Multiscale Analysis of Biological Systems

It is argued that multiscale approaches are necessary for an explanatory modeling of biological systems. A first step, besides common to the multiscale modeling of physical and living systems, is a bottom-up integration based on the notions of effective parameters and minimal models. Top-down effects can be accounted for in terms of effective constraints and inputs. Biological systems are essentially characterized by an entanglement of bottom-up and top-down influences following from their evolutionary history. A self-consistent multiscale scheme is proposed to capture the ensuing circular causality. Its differences with standard mean-field self-consistent equations and slow-fast decompositions are discussed. As such, this scheme offers a way to unravel the multilevel architecture of living systems and their regulation. Two examples, genome functions and biofilms, are detailed.     

Papuan Pasts: Cultural, Linguistic and Biological Histories of Papuan-Speaking Peoples

Papuan Pasts: Cultural, Linguistic and Biological Histories of Papuan-Speaking Peoples . Andrew Pawley, Robert Attenborough, Jack Golson, and Robin Hide, eds. Canberra: Pacific Linguistics, 2006. 817 pp.     

Multiscale Adaptive Marginal Analysis of Longitudinal Neuroimaging Data with Time‐Varying Covariates

Summary Neuroimaging data collected at repeated occasions are gaining increasing attention in the neuroimaging community due to their potential in answering questions regarding brain development, aging, and neurodegeneration. These datasets are large and complicated, characterized by the intricate spatial dependence structure of each response image, multiple response images per subject, and covariates that may vary with time. We propose a multiscale adaptive generalized method of moments (MA‐GMM) approach to estimate marginal regression models for imaging datasets that contain time‐varying, spatially related responses and some time‐varying covariates. Our method categorizes covariates into types to determine the valid moment conditions to combine during estimation. Further, instead of assuming independence of voxels (the components that make up each subject’s response image at each time point) as many current neuroimaging analysis techniques do, this method “adaptively smoothes” neuroimaging response data, computing parameter estimates by iteratively building spheres around each voxel and combining observations within the spheres with weights. MA‐GMM’s development adds to the few available modeling approaches intended for longitudinal imaging data analysis. Simulation studies and an analysis of a real longitudinal imaging dataset from the Alzheimer’s Disease Neuroimaging Initiative are used to assess the performance of MA‐GMM. Martha Skup, Hongtu Zhu, and Heping Zhang for the Alzheimer’s Disease Neuroimaging Initiative.     

Using Biological Pathway Data with Paxtools

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.

This is a PLOS Computational Biology Software Article

     

Biological degradation of Ascophyllum nodosum

The alginate forms the major structural component of the cell wall and the intercellular matrix of the brown alga Ascophyllum nodosum. Successful biological degradation of A. nodosum would largely depend on the dissolution of the alginate, but reactive compounds in the alga such as polyphenols may also have toxic effects on the microbial population involved. Aerobic and anaerobic batch reactors, operated at 35°C and pH 7, were fed milled A. nodosum, nutrients and inocula adapted to seaweed degradation. The dominant factor for conversion of organic matter during anaerobic digestion was the inhibitory effect of the polyphenols on alginate lyases and methane production. Probably, the relative large fraction of high molecular weight polyphenols (>10 kDa) in this alga gave efficient binding of proteins during digestion. The anaerobic degradation was greatly stimulated when the polyphenols were fixed with low amounts of formaldehyde. An accumulated content of guluronate in the remaining alginate indicated that Ca-crosslinking also limited the guluronate lyase access to the polymer. In contrast, the aerobic digestion of alga gave no increase in the guluronate content of the residual alginate. Compared to anaerobic conditions, the phenols had a much lower influence on the hydrolytic rate of organic matter during aerobic conditions. This revised version was published online in August 2006 with corrections to the Cover Date.     

