大数据时代的整合生物信息学

随着生物数据测量技术的不断发展,生物数据的类型、内容、复杂度不断增加,生物信息学已迈入大数据时代。面对大数据时代多模态、多层次、高维度、非线性的复杂生物数据,生物信息学需要发展相应的方法和技术进行有效整合生物信息学研究与应用。本文对大数据时代整合生物信息学所涉及的数据整合、方法整合、系统整合及相关问题进行梳理和探讨。     

Recognition of facial expressions in a Japanese monkey (Macaca fuscata) and humans (Homo sapiens)

Recognition of facial expressions by a Japanese monkey and two humans was studied. The monkey subject matched 20 photographs of monkey facial expressions and 20 photographs of human facial expressions. Humans sorted the same pictures. Matching accuracy by the monkey was about 80% correct for both human and monkey facial expressions. The confusion matrices of those facial expressions were analyzed by a multi-dimensional scaling procedure (MDSCAL). The resulting MDS plots suggested that the important cues in recognizing facial expressions of monkeys were “thrusting the mouth” and ‘raising the eyebrows.” Comparison of the MDS plots by the monkey subject with those by human subjects suggested that the monkey categorized the human “happiness” faces. This may suggest that the monkey has an ability to recognize human smile face even though it is learned. However, the monkey did not differentiate the human “anger/disgust” faces from the human “sad” faces, while human subjects clearly did. This may correlate with the lack of eyebrow movement in monkeys.     

纤维素乙醇高温发酵的研究进展与展望

利用高温细菌发酵,纤维素乙醇生产有望实现“生物质降解-乙醇发酵-乙醇蒸馏”过程的同步化,从而最大限度地降低纤维素乙醇的生产成本;这是一个目标更高、道路更远、科学性更强的可再生能源发展策略.纤维素乙醇高温发酵研究已经取得了重要进展,目前面临的主要挑战包括发酵乙醇的高温细菌的遗传转化系统不够稳定、缺少内源的高活性和耐热性纤维素酶,以及乙醇代谢调控机理有待进一步解析.这些科技难题将会在DNA生物合成和进化技术、细胞生物学技术,以及合成生物学技术的发展中得到解决.     

Intermediate host specificity in Schistosoma mansoni

Miracidia of Schistosoma mansoni penetrate into many kinds of snails, but development of normal sporocysts takes place only in certain species of Biomphalaria. Different populations of this snail vary greatly in laboratory infection rates with S. mansoni originating from diverse geographic localities. Cross-exposure experiments show that compatibility factors exist in both snails and parasites. Susceptibility of stocks of Biomphalaria to particular strains of S. mansoni is genetically determined and may be modified by selection in the laboratory. In a compatible snail, the sporocyst develops without host tissue reaction; in incompatible snails the early larvae are rapidly surrounded by amebocytes and fibroblasts, and destroyed. This reaction resembles the generalized host cellular response elicited by any foreign body. An individual snail exposed to many miracidia may have both developing and encapsulated sporocysts side by side within its tissues. The weight of current evidence suggests that elicitation or absence of this cellular response resides in the recognition or nonrecognition of the sporocyst as a foreign body. The sporocyst tegument surface, which forms within a few hours after miracidial penetration, may have a molecular conformation identical with that of the snail, or may be able to bind specific host molecules, so that detection and subsequent encapsulation by host cells are averted. Presuming genetic determination of the sporocyst surface structure and of the host cell detection capability, differing infection rates would result from the particular frequencies of relevant genes in the populations concerned.     

Analyzing the biology on the system level

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology--systemic structures, dynamics, control methods, and design principles.     

Three‐dimensional cell culture model utilization in cancer stem cell research

Three‐dimensional (3D) cell culture models are becoming increasingly popular in contemporary cancer research and drug resistance studies. Recently, scientists have begun incorporating cancer stem cells (CSCs) into 3D models and modifying culture components in order to mimic in vivo conditions better. Currently, the global cell culture market is primarily focused on either 3D cancer cell cultures or stem cell cultures, with less focus on CSCs. This is evident in the low product availability officially indicated for 3D CSC model research. This review discusses the currently available commercial products for CSC 3D culture model research. Additionally, we discuss different culture media and components that result in higher levels of stem cell subpopulations while better recreating the tumor microenvironment. In summary, although progress has been made applying 3D technology to CSC research, this technology could be further utilized and a greater number of 3D kits dedicated specifically to CSCs should be implemented.     

A novel method for quantifying overdispersion in count data and its application to farmland birds

The statistical modelling of count data permeates the discipline of ecology. Such data often exhibit overdispersion compared with a standard Poisson distribution, so that the variance of the counts is greater than that of the mean. Whereas modelling to reveal the effects of explanatory variables on the mean is commonplace, overdispersion is generally regarded as a nuisance parameter to be accounted for and subsequently ignored. Instead, we propose a method that models the overdispersion as a biologically interesting property of a data set and show how novel inference is provided as a result. We adapted the double hierarchical generalized linear model approach to create an easily extendible model structure that quantifies the influence of explanatory variables on the overdispersion of count data, and apply it to farmland birds. These data were from a study within Irish agricultural ecosystems, in which total bird species abundance and the abundance of farmland indicator species were compared on dairy and non‐dairy farms in the winter and breeding seasons. In general, overdispersion in bird counts was greater on dairy farms than on non‐dairy farms, and for total bird numbers, overdispersion was greatest on dairy farms in winter. Our code is fitted using the Bayesian package Rstan, and we make all code and data available in a GitHub repository. Within a Bayesian framework, this approach facilitates a meaningful quantification of the effects of categorical explanatory variables on any response variable with a tendency to overdispersion that has a meaningful biological or ecological explanation.     

