Make Histri: reconstructing the exchange history of bacterial and archaeal type strains

Each transfer of a microbial strain between a Biological Resource Center (BRC) and an individual researcher or another BRC imposes a risk of contamination or human error. Such artifacts jeopardize the quality of scientific results. In order to trace back possible scientific discrepancies that can be linked to failure of authenticity of the biological material involved, we launched the 'Make Histri' project that aims at reconstructing the exchange history ('Histri') of all bacterial and archaeal type strains as can be deduced from the information contained in BRC online catalogs. A Histri, visualized as a rooted tree, contains all known strain numbers attributed to the various cultures of a given strain, annotated with additional information about each transfer of microbial material.     

A communication channel model for information transmission in the blowfly photoreceptor

Biological photoreceptors transduce and communicate information about visual stimuli to other neurons through a series of signal transformations among physical states such as concentration of a chemical species, current, or the number of open ion channels. We present a communication channel model to quantify the transmission and degradation of visual information in the blowfly photoreceptor cell. The model is a cascade of linear transfer functions and noise sources that are derived from fundamental principles whenever possible, and whose parameters are estimated from physiological data. We employ the model to calculate the information capacity of blowfly phototransduction; our results compare favorably with estimates of the capacity derived from experimental measurements by de Ruyter van Steveninck and Laughlin (Nature 379 (1996) 642-645) and Juusola (J. Gen. Physiol. 104 (1994) 593-621). The model predicts that photon shot noise and ion channel noise are the dominant noise sources that limits information transmission in the blowfly photoreceptor.     

Cues for communal egg‐laying in lizards (Bassiana duperreyi,Scincidae)

Animals may aggregate either because the presence of conspecifics provides information about habitat suitability, or because the presence of conspecifics directly enhances individual viability. For a female lizard, the advantage of laying her eggs in a communal nest may entail either information transfer (hatched eggshells show that the site has been successful in previous seasons) or direct physiological benefits (recently‐laid eggs can enhance water availability to other eggs). We tested the relative importance of these two mechanisms in the three‐lined alpine skink (Bassiana duperreyi Gray, 1838) by offering gravid females a choice between sites with hatched eggshells versus freshly‐laid eggs. Females selectively oviposited beside fresh eggs. In this species, early‐nesting females use information transfer (i.e. the presence of old eggshells) as a nest‐site criterion, whereas later nesters switch to a reliance on direct benefits of conspecific presence (i.e. the presence of freshly‐laid eggs). © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 839–842.     

An overview of indexes to evaluate terrestrial plants for phytoremediation purposes (Review)

This paper reviews the various factors, coefficients and indexes developed to evaluate terrestrial plant performance in respect to phytoremediation.A brief list of indexes includes the Accumulation factor, Bioabsorption coefficient, Bioaccumulation coefficient, Bioaccumulation factor, Bioconcentration, Bioconcentration coefficient, Bioconcentration factor, Biological absorption coefficient, Biological accumulation coefficient, Biological concentration factor, Biological transfer coefficient, Concentration factor, Enrichment coefficient, Enrichment factor, Extraction coefficient, Index of bioaccumulation, Mobility index, Shoot accumulation factor, Soil host transfer factor, Soil-plant transfer coefficient, Soil-plant transfer factor, Transfer factor and Translocation factor.These indexes represent the result of a ratio calculation between element concentrations in plant parts to that of substrata. In other cases indexes arise from the ratio calculation of element concentrations in two distinct plant parts.In the literature different terms have been attributed to the same ratio and this often represents an overlap in terminology. On the other hand the same term corresponds to several different ratios and this could create confusion and misinterpretation in data comparison.Furthermore, the evaluation of hyperaccumulation, phytostabilization or phytoextraction of plant species is not always performed in the same way. Different plant parts are considered as well as different extraction procedures for both plant and substrata element assessment. As a consequence, a direct comparison between obtained data is not always reliable and possible.In this paper the various available indexes are reviewed, highlighting both the similarity and differences between them with the aim of helping the community in choosing the appropriate term for both data evaluation and comparison. In this author’s opinion there is no need of new terms to define indexes. I would stress the need for conformity to the original definitions and criteria.     

Is matter inanimate?: Protobiological information from within

Biological information refers to the process of how matter informs matter through endogenous boundary conditions, exhibiting a sharp contrast to Shannon's information referring to the process of how coded messages inform a human receiver or observer. The origin and evolution of protobiological and biological information occur because prior polymeric products successively provide new boundary conditions to the subsequent production process. The transition from what looks like inanimate matter to living beings is a continuous process. The underlying mechanism is the physical process that prior products provide new boundary conditions to the subsequent production process in a successive manner. Biological information resides in perpetuating cellular production process which eventually leads to an enhancement of evolutionary specificity. Cellular units are prerequisite to biological evolution, not vice versa.     