A Comprehensive Specimen-Specific Multiscale Data Set for Anatomical and Mechanical Characterization of the Tibiofemoral Joint

Understanding of tibiofemoral joint mechanics at multiple spatial scales is essential for developing effective preventive measures and treatments for both pathology and injury management. Currently, there is a distinct lack of specimen-specific biomechanical data at multiple spatial scales, e.g., joint, tissue, and cell scales. Comprehensive multiscale data may improve the understanding of the relationship between biomechanical and anatomical markers across various scales. Furthermore, specimen-specific multiscale data for the tibiofemoral joint may assist development and validation of specimen-specific computational models that may be useful for more thorough analyses of the biomechanical behavior of the joint. This study describes an aggregation of procedures for acquisition of multiscale anatomical and biomechanical data for the tibiofemoral joint. Magnetic resonance imaging was used to acquire anatomical morphology at the joint scale. A robotic testing system was used to quantify joint level biomechanical response under various loading scenarios. Tissue level material properties were obtained from the same specimen for the femoral and tibial articular cartilage, medial and lateral menisci, anterior and posterior cruciate ligaments, and medial and lateral collateral ligaments. Histology data were also obtained for all tissue types to measure specimen-specific cell scale information, e.g., cellular distribution. This study is the first of its kind to establish a comprehensive multiscale data set for a musculoskeletal joint and the presented data collection approach can be used as a general template to guide acquisition of specimen-specific comprehensive multiscale data for musculoskeletal joints.     

Investigation of the Effect of Data Error in the Analysis of Biological Tracer Data

Data obtained from tracer studies often consist of serial measurements after administration of radioisotope. Very little work has been published on how the error in the data affects the mathematical analysis. Computer simulation was here employed to produce data with error of different magnitude and form for each of several values of rate constant and amplitude. The data were terminated when the value of the last point was 5% of the value of the first point, and also in other ways arranged to simulate experimental situations. The sets of simulated data for a two compartment system were analyzed by the gaussian iterative technique. With a rate constant ratio of at least four the technique converged for data errors of 5% or less. The calculated error in the rate constants ranged from 2 to 85%, and in the amplitudes from 1 to 50%, for data error of 0.5 to 10%. The lesser rate constant and amplitude had the greater errors. If a wrong assumption was made in the analysis about the variation of data error over the time interval of measurement, then the calculated values of parameter standard deviations were greatly in error. The results can be used to decide what experimental accuracy is needed for a given accuracy of model parameters for a variety of biological problems.     

Biological notes on a fungus-growing ant, Trachymyrmex cf. zeteki (Hymenoptera, Formicidae, Attini) attacked by a diverse community of parasitoid wasps (Hymenoptera, Diapriidae)

A number of wasps in the family Diapriidae, subfamily Diapriinae (Proctotrupoidea), are parasitoids that specialize on ant larvae. These wasps are abundant and diverse in the Neotropics, but little is known about their biology. We studied parasitism rates by an array of diapriine wasps that attack the larvae of fungus-growing ants, Trachymyrmex cf. zeteki, in a single population (near Gamboa, Panamá). Relatively little is known about the biology and natural history of these ants, so we also present data on colony size and nest architecture. We excavated 136 colonies in central Panamá from June to September 2006, and 20 nests from July 2009. We reared six wasp morphotypes; two of them in the genus Mimopriella Masner and Garcia, one Oxypria Kieffer, two Szelenyiopria Fabritius and one Acanthopria Ashmead. The mean intensity of larval parasitism per ant colony was 33.9% (2006), and its prevalence across all ant populations was 27.2% (2006 and 2009). Parasitism rates were not positively correlated with host colony size. A single case of super-parasitism was documented in which two Oxypria males were reared from the same host larva.     

