Contributions to the binding free energy of ligands to avidin and streptavidin

The free energy of binding of a ligand to a macromolecule is here formally decomposed into the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand. Molecular dynamics simulations with implicit solvation are used to evaluate these contributions in the binding of biotin, biotin analogs, and two peptides to avidin and streptavidin. We find that the largest contribution opposing binding is the protein reorganization energy, which is calculated to be from 10 to 30 kcal/mol for the ligands considered here. The ligand reorganization energy is also significant for flexible ligands. The translational/rotational entropy is 4.5-6 kcal/mol at 1 M standard state and room temperature. The calculated binding free energies are in the correct range, but the large statistical uncertainty in the protein reorganization energy precludes precise predictions. For some complexes, the simulations show multiple binding modes, different from the one observed in the crystal structure. This finding is probably due to deficiencies in the force field but may also reflect considerable ligand flexibility.     

Mapping the Shapes of Phylogenetic Trees from Human and Zoonotic RNA Viruses

A phylogeny is a tree-based model of common ancestry that is an indispensable tool for studying biological variation. Phylogenies play a special role in the study of rapidly evolving populations such as viruses, where the proliferation of lineages is constantly being shaped by the mode of virus transmission, by adaptation to immune systems, and by patterns of human migration and contact. These processes may leave an imprint on the shapes of virus phylogenies that can be extracted for comparative study; however, tree shapes are intrinsically difficult to quantify. Here we present a comprehensive study of phylogenies reconstructed from 38 different RNA viruses from 12 taxonomic families that are associated with human pathologies. To accomplish this, we have developed a new procedure for studying phylogenetic tree shapes based on the ‘kernel trick’, a technique that maps complex objects into a statistically convenient space. We show that our kernel method outperforms nine different tree balance statistics at correctly classifying phylogenies that were simulated under different evolutionary scenarios. Using the kernel method, we observe patterns in the distribution of RNA virus phylogenies in this space that reflect modes of transmission and pathogenesis. For example, viruses that can establish persistent chronic infections (such as HIV and hepatitis C virus) form a distinct cluster. Although the visibly ‘star-like’ shape characteristic of trees from these viruses has been well-documented, we show that established methods for quantifying tree shape fail to distinguish these trees from those of other viruses. The kernel approach presented here potentially represents an important new tool for characterizing the evolution and epidemiology of RNA viruses.     

The containment of the radical right in Western Europe: a response to Carvalho

Do extreme right parties in contemporary Europe shape policy in meaningful ways? Carvalho's book charts complicated intellectual terrain, and the author demonstrates that while radical right parties have made a modest political impact in some states, they have achieved much less than one might have expected in their central policy area (immigration). After reviewing the strengths and weaknesses of Carvalho's analysis, I suggest that his findings are consistent with the general ‘containment’ (as opposed to ‘contagion’) of the radical right in (Western) Europe. The notion that the populist right has been ‘contained’ in Europe may seem odd at first blush, but a comparison with the USA suggests that it may be a fruitful theoretical starting point.     

Maresin-1 reduces the pro-inflammatory response of bronchial epithelial cells to organic dust

Background

Exposure to organic dust causes detrimental airway inflammation. Current preventative and therapeutic measures do not adequately treat resulting disease, necessitating novel therapeutic interventions. Recently identified mediators derived from polyunsaturated fatty acids exhibit anti-inflammatory and pro-resolving actions. We tested the potential of one of these mediators, maresin-1 (MaR1), in reducing organic dust-associated airway inflammation.

Methods

As bronchial epithelial cells (BECs) are pivotal in initiating organic dust-induced inflammation, we investigated the in vitro effects of MaR1 on a human BEC cell line (BEAS-2B). Cells were pretreated for 1 hour with 0–200 nM MaR1, followed by 1–24 hour treatment with 5% hog confinement facility-derived organic dust extract (HDE). Alternatively, a mouse lung slice model was utilized in supportive cytokine studies. Supernatants were harvested and cytokine levels determined via enzyme-linked immunosorbent assays. Epithelial cell protein kinase C (PKC) isoforms α and ϵ, and PKA activities were assessed via radioactivity assays, and NFκB and MAPK-related signaling mechanisms were investigated using luciferase vector reporters.

