Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school

Background

The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks.

Results

The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities.

Conclusions

There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.

     

Economies of Growth or Ecologies of Survival?

ABSTRACT

The article presents the analytical framework, notably Bateson’s concepts of the double-bind and flexibility, in the context of a discussion of the Anthropocene, and outlines the subsequent articles and their internal relationships.     

A systems approach to morphogenesis in Arabidopsis thaliana: II. Modeling the regulation of shoot apical meristem structure

Two models of the mechanism maintaining a zonal structure in the shoot apical meristem (SAM) were built based on the analysis of experimental data on the interactions between CLV1, CLV2, CLV3, and WUS genes and the concepts of their role in this mechanism. The first model, a simple one-dimensional model with two morphogens, which is a variant of Wolpert’s French flag model [1], describes the regulation of zone distribution along the SAM vertical axis. Despite a number of simplifications, this model has stationary solutions with biologically meaningful interpretation. The simplifying assumptions were successively abandoned in constructing a two-dimensional model of the mechanism underlying the regulation of SAM structure. This model provides a better understanding of the distributed system that regulates the SAM structure, and allows more detailed formalization of the modern concepts and experimental data concerning this mechanism.

     

The production of extracellular copper-complexing ligands by marine and estuarine fungi

Abstract

Potentiometric titrations of filtrates from cultures of intertidal and marine fungi revealed extracellular production of strong copper-complexing ligands for 8 of 11 species tested. Conditional stability constants for these ligands at pH 7 ranged from 10⁹ to 10¹², similar to previously published constants for organic ligands from natural waters and sediments. Our results indicate that fungi could be an important source of natural chelating substances, and could play an important role in controlling the biological availability and geochemical behavior of copper in many natural systems.     

Supply of Nutrients to Cells in Engineered Tissues

Abstract

A proper supply of nutrients to cells in engineered tissues is paramount for an optimal development and survival of these tissues. However, especially in tissues with clinically relevant sizes, the mass transport of nutrients into the tissue is often insufficient to sustain all the cells within the tissue. This is not only the case during in vitro culture. After implantation of an engineered tissue, a vascular network is not directly established. Therefore, the mass transport of nutrients is also critical during the initial period after implantation.

This review introduces the basics of mass transport, leading to the conclusion that three main concepts can be used to increase nutrient supply in tissue engineering. These are; increasing the overall diffusion coefficient, decreasing the diffusion distance, or increasing convective transport. Based on these concepts, the main strategies that have been developed to enhance the supply of nutrients to cells in engineered tissues will be discussed.     

Proteome microarray technology and application: higher,wider, and deeper

ABSTRACT

Introduction: Protein microarray is a powerful tool for both biological study and clinical research. The most useful features of protein microarrays are their miniaturized size (low reagent and sample consumption), high sensitivity and their capability for parallel/high-throughput analysis. The major focus of this review is functional proteome microarray.

Areas covered: For proteome microarray, this review will discuss some recently constructed proteome microarrays and new concepts that have been used for constructing proteome microarrays and data interpretation in past few years, such as PAGES, M-NAPPA strategy, VirD technology, and the first protein microarray database. this review will summarize recent proteomic scale applications and address the limitations and future directions of proteome microarray technology.

Expert opinion: Proteome microarray is a powerful tool for basic biological and clinical research. It is expected to see improvements in the currently used proteome microarrays and the construction of more proteome microarrays for other species by using traditional strategies or novel concepts. It is anticipated that the maximum number of features on a single microarray and the number of possible applications will be increased, and the information that can be obtained from proteome microarray experiments will more in-depth in the future.     

Classroom Education and the Development of Units of Verbal Thinking: Interpreting the Results of Comparative Experimental Studies of People Who Did or Did Not Attend School

Abstract

This article discusses the performance of adults who did and did not attend school in experiments involving the definition of concepts, the finding of word-pair similarities, classification, and language objectivation. Most of the differences described correspond to the differences between every day and scientific concepts identified by L.S. Vygotsky. The existing data are insufficient to determine whether all the qualitative differences listed by Vygotsky exist between units of verbal thinking in those who did and did not attend school. In some cases, the thinking of people who did not attend school exhibits features that, according to Vygotsky, should emerge only in school with the assimilation of scientific knowledge (language objectivation and the “super-empirical” connections between concepts).     

