Realignment of the Genetic Map of the Terminus of the rIIB Cistron of Bacteriophage T4

Duplication end-point mapping in the rIIB cistron indicates that the order of the BS-B10b segments is the inverse of that presented in Benzer's (1961) genetic maps. This findings is supported by two- and three-factor crosses and the phenotypes of rII deletions extending into the D region.     

The flexibility in the proline ring couples to the protein backbone

In proteins, the proline ring exists predominantly in two discrete states. However, there is also a small but significant amount of flexibility in the proline ring of high-resolution protein structures. We have found that this side-chain flexibility is coupled to the backbone conformation. To study this coupling, we have developed a model that is simply based on geometric and steric factors and not on energetics. We show that the coupling between phi and chi1 torsions in the proline ring can be described by an analytic equation that was developed by Bricard in 1897, and we describe a computer algorithm that implements the equation. The model predicts the observed coupling very well. The strain in the C(gamma)-C(delta)-N angle appears to be the principal barrier between the UP and DOWN pucker. This strain is relaxed to allow the proline ring to flatten in the rare PLANAR conformation.     

Quantifying optimal accuracy of local primary sequence bioinformatics methods

MOTIVATION: Traditional bioinformatics methods scan primary sequences for local patterns. It is important to assess how accurate local primary sequence methods can be. RESULTS: We study the problem of donor pre-mRNA splice site recognition, where the sequence overlaps between real and decoy datasets can be quantified, exposing the intrinsic limitations of the performance of local primary sequence methods. We assess the accuracy of primary sequence methods generally by studying how they scale with dataset size and demonstrate that our new primary sequence ranking methods have superior performance.     

Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases

Alpha-lytic protease (alpha LP) and Streptomyces griseus protease B (SGPB) are two extracellular serine proteases whose folding is absolutely dependent on the existence of their companion pro regions. Moreover, the native states of these proteins are, at best, marginally stable, with the apparent stability resulting from being kinetically trapped in the native state by large barriers to unfolding. Here, in an effort to understand the physical properties that distinguish kinetically and thermodynamically stable proteins, we study the temperature-dependences of the folding and unfolding kinetics of alpha LP and SGPB without their pro regions, and compare their behavior to a comprehensive set of other proteins. For the folding activation thermodynamics, we find some remarkable universal behaviors in the thermodynamically stable proteins that are violated dramatically by alpha LP. Despite significant variations in deltaC(P,F)++, the maximal folding speed occurs within the narrow biological temperature range for all proteins, except for alpha LP, with its maximal folding speed shifted lower by 200 K. This implies evolutionary pressures on folding speed for typical proteins, but not for alpha LP. In addition, the folding free energy barrier in the biological temperature range for most proteins is predominantly enthalpic, but purely entropic for alpha LP. The unfolding of alpha LP and SGPB is distinguished by three properties: a remarkably large deltaC(P,U)++, a very high deltaG(U)++, and a maximum deltaG(u)++ at the optimal growth temperature for the organism. While other proteins display each of these traits to some approximation, the simultaneous optimization of all three occurs only in the kinetically stable proteins, and appears to be required to maximize their unfolding cooperativity, by suppressing local unfolding events, and slowing the rate of global unfolding. Together, these properties extend the lifetime of these enzymes in the highly proteolytic extracellular environment. Attaining such functional properties seems possible only through the gross perturbation of the folding thermodynamics, which in turn has required the co-evolution of pro regions as folding catalysts.     

Pacific and Atlantic herring produce burst pulse sounds

The commercial importance of Pacific and Atlantic herring (Clupea pallasii and Clupea harengus) has ensured that much of their biology has received attention. However, their sound production remains poorly studied. We describe the sounds made by captive wild-caught herring. Pacific herring produce distinctive bursts of pulses, termed Fast Repetitive Tick (FRT) sounds. These trains of broadband pulses (1.7-22 kHz) lasted between 0.6 s and 7.6 s. Most were produced at night; feeding regime did not affect their frequency, and fish produced FRT sounds without direct access to the air. Digestive gas or gulped air transfer to the swim bladder, therefore, do not appear to be responsible for FRT sound generation. Atlantic herring also produce FRT sounds, and video analysis showed an association with bubble expulsion from the anal duct region (i.e. from the gut or swim bladder). To the best of the authors' knowledge, sound production by such means has not previously been described. The function(s) of these sounds are unknown, but as the per capita rates of sound production by fish at higher densities were greater, social mediation appears likely. These sounds may have consequences for our understanding of herring behaviour and the effects of noise pollution.     

The Influence of Substrate Color on the Alarm Response of Tidepool Sculpins (Oligocottus maculosus; Pisces,Cottidae)

For animals that use crypsis to avoid predators, immobility reduces the risk of detection. The magnitude of this immobility benefit depends upon the probability that a predator is present, since a predator must be present for crypsis to be valuable. Thus, cryptic animals typically reduce their movement rates upon detection of a nearby predator or signs of its activity. Such a response occurs in tidepool sculpins (Oligocottus maculosus) when presented with water-borne compounds released from the skin of injured conspecifics (Hugie et al. 1991). The benefit of immobility should also depend upon the animal's background, or substrate, since animals on a matching substrate achieve a higher level of crypticity than those on a nonmatching substrate, and have more to gain by remaining still. Therefore, we predicted that the response of tidepool sculpins to conspecific skin extract would involve a greater reduction in movement rates for fish on sand (matching) than for those on white (nonmatching) substrate. The results of a laboratory experiment supported this prediction, with fish on sand showing a large decrease in movement rates in response to skin extract, while the movement rates of those on white substrate remained unchanged.     

Evidence for crypsis in coho salmon, Oncorhynchus kisutch (Walbaum), parr: substrate colour preference and achromatic reflectance

The crypsis hypothesis of salmonid parr coloration and behaviour is evaluated in light of the criteria for protective resemblance. A review of the literature indicates that salmonid parr coloration and behaviour correspond to a cryptic interpretation. Experiments on coho salmon, Oncorhynchus kisutch , parr substrate colour preference indicate that the behavioural correlate of appropriate background choice is satisfied. Absorption spectrophotometry of diapositives of fish and experimental substrates suggests that background matching is achieved through achromatic reflectance and absorption of wavelengths by the silvery sides and parr marks, respectively.     

Extracting representative structures from protein conformational ensembles

A large number of methods generate conformational ensembles of biomolecules. Often one structure is selected to be representative of the whole ensemble, usually by clustering and selecting the structure closest to the center of the most populated cluster. We find that this structure is not necessarily the best representation of the cluster and present here two computationally inexpensive averaging protocols that can systematically provide better representations of the system, which can be more directly compared with structures from X‐ray crystallography. In practice, systematic errors in the generated conformational ensembles appear to limit the maximum improvement of averaging methods. Proteins 2014; 82:2671–2680. © 2014 Wiley Periodicals, Inc.