Landscape Pattern Dynamics and Mechanisms during Vegetation Restoration: A Multiscale,Hierarchical Patch Dynamics Approach

The spatial pattern of vegetation changes during ecological restoration, and these changes are affected by the process of restoration. The objective of this study was to integrate the pattern and mechanism of forest restoration in the Dinghushan Nature Reserve (DNR), Guangdong, China, based on data from remote sensing and long‐term field observations. We studied the pattern dynamics of three main forest types and their underlying mechanisms during restoration following a multiscale, hierarchical patch dynamics framework that integrates population, community, and landscape processes. Remote sensing data were used to determine the changes in landscape pattern during different periods of forest restoration from 1978 to 2006. At the landscape scale, the number, area, and perimeter of the needle/broad‐leaved mixed forest (MF) and the evergreen broad‐leaved forest (BF) increased, whereas those of the tropical needle‐leaved forest (NF) decreased during succession. Our analysis based on long‐term field observations indicated that the change rate of NF was lower than that of MF during 1981–1996, but became much higher during 1996–2007. The rate of change in landscape pattern and the progression of succession stages were consistent with each other. Our results also showed that species regeneration and community succession are the biological basis of forest landscape dynamics during vegetation restoration. Landscape pattern analysis allowed us to show “what” happened during vegetation restoration and “where,” and population and community analysis indicated “why” and “how” it happened.     

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea

Proteomics Data Collection (ProDaC) is an EU-funded "Coordination Action" within the 6th framework programme. It aims to simplify the publication, dissemination and utilization of proteomics data by establishing standards that will support broad data collection from the research community. As a part of ProDaC, regular workshops are organized on a half-yearly basis to enable communication and discussion of the involved partners and to report on project progress. After the kick-off meeting (October 2006) in Long Beach, CA, USA and the 1st workshop in Lyon, France (April 2007), the 2nd ProDaC workshop took place at the COEX InterContinental Hotel in Seoul, Korea, on 5th October 2007, shortly before the HUPO World Congress. The progress achieved within the first year was presented by the leaders of the work packages. Additionally, a Journal's representative talked about his experiences and future plans concerning Proteomics standards; and two further external speakers presented their research related to data handling and Proteomics repositories.     

Predicting Biological Invasions

There are various approaches to explain the mechanisms of biological invasions. It is possible (1) to focus on the characteristics of invading species and (2) on those of the ecosystems invaded, (3) to investigate the relationship between these two factors (key–lock approach), or (4) to differentiate the invasion process in time. Each of these approaches may serve to improve the understanding of some aspects of biological invasions, and each of them is in some way suitable for the purpose of predicting invasions. We discuss the usefulness and the limitations of these approaches, focusing on case studies from central Europe. An example of the fourth approach, a model of steps and stages of plant invasions that describes the invasion process in greater detail, illustrates some general limitations in predicting biological invasions. This revised version was published online in July 2006 with corrections to the Cover Date.     

生物实验数据的两因素方差分析

结合实例详细地叙述了生物实验数据的两因素方差分析计算方法,具有较强的实用意义。并介绍了如何分析计算结果。     

Glass frogs (Centrolenidae) of Yanayacu Biological Station, Ecuador, with the description of a new species and comments on centrolenid systematics

We describe Centrolene bacatum , C. buckleyi , Cochranella posadae , and a new species of Cochranella from Yanayacu Biological Station on the Amazonian slopes of the Ecuadorian Andes. The new species differs from other species in Centrolenidae by a combination of characters, including reduced webbing between Fingers III and IV, and kidneys covered with white peritoneum. We summarize the current generic and infrageneric classification in Centrolenidae and discuss some of its problems. A phylogenetic analysis of morphological and behavioural data shows that the genera Centrolene and Cochranella might not be monophyletic; the genus Hyalinobatrachium and, in particular, the group H. fleischmanni seem to be monophyletic. However, an analysis with many more characters is needed to resolve the relationships of glass frogs.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 489–513.     