DIGITAL FILTERS IN AUDITORY PHYSIOLOGY

ABSTRACT

In auditory research, the manipulation of signals by filtering with analog electronic filters plays an important role. Recently, digital filters that compute signal modifications in realtime became available. They can mimic all functions of analog filters, and additionally make possible new experimental concepts.

This tutorial paper introduces the concept of digital filters by using analogies from acoustics. Even complex acoustical environments can be simulated with digital filters, as they allow the programming of almost arbitrary frequency and phase responses.     

The Skeleton in the Physical Anthropology Closet1

Abstract

The “new” and “newer” concepts of physical anthropology are oriented to biochemical, genetic and evolutionary studies. While theseareneededand welcome concepts, they often slight the basic tools of anthropometry and typology. Also, the new and newer physical anthropology tends to separate biological factors from their cultural contexts. The writer discusses several questions posed by this shift in emphasis and suggests that the lack of a functional approach lessens the effectiveness of both biologically and culturally oriented investigators.     

Serum metabolomics identifies metabolite panels that differentiate lame dairy cows from healthy ones

Background

Metabolomics provides measurement of numerous metabolites in human samples, which can be a useful tool in clinical research. Blood and urine are regarded as preferred subjects of study because of their minimally invasive collection and simple preprocessing methods. Adhering to standard operating procedures is an essential factor in ensuring excellent sample quality and reliable results.

Aim of review

In this review, we summarize the studies about the impacts of various preprocessing factors on metabolomics studies involving clinical blood and urine samples in order to provide guidance for sample collection and preprocessing.

Key scientific concepts of review

Clinical information is important for sample grouping and data analysis which deserves attention before sample collection. Plasma and serum as well as urine samples are appropriate for metabolomics analysis. Collection tubes, hemolysis, delay at room temperature, and freeze–thaw cycles may affect metabolic profiles of blood samples. Collection time, time between sampling and examination, contamination, normalization strategies, and storage conditions may alter analysis results of urine samples. Taking these collection and preprocessing factors into account, this review provides suggestions of standard sample preprocessing.

     

The Southwest and the Plains: Ecology and Economics

Abstract

The ecological concept of niche is used to provide a better understanding of prehistoric interactions between the Plains and the Puebloan Southwest. A diachronic model is presented based on concepts of energy flow and regional microvariation in net energy input. At a general level, such use of ecological models and principles enables changes in human systems to be seen as an example of a general increase in ecosystem complexity. The application of more powerful theoretic and methodological concepts and constructs can then lead to a more powerful theory of human cultural evolution.     

Panbiogeography and the public

Abstract

Progress is reported on the systematics and biogeography of some small land snails in Australasia. Observed patterns of dispersal and massings of taxa appear to support basic concepts in panbiogeographic methodology. The role of the amateur in science is related to the use of computers, curatorial systems, and the current political environment for science.     

Programmed cell death lives

Research on cell death mechanisms gets a lot of attention. This is understandable as it underlies biology in general, as well as the insight in pathological conditions and the development of opportunities for therapeutic intervention. Over the last years a steady rise in the number of scientific reports and in the impact of this literature on the different mechanisms of programmed cell death can be observed. A number of new concepts are highlighted.

     

Application of Pb isotopic mapping to environment evaluation in China

Abstract

Quantitative criterion of Pb pollution sources and levels from Pb isotopic tracing must depend on the establishment of a natural Pb isotopic background. Lead isotopic mapping for Continental China and the neighborhood sea areas is being completed. Seven major isotopic provinces in the continent (Cathaysia, Indochina, Yangtze, North China, Northeast China, North Xinjiang and Tibet) have been identified. The Pb isotopic mapping in the South China Sea shows two depositing areas; sediments from the Red River is related to the Indochina geochemical province; sediments from the Pearl River system is related to the Cathaysia geochemical province. Pb isotopic evidence indicates that the major Pb pollution sources of aerosols in the Eastern China are from local Pb–Zn–Cu resource consumption in various industries. The Pb pollution from aerosols, eolian dusts, and acid leachable components in soils and sediments around the South China Sea shows two major sources: application of lead metal in various industries and automobile exhausts.     

