The relationship between microsatellite slippage mutation rate and the number of repeat units

Microsatellite markers are widely used for genetic studies, but the relationship between microsatellite slippage mutation rate and the number of repeat units remains unclear. In this study, microsatellite distributions in the human genome are collected from public sequence databases. We observe that there is a threshold size for slippage mutations. We consider a model of microsatellite mutation consisting of point mutations and single stepwise slippage mutations. From two sets of equations based on two stochastic processes and equilibrium assumptions, we estimate microsatellite slippage mutation rates without assuming any relationship between microsatellite slippage mutation rate and the number of repeat units. We use the least squares method with constraints to estimate expansion and contraction mutation rates. The estimated slippage mutation rate increases exponentially as the number of repeat units increases. When slippage mutations happen, expansion occurs more frequently for short microsatellites and contraction occurs more frequently for long microsatellites. Our results agree with the length-dependent mutation pattern observed from experimental data, and they explain the scarcity of long microsatellites.     

Winery wastewater treatment: a critical overview of advanced biological processes

Wine production is one of the leading sectors of the food processing industry. The wine industry produces a large amount of wastewater characterized by a high strength in terms of organic pollution and large variability throughout the year. Most of the organic matter is soluble and easily biodegradable. On the other hand, nitrogen and phosphorous are lacking. The aerobic and anaerobic processes are largely applied for winery wastewater treatment because they can quickly react to changes in the organic loading. This review analyzes e applied biological systems, considering both aerobic and anaerobic processes, and different reactor configurations. The performances of different biological processes are evaluated in terms of operational conditions (organic loading rate and hydraulic retention time). Aerobic processes can guarantee chemical oxygen demand removal up to 98% for organic loading rates of some 1-2?kg of chemical oxygen demand m^?3d^?1 but requires good aeration systems to supply the required process oxygen. The management cost of these processes could be high considering the power density in the range 60-70?W m^?3_reactor and that nutrients should be added to support biomass growth. On the other hand, anaerobic processes are able to face high organic loads with low running costs, but COD removal is generally limited to 90%. Combination of the two treatment systems (anaerobic followed by aerobic) could reduce management costs and meet high discharge standards.     

溪流生态系统生态学研究

本文根据6年定位研究的结果,讨论了有关东北山溪生态系统生态学方面的问题,诸如溪流生态系统的组成、结构、能量流动、物质循环、食物网结构与营养能级等。调查了组成生物并对其做了定量分析;描述了能量的消耗途径并绘制了生态系统的能流框图;按营养关系划分了食物链和食物网结构,并根据各类群的生物量计算了不同营养能级的转换效率;按照水体中溶氧变化和水分循环规律建立了相应的动态模型。最后,对经典的将生态系统中生物类群划分为生产者、消费者和分解者三大集团进行了讨论,鉴于事实上每一生物类群分别具有生产、消费和分解等三重作用,因此,建议用生产过程、消费过程和分解过程来表述生物类群在生态系统中的功能作用。       

亚高山森林生态系统过程研究进展

亚高山森林是以冷、云杉属为建群种或优势种的暗针叶林为主体的森林植被。亚高山森林在庇护邻近脆弱生态系统、保育生物多样性、涵养水源、碳吸存和指示全球气候变化等方面具有十分重要且不可替代的作用和地位,其多样化的植被和土壤组合为研究生态系统过程提供了天然的实验室。亚高山森林的群落演替与更新、生物多样性保育、水文生态过程、生物元素的生物地球化学循环以及亚高山森林生态过程对气候变化的响应等研究已取得了明显的进展。但有关全球变化条件下的亚高山森林土壤生物多样性和冬季生态学过程等研究明显不足。全球气候变化背景下的冬季生态学过程、极端灾害事件对亚高山森林生态系统过程的影响、亚高山森林生物多样性的保育机制、亚高山森林土壤生物多样性与生态系统过程的耦合机制等可能是未来研究的前沿科学问题。     

A model of plant strategies in fluvial hydrosystems

1. We propose a model of plant strategies in temperate fluvial hydrosystems that considers the hydraulic and geomorphic features that control plant recruitment, establishment and growth in river floodplains.
2. The model describes first how the disturbance gradient and the grain-size of the river bed load affect the relative proportion of erosion and deposition processes, and how the frequency of flood disturbance affects the intensity of such processes.
3. Secondly, the model predicts plant strategies according to direct and indirect effects of floods (disturbances through erosion versus deposition processes, and associated nutrient excess or limitation).
4. The relevance of the model as a prediction tool is discussed. Some proposals are made to validate the model, and traits are proposed that should be considered in future research for improving the predicting value of the model.     