Results

MaR1 dose-dependently reduced IL-6 and IL-8 production following HDE treatment of BECs. MaR1 also reduced HDE-stimulated cytokine release including TNF-α in a mouse lung slice model when given before or following HDE treatment. Previous studies have established that HDE sequentially activates epithelial PKCα and PKCϵ at 1 and 6 hours, respectively that regulated TNF-α, IL-6, and IL-8 release. MaR1 pretreatment abrogated these HDE-induced PKC activities. Furthermore, HDE treatment over a 24-hour period revealed temporal increases in NFκB, AP-1, SP-1, and SRE DNA binding activities, using luciferase reporter assays. MaR1 pretreatment did not alter the activation of NFκB, AP-1, or SP-1, but did reduce the activation of DNA binding at SRE.

Conclusions

These observations indicate a role for MaR1 in attenuating the pro-inflammatory responses of BECs to organic dust extract, through a mechanism that does not appear to rely on reduced NFκB, AP-1, or SP-1-related signaling, but may be mediated partly through SRE-related signaling. These data offer insights for a novel mechanistic action of MaR1 in bronchial epithelial cells, and support future in vivo studies to test MaR1’s utility in reducing the deleterious inflammatory effects of environmental dust exposures.     

Commercial techniques for preserving date palm (Phoenix dactylifera) fruit quality and safety: A review

The popularity of date palm (Phoenix dactylifera) fruit is increasing, therefore the demand for high-quality date palm fruit with less or no chemical treatment is the topic of interest for date producers and consumers. The quality of date palm fruit is much dependent on its postharvest handling and processing. For preventing the degradation and maintenance of the high quality of dates during the storage an appropriate harvest and post-harvest processes are required. The process should control the biotic and abiotic factors like insects, fungus, temperature, as well as handling and processing of dates. Therefore, in this work, we reviewed the literature related to the protection of date fruits during their post-harvest life. The commercially viable advance and updated techniques that can be used to avoid storage losses and problems while keeping fruit quality (nutritional, color, flavor, and texture) and microbial safety under optimal conditions are discussed.     

HIV-1 nef protein structures associated with brain infection and dementia pathogenesis

The difference between regional rates of HIV-associated dementia (HAD) in patients infected with different subtypes of HIV suggests that genetic determinants exist within HIV that influence the ability of the virus to replicate in the central nervous system (in Uganda, Africa, subtype D HAD rate is 89%, while subtype A HAD rate is 24%). HIV-1 nef is a multifunctional protein with known toxic effects in the brain compartment. The goal of the current study was to identify if specific three-dimensional nef structures may be linked to patients who developed HAD. HIV-1 nef structures were computationally derived for consensus brain and non-brain sequences from a panel of patients infected with subtype B who died due to varied disease pathologies and consensus subtype A and subtype D sequences from Uganda. Site directed mutation analysis identified signatures in brain structures that appear to change binding potentials and could affect folding conformations of brain-associated structures. Despite the large sequence variation between HIV subtypes, structural alignments confirmed that viral structures derived from patients with HAD were more similar to subtype D structures than to structures derived from patient sequences without HAD. Furthermore, structures derived from brain sequences of patients with HAD were more similar to subtype D structures than they were to their own non-brain structures. The potential finding of a brain-specific nef structure indicates that HAD may result from genetic alterations that alter the folding or binding potential of the protein.     

Actin motility: formin a SCAry tail

A new biochemical analysis has revealed that the Rickettsia bacterial protein Sca2--recently shown to be essential for virulence and actin-dependent motility--assembles actin filaments using a mechanism that functionally resembles the processive elongation tactics used by formins.     

Does cutting herbicide rates threaten the sustainability of weed management in cropping systems?

Evolution of herbicide resistance in weeds is a growing problem across the world, and it has been suggested that low herbicide rates may be contributing to this problem. An individual-based simulation model that represents weed population dynamics and the evolution of polygenic herbicide resistance was constructed and used to investigate whether using lower herbicide rates or standard rates at reduced efficacy could reduce the sustainability of cropping systems by causing faster increases in weed population density as herbicide resistance develops. A number of different possible genetic bases for resistance were considered, including monogenic resistance and polygenic resistance conferred by several genes. The results show that cutting herbicide rates does not affect the rate at which weed densities reach critical levels when resistance is conferred exclusively by a single dominant gene. In some polygenic situations, cutting herbicide rates substantially reduces sustainability, due to a combination of faster increase in resistance gene frequency and reduced kill rates in all genotypes, while in other polygenic situations the effect is small. Differences in sustainability depend on combined strength of the resistance genes, variability in phenotypic susceptibility and rate delivered, level of control due to alternative measures, and degree of genetic dominance and epistasis. In the situation where resistance can be conferred by both a single dominant major gene or a number of co-dominant minor genes in combination, the difference made by low rates depends on the relative initial frequency of the major and minor genes. These results show that careful consideration of herbicide rate and understanding the genetic basis of resistance are important aspects of weed management.