On the limitations of standard statistical modeling in biological systems: A full Bayesian approach for biology

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist.     

藏鹀的自然历史、威胁和保护

藏鹀(Emberiza koslowi)是我国青藏高原东部的特有珍稀鸟种,目前关于它的资料非常匮乏.为了解藏鹀的分布、数量和基本生活史特征,促进对于该物种的有效保护,自2005年起以青海省果洛州久治县白玉乡为中心对藏鹀进行了持续6年的观察,并针对其面临的威胁采取了相应的保护措施.结果显示,藏鹀主要分布在青海的玉树、果洛和四川的阿坝一带海拔3 500～4 700 m范围内的适宜栖息地,该分布区比原有认知更靠东北,更为狭小且海拔更高.用样线法开展的藏鹀数量监测,在7.4 km2的调查范围内记录到一个18 ～33只的稳定种群.此外,还对藏鹀的筑巢、育雏和争斗等行为进行了详细描述.食肉动物的捕食、冬季食物缺乏和牲畜踩踏鸟卵是藏鹀面临的最直接威胁.通过持续监测、与当地牧民协商、建立保护小区并开展有针对性的保护,藏鹀种群趋于稳定.     

Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations

The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations and to look for genomic regions with outstanding genetic differentiation between these populations. Genetic differentiation is generally based on allele frequency differences between populations, which are measured by F_ST or related statistics. Here we introduce a new statistic, denoted hapFLK, which focuses instead on the differences of haplotype frequencies between populations. In contrast to most existing statistics, hapFLK accounts for the hierarchical structure of the sampled populations. Using computer simulations, we show that each of these two features—the use of haplotype information and of the hierarchical structure of populations—significantly improves the detection power of selected loci and that combining them in the hapFLK statistic provides even greater power. We also show that hapFLK is robust with respect to bottlenecks and migration and improves over existing approaches in many situations. Finally, we apply hapFLK to a set of six sheep breeds from Northern Europe and identify seven regions under selection, which include already reported regions but also several new ones. We propose a method to help identifying the population(s) under selection in a detected region, which reveals that in many of these regions selection most likely occurred in more than one population. Furthermore, several of the detected regions correspond to incomplete sweeps, where the favorable haplotype is only at intermediate frequency in the population(s) under selection.     

The diagnostic value of reproductive organs in some genera of articulated Coralline red algae

Clearcut differences exist between the reproductive organs of Corallina and Jania. Fully formed spermatangial conceptacles in Corallina have low ceillings and pronounced beaks whereas in Jania they have high ceilings and lack beaks. Fusion cells in carposporophytic conceptacles are thin and broad in the former genus and thick and narrow in the latter. Tetrasporangial conceptacles have less capacity in Jania than in Corallina and the fertile areas in young conceptacles cover a smaller area.

Haliptylon is changed from group to generic status and Corallina subulata is transferred to this genus. Haliptylon is characterised by conceptacles similar in all known respects to those of Jania, but the branching is pinnate, as in Corallina.

From the available evidence it appears possible that organisms having Corallina-type conceptacles diverged phylogenetically long ago from those having Jania-type conceptacles.     

Process model comparison and transferability across bioreactor scales and modes of operation for a mammalian cell bioprocess

A Monod kinetic model, logistic equation model, and statistical regression model were developed for a Chinese hamster ovary cell bioprocess operated under three different modes of operation (batch, bolus fed‐batch, and continuous fed‐batch) and grown on two different bioreactor scales (3 L bench‐top and 15 L pilot‐scale). The Monod kinetic model was developed for all modes of operation under study and predicted cell density, glucose glutamine, lactate, and ammonia concentrations well for the bioprocess. However, it was computationally demanding due to the large number of parameters necessary to produce a good model fit. The transferability of the Monod kinetic model structure and parameter set across bioreactor scales and modes of operation was investigated and a parameter sensitivity analysis performed. The experimentally determined parameters had the greatest influence on model performance. They changed with scale and mode of operation, but were easily calculated. The remaining parameters, which were fitted using a differential evolutionary algorithm, were not as crucial. Logistic equation and statistical regression models were investigated as alternatives to the Monod kinetic model. They were less computationally intensive to develop due to the absence of a large parameter set. However, modeling of the nutrient and metabolite concentrations proved to be troublesome due to the logistic equation model structure and the inability of both models to incorporate a feed. The complexity, computational load, and effort required for model development has to be balanced with the necessary level of model sophistication when choosing which model type to develop for a particular application. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

