Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

Molecular entities present in a cell (mRNA, proteins, metabolites,…) do not act in isolation, but rather in cooperation with each other to define an organisms form and function. Their concerted action can be viewed as networks of interacting entities that are active under certain conditions within the cell or upon certain environmental signals. A main challenge in systems biology is to model these networks, or in other words studying which entities interact to form cellular systems or accomplish similar functions. On the contrary, viewing a single entity or an experimental dataset in the light of an interaction network can reveal previous unknown insights in biological processes. In this review we give an overview of how integrated networks can be reconstructed from multiple omics data and how they can subsequently be used for network-based modeling of cellular function in bacteria.     

Adaptedness, evolution and a hierarchical concept of fitness.

Fitness is a consequence of the adaptedness of an entity to its environment. The fitness of an evolutionary entity, when the entity is defined by a set of attributes determining how it interacts with its environment, is manifested as persistence of those attributes. Two measures of fitness are presented to explicate this concept: (1) an extensive measure of the persistence of the original set of attributes in the individual entity and its descendants, but corrected for evolution; this includes as a special case fitness as used in population genetics; and, (2) an intensive measure that is independent of the abundance of descendant exemplars. Fitness as conceived here is a function of survival time, degree of evolution, and when applicable, reproductive contribution. The rate of fitness increase of an entity will vary inversely with the degree of evolutionary change experienced by the entity, its descendants, or both through time. Adaptive evolution can increase the length of time that fitness accumulates by increasing the survival of descendants possessing all or some of the ancestral attributes. Reproduction, where possible, can increase the number of descendants. This concept of fitness is simple, unambiguous, coherent, and applicable to entities at any hierarchical level of interest to ecologists and evolutionary biologists.     

Integration, individuality and species concepts

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. This revised version was published online in July 2006 with corrections to the Cover Date.     

A COMPARATIVE STUDY OF THE RED ALGA GRATELOUPIA FILICINA (HALYMENIACEAE) FROM THE NORTHWESTERN PACIFIC AND MEDITERRANEAN WITH THE DESCRIPTION OF GRATELOUPIA ASIATICA, SP. NOV.

Morphological observations and molecular analyses of the red alga Grateloupia filicina (Halymeniaceae) from two geographically distant regions, eastern Asia (Japan and northern China) in the northwestern Pacific and Italy in the Mediterranean, reveal the presence of two distinct entities. Morphologically, the eastern Asian entity differs substantially from the Italian entity in the following ways: 1) thin and soft thalli with wider axes, 2) denser medullary filaments, 3) scattered reproductive structures over the entire thallus, and 4) a mature auxiliary cell that is oval and slightly larger than other ampullary cells. Phylogenetic analysis based on the ribulose-1,5-bisphosphate carboxylase/oxygenase gene ( rbc L) sequences revealed that the eastern Asian and Italian entities are phylogenetically far apart, strongly supporting the differentiation of these two entities at the species level. The eastern Asian entity is therefore described as a new species, Grateloupia asiatica. This species can be distinguished from most known species of Grateloupia that have widely flattened thalli by its compressed to narrowly flattened axes with numerous pinnate proliferations and from a few species with similar thalli by a particular combination of features, including a gelatinous texture, mostly simple and narrower axes, a thinner cortex, and the absence of catenate proliferations.     

Colon-Derived Liver Metastasis,Colorectal Carcinoma,and Hepatocellular Carcinoma Can Be Discriminated by the Ca2+-Binding Proteins S100A6 and S100A11

Background

It is unknown, on the proteomic level, whether the protein patterns of tumors change during metastasis or whether markers are present that allow metastases to be allocated to a specific tumor entity. The latter is of clinical interest if the primary tumor is not known.

