Population density and growth of the newly introduced Atlantic rock crab Cancer irroratus Say, 1817 (Decapoda,Brachyura) in Iceland: a four-year mark-recapture study

The Atlantic rock crab Cancer irroratus was discovered in Icelandic waters in August 2006 and spread rapidly along the coastline. The species has reproduced successfully in Iceland, and there have been strong indications that C. irroratus has become common on soft-bottom coastal habitats in south-western Iceland. To be able to evaluate the effect of such non-indigenous species on the ecosystem, population density estimates are required. In the years 2011 to 2014, a mark-recapture study was carried out on C. irroratus in a small inlet in the Kollafjörður fjord, south-western Iceland. In total, 6475 C. irroratus were captured and of them 4670 were tagged with sequentially numbered T-bar anchor tags. Of the crabs tagged, 155 were recaptured over the four years (3.3%), 34 had moulted and one of them presumably twice over the four-year period. The size range of recaptured crabs was 7.3–12.8?cm carapace width and the growth increment per moult ranged from 1.2 to 2.6?cm, with an average of 2?cm. Based on the mark-recapture analysis, the population at the study area in Kollafjörður was estimated to be about 107,000 individuals.     

Size distribution,length–weight relationship and size at the onset of sexual maturity of the orange mud crab,Scylla olivacea,in Malaysian waters

The size distribution, length–weight relationship and size at the onset of sexual maturity of the orange mud crab (Scylla olivacea) from four geographically distinct locations (Taiping, Setiu, Kota Marudu and Lundu) representing Malaysian waters were analysed and estimated. Scylla olivacea was found in the size range of 47–134?mm carapace width. Males were significantly smaller in size but heavier than females. Geographical variation in carapace width and body weight were significant, but no interaction was found between sexes and locations. As shown by the length–weight relationships of S. olivacea, the males exhibited positive growth allometry whereas the females exhibited negative growth allometry. Males mature physiologically prior to attaining morphometric sexual maturity. Females, however, achieve physiological and morphometric sexual maturity in synchrony. No significant variation was found in the estimates of size at the onset of sexual maturity of males and females among different locations. We recommend the use of the third right walking leg merus length and carapace width to estimate the size at the onset of sexual maturity (morphometric maturity) for S. olivacea. Data obtained in this study serve as important baseline data for future mud crab resource management in Malaysia and were used to recommend minimum landing sizes for S. olivacea in each respective location based on the largest size at the onset of sexual maturity estimates were suggested.     

Moulting synchrony in green crabs (Carcinus maenas) from Prince Edward Island,Canada

The growth and spread of non-indigenous green crabs (Carcinus maenas) in Atlantic Canada is of concern to the sustainability of shellfish resources, particularly in areas recently invaded. Commercial green crab fishing has been initiated on Prince Edward Island to help control this species and provide a new resource for inshore fishermen. Developing a soft-shell crab product modelled after the Venetian ‘Moleche’ would provide an economic incentive beyond the existing hard-shell crab bait market. However, answers to questions such as the timing and characteristics of green crab moulting are required. A pilot study conducted in 2014–2015 collected seven groups of crabs and held them in individual compartments for 2–4 weeks to record moulting rates and physical characteristics. We found that a synchronized ‘moulting window’ occurs during July for male crabs. Field experiments in 2015 had an average moulting rate of 34%, with group-specific rates as high as 60%. The same cohort of crabs held in the laboratory had an average moulting rate of 48%, with group-specific rates as high as 75%. We observed a gradual increase in moulting rates from early to mid-July, after which all crabs caught had recently moulted, with evidence of new carapaces on all crabs. In 2015, the moulting window followed a 5°C increase in water temperature. Regarding morphology, the presence of a ‘halo’ on the episternites of the carapace was an indicator that a crab would soon moult. These promising results represent the first step in assessing the feasibility of a soft-shell, green crab industry.     