系统生物学研究中不同组学数据的整合

高通量实验方法的发展导致大量基因组、转录组、代谢组等组学数据的出现,组学数据的整合为全面了解生物学系统提供了条件.但是,由于当前实验技术手段的限制,高通量组学数据大多存在系统偏差,数据类型和可靠程度也各不相同,这给组学数据的整合带来了困难.本文以转录组、蛋白质组和代谢组为重点,综述了近年来组学数据整合方面的研究进展,包括新的数据整合方法和分析平台.虽然现存的数据统计和网络分析的方法有助于发现不同组学数据之间的关联,但是生物学意义上的深层次的数据整合还有待于生物、数学、计算机等各种领域的全面发展.     

Topological Data Analysis of Biological Aggregation Models

We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D''Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters.     

What,if anything,is a ‘typical’ viper? Biological attributes of basal viperid snakes (genus Causus Wagler, 1830)

For many major phylogenetic radiations of organisms, the available ecological knowledge is disproportionately derived from a small minority of taxa, and sometimes from organisms that are highly atypical. Viperid snakes provide a good example of this situation; high-latitude cold-climate taxa in northern Europe (vipers) and North America (rattlesnakes) have been studied intensively, but more speciose radiations in tropical Africa, Asia, and Central America remain poorly known. We dissected > 500 specimens (six species) of night adders (genus Causus ), mostly from Cameroon (68%) in equatorial Africa, to quantify morphology, diets, and reproductive biology. By contrast to the 'slow' life-histories of cold-climate viperids, night adders feed frequently on frogs (rather than infrequently on mammals), and produce frequent large clutches of relatively small eggs (rather than infrequent small litters of relatively large live young). Thus, putatively 'typical' viperid attributes such as low fecundity, viviparity, and predation on mammals reflect adaptations to the invasion of cold environments by a small and perhaps atypical subset of viperid taxa. Our data on prey size suggest that one of the critical innovations of early viperids may have been an ability to subdue and ingest relatively large prey.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 575–588.     

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain

The "Coordination Action" ProDaC (Proteomics Data Collection) - funded by the EU within the 6th framework programme - was created to support the dissemination, utilization and publication of proteomics data. Within this international consortium, standards are developed and maintained to support extensive data collection by the proteomics community. An important part of ProDaC are workshops organized on a regular basis (two per year) to allow discussions and communication between the ProDaC partners and to report on the progress of the project. The kick-off meeting took place in October 2006 in Long Beach, CA, USA. The 1st ProDaC workshop was held in Lyon, France (April 2007) and the 2nd in Seoul, Korea in October 2007. ProDaC organized the 3rd ProDaC workshop at the Beatriz Hotel, Toledo, on 22nd April, 2008, directly before the HUPO - PSI spring meeting (Human Proteome Organisation - Proteomics Standards Initiative). The work package coordinators presented talks about the progress achieved during the past six months. Additionally four external speakers presented their work on data conversion and data repositories. The concluding discussion session was chaired by the Journal's representative.     

Biological evaluation of running waters in Korea, with special reference to bioassessment using the PFU system

A total of six stations in the Han River system were selected for establishing polyurethane foam units (PFUs) to collect protozoans, including phytomastigophorans, zoomastigophorans, amoebas and ciliates, in July 1993. In the bioassessment of microbial communities using the PFUs, the number of species decreased as pollution intensity increased. The diversity index values calculated at the main stations generally agreed with the pollution status of the stations. Anyang-Chon (Chon means stream) showed the lowest diversity value (1.89), and all stations, except Masok and Anyang-Chon, showed diversity index values ranging from 3.15 to 3.93. The highest heterotrophic index (HI) value was detected in Anyang-Chon followed by Masok-Chon. The number of species at the main stations reached a maximum on day 11 of being exposed to PFUs. The results of _eq, G and T_90% all suggest that bioassessments using the PFU system were well matched with pollution status of the water. All microbial variables were significantly correlated with comprehensive chemical pollution indices, P_a and P_b , with correlation coefficients ranging from r =0.87 to r=0.96. This revised version was published online in July 2006 with corrections to the Cover Date.