Anisotropic lattice distortions in the mollusk-made aragonite: a widespread phenomenon

In this paper, we present experimental results demonstrating systematic structural distinctions between biogenic and non-biogenic calcium carbonate. Specifically we show, by high-resolution X-ray powder diffraction on dedicated synchrotron beam lines, that the orthorhombic unit cell of the mollusk-made aragonite is anisotropically distorted as compared with that one of geological aragonite. In all investigated shells, belonging to different classes (bivalve, gastropod, and cephalopod) and taken from different habitat origins (sea, fresh water, and land), the maximum elongation of about 0.1-0.2% was found along the c-axis. The lattice distortions along the a-axis were also of the positive sign (elongation) but lower than those along the c-axis, whereas lattice distortions along the b-axis were always negative (contraction). Supporting experiments, including structural analysis after a bleach procedure, measurements of temperature-dependent lattice relaxation, measurements of the CO(2) release at elevated temperatures, signify that the observed structural distinctions are most probably caused by the organic molecules intercalating into the aragonite lattice during biomineralization. Our findings show that in some sense organisms control the atomic structure of the crystals. Deeper understanding of this phenomenon will aid in the development of new approaches to grow biomimetic composites and tailor their properties on a molecular level.     

Capitula in the Asteridae: A widespread and varied phenomenon

The presence of capitula, the head-type of inflorescences, is widespread in the Asterideae. Several families, predominantly terminal in the clade, display the tendency of maximizing reproductive output by condensing indeterminate inflorescences to the point of capitulum formation. This is accomplished by the process of halting or suppressing development of the internodes, an example of paedomorphosis of the progenesis type. This tendency is either infrequent or absent in the basal members of the Asteridae. When inflorescence condensation is present, closely related taxa often demonstrate the progression of the paedomorphosis. More examples of capitulum formation are found in the more advanced families, culminating with the Asteraceae, almost all of which display fully condensed capitula of some sort. Other phenomena are also apparent besides the basic inflorescence condensation. Edge effects are often seen, ranging from a mere crowding of the outermost flowers to the formation of additional flower types. In some taxa, inflorescence condensation continues beyond the basic capitulum form, yielding even more condensed inflorescences that then become determinate. More highly condensed inflorescences have independently evolved several times in the Asteraceae, and some tertiarily condensed inflorescences have evolved as well.     

Towards social life cycle assessment: a quantitative product social impact assessment

Purpose

The main goal of this paper is to present the feasibility of the quantitative method presented in the Product Social Impact Assessment (PSIA) handbook throughout a case study. The case study was developed to assess the social impacts of a tire throughout its entire life cycle. We carried out this case study in the context of the Roundtable for the Product Social Metrics project in which 13 companies develop two methodologies, a qualitative and a quantitative one, for assessing the social impact of product life cycle.

Methods

The quantitative methodology implemented for assessing the social impact of a Run On Flat tire mounted in a BMW 3 series consists of 26 indicators split in three groups. Each group represents a stakeholder group. Primary data of the quantitative indicators were collected along the product life cycle of the Run On Flat by involving the companies, which owned the main steps of the product life cycle. Throughout this case study, an ideal/worst-case scenario was defined for the distance-to-target approach to compare the social performances of more products when they are available.

Results and discussion

The implementation of the PSIA quantitative method to a Run On Flat illustrated the necessity to have a referencing step in order to interpret the results. This is particularly important when the results are used to support decision-making process in which no experts are involved. It frequently happens in a big company where the management level has to take often decisions on different topics. Reference values were defined using ideal or worst-case-target scenarios (Fontes et al. 2014). For those topics where it was possible, an ideal/ethical scenario was defined, e.g., 0 h of child labor per product. In other cases, we defined a worst-case scenario, e.g., 0 training hours per product. It was then possible to interpret the results using a distance-to-target approach. A matrix was developed in the case study for identifying in which step of the product life cycle data is not available; that means we need more transparency in the supply chain.

Conclusions

Each value of the matrix can be compared to the ideal/worst scenario to compare the step to each other and to identify along the product life cycle which step and the relative supplier that needs further measures to improve the product performance. Furthermore, a quantitative value for each indicator related to the product life cycle is calculated and compared with the ideal/worst scenario. The case study on Run On Flat represents the first implementation of the quantitative method of PSIA.