Methodology/Principal Findings

In this study, tissue from colon-derived liver metastases (n = 17) were classified, laser-microdissected, and analysed by ProteinChip arrays (SELDI). The resulting spectra were compared with data for primary colorectal (CRC) and hepatocellular carcinomas (HCC) from our former studies. Of 49 signals differentially expressed in primary HCC, primary CRC, and liver metastases, two were identified by immunodepletion as S100A6 and S100A11. Both proteins were precisely localized immunohistochemically in cells. S100A6 and S100A11 can discriminate significantly between the two primary tumor entities, CRC and HCC, whereas S100A6 allows the discrimination of metastases and HCC.

Conclusions

Both identified proteins can be used to discriminate different tumor entities. Specific markers or proteomic patterns for the metastases of different primary cancers will allow us to determine the biological characteristics of metastasis in general. It is unknown how the protein patterns of tumors change during metastasis or whether markers are present that allow metastases to be allocated to a specific tumor entity. The latter is of clinical interest if the primary tumor is not known.     

Mass, volume and dimensional distributions in biology, with special reference to cells

The positively skewed distribution of mass (weight) in biology was examined, and it was concluded all weight or masses can best be described by lognormal theory. Examples are given ranging in weight from viruses to humans. The accretion of mass proceeds as "more of the same" and primarily does not alter function. Immunologic properties must be carefully preserved. Small biologic entities can afford only small mass gains or losses while preserving their functionality; the larger the entity, the larger is the variability of mass functionally permitted. A well-established, convenient graphic method of analyzing a sample is described, with the advantages and pitfalls discussed. At the cellular level, volume and dimensions are lognormally distributed whenever the specific gravity (g/cu cm) is nearly homogenous among the particles or cells. In multicellular organisms, dimensions and forms (such as height and cranial circumference) are primarily the product of multifactorial genetic determinants and frequently appear as normal distributions. This paper discusses the meaning of the law of proportionate effects for small biologic objects, especially cells, and how an initial or "elementary" distribution may be conceived.     

Entity Normalization in Life Cycle Assessment: Hybrid Schemes Applied to a Transportation Agency Case Study

Government agencies, companies, and other entities are using environmental assessments, like life cycle assessment (LCA), as an input to decision‐making processes. Communicating the esoteric results of an LCA to these decision makers can present challenges, and interpretation aids are commonly provided to increase understanding. One such method is normalizing results as a means of providing context for interpreting magnitudes of environmental impacts. Normalization is mostly carried out by relating the environmental impacts of a product (or process) under study to those of another product or a spatial reference area (e.g., the United States). This research is based on the idea that decision makers might also benefit from normalization that considers comparisons to their entity's (agency, company, organization, etc.) total impacts to provide additional meaning and aid in comprehension. Two hybrid normalization schemes have been developed, which include aspects of normalization to both spatially based and entity‐based impacts. These have been named entity‐overlaid and entity‐accentuated normalization, and the schemes allow for performance‐based planning or emphasizing environmental impact types that are most relevant to an entity's operational profile, respectively. A hypothetical case study is presented to demonstrate these schemes, which uses environmental data from a U.S. transportation agency as the basis for entity normalization factors. Results of this case study illustrate how entity‐related references may be developed, and how this additional information may enhance the presentation of LCA results using the hybrid normalization schemes.     

Response misclassification in studies on bilateral diseases

Misclassification in binary outcomes can severely bias effect estimates of regression models when the models are naively applied to error‐prone data. Here, we discuss response misclassification in studies on the special class of bilateral diseases. Such diseases can affect neither, one, or both entities of a paired organ, for example, the eyes or ears. If measurements are available on both organ entities, disease occurrence in a person is often defined as disease occurrence in at least one entity. In this setting, there are two reasons for response misclassification: (a) ignorance of missing disease assessment in one of the two entities and (b) error‐prone disease assessment in the single entities. We investigate the consequences of ignoring both types of response misclassification and present an approach to adjust the bias from misclassification by optimizing an adequate likelihood function. The inherent modelling assumptions and problems in case of entity‐specific misclassification are discussed. This work was motivated by studies on age‐related macular degeneration (AMD), a disease that can occur separately in each eye of a person. We illustrate and discuss the proposed analysis approach based on real‐world data of a study on AMD and simulated data.     