Is matter inanimate? Protobiological information from within

Biological information refers to the process of how matter informs matter through endogenous boundary conditions, exhibiting a sharp contrast to Shannon's information referring to the process of how coded messages inform a human receiver or observer. The origin and evolution of protobiological and biological information occur because prior polymeric products successively provide new boundary conditions to the subsequent production process. The transition from what looks like inanimate matter to living beings is a continuous process. The underlying mechanism is the physical process that prior products provide new boundary conditions to the subsequent production process in a successive manner. Biological information resides in perpetuating cellular production process which eventually leads to an enhancement of evolutionary specificity. Cellular units are prerequisite to biological evolution, not vice versa.     

Unbalanced resting-state networks activity in psychophysiological insomnia

Sleep and Biological Rhythms - Psychophysiological insomnia (PI) is a clinical condition characterized by sleep-related disturbing cognitive activity and biased self-related information processing....     

Lead and Mercury Levels in Preterm Infants Before and After Blood Transfusions

Biological Trace Element Research - Very low birth weight (VLBW) infants usually receive packed red blood cell unit (pRBC) transfusions. Heavy metal transfer via pRBCs is not widely discussed...     

Interoperability of CABRI Services and Biochemical Pathways Databases

Common Access to Biological Resources and Information (CABRI) service is a 'one-stop-shop' for materials that are collected by a number of European culture collections that engage themselves in a quality service for the scientific community by adhering to Quality Guidelines for the management of resources and related information. It includes collections' catalogues that can be searched in an SRS implementation. A simple search facility, including a synonym search and a shopping cart, is also available. Within the European Biological Resource Centres Network (EBRCN) project, an extension and improvement of the catalogues' information is under way. This includes adding links to bibliographic databanks and sequence databases. Revision of 'in-house' controlled vocabularies used by data annotators is under way, in order to improve the setting up of external links, and new links to biochemical pathways databases are being set up for some of the catalogues.     

News from the Biological Stain Commission No. 11

The 11th issue of News from the Biological Stain Commission (BSC) provides our first impressions of the REACH and ECHA programs. We intend to give a more thorough account of what these important programs actually mean in later editions of News from the Biological Stain Commission. Under the heading of Regulatory Affairs, the Biological Stain Commission's International Affairs Committee presents information from the opening session of the meeting of the International Standards Organization ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test systems held on 2-4 June 2010 in Seoul, Republic of Korea.     

Correction to: Effect of Selenium on Lipid and Amino Acid Metabolism in Yeast Cells

Biological Trace Element Research - The authors forgot to include the following information in Materials and Methods.     

News from the Biological Stain Commission No. 11

The 11th issue of News from the Biological Stain Commission (BSC) provides our first impressions of the REACH and ECHA programs. We intend to give a more thorough account of what these important programs actually mean in later editions of News from the Biological Stain Commission. Under the heading of Regulatory Affairs, the Biological Stain Commission’s International Affairs Committee presents information from the opening session of the meeting of the International Standards Organization ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test systems held on 2-4 June 2010 in Seoul, Republic of Korea.     

A taxonomy of biological information

Reproduction, and thus information transfer across generations, is the most essential process of life, yet biologists lack a consensus on terms to define biological information. Unfortunately, multiple definitions of the same terms and other disagreements have long inhibited the development of a general framework for integrating the various categories of biological information. Currently, the only consensus is over two general categories, genetic information, which is encoded in DNA, and non‐genetic information, which is extracted from the environment. Non‐genetic information is the key to understanding gene‐environment interactions and is the raw material of fields such as developmental plasticity, behavior, communication, social learning and cultural evolution. In effect, differences in information possessed by individuals produce phenotypic variation. We thus define biological information as ‘factors that can affect the phenotype in ways that may influence fitness’. This definition encompasses all information that is potentially relevant to organisms, which includes the physical environment. Biological information can be acquired passively from genes or via processes such as epigenetics, parental effects and habitat inheritance, or actively by organisms sensing facts about their environment. The confusion over definitions mainly concerns non‐genetic information, which takes many more forms than genetic information. Much of the confusion derives from definitions based on how information is used rather than on the facts from which it is extracted. We recognize that a fact becomes information once it is detected. Information can thus be viewed analogously to energy in being either potential or realized. Another source of confusion is in the use of words outside their usual meanings. We therefore present intuitive definitions and classify them according to categories of facts in a hierarchical framework. Clarifying these concepts and terms may help researchers to manipulate facts, allowing a fuller study of biological information.     