     

Mitochondrial targeting of farnesyl diphosphate synthase is a widespread phenomenon in eukaryotes

Cellular internalization of cell-penetrating peptide HIV-1 Tat basic domain (RKKRRQRRR) was studied in Triticale cv AC Alta mesophyll protoplasts. Fluorescently labeled monomer (Tat) and dimer (Tat(2)) of Tat basic domain efficiently translocated through the plasma membrane of mesophyll protoplast and showed distinct nuclear accumulation within 10 min of incubation. Substitution of first arginine residue with alanine in Tat basic domain (M-Tat) severely reduced cellular uptake of the peptide (3.8 times less than Tat). Tat(2) showed greater cellular internalization than Tat (1.6 times higher). However, characteristics of cellular uptake remained same for Tat and Tat(2). Cellular internalization of Tat and Tat(2) was concentration dependent and non-saturable whereas no significant change in cellular uptake was observed even at higher concentrations of M-Tat. Low temperature (4 degrees C) remarkably increased cellular internalization of Tat as well as Tat(2) but M-Tat showed no enhanced uptake. Viability test showed that peptide treatment had no cytotoxic effect on protoplasts further indicating involvement of a common mechanism of peptide uptake at all the temperatures. Endocytic inhibitors nocodazole (10 muM), chloroquine (100 muM) and sodium azide (5 mM) did not show any significant inhibitory effect on cellular internalization of either Tat or Tat(2). These results along with stimulated cellular uptake at low temperature indicate that Tat peptide is internalized in the plant protoplasts in a non-endocytic and energy-independent manner. Competition experiments showed that non-labeled peptide did not inhibit or alter nuclear accumulation of fluorescent Tat or Tat(2) suggesting active transport to the nucleus was not involved. Studies in mesophyll protoplasts show that internalization pattern of Tat peptide is apparently similar to that observed in mammalian cell lines.     

Ostracism as a social and biological phenomenon: An introduction

Ostracism refers to the general process of rejection and exclusion, observed in human groups and in many other species. It occurs as “shunning” in small homogenous groups like the Amish or as rejection among children. Ostracism in various forms is also deeply embedded in our own legal tradition, and is used in the formal and informal legal procedures of other cultures, used to maintain order, to punish deviance, and to increase social cohesion. Hence, it is plausible to hypothesize that human ostracism may have physiological substrates or biological functions in addition to cultural, moral, and legal dimensions. Biological research shows that human emotions (anger, fear, reassurance, self-confidence) involve responses of the limbic system as well as ideas or thoughts in the cerebral cortex and that human behavior continually integrates biological and cultural factors. The legal system expresses and channels human behavior. For this reason laws should be more effective if their functions complement (rather than ignore) the function of the behavior being regulated. To look at law as it affects human behavior in the light of the life sciences does not imply the intention of finding a universally valid “natural law,” akin to theological or ideological doctrine. On the contrary, we find that humans can form radically different social systems due to the plasticity of their behavior. However, an interdisciplinary analysis of ostracism as a common area of behavior, combining biology, law, and the social sciences can produce insights that none of these fields alone can provide. Such an approach should increase our understanding of human nature and the functions of law.     

New techniques for the assessment of canine semen quality: a review

Until recently, canine semen assessment was routinely performed by conventional light microscopic techniques. The limitations of these methods include subjectivity, variability, the small number of spermatozoa analyzed, and poor correlation with fertilizing potential. The last decade, several new in vitro techniques have been introduced for canine semen assessment that enable a more detailed evaluation of several sperm characteristics. Numerous fluorescent staining techniques have been developed for the evaluation of specific sperm characteristics and functions, including plasma membrane integrity, capacitation status and the acrosome reaction. By combining fluorescent stains, several functional sperm characteristics can be assessed simultaneously. Moreover, by means of flow cytometry, large numbers of fluorescently labelled spermatozoa can be analysed in a short interval. Following thorough standardization and validation, computer-assisted sperm analysis systems provide objective and detailed information on various motility characteristics and morphometric dimensions that cannot be identified by conventional light microscopic semen analysis. In vitro assays, evaluating the capacity of canine spermatozoa to bind to the zona pellucida or oviductal explants, or to penetrate the oocyte, provide additional information on canine gamete interaction that may be useful in predicting the fertilizing potential of spermatozoa. Although substantial improvements have been made in canine semen assessment, surprisingly few parameters were correlated with in vivo fertility. Therefore, further research is required to determine which sperm characteristics are of clinical value for predicting the in vivo fertility in dogs.     

Electromagnetic information in the phenomenon of life

The author's original experiments and ideas have been summarized, which concern the role of natural background radiation in maintenance of electromagnetic information essential for existence of the living organism as an integral whole.     

BIGpre: a quality assessment package for next-generation sequencing data

The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn’t taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net/.     