广谱流感疫苗的研究进展

流行性感冒(简称流感)的频频暴发严重危害人类健康和公共卫生,已引起全球范围内的高度关注。预防流感最有效和经济的措施是接种疫苗,但流感病毒的持续变异可逃逸人群已有的免疫应答,目前使用的季节性流感疫苗仅对亚型内抗原匹配较好的毒株产生免疫保护作用,难以有效应对因抗原漂移或抗原转换而产生的无法预料的流感大流行。因此,研发对流感病毒不同亚型均具有交叉免疫保护作用的广谱流感疫苗具有重要意义。近年来,流感病毒广谱中和抗体的发现、对流感病毒抗原保守区域及细胞免疫机制的深入研究、疫苗免疫策略的优化等都为广谱流感疫苗的研发提供了新思路。本文简述了近几年基于血凝素、基质蛋白、核蛋白等多种流感靶抗原的广谱流感疫苗的研究进展。     

Chemical Composition of Ballota macedonica Vandas and Ballota nigra L. ssp. foetida (Vis.) Hayek Essential Oils – The Chemotaxonomic Approach

The essential oils isolated from fresh aerial parts of Ballota macedonica (two populations) and Ballota nigra ssp. foetida were analyzed by GC and GC/MS. Eighty five components were identified in total; 60 components in B. macedonica oil (population from the Former Yugoslav Republic of Macedonia), 34 components in B. macedonica oil (population from the Republic of Serbia), and 33 components in the oil of B. nigra ssp. foetida accounting for 93.9%, 98.4%, and 95.8% of the total oils, respectively. The most abundant components in B. macedonica oils were carotol (13.7 – 52.1%), germacrene D (8.6 – 24.6%), and (E)‐caryophyllene (6.5 – 16.5%), while B. nigra ssp. foetida oil was dominated by (E)‐phytol (56.9%), germacrene D (10.0%), and (E)‐caryophyllene (4.7%). Multivariate statistical analyses (agglomerative hierarchical cluster analysis and principal component analysis) were used to compare and discuss relationships among Ballota species examined so far based on their volatile profiles. The chemical compositions of B. macedonica essential oils are reported for the first time.     

Quantative analysis and paleoecology of Middle to Upper Eocene Ostracods from Jebel Jebil,central Tunisia

One hundred and seventy collected samples from Jebil section have been carefully studied for their ostracod content and referred to 41 species belonging to 20 genera. Their vertical distribution allowed to distinguish five successive associations of ostracod assemblages; two of which are correlated with the Early Lutetian, one with the Late Lutetian, another association with the Bartonian and the last one with the Priabonian. Community structure of the collected ostracod fauna has been studied; three indices have been calculated for each sample: Shannon (diversity), Margalef (richness) and Equitability indexes. In the lower and the middle part of the Formation, they indicate a stable environment supporting high diversity ostracod communities; whereas in the upper portion the environmental conditions were unstable characterized by low diversity. The results of a multivariate statistical method, using the cluster analysis and the Detrended Correspondence Analysis of the 41 ostracod species and the 170 samples, have led to conclude that the most effective environmental factor in the study area is the paleodepth and of less importance oxygenation and salinity. Thus, it allowed to distinguish four palaeoenvironmental intervals within the Cherahil Formation: the first one represented by taxa that are known from the shallower parts of the shelf; the second interval includes the majority of the encountered species of inner neritic shelf with normal salinity; the third one, corresponding to an outer neritic domain; and the last interval refers to a circalittoral environment, is comprised mainly of Cytherella angulata and of Soudanella laciniosa triangulata.     

Ecological total-factor energy efficiency of China’s energy intensive industries

This paper uses a meta-frontier slack-based DEA model to measure the ecological total-factor energy efficiency as well as the energy conservation potential of China’s four energy intensive subsectors. We incorporate both desirable and undesirable output together in the period, 2000–2013. The conclusions are: firstly, under the meta-frontier, the four subsectors of energy intensive industries have low average level of ecological total-factor energy efficiencies. They are 0.137, 0.212, 0.238, and 0.307 in the non-metallic mineral products manufacturing industry, raw chemical materials and chemical products manufacturing industry, smelting and pressing of ferrous metals industry, and smelting and pressing of non-ferrous metals industry, respectively. Secondly, the ecological energy efficiency in East China is the highest among three regions. Central China and West China are behind, but they are extremely close to each other. Thirdly, East China almost has no technology gap pertaining to energy efficiency, while Central China and West China almost have the same gap. Finally, Sichuan is considered to be the best province in West China under group frontier due to its perform in the three energy intensive subsectors. For Central and East China, no province has higher ecological energy efficiency in more than two energy intensive subsectors.