIDS, tuberculosis, and infant and child mortality targets for the year 2005 using the United Nations MDG database for 227 countries from 1990 to the present. We studied the association of economic development (gross domestic product [GDP] per capita in purchasing-power-parity), the relative priority placed on health (health spending as a percentage of GDP), real health spending (health system expenditures in purchasing-power-parity), HIV/AIDS burden (prevalence rates among ages 15–49 y), and NCD burden (age-standardised chronic disease mortality rates), with measures of distance from attainment of health MDGs. To avoid spurious correlations that may exist simply because countries with high disease burdens would be expected to have low MDG progress, and to adjust for potential confounding arising from differences in countries'' initial disease burdens, we analysed the variations in rates of change in MDG progress versus expected rates for each country. While economic development, health priority, health spending, and health infrastructure did not explain more than one-fifth of the differences in progress to health MDGs among countries, burdens of HIV and NCDs explained more than half of between-country inequalities in child mortality progress (R ²-infant mortality  = 0.57, R ²-under 5 mortality  = 0.54). HIV/AIDS and NCD burdens were also the strongest correlates of unequal progress towards tuberculosis goals (R ² = 0.57), with NCDs having an effect independent of HIV/AIDS, consistent with micro-level studies of the influence of tobacco and diabetes on tuberculosis risks. Even after correcting for health system variables, initial child mortality, and tuberculosis diseases, we found that lower burdens of HIV/AIDS and NCDs were associated with much greater progress towards attainment of child mortality and tuberculosis MDGs than were gains in GDP. An estimated 1% lower HIV prevalence or 10% lower mortality rate from NCDs would have a similar impact on progress towards the tuberculosis MDG as an 80% or greater rise in GDP, corresponding to at least a decade of economic growth in low-income countries.

Conclusions

Unequal progress in health MDGs in low-income countries appears significantly related to burdens of HIV and NCDs in a population, after correcting for potentially confounding socioeconomic, disease burden, political, and health system variables. The common separation between NCDs, child mortality, and infectious syndromes among development programs may obscure interrelationships of illness affecting those living in poor households—whether economic (e.g., as money spent on tobacco is lost from child health expenditures) or biological (e.g., as diabetes or HIV enhance the risk of tuberculosis). Please see later in the article for the Editors'' Summary     

Optimization and Technological Development Strategies of an Antimicrobial Extract from Achyrocline alata Assisted by Statistical Design

Achyrocline alata, known as Jateí-ka-há, is traditionally used to treat several health problems, including inflammations and infections. This study aimed to optimize an active extract against Streptococcus mutans, the main bacteria that causes caries. The extract was developed using an accelerated solvent extraction and chemometric calculations. Factorial design and response surface methodologies were used to determine the most important variables, such as active compound selectivity. The standardized extraction recovered 99% of the four main compounds, gnaphaliin, helipyrone, obtusifolin and lepidissipyrone, which represent 44% of the extract. The optimized extract of A. alata has a MIC of 62.5 μg/mL against S. mutans and could be used in mouth care products.     

Basis functions for object-centered representations

In an object-centered representation, the position of the subparts of an object are encoded with respect to a set of axes and an origin centered on the object. Several physiological and neuropsychological results support the existence of such representations in humans and monkeys. An explicit representation would involve neurons with invariant response properties in object-centered coordinates. We consider an alternative scheme using basis functions in which the cells have retinotopic receptive fields modulated by the orientation of the object and task-related signals. We show that this alternative is consistent with single-cell data, is computationally efficient, and accounts for object-centered hemineglect, a syndrome observed in humans after fronto-parietal lesions.     

Statistical Genetics of an Annual Plant, Impatiens Capensis. I. Genetic Basis of Quantitative Variation

Analysis of quantitative genetics in natural populations has been hindered by computational and methodological problems in statistical analysis. We developed and validated a jackknife procedure to test for existence of broad sense heritabilities and dominance or maternal effects influencing quantitative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and/or maternal effects, while later characters exhibited predominantly environmental variation. Monte Carlo simulations demonstrate that these jackknife tests of variance components are extremely robust to heterogeneous error variances. Statistical methods from human genetics provide evidence for either a major locus influencing germination date, or genes that affect phenotypic variability per se. We urge explicit consideration of statistical behavior of estimation and testing procedures for proper biological interpretation of statistical results.     

Statistical inference for multi-pathogen systems

There is growing interest in understanding the nature and consequences of interactions among infectious agents. Pathogen interactions can be operational at different scales, either within a co-infected host or in host populations where they co-circulate, and can be either cooperative or competitive. The detection of interactions among pathogens has typically involved the study of synchrony in the oscillations of the protagonists, but as we show here, phase association provides an unreliable dynamical fingerprint for this task. We assess the capacity of a likelihood-based inference framework to accurately detect and quantify the presence and nature of pathogen interactions on the basis of realistic amounts and kinds of simulated data. We show that when epidemiological and demographic processes are well understood, noisy time series data can contain sufficient information to allow correct inference of interactions in multi-pathogen systems. The inference power is dependent on the strength and time-course of the underlying mechanism: stronger and longer-lasting interactions are more easily and more precisely quantified. We examine the limitations of our approach to stochastic temporal variation, under-reporting, and over-aggregation of data. We propose that likelihood shows promise as a basis for detection and quantification of the effects of pathogen interactions and the determination of their (competitive or cooperative) nature on the basis of population-level time-series data.     