Dectin-1 Activation Controls Maturation of β-1,3-Glucan-containing Phagosomes

Elimination of fungal pathogens by phagocytes requires phagosome maturation, a process that involves the recruitment and fusion of intracellular proteins. The role of Dectin-1, a β-1,3-glucan receptor, critical for fungal recognition and triggering of Th17 responses, to phagosomal maturation has not been defined. We show that GFP-Dectin-1 translocates to the fungal phagosome, but its signal decays after 2 h. Inhibition of acidification results in retention of GFP-Dectin-1 to phagosome membranes highlighting the requirement for an acidic pH. Following β-1,3-glucan recognition, GFP-Dectin-1 undergoes tyrosine phosphorylation by Src kinases with subsequent Syk activation. Our results demonstrate that Syk is activated independently of intraphagosomal pH. Inhibition of Src or Syk results in prolonged retention of GFP-Dectin-1 to the phagosome signifying a link between Syk and intraphagosomal pH. β-1,3-glucan phagosomes expressing a signaling incompetent Dectin-1 failed to mature as demonstrated by prolonged Dectin-1 retention, presence of Rab5B, failure to acquire LAMP-1 and inability to acidify. Phagosomes containing Candida albicans also require Dectin-1-dependent Syk activation for phagosomal maturation. Taken together, these results support a model where Dectin-1 not only controls internalization of β-1,3-glucan containing cargo and triggers proinflammatory cytokines, but also acts as a master regulator for subsequent phagolysosomal maturation through Syk activation.     

Revealing turning points in ecosystem functioning over the Northern Eurasian agricultural frontier

The collapse of the Soviet Union in 1991 has been a turning point in the World history that left a unique footprint on the Northern Eurasian ecosystems. Conducting large scale mapping of environmental change and separating between naturogenic and anthropogenic drivers is a difficult endeavor in such highly complex systems. In this research a piece‐wise linear regression method was used for breakpoint detection in Rain‐Use Efficiency (RUE) time series and a classification of ecosystem response types was produced. Supported by earth observation data, field data, and expert knowledge, this study provides empirical evidence regarding the occurrence of drastic changes in RUE (assessment of the timing, the direction and the significance of these changes) in Northern Eurasian ecosystems between 1982 and 2011. About 36% of the study area (3.4 million km²) showed significant (P < 0.05) trends and/or turning points in RUE during the observation period. A large proportion of detected turning points in RUE occurred around the fall of the Soviet Union in 1991 and in the following years which were attributed to widespread agricultural land abandonment. Our study also showed that recurrent droughts deeply affected vegetation productivity throughout the observation period, with a general worsening of the drought conditions in recent years. Moreover, recent human‐induced turning points in ecosystem functioning were detected and attributed to ongoing recultivation and change in irrigation practices in the Volgograd region, and to increased salinization and increased grazing intensity around Lake Balkhash. The ecosystem‐state assessment method introduced here proved to be a valuable support that highlighted hotspots of potentially altered ecosystems and allowed for disentangling human from climatic disturbances.     

Bacterial and phytoplankton dynamics in a sub-tropical estuary

Heterotrophic bacterial and phytoplankton biomass, production, specific growth rates and growth efficiencies were studied in July 2001 and January 2002 during both spring and neap tides, along a tidal cycle, at three sites in a subtropical estuary. Major freshwater inputs located in the Northern region led to differences in both phytoplankton and bacterioplankton biomass and activity along the estuary. While in the Northern region phytoplankton is light-limited, with mean phytoplankton production (PP) between 1.1 and 1.9 μg C l⁻¹ h⁻¹ and mean specific growth rates (PSG) between 0.14 and 0.16 d⁻¹, the Southern region registered values as high as 24.7 μg C l⁻¹ h⁻¹ for PP and 2.45 d⁻¹ (mean PP between 3.4 and 7.3 μg C l⁻¹ h⁻¹; mean PSG between 0.28 and 0.57 d⁻¹). On the other hand, maximum bacterial production (BP: 63.8 μg C l⁻¹ h⁻¹) and specific growth rate (BSG: 32.26 d⁻¹) were observed in the Northern region (mean BP between 3.4 and 12.8 μg C l⁻¹ h⁻¹; mean BSG between 1.98 and 6.67 day⁻¹). These bacterial activity rates are among the highest recorded rates in estuarine and coastal waters, indicating that this system can be highly heterotrophic, due to high loads of allochthonous carbon (mainly derived from mangrove forest). Our results also showed that, despite that BP rates usually exceeded PP, in the Southern region BP may be partially supported (∼45%) by PP, since a significant regression was observed between BP and PP (r = 0.455, P < 0.001). Handling editor: P. Viaroli