Kybernetik und psychophysisches Grundproblem

Summary It is shown that the traditional antithesis of mind and matter stems from a grave misunderstanding or rather misarrangement of empirical facts. This oblique antithesis and numerous well-known contradictions connected with it are eliminated by careful analysis of the intricate situation from which they arose. The solution of the problem leads to a clear understanding of fundamental concepts upon which Cybernetics is founded, and of the achievements potentially within its reach.

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Die folgenden Ausführungen stellen die stark komprimierte Fassung eines Aufsatzes dar, schon 1949 einem kleinen Kreis Interessierter in den USA und Deutschland zugänglich gemacht wurde.     

Parallel sequence tagging for concept recognition

Background

Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial way, which is inherently prone to error propagation from NER to NEN. We propose a parallel architecture, where both NER and NEN are modeled as a sequence-labeling task, operating directly on the source text. We examine different harmonisation strategies for merging the predictions of the two classifiers into a single output sequence.

Results

We test our approach on the recent Version 4 of the CRAFT corpus. In all 20 annotation sets of the concept-annotation task, our system outperforms the pipeline system reported as a baseline in the CRAFT shared task, a competition of the BioNLP Open Shared Tasks 2019. We further refine the systems from the shared task by optimising the harmonisation strategy separately for each annotation set.

Conclusions

Our analysis shows that the strengths of the two classifiers can be combined in a fruitful way. However, prediction harmonisation requires individual calibration on a development set for each annotation set. This allows achieving a good trade-off between established knowledge (training set) and novel information (unseen concepts).

     

More or Less Integrated Ocean Management: Multiple Integrated Approaches and Two Norms

Abstract

Through a normative lens, this article investigates integrated ocean management and the multiple concepts that it involves. Although international law provides legal authority to coastal states to manage their ocean area entitlements, no single legally binding norm specific to integrated ocean management exists. Nevertheless, by combining different internationally recognized sources, this article identifies and discusses two normative concepts applicable in coastal state integrated ocean management. These are (1) the framing of integrated ocean management as a management process and (2) the incorporation of environmental, economic, and social concerns into an ocean management policy.     

Epidemiological Concepts Regarding Disease Monitoring and Surveillance

Definitions of epidemiological concepts regarding disease monitoring and surveillance can be found in textbooks on veterinary epidemiology. This paper gives a review of how the concepts: monitoring, surveillance, and disease control strategies are defined. Monitoring and surveillance systems (MO&SS) involve measurements of disease occurrence, and the design of the monitoring determines which types of disease occurrence measures can be applied. However, the knowledge of the performance of diagnostic tests (sensitivity and specificity) is essential to estimate the true occurrence of the disease. The terms, disease control programme (DCP) or disease eradication programme (DEP), are defined, and the steps of DCP/DEP are described to illustrate that they are a process rather than a static MO&SS.

     

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations

The ability of Halomonas maura to bioprecipitate carbonate and sulphate crystals in solid media at different manganese concentrations has been demonstrated in this study for the first time. The precipitated minerals were studied by X-ray diffraction, scanning and transmission electron microscopy, and energy-dispersive X-ray spectroscopy. The precipitated minerals were different based on the manganese concentration present in the medium and the incubation time. In the absence of manganese, H. maura formed pseudokutnahorite crystals; in the presence of manganese, the concentration in the culture medium determined the precipitation carbonates, such as rhodochrosite and dolomites. However, in the presence of low concentrations of manganese chloride (MnCl₂) (5 g/l), kutnohorite crystals were also formed. Finally, when H. maura was grown in the presence of manganese, small amounts of sulphate crystals (such as bassanite and gypsum) were detected. Our study of the precipitated minerals showed an active role of H. maura in the biomineralisation process, but the geochemical conditions, and the manganese concentrations in particular, were clearly influential.