Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs

The N¹-methyl-Adenosine (m¹A58) modification at the conserved nucleotide 58 in the TΨC loop is present in most eukaryotic tRNAs. In yeast, m¹A58 modification is essential for viability because it is required for the stability of the initiator-tRNA^Met. However, m¹A58 modification is not required for the stability of several other tRNAs in yeast. This differential m¹A58 response for different tRNA species raises the question of whether some tRNAs are hypomodified at A58 in normal cells, and how hypomodification at A58 may affect the stability and function of tRNA. Here, we apply a genomic approach to determine the presence of m¹A58 hypomodified tRNAs in human cell lines and show how A58 hypomodification affects stability and involvement of tRNAs in translation. Our microarray-based method detects the presence of m¹A58 hypomodified tRNA species on the basis of their permissiveness in primer extension. Among five human cell lines examined, approximately one-quarter of all tRNA species are hypomodified in varying amounts, and the pattern of the hypomodified tRNAs is quite similar. In all cases, no hypomodified initiator-tRNA^Met is detected, consistent with the requirement of this modification in stabilizing this tRNA in human cells. siRNA knockdown of either subunit of the m¹A58-methyltransferase results in a slow-growth phenotype, and a marked increase in the amount of m¹A58 hypomodified tRNAs. Most m¹A58 hypomodified tRNAs can associate with polysomes in varying extents. Our results show a distinct pattern for m¹A58 hypomodification in human tRNAs, and are consistent with the notion that this modification fine tunes tRNA functions in different contexts.     

Mitochondrial haplogroup N1a phylogeography,with implication to the origin of European farmers

Background  

Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations.     

Correlation of <Emphasis Type="Italic">trans</Emphasis>-Lycopene Measurements by the HPLC Method with the Optothermal and Photoacoustic Signals and the Color Readings of Fresh Tomato Homogenates

The trans-lycopene content of fresh tomato homogenates was assessed by means of the laser photoacoustic spectroscopy, the laser optothermal window, micro-Raman spectroscopy, and colorimetry; none of these methods require the extraction from the product matrix prior to the analysis. The wet chemistry method (high-performance liquid chromatography) was used as the absolute quantitative method. Analytical figures of merit for all methods were compared statistically; best linear correlation was achieved for the chromaticity index a* and chroma C*.     

A multi-criteria decision-making model for classifying wood products with respect to their impact on environment

Background, aim and scope  

Although life cycle assessment is frequently used in scientific studies of product comparison, many practitioners are looking for improvements in the normalisation, grouping and weighting of life cycle inventory results. Local conditions, which are well known to local experts, are very important to these steps. The goal of this work was to develop a computer-based decision support system for classifying wood products according to their influence on the environment in their whole life cycle. The model specifically addresses local conditions in the Republic of Slovenia and was developed by Slovenian experts.     

Inclusion of carbonation during the life cycle of built and recycled concrete: influence on their carbon footprint

Background, aim, and scope  

When the service life (or primary life) of built concrete infrastructure has elapsed, a common practice is that the demolished concrete is crushed and recycled, then incorporated into new construction. LCA studies of CO₂ emissions focus on the manufacturing and construction and occupancy/utilization phases, without consideration of the demolition and application of recycled concrete into a secondary construction application. Concrete has a documented ability to chemically react with airborne carbon dioxide (CO₂); however, carbon capture (or carbonation) by concrete during the primary and secondary life, is not considered in LCA models. This paper incorporates CO₂ capture during both primary and secondary life into an LCA model for built concrete.     

Rigorous proof of fuzzy error propagation with matrix-based LCI

Background, aim, and scope  

Propagation of parametric uncertainty in life cycle inventory (LCI) models is usually performed based on probabilistic Monte Carlo techniques. However, alternative approaches using interval or fuzzy numbers have been proposed based on the argument that these provide a better reflection of epistemological uncertainties inherent in some process data. Recent progress has been made to integrate fuzzy arithmetic into matrix-based LCI using decomposition into α-cut intervals. However, the proposed technique implicitly assumes that the lower bounds of the technology matrix elements give the highest inventory results, and vice versa, without providing rigorous proof.     

Recurrences and Human Agential Meaning Grounding: Laying a Path in Walking

This article addresses the semiotic problem of how meaning is agentially grounded: how actual meaning is possible and is justifiably supported by agents’ capabilities and purposes. This article is particularly focused on human agential grounding; however, to a great degree, insights presented here can be extended to other living beings. Specifically, agential meaning is examined here inside the framework of agentive semiotics and embodied, situated and enactive cognition theories, in line with the mind-life continuity general thesis (which intends to naturalize mind and experience). To offer clarity and methodological precision about agential grounding, three explanation categories (called recurrences) are proposed: phylogenetic recurrence, the evolutionary basis for corporal/embodied grounding; ontogenetic recurrence, the developmental basis for individual meaning grounding; and collective recurrence, the basis for meaning recognized, attributed and assigned inside social contexts. These recurrences are conceived as three types of general processes that constantly enclose possibilities for purpose and meaning emergence in humans. As a result of these types of recurrences, two categories of human agendas or purposes are also proposed: individual and collective. Finally, remarks about how these categories can be useful for semiotic analysis and further research are suggested.     

Relationship Between Molecular Structure and Thermo-mechanical Properties of Candelilla Wax and Amides Derived from (<Emphasis Type="Italic">R</Emphasis>)-12-Hydroxystearic Acid as Gelators of Safflower Oil

In this research, we studied the relationship between the molecular structure of (R)-12-hydroxyoctadecanamide, (R)-N-propyl-12-hydroxyoctadecanamide, and (R)-N-octadecyl-12-hydroxyoctadecanamide and the thermo-mechanical properties of their 2% (wt/wt) organogels developed using safflower oil high in oleic acid (HOSFO) as the liquid phase. Candelilla wax (CW), a well-known edible gelling additive whose main component is hentriacontane, also was studied for comparative purposes. The results obtained show that the attractive interactions (i.e., hydrogen bonding and dipolar interactions) between amide groups and between hydroxyl groups present in the amides resulted in organogels with higher melting temperature, heat of melting, and crystallization parameters than those found in the CW organogel. The rheological parameters associated to the strength of the amide or CW-based gels developed in HOSFO (i.e., yield stress and elastic modulus) seem to be associated with the nature of amide groups (i.e., primary or secondary amide) and the increase in the length of the self-assembly molecular unit (i.e., L value determined by X-ray diffraction) and therefore to the extent of London dispersion forces along the hydrocarbon chain. The creep and recovery measurements allowed an evaluation among the internal structures of the different organogels and demonstrated that independent of the hydrogen bonding and dipolar interaction provided by the amide and the hydroxyl groups, the increase in the hydrocarbon chain length results in higher organogel resistance to deformation and higher instant recovery capacity. However, the stabilization of the self-assembly unit through polar groups (i.e., –CONH₂ in HOA) reduces organogel elasticity but provides a higher extended recovery capacity. The results reported in this investigation showed some relationships between gelator structure and the thermo-mechanical properties of low-molecular-mass organic gelator amides. Our long-term objective is to understand the organogelation process to eventually develop trans-free vegetable oil-based food products with novel textures for the consumers.