On the Application of Ordinate Characterizing of Approximately Periodical Functions in Analyzing Biological Records

As a possible alternative to spectral analysis of biological processes the method of thresholding the recorded function is reconsidered. The frequencies of the section length for a finite set of levels form the frequency surface which is the starting point for inference and reasoning. The paper presents ideas and examples to stimulate the development and use of a suitable electronic equipment.     

Model of two noise source dependent Ornstein-Uhlenbeck processes applied to postural sway

In this study the postural control system is modeled in terms of two counteracting bio-subsystems. Their activities are described by two Ornstein-Uhlenbeck processes with different-in-magnitude noise sources. The model is constructed as a sum of these processes, where in each of them the same noise source with opposite sign of the noise coefficients was introduced. Since the friction coefficients are also different for these processes, the delay of a crossover from ballistic to diffusive motion for one of the subsystems is greater than for its counterpart. It turns out that for smaller time intervals a superdiffusive behavior is observed, whereas, counteraction of subsystems is called into play for a larger time intervals, what for investigated range of data, is exhibited as a slow, subdiffusive behavior.     

Continuous time-interaction processes for population size estimation,with an application to drug dealing in Italy

We introduce a time-interaction point process where the occurrence of an event can increase (self-excitement) or reduce (self-correction) the probability of future events. Self-excitement and self-correction are allowed to be triggered by the same event, at different timescales; other effects such as those of covariates, unobserved heterogeneity, and temporal dependence are also allowed in the model. We focus on capture-recapture data, as our work is motivated by an original example about the estimation of the total number of drug dealers in Italy. To do so, we derive a conditional likelihood formulation where only subjects with at least one capture are involved in the inference process. The result is a novel and flexible continuous-time population size estimator. A simulation study and the analysis of our motivating example illustrate the validity of our approach in several scenarios.     

一类受马氏调制的连续型传染病模型

本文借鉴保险上的方法来考虑这样一个传染病模型,即在一个区域中,初始有一定的传染病人,假设一方面病人不断增加,且传染率受当时病人数目的影响;另一方面病人减少（死亡或治愈）的发生频率及数目受一外界环境的影响,而外界环境假定为一有限状态的马氏过程。在这些假设下,我们得出初始状态为i时疾病灭绝的概率以及平稳状态下的疾病灭绝概率。     

Testing equality of survival functions of quality-adjusted lifetime

We present a method for comparing the survival functions of quality-adjusted lifetime from two treatments. This test statistic becomes the ordinary log-rank test when quality-adjusted lifetime is the same as the survival time. Simulation experiments are conducted to examine the behavior of our proposed test statistic under both null and alternative hypotheses. In addition, we apply our method to a breast cancer trial for comparing the distribution of quality-adjusted lifetime between two treatment regimes.     

Possible use of Biolog methodology for monitoring yeast presence in alcoholic fermentation for wine‐making

Aims: A research was undertaken to explore the possibility to use Biolog system of microbial metabolic characterization for the monitoring of yeast population evolution during alcoholic fermentation for wine production. Methods and Results: An application of Biolog system was employed for the characterization of yeasts of oenological interest, in pure cultures and mixed consortia, in various cell concentrations. The system’s capacity to discriminate among different cell concentrations of the same yeast strain was ascertained, along with the capacity to discriminate between mixed and pure populations. Conclusions: The tested application of Biolog system resulted suitable for a quick recognition (24 h) of the presence of starter cultures within mixed populations of autochthonous yeasts. Such discrimination was confirmed with the one resulting from molecular techniques. Significance and Impact of the Study: The study suggests the possibility to employ Biolog system for an early monitoring of yeast evolution in modern wine‐making fermentations, where specialized yeasts are more and more frequently used as starters and their ability to overcome autochthonous yeast populations is crucial.     

Biogeochemical and hydrological controls on carbon export from a forested catchment in central Japan

Here we review research on the links between hydrological processes and the biogeochemical environment controlling the dynamics of dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) in temperate forested catchments. In addition, we present the results of original experiments. The spatial and temporal changes in DIC and DOC concentrations were investigated in tandem with observations of elementary belowground hydrological processes for a forested headwater catchment in central Japan. The soil CO₂ gas concentration, which is the source of DIC, increased with depth. The hydrological characteristics of groundwater also affected the spatial variation of partial pressure of dissolved CO₂ (pCO₂) in groundwater. The temporal variations in the soil CO₂ gas concentration and the pCO₂ values of groundwater suggested that the dynamics of DIC were strongly affected by biological activity. However, the geographical differences in DIC leaching were affected not only by the link between climatological conditions and biological activity, but also by other factors such as geomorphologic conditions. The DOC concentrations decreased with selective removal of hydrophobic acid during vertical infiltration. The major DOC-removal mechanisms were retention of metal-organic complexes to soil solids in the upper mineral soil layer and decomposition of DOC in the lower mineral soil layer. The responses of the DIC and DOC concentrations to changes in discharge during storm events were explained by the spatial variation in the DIC and DOC concentrations. Seasonal variation, which represents a long-term change, in stream water DOC concentrations was affected not only by the temporal variation in DOC concentrations in the topsoil, which may be affected by biological activity, but also by water movement, which transports DOC from the topsoil to stream water. These results indicate that both a biogeochemical approach and a method for evaluating the hydrological effects on carbon dynamics are critical for clarifying the carbon accumulation-and-release processes in forested ecosystems.     