News from the Biological Stain Commission No. 7

Abstract

In this issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory affairs, the Biological Stain Commission's International Affairs Committee presents information from a meeting held in Berlin by the International Standards Organization ISO/TC 212/WG 1, “Quality and Competence in the Medical Laboratory,” on 11–12 December 2008. After this, we turn again to problems with impure dyes and find that solvent dyes are impure even for non-biological use.     

Differential electrodermal and phasic heart rate responses to personally relevant information: Comparing sleep and wakefulness

Sleep and Biological Rhythms - This study examined autonomic physiological responses to personally relevant information presented during sleep and wakefulness. Heart rate and electrodermal...     

Some effects of metal ions on DNA structure and genetic information transfer

The reaction of metal ions with nucleic acids can lead to a variety of dramatic effects on nucleic acid structure, e.g., crosslinking of the polymer strands, degradation to oligomers and monomers, stabilization or destabilization, and the mispairing of bases. These effects have important implications for genetic information transfer. Metal ions are involved in many aspects of this transfer; we are presently concerned with the effect of metal ions on the orientation of the active site of RNA polymerase. Many of the effects of metal ions on nucleic acid structure involve changes in the conformation of the macromolecules. We have found that conditions that have been used to convert B DNA to Z DNA lead to at least two other conformational changes, and phase diagrams delineate the realms of stability of each of the forms. We have carried out a number of studies that demonstrate that the conversion of B to Z DNA is very closely correlated with a substantial decrease in the ability of the DNA to act as a template for RNA synthesis. A portion of this paper has been taken from another paper on “Changes of Biological Significance Induced by Metal Ions in the Structure of Nucleic Acids,” published in Annali dell' lstituto Superiore di Sanita.     

News from the Biological Stain Commission no. 12

In this 12(th) issue of News from the Biological Stain Commission (BSC) under the heading of Regulatory affairs, the Biological Stain Commission's International Affairs Committee presents information from the meetings of ISO/TC 212/WG 1 Quality and competence in the medical laboratory and ISO/TC 212/WG 3 In vitro diagnostic products both held on 2 - 3 June 2010, plus information on the second plenary meeting of ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test systems held on 4 June 2010. All meetings took place in Seoul, Republic of Korea. Finally, information is provided concerning the 25(th) meeting of CEN/TC 140 In vitro diagnostic medical devices held on 23 June 2010 in Berlin, Germany.     

Nicotinamide-dependent one-electron and two-electron (flavin) oxidoreduction: thermodynamics, kinetics, and mechanism.

1. Biological nicotinamide-dependent oxidoreduction consists of reversible 2e- oxidoreduction of substrates. A mechanism involving subsequent 1e- steps is shown to be very unfavourable due to the high energy of the nicotinamide radical. 2. Free energy relationships provide a convenient tool, allowing one to differentiate between hydride transfer and hydrogen atom transfer. It is concluded that biological nicotinamide-dependent, as well as flavin-nicotinamide oxidoreduction, proceed via hydride transfer but not via hydrogen atom transfer. 3. In flavin-nicotinamide oxidoreduction, flavin-nicotinamide charge transfer complexes are very likely the catalytic intermediates, preceding transfer of hydride ion. The energy of the long-wavelength charge transfer transition of zwitterionic oxidized-nicotinamide/reduced-flavin complexes is strongly dependent on polarity. It is maximal in a highly polar environment. 4. 5-Deazaflavins show the high thermodynamic radical instability of nicotinamides. They have to be considered as nicotinamide analog 2e- oxidoreductants rather than flavin analogs, therefore, lacking the ability to catalyze reversible 1e- oxidoreduction, essential for many flavoenzymes.     

A Flexible Integration and Visualisation System for Biomarker Discovery

Biological data have accumulated at an unprecedented pace as a result of improvements in molecular technologies. However, the translation of data into information, and subsequently into knowledge, requires the intricate interplay of data access, visualisation and interpretation. Biological data are complex and are organised either hierarchically or non-hierarchically. For non-hierarchically organised data, it is difficult to view relationships among biological facts. In addition, it is difficult to make changes in underlying data storage without affecting the visualisation interface. Here, we demonstrate a platform where non-hierarchically organised data can be visualised through the application of a customised hierarchy incorporating medical subject headings (MeSH) classifications. This platform gives users flexibility in updating and manipulation. It can also facilitate fresh scientific insight by highlighting biological impacts across different hierarchical branches. An example of the integration of biomarker information from the curated Proteome database using MeSH and the StarTree visualisation tool is presented.