Figure 9: Alternative representations of the Ramachandran plot.

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity

BIOS approach tested for controlling walnut pests in San Joaquin Valley

As concerns increase over changes in pesticide regulations, farmworker safety, surface and groundwater contamination and escalating costs and uncertainties associated with chemical controls, walnut growers need effective and cost-efficient ways to produce walnuts with minimal use of pesticides. This study compared the effectiveness of Biologically Integrated Orchard Systems (BIOS) with conventionally managed walnut orchards in the northern San Joaquin Valley from 1999 to 2001. We found no significant differences between BIOS and conventional blocks in nut quality or yields. Codling moth was effectively controlled by pheromone disruption and alternative pest-control methods. Mating disruption, by itself, appears to provide good control of codling moth in many orchards. However, it is still more expensive for growers than conventional pest-control methods

Vine Mealybug: What You Should Know

Vine mealybug (VMB), a vineyard pest throughout the world, damages grape foliage and fruit, rendering the fruit unmarketable. This publication helps you identify and control VMB in California vineyards

Bait formulations and longevity of navel orangeworm egg traps tested

Standardization of pest monitoring practices and materials to maximize sensitivity to pest populations in the field is a foundation of effective integrated pest management (IPM). In response to changes in the availability of commercial bait material for navel orangeworm (NOW) egg traps, we evaluated potential alternative bait materials for use in monitoring this key pest of almonds, pistachios, walnuts and figs. Navel orangeworm egg traps baited with uninfested nutmeats were as effective as almond meal plus 10% crude almond oil, whereas traps baited with freeze-killed, navel orangeworm-infested nutmeats were less effective. The use of nut mummies (culled during winter orchard sanitation) as trap bait may not produce consistent results since the level of navel orangeworm infestation of these nuts is typically unknown. Three seasons of field tests showed that egg traps baited with almond meal plus 3% or 10% crude almond oil received similar numbers of navel orangeworm eggs, and these traps were equally effective for at least 10 weeks