Formation of Levan from Raffinose by Levansucrase of Zymomonas mobilis

Levansucrase (EC 2.4.1.10.) of Zymomonas mobilis 113S can perform the polymerisation of fructose moiety from raffinose to levan concomitantly with a release of non‐catabolised melibiose into the medium. The kinetic parameters of the levansucrase‐catalysed reaction provide even higher reaction velocities on raffinose as compared to sucrose, particularly at low substrate concentrations. A decreased value in the number of the average molecular mass (M_n = 1693 kDa), an increased intrinsic viscosity (η = 49.47 cm³/g), and a diminished Huggin's constant (K^' = 0.67) are intrinsic to the levan synthesis from raffinose, indicating certain structural peculiarities compared to a polysaccharide obtained from sucrose (M_n = 1851 kDa, [η] = 42.47 cm³/g, K' = 1.21).     

Do isolation and local habitat jointly limit the structure of stream invertebrate assemblages?

1. Both local and regional processes simultaneously control species assemblages depending on spatial habitat configuration. In dendritic networks like streams, the unique spatial arrangement of habitats produces various combinations of local habitat size and isolation. Stream invertebrate assemblages could therefore be controlled by different combinations of local and regional processes, depending on their location in the network. 2. Using quantile regression, we investigated how local habitat size, local environmental conditions and spatial isolation influenced variation in assemblage composition. Adult Trichoptera and benthic macroinvertebrate assemblages were represented by non‐metric multidimensional scaling (NMDS) ordination scores, as were local environmental conditions, in four headwater stream networks in New Zealand. 3. With increasing local habitat size, there was a decrease in variation in assemblage composition (NMDS scores) of both adult Trichoptera and benthic macroinvertebrates. This relationship between habitat size and assemblage variation was related to local habitat conditions at the upper limit of assemblage variability and spatial isolation at the lower limit of assemblage variability, for both adult Trichoptera and benthic assemblages, indicating joint local and regional controls on stream invertebrate assemblages. 4. The relationships between local assemblages and their neighbours, based on community similarity scores, differed between benthic macroinvertebrates and adult Trichoptera. For benthic assemblages, the larger the stream, the more similar assemblages were to neighbouring assemblages, whereas there was no consistent relationship between assemblage similarity and stream size for adult Trichoptera. This difference in structuring could be attributed to contrasting spatial influences linked to the different dispersal modes of adults and larvae. However, because adult and benthic assemblages are not independent, the influence of life stage on spatial distribution is difficult to determine (i.e. it is essentially a ‘chicken and egg’ argument). 5. Overall, our approach using quantile regression to evaluate limit responses, rather than regressions on means, has highlighted the joint importance of local habitat and spatial processes in structuring stream invertebrate assemblages. Furthermore, we have provided evidence for the importance of the spatial network arrangement and interactions between life stages and dispersal processes, in structuring stream assemblages.     

A new methodical approach to determine the quantum yield of the conversion of electronic excitation in the reaction centers of purple bacteria

A new methodical approach is proposed for precise determination (better than ± 2%) of the quantum yield of charge separation in the reaction centers of purple bacteria; for Rhodospirillum rubrum this value proves to be 93.5%.     

The importance of meiofauna to lotic ecosystem functioning

• 1 Although meiofauna occur in large numbers in many streams, almost nothing is known about their functional role.
• 2 In other systems, meiofauna influence microbial and organic matter dynamics through consumption and bioturbation. Given that these are important processes in streams, meiofauna have the potential to influence lotic function by changing the quality and availability of organic matter as well as the number and biotic activity of benthic microbes. Selective feeding by meiofauna has the potential to alter the availability of nutrients and organic carbon.
• 3 Meiofauna generally contribute only a small amount to metazoan production and biomass in streams, although exceptions occur. Within a stream, the relative importance of meiofauna may reflect whether the temporary or permanent meiofauna dominate the meiobenthos as well as the season when samples are collected.
• 4 We suggest stream conditions (small sediment grain size, restricted interstitial flow) under which meiofauna have the greatest likelihood of influencing stream ecosystem function.
• 5 Important areas for future research include addressing whether meiofauna feed selectively, whether meiofauna are links or sinks for carbon in streams, and whether bioturbation by meiofauna influences stream ecosystem processes in a predictable manner.