New Indices for Predicting Glycaemic Variability

Blood glucose variability is known to be associated with increased risk of long-term complications. Reliable indices for predicting hyperglycaemic and hypoglycaemic fluctuations are therefore needed. Glycaemic standard deviation (SD) obtained by continuous glucose monitoring correlates closely with nine previously described glycaemic variability formulas. Here, new indices predictive of glycaemic variability were developed, which can be calculated from laboratory measures based on a single blood draw. The indices included the glycated albumin (GA) to HbA1c ratio (GA/A1c ratio) and the fasting C-peptide immunoreactivity (FCPR) to fasting plasma glucose (FPG) ratio (FCPR index). Predictive values of these indices were assessed in 100 adults with diabetes. GA/A1c ratio and FCPR index showed close associations with glycaemic SD in addition to the nine existing glucose variability formulas. Subjects with a GA/A1c ratio ≥2.8 and FCPR index <3.0 showed the greatest SD and longest durations of hypoglycaemia, while those with a GA/A1c ratio <2.8 and FCPR index ≥3.0 had smaller SDs and little sign of hypoglycaemia. In adults with diabetes, a high GA/A1c ratio and low FCPR index value reflect higher glycaemic excursions, irrespective of diabetes type. Simultaneous measurements of GA, HbA1c, FPG and FCPR may help to identify a group of patients who warrant closer monitoring in relation to glycaemic variability and hypoglycaemia.     

Predicting structures for genome proteins.

Assigning three-dimensional protein folds to genome sequences is essential to understanding protein function. Although experimental three-dimensional structures are currently available for only a very small fraction of these sequences, computational fold assignment is able to assign folds to 20-30% of the sequences in various genomes. This percentage varies depending on the particular organism under analysis, on the sensitivities of the methods used and on the number of experimental structures available at the time the assignment is carried out. The fraction of assignable sequences is currently increasing at an annual rate of roughly 18%. If this rate is sustained throughout the coming years, three-dimensional computational models for more than half of the genome sequences may be available by the year 2003.     

Electrocardiogram for Predicting Cardiac Functional Recovery

To investigate if the 12-lead resting electrocardiogram (ECG) is a predictor of left ventricular (LV) functional recovery after revascularization of chronic total coronary artery occlusions (CTO). Revascularization was performed in 58 CTO patients who had impaired regional wall motion. The 12-lead resting ECG was used to evaluate Q-wave, QT dispersion, and other parameters. Pre- and postoperative LV regional wall motions were evaluated by real-time three-dimensional echocardiography (RT-3DE). In patients with non-Q-wave, the wall motion score index (WMSI) was dropped from 1.56 ± 0.31 to 1.12 ± 0.21 (P < 0.05), while there was no significant changes (1.73 ± 0.12 and 1.59 ± 0.23, P > 0.05) for WMSI in patients with Q-wave. Preoperative non-Q-wave at baseline was predicted recovery with 88 % sensitivity and 68 % specificity. Positive predictive value for recovery was 67 % in patients with non-Q-wave. The presence of Q-wave can predict non-recovery of the regional wall motion with 68 % sensitivity and 88 % specificity. For CTO patients treated by revascularization, recovery can be predicted reliably through the analysis of pathological Q-wave on the 12-lead resting ECG.     

Predicting survival time for cold exposure

The prediction of survival time (ST) for cold exposure is speculative as reliable controlled data of deep hypothermia are unavailable. At best, guidance can be obtained from case histories of accidental exposure. This study describes the development of a mathematical model for the prediction of ST under sedentary conditions in the cold. The model is based on steady-state heat conduction in a single cylinder comprised of a core and two concentric annular shells representing the fat plus skin and the clothing plus still boundary layer, respectively. The ambient condition can be either air or water; the distinction is made by assigning different values of insulation to the still boundary layer. Metabolic heat production (M) is comprised of resting and shivering components with the latter predicted by temperature signals from the core and skin. Where the cold exposure is too severe forM to balance heat loss, ST is largely determined by the rate of heat loss from the body. Where a balance occurs, ST is governed by the endurance time for shivering. End of survival is marked by the deep core temperature reaching a value of 30° C. The model was calibrated against survival data of cold water (0 to 20° C) immersion and then applied to cold air exposure. A sampling of ST predictions for the nude exposure of an average healthy male in relatively calm air (1 km/h wind speed) are the following: 1.8, 2.5, 4.1, 9.0, and >24 h for –30, –20, –10, 0, and 10° C, respectively. With two layers of loose clothing (average thickness of 1 mm each) in a 5 km/h wind, STs are 4.0, 5.6, 8.6, 15.4, and >24 h for –50, –40, –30, –20, and –10° C. The predicted STs must be weighted against the extrapolative nature of the model. At present, it would be prudent to use the predictions in a relative sense, that is, to compare or rank-order predicted STs for various combinations of ambient conditions and clothing protection.