Mineralogical Transformations and Soil Development in Shale Across a Latitudinal Climosequence

To investigate factors controlling soil formation, we established a climosequence as part of the Susquehanna-Shale Hills Critical Zone Observatory (SSHCZO) in central Pennsylvania, USA. Sites were located on organic matter-poor, iron-rich Silurian-aged shale in Wales, Pennsylvania, Virginia, Tennessee, Alabama, and Puerto Rico, although this last site is underlain by a younger shale. Across the climosequence, mean annual temperature (MAT) increases from 7 to 24°C and mean annual precipitation (MAP) ranges from 100 to 250 cm. Variations in soil characteristics along the climosequence, including depth, morphology, particle-size distribution, geochemistry, and bulk and clay mineralogy, were characterized to investigate the role of climate in controlling mineral transformations and soil formation. Overall, soil horizonation, depth, clay content, and chemical depletion increase with increasing temperature and precipitation, consistent with enhanced soil development and weathering processes in warmer and wetter locations. Secondary minerals are present at higher concentrations at the warmest sites of the climosequence; kaolinite increases from \u3c5% at northern sites in Wales and Pennsylvania to 30% in Puerto Rico. The deepest observed weathering reaction is plagioclase feldspar dissolution followed by the transformation of chlorite and illite to vermiculite and hydroxy-interlayered vermiculite. Plagioclase, although constituting \u3c12% of the initial shale mineralogy, may be the profile initiating reaction that begins shale bedrock transformation to weathered regolith. Weathering of the more abundant chlorite and illite minerals (∼70% of initial mineralogy), however, are more likely controlling regolith thickness. Climate appears to play a central role in driving soil formation and mineral weathering reactions across the climosequence

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.Comment: 25 pages, 7 figure

Numerical modelling of the shoulder for clinical applications

Research activity involving numerical models of the shoulder is dramatically increasing, driven by growing rates of injury and the need to better understand shoulder joint pathologies to develop therapeutic strategies. Based on the type of clinical question they can address, existing models can be broadly categorized into three groups: (i) rigid body models that can simulate kinematics, collisions between entities or wrapping of the muscles over the bones, and which have been used to investigate joint kinematics and ergonomics, and are often coupled with (ii) muscle force estimation techniques, consisting mainly of optimization methods and electromyography-driven models, to simulate muscular action and joint reaction forces to address issues in joint stability, muscular rehabilitation or muscle transfer, and (iii) deformable models that account for stress-strain distributions in the component structures to study articular degeneration, implant failure or muscle/tendon/bone integrity. The state of the art in numerical modelling of the shoulder is reviewed, and the advantages, limitations and potential clinical applications of these modelling approaches are critically discussed. This review concentrates primarily on muscle force estimation modelling, with emphasis on a novel muscle recruitment paradigm, compared with traditionally applied optimization methods. Finally, the necessary benchmarks for validating shoulder models, the emerging technologies that will enable further advances and the future challenges in the field are described

The VP3 gene of human group C rotavirus

The complete nucleotide sequence of genome segment 4 from the human group C rotavirus (Bristol strain) was determined. Comparison of the nucleotide sequences of the genome termini with the consensus 5' and 3' terminal non-coding sequences of the human group C rotavirus genome revealed characteristic 5' and 3' sequence motifs. Human group C rotavirus genome segment 4 is 2,166bp long and encodes a single open reading frame of 2,082 nucleotides (693 amino acids) starting at nucleotide 55 and terminating at nucleotide 2,136 giving a 3' untranslated region of 30 nucleotides. Alignment with the porcine group C VP3 equivalent gene showed the human gene is one amino acid longer, and that the proteins have 84.1% amino acid sequence identity. A conserved potential nucleotide binding motif shared with the porcine VP3 sequence was identified. Analogy with the group A rotaviruses suggested that the genome segment 4 encodes the group C rotavirus guanylyltransferase