Searching and review on the Three Rs information in Korea: time for quality assessment and continued education

Scientists planning research that involves the use of animals are required by international and/or national law to examine the possibilities for the implementation of Replacement, Reduction and/or Refinement (the Three Rs principles of Russell and Burch) in experiments for research, testing, and education. There are two Korean laws legislating humane use of animals and ethical review prior to animal experiments. This report reviews current practice of the literature search by the researchers and protocol review by the Institutional Animal Care and Use Committees on the Replacement, Reduction and Refinement alternatives in Korea. The promotion and protection of the laboratory animals are one of the core competencies of investigators exploring the ethical conduct of research and good science. [BMB Reports 2013; 46(7): 335-337]     

Unleashing the BEAST: a brief measure of human social information use

Social information enables individuals to reduce uncertainty and increase decision accuracy across a broad range of domains. Intriguingly, individuals and populations consistently differ in social information use. Understanding the underlying causes of this variation has proven challenging due to the lack of a standardized paradigm to quantify social information use. Here we introduce the BEAST (Berlin Estimate AdjuStment Task); a brief (∼5-min), simple, and incentive-compatible behavioural task to quantify individuals' propensities to use social information. In the task, participants observe an image with a number of animals and estimate the total number. Next, they receive another person's estimate, after which they provide a second estimate. An individual's average adjustment quantifies their propensity to use social information. We found that individuals' propensity to use social information is consistent within the task, has considerable test–retest reliability over 9 months, generalizes to other social learning tasks, and correlates with established self-reported measures of social conformity and social proximity. The BEAST thus reliably captures individual variation in social information use. We conclude by highlighting the BEAST's potential to serve as a flexible framework to assess the determinants of human social information use.     

MDQC: a new quality assessment method for microarrays based on quality control reports

MOTIVATION: The process of producing microarray data involves multiple steps, some of which may suffer from technical problems and seriously damage the quality of the data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how to assess the quality of a microarray dataset using the measures provided in quality control (QC) reports; (2) how to identify possible sources of the quality problems. RESULTS: We propose a novel multivariate approach to evaluate the quality of an array that examines the 'Mahalanobis distance' of its quality attributes from those of other arrays. Thus, we call it Mahalanobis Distance Quality Control (MDQC) and examine different approaches of this method. MDQC flags problematic arrays based on the idea of outlier detection, i.e. it flags those arrays whose quality attributes jointly depart from those of the bulk of the data. Using two case studies, we show that a multivariate analysis gives substantially richer information than analyzing each parameter of the QC report in isolation. Moreover, once the QC report is produced, our quality assessment method is computationally inexpensive and the results can be easily visualized and interpreted. Finally, we show that computing these distances on subsets of the quality measures in the report may increase the method's ability to detect unusual arrays and helps to identify possible reasons of the quality problems. AVAILABILITY: The library to implement MDQC will soon be available from Bioconductor.     

Applying geographic information systems and remote sensing for water quality assessment of mangrove forest

The study of environmental conditions is one of the most important measures in the field of reforestation. The present study was undertaken to assess the environmental status of the mangrove forest of Alibaug, Maharashtra, India with respect to different sixteen physicochemical parameters of water using Geographical information system (GIS) for rehabilitation, conservation and development of the destructed area of the mangrove forest. The Base map of study area was prepared using topographic map and the remote sensing data of Landsat 7 ETM + for spatial analysis. The distributions of water pollutants were assigned using a GIS approach of Inverse Distance Weighted (IDW). The results showed that the amounts of EC, COD, hardness, O&G, Cl^?, Na⁺, Ca^2 +, Mg^2 +, NO₃^? and PO₄^3? are higher than the normal ranges in mangrove forest due to natural processes and human activity, industrial and domestic wastewater disposal, oil spillage and agricultural runoff which all eventually affect the water quality of mangrove forest of Alibaug. To identify the areas within the normal ranges of 16 studied parameter, suitability map of water was prepared through an integration of 16 suitability maps of the studied parameters. The suitability map of water classified the water to six classes of suitability in order of moderate > moderate to high > low to moderate > high > low suitable. The areas with classes of 1 and 2 were suitable for the protective measures. Classes 3 and 4 were suitable for replantation and restoration of native mangrove species as well as local communities' cooperation in the participatory protection measures. The areas of classes 5 and 0 need to be designed an urgent management and mitigation plan to reduce impact of human activities. The result of the study also proves the use of GIS as a powerful tool in addressing assessment and monitoring programs of the water quality in the mangrove ecosystems.