Anatomical Entity Recognition with a Hierarchical Framework Augmented by External Resources

References to anatomical entities in medical records consist not only of explicit references to anatomical locations, but also other diverse types of expressions, such as specific diseases, clinical tests, clinical treatments, which constitute implicit references to anatomical entities. In order to identify these implicit anatomical entities, we propose a hierarchical framework, in which two layers of named entity recognizers (NERs) work in a cooperative manner. Each of the NERs is implemented using the Conditional Random Fields (CRF) model, which use a range of external resources to generate features. We constructed a dictionary of anatomical entity expressions by exploiting four existing resources, i.e., UMLS, MeSH, RadLex and BodyPart3D, and supplemented information from two external knowledge bases, i.e., Wikipedia and WordNet, to improve inference of anatomical entities from implicit expressions. Experiments conducted on 300 discharge summaries showed a micro-averaged performance of 0.8509 Precision, 0.7796 Recall and 0.8137 F1 for explicit anatomical entity recognition, and 0.8695 Precision, 0.6893 Recall and 0.7690 F1 for implicit anatomical entity recognition. The use of the hierarchical framework, which combines the recognition of named entities of various types (diseases, clinical tests, treatments) with information embedded in external knowledge bases, resulted in a 5.08% increment in F1. The resources constructed for this research will be made publicly available.     

Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement

Background  

Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used to classify the same set of entities and methods allowing the comparison of the performance of two data sources or the determination of how well a given classification agrees with another are frequently needed, especially in the absence of a universally accepted "gold standard" classification.     

On the use of the word 'epigenetic'

Over the past few years we have seen an odd change, or extension, in the use of the word 'epigenetic' when describing matters of gene regulation in eukaryotes. Although it may generally be that it is not worth arguing over definitions, this is true only insofar as the participants in the discussion know what each other means. I believe the altered use of the term carries baggage from the standard definition that can have misleading implications. Here I wish to probe our use of language in this way, and to show how such a discussion leads to some more general considerations concerning gene regulation.     

In vitro tests for the measurement of clostridial toxins, toxoids and antisera. II. Titration of Clostridium perfringens toxins and antitoxins in cell culture

The usefulness of cytopathic indicators for the titration of Cl perfringens beta and epsilon toxins has been investigated. Neutralization experiments with monoclonal antibodies have shown that the entities responsible for the lethal and dermonecrotic effects of Cl perfringens beta toxin preparations are identical. However, the cytopathic effects of the same preparations are caused by other entities. Therefore, titrations based upon lethal and dermonecrotic indicators of beta toxin are equally valid but those based on cytopathic effects are not. Similar experiments with Cl perfringens epsilon preparations have shown that their lethal, dermonecrotic and cytopathic activities are all caused by the same entity. It follows that all three activities can be valid indicators for toxin neutralization tests. Cell culture titrations of Cl perfringens epsilon antitoxin performed on rabbit sera at the levels of test prescribed by the European Pharmacopoeia have produced consistent results which agree closely with the dermonecrotic test. This test has, in turn, been shown to reflect the results of the mouse lethal test accurately. Titrations of cattle and sheep sera at lower levels of test have also produced results in close agreement with the in vivo test. It is concluded that cell culture titration offers a valid in vitro alternative to the use of mouse lethal and guinea-pig dermonecrotic indicators for the titration of sera generated in the course of potency tests and field trials of Cl perfringens epsilon vaccines.     

Cephalo-adrenal interactions in the broader context of pragmatic and theoretical rhythm models

Some of the literature on modeling of biological rhythms with mathematical, physical, chemical, biochemical, in vivo and in vitro oscillations is succintly annotated. The need for biologic models that account for the interaction of 3 or more periodic entities is indicated, documented and illustrated, with emphasis on the cephalo-adrenal network of rodents. Patterns of interaction, in this context, involve attenuation, no-effect and/or amplification by a third entity, the modulator, of the effect of an actor upon the reactor. Such feedsidewards lead to chronomodulation, a phenomenon accounting for qualitatively as well as quantitatively different modulatory effects of the same drug or other stimulus. Controversies of long standing can thus be resolved and novel effects uncovered.     

