Structural relatedness of lysis proteins from colicinogenic plasmids and icosahedral coliphages.

The host-lysis-inducing functions of phi X174 protein E and MS2 protein L were recently shown to reside on the N-terminal and C-terminal halves of the two respective lysis proteins. In the present study it is shown that the small lysis proteins encoded in various colicinogenic plasmids share local sequence similarities and certain structural characteristics with the essential peptides of their coliphage-coded counterparts. Despite their dissimilar sizes and origins, it is suggested that the colicinogenic lysis proteins are functionally analogous and evolutionarily related to those of icosahedral single-stranded DNA and RNA phages

Passive CO₂ removal in urban soils:evidence from brownfield sites

Management of urban brownfield land can contribute to significant removal of atmospheric CO2 through the development of soil carbonate minerals. However, the potential magnitude and stability of this carbon sink is poorly quantified as previous studies address a limited range of conditions and short durations. Furthermore, the suitability of carbonate-sequestering soils for construction has not been investigated. To address these issues we measured total inorganic carbon, permeability and ground strength in the top 20 cm of soil at 20 brownfield sites in northern England, between 2015 and 2017. Across all sites accumulation occurred at a rate of 1–16 t C ha−1 yr−1, as calcite (CaCO3), corresponding to removal of approximately 4–59 t CO2 ha−1 yr−1, with the highest rate in the first 15 years after demolition. C and O stable isotope analysis of calcite confirms the atmospheric origin of the measured inorganic carbon. Statistical modelling found that pH and the content of fine materials (combined silt and clay content) were the best predictors of the total inorganic carbon content of the samples. Measurement of permeability shows that sites with carbonated soils possess a similar risk of run-off or flooding to sandy soils. Soil strength, measured as in-situ bearing capacity, increased with carbonation. These results demonstrate that the management of urban brownfield land to retain fine material derived from concrete crushing on site following demolition will promote calcite precipitation in soils, and so offers an additional CO2 removal mechanism, with no detrimental effect on drainage and possible improvements in strength. Given the large area of brownfield land that is available for development, the contribution of this process to CO2 removal by urban soils needs to be recognised in CO2 mitigation policies

Developing a contactless bankcard fare engine for Transport for London

Thesis (S.M. in Transportation)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2009.Includes bibliographical references (p. 192-193).This thesis investigates the design of a fare engine which operates within the constraints of using contactless bankcards as a fare instrument, while satisfying the complex current and future fare requirements of Transport for London (TfL). A fare engine is a system which transforms user transactions at fare gates and validators into chargeable fares. Contactless bankcard fare payment differs from current fare smartcard systems by requiring a centralized fare engine. The proposed fare engine utilizes a data structure which maintains each user's journey history in three successive tiers of linked objects. This structure enables transactions to be correctly sequenced without a guarantee of in-order arrival of gate and validator transactions. A cleanup routine prevents the data structure from growing without bound as journey history accumulates. A dynamic journey linking mechanism allows the effect of inserted transactions to be propagated throughout the data structure and reflected in the affected journeys with near-constant time complexity. This ensures scalability while providing real-time feedback for customer service and payment authorization needs. A solution is devised for the coupling of arbitrary origin-destination fares with zonal period tickets. The paradigm of automatic ticket selection is introduced, overcoming the limitations of the existing capping algorithm used by TfL. Through the tracking of parallel fare scenarios, passengers are guaranteed a total fare no higher than if they had purchased the optimal period ticket for their usage profile. With the solutions proposed in this thesis, a contactless bankcard fare engine for TfL appears feasible.by Peter S.C. Lau.S.M.in Transportatio

Dietary Strategies to Optimize Wound Healing after Periodontal and Dental Implant Surgery: An Evidence-Based Review

Methods to optimize healing through dietary strategies present an attractive option for patients, such that healing from delicate oral surgeries occurs as optimally as possible with minimal patient-meditated complications through improper food choices. This review discusses findings from studies that have investigated the role of diet, either whole foods or individual dietary components, on periodontal health and their potential role in wound healing after periodontal surgery. To date, research in this area has largely focused on foods or individual dietary components that may attenuate inflammation or oxidant stress, or foster de novo bone formation. These studies suggest that a wide variety of dietary components, including macronutrients and micronutrients, are integral for optimal periodontal health and have the potential to accelerate oral wound healing after periodontal procedures. Moreover, this review provides guidance regarding dietary considerations that may help a patient achieve the best possible outcome after a periodontal procedure

An MHC-I Cytoplasmic Domain/HIV-1 Nef Fusion Protein Binds Directly to the μ Subunit of the AP-1 Endosomal Coat Complex

The down-regulation of the major histocompatibility complex class I (MHC-I) from the surface of infected cells by the Nef proteins of primate immunodeficiency viruses likely contributes to pathogenesis by providing evasion of cell-mediated immunity. HIV-1 Nef-induced down-regulation involves endosomal trafficking and a cooperative interaction between the cytoplasmic domain (CD) of MHC-I, Nef, and the clathrin adaptor protein complex-1 (AP-1). The CD of MHC-I contains a key tyrosine within the sequence YSQA that is required for down-regulation by Nef, but this sequence does not conform to the canonical AP-binding tyrosine-based motif Yxxphi, which mediates binding to the medium (micro) subunits of AP complexes. We previously proposed that Nef allows the MHC-I CD to bind the mu subunit of AP-1 (micro1) as if it contained a Yxxphimotif.Here, we show that a direct interaction between the MHC-I CD/Nef and micro1 plays a primary role in the down-regulation of MHC-I: GST pulldown assays using recombinant proteins indicated that most of the MHC-I CD and Nef residues that are required for the down-regulation in human cells contribute to direct interactions with a truncated version of micro1. Specifically, the tyrosine residue of the YSQA sequence in the MHC-I CD as well as Nef residues E62-65 and P78 each contributed to the interaction between MHC-I CD/Nef and micro1 in vitro, whereas Nef M20 had little to no role. Conversely, residues F172/D174 and V392/L395 of the binding pocket on micro1 for Yxxphi motifs were required for a robust interaction.These data indicate that the MHC-I cytoplasmic domain, Nef, and the C-terminal two thirds of the mu subunit of AP-1 are sufficient to constitute a biologically relevant interaction. The data also reveal an unexpected role for a hydrophobic pocket in micro1 for interaction with MHC-I CD/Nef

Café Mesoamericano: desarrollo de una estrategia de adaptación al cambio climático

La producción de café en Mesoamérica es parte importante de la economía y la sociedad, al ser eje del bienestar de miles de familias y contribuir significativamente al PIB agrícola de diversos países. Pero las proyecciones indican que es en México y América Central donde el cambio climático tendrá los impactos más severos. Los modelos climáticos y los indicadores de aptitud climática del nicho en relación con el cultivo muestran cambios considerables, tanto en la calidad del café como en las zonas altitudinales apropiadas para la producción. Si hoy no se hacen esfuerzos para fortalecer la capacidad adaptativa, probablemente habrá grandes pérdidas económicas en toda la cadena de abastecimiento de café, así como la desaparición de importantes servicios ambientales

A New Monte Carlo Algorithm for Protein Folding

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for lattice heteropolymers, and compare to published Monte Carlo studies. In all cases our algorithms are faster than all previous ones, and in several cases we find new minimal energy states. In addition to ground states, our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett., revised version with changes in the tex