A new hermit crab of the Paguristes tortugae complex (Crustacea: Anomura: Diogenidae), with a key to the western Atlantic species

A new hermit crab species, Paguristes scarabinoi sp. nov. is described and illustrated based on specimens collected in Uruguay. The new species is assigned to the Paguristes tortugae species complex based on the characteristic dense fringe of long plumose setae present on ambulatory legs and dorsolateral margins of chelae. The new species can be differentiated from all other species currently placed in the P. tortugae complex by the combination of the following features: antennal flagellum with short and long setae on each article; antennular peduncles short to moderately long, not exceeding one-third of ocular peduncles including the corneas; dactyl of ambulatory legs long, slender, slightly convex and without a longitudinal sulcus flanked by corneous spines or spinules on the mesial face; and female brood pouch elongate, slender, blade-shaped. A key to the western Atlantic species of the P. tortugae complex is provided.

http://zoobank.org/urn:lsid:zoobank.org:pub:4B3298F3-D5DF-40E5-A2AB-9B457AB8BE0E     

Monte Carlo Study of the Buckingham Exponential-six Fluid

Abstract

In this paper we report the results of extensive Monte Carlo simulations of a pure fluid of Buckingham modified exponential-six molecules. Data are presented for the configurational energy and pressure covering a wide range of temperatures and densities. These data are interpreted using the generalized van der Waals partition function with a novel separation into free volume and mean potential terms. We find, surprisingly, that the Buckingham fluid is described by a simple van der Waals-like equation of state provided that the b parameter is temperature dependent and chosen in a theoretically correct manner.     

Sampling the Initial Conditions for Quasiclassical Trajectory Studies of Vibrational Predissociation Dynamics

A method is proposed for selecting initial conditions in order to study the classical dynamics of vibrational predissociation of van der Waals (vdW) clusters. The method starts from the quantum initial state of the system, which is used to sample and weight the initial positions of the different modes. The initial values of the associated momenta are calculated in such a way that they correspond with the total energy and angular momentum of the system initial state, at which the classical trajectory simulation is to be carried out. An application to the case of Cl2–-He2 is presented and discussed.     

A novel approach to the van der pol oscillator: Natural frequency and entrainment

Abstract

The physics of the van der Pol oscillator as realized by the Meissner circuit is discussed by analogy to the beat phenomenon and by a consequent analysis of current balance. The current balance method leads to a new, very accurate equation for the dependence of the oscillator frequency on the feedback parameter. Several aspects of entrainment (existence, limited frequency range, dependence on parameters, phase shift) can be explained, too. Numerical results are presented which have been obtained by solving the homogeneous and inhomogeneous van der Pol equation with a Runge‐Kutta method.     

ProteinVolume: calculating molecular van der Waals and void volumes in proteins

Background

Voids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.

Results

We developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.

Conclusions

ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu. Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0531-2) contains supplementary material, which is available to authorized users.     

Methyl 6-deoxy-6-iodo-α-d-glucopyranoside: crystal structure and high-resolution NMR spectroscopy

Single-crystal X-ray diffraction and high-resolution ¹H and ¹³C NMR spectral data for methyl 6-deoxy-6-iodo-α-d-glucopyranoside are reported. The ⁴C₁ conformation was found to be the preferred form for this compound, both in the crystal lattice and in solution. The rotational preferences of all the groups bound to the pyranose ring are presented. The stabilization of the crystal structure by a network of O-H···O intra- and intermolecular interactions as well as the short contacts of the iodine atoms is discussed.     

A Mathematical Model of the Human Circadian System and Its Application to Jet Lag

A mathematical model of the circadian system is described that is appropriate for application to jet lag. The core of the model is a van der Pol equation with an external force. Approximate solutions of this equation in which the external force is composed of a constant and an oscillating term are investigated. They lead to analytical expressions for the amplitude and period of free-running rhythms and for the frequency limits of the entrainment region. The free-running period increases quadratically with stiffness. Both period and amplitude depend on the value of the constant external force. The width of the range of entrainment is mostly determined by the external force, whereas the relative position of this range follows the intrinsic period of the oscillator. Experiments with forced and spontaneous internal desynchronization were evaluated using these analytical expressions, and estimates were obtained for the intrinsic period of the oscillator, its stiffness, and the external force. A knowledge of these model parameters is essential for predictions about circadian dynamics, and there are practical implications for the assessment of the adaptation after rapid transmeridian travel.     

