Variation of reproductive behaviour and success of males adopting different tactics in Atlantic salmon

  The use of video photography normally involves sub‐aqua recording via a camcorder device. The problem is that the scientist needs to be directly involved in the recording underwater or else viewing the results of the footage after the event. The system we have developed enables real time images to be relayed to a boat, satellite of shore‐based recorder. With a two‐way audio communication system, it is possible for the scientist/team to direct the camera work of the divers, remotely. The configuration of this system are discussed, and a wide range of scientific applications suggested.     

Tree‐sequence recording in SLiM opens new horizons for forward‐time simulation of whole genomes

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual‐based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree‐sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward‐time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn‐in to be constructed extremely efficiently after the fact, using “recapitation”; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree‐sequence recording method in SLiM 3 (a free, open‐source evolutionary simulation software package) and extended it to allow the recording of non‐neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.     

Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls

The last decade has seen a dramatic increase in the use of small‐angle scattering for the study of biological macromolecules in solution. The drive for