Towards a general theory of adaptive walks on rugged landscapes

Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive "walks" via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are "close" to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.     

What is hierarchical selection?

It has been proposed that natural selection occurs on a hierarchy of levels, of which the organismic level is neither the top nor the bottom. This hypothesis leads to the following practical problem: in general, how does one tell if a given phenomenon is a result of selection on level X or level Y. How does one tell what the units of selection actually are? It is convenient to assume that a unit of selection may be defined as a type of entity for which there exists, among all entities on the same “level” as that entity, an additive component of variance for some specific component F of fitness which does not appear as an additive component of variance in any decomposition of this F among entities at any lower level. But such a definition implicitly assumes that if f(x, y) depends nonadditively on its arguments, there must be interaction between the quantities which x and y represent. This assumption is incorrect. And one cannot avoid this error by speaking of “transformability to additivity” instead of merely “additivity”. A general mathematical formulation of the concepts of interaction and non-interaction is proposed, followed by a correspondingly modified approach to the definition of a unit of selection. The practical difficulty of verifying the presence of hierarchical selection is discussed.     

土壤动物知识图谱构建理论、方法与技术——以浙江天目山土壤螨类为例

土壤动物学面临以全新知识体系为科学研究框架的变革时期,其核心内容是以数据驱动为主要特征的人工智能技术方法。目前广泛应用的基于数据库的数据处理分析方法,面临着数据多源异构、快速增长和处理能力不足之间的矛盾。基于快速发展的大数据科学和人工智能技术的数据挖掘方法在解决前述矛盾中有突出优势,但需要依赖一个强大的领域知识库,然而土壤动物领域知识图谱的研究十分匮乏。土壤动物知识图谱是一个具有有向图结构的知识库,其中图的节点代表与土壤动物相关的实体或概念,图的边代表实体或概念之间的各种语义关系。提出了土壤动物知识图谱的定义、内涵、理论模型和构建方法,以浙江天目山土壤螨类多样性为例,分析了构建山地土壤动物知识图谱的技术方法;以土壤动物多样性研究关注的物种分布、物种共存、环境条件对物种的影响作用为例,探讨了基于山地土壤动物知识图谱可以解决的相关科学问题。研究表明,土壤动物知识图谱在解决生物多样性重要科学问题方面具有独特的潜力和优势,有力推动了土壤动物学、信息科学和数据科学交叉的土壤动物信息学的发展。     

Fluorophore(s) Appended Fullerene Dyads and Triads for Probing Photoinduced Energy Transfer: Syntheses, Electronic Structure, and Fluorescence Studies

Fullerene, C₆₀ was functionalized to possess one or two fluorophore entities. The fluorophore–fullerene dyads thus synthesized contain either a naphthalene, pyrene, or fluorene entity while the triads contain either a pyrene or fluorene entity in addition to a naphthalene entity. The redox behavior of these dyads and triads were probed by cyclic voltammetric technique, while the geometry and electronic structures were deduced from ab initio B3LYP/3-21G(*) method. Steady-state emission studies revealed the occurrence of energy transfer from the singlet excited fluorophore to the fullerene entity in the case of the dyads while the occurrence of step-by-step sequential energy transfer is envisioned in the case of the triads. A better ‘antenna-effect’ owing to the extended range of excitation wavelength to induce energy transfer to the appended fullerene has been achieved in the case of the triads.     

Accommodating ontologies to biological reality--top-level categories of cumulative-constitutively organized material entities

Background

The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO''s three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity.

Methodology/Principal Findings

Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities.

Conclusions/Significance

We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.