A Mathematical Model of the Human Circadian System and Its Application to Jet Lag

A mathematical model of the circadian system is described that is appropriate for application to jet lag. The core of the model is a van der Pol equation with an external force. Approximate solutions of this equation in which the external force is composed of a constant and an oscillating term are investigated. They lead to analytical expressions for the amplitude and period of free-running rhythms and for the frequency limits of the entrainment region. The free-running period increases quadratically with stiffness. Both period and amplitude depend on the value of the constant external force. The width of the range of entrainment is mostly determined by the external force, whereas the relative position of this range follows the intrinsic period of the oscillator. Experiments with forced and spontaneous internal desynchronization were evaluated using these analytical expressions, and estimates were obtained for the intrinsic period of the oscillator, its stiffness, and the external force. A knowledge of these model parameters is essential for predictions about circadian dynamics, and there are practical implications for the assessment of the adaptation after rapid transmeridian travel.     

On the existence of MHn species with M=Al, Ga and n=4, 5, 6. Computational study of structures, stabilities and bonding

Based on second-order perturbation theory (MP2) predictions with large 6-311++G(3df, 3pd) basis set we have reviewed the possible structures and stabilities of a series of neutral MH_n(M=Al, Ga; n=4, 5, 6) species. For AlH₄ and AlH₅, our results confirm the previous theoretical findings, which indicate the dihydrogen C_s complexes (²A′) AlH₂(H₂) and (¹A′) AlH₃(H₂), respectively, as the lowest energy isomers. We found, similarly, C_s (²A′) GaH₂(H₂) and (¹A′) GaH₃(H₂) van der Waals complexes as the most stable species of the gallium analogues GaH₄ and GaH₅. The calculated H₂ dissociation energies (D_e) for AlH₂(H₂) and AlH₃(H₂) are of the order 1.8–2.5 kcalmol¹, whereas this range of values for GaH₂(H₂) and GaH₃(H₂) is 1.4–1.8 kcalmol¹ . Symmetry-adapted perturbation theory (SAPT) was used to analyze the interaction energies of these dihydrogen complexes (for n=5) to determine why the Ga species show a smaller binding energy than the Al species. The SAPT partitioning of the interaction energy showed significant differences between AlH₃(H₂) and GaH₃(H₂), resulting from the much stronger “hydride” character of the aluminum species. The experimental observation of AlH₂(H₂) and AlH₃(H₂), and likely GaH₃(H₂), via low-temperature matrix isolation has been reported recently by Pullumbi et al. and Andrews et al., supporting the theoretical predictions. For n=6, we found the degenerate C₂(²A) and C_s(²A′) MH₂(H₂)₂ “double H₂” type van der Waals complexes as the lowest energy species for both M=Al and Ga.Electronic Supplementary Material Supplementary material is available for this article at     

Side-chain contributions to membrane protein structure and stability

The molecular forces that stabilize membrane protein structure are poorly understood. To investigate these forces we introduced alanine substitutions at 24 positions in the B helix of bacteriorhodopsin and examined their effects on structure and stability. Although most of the results can be rationalized in terms of the folded structure, there are a number of surprises. (1) We find a remarkably high frequency of stabilizing mutations (17%), indicating that membrane proteins are not highly optimized for stability. (2) Helix B is kinked, with the kink centered around Pro50. The P50A mutation has no effect on stability, however, and a crystal structure reveals that the helix remains bent, indicating that tertiary contacts dominate in the distortion of this helix. (3) We find that the protein is stabilized by about 1kcal/mol for every 38A(2) of surface area buried, which is quite similar to soluble proteins in spite of their dramatically different environments. (4) We find little energetic difference, on average, in the burial of apolar surface or polar surface area, implying that van der Waals packing is the dominant force that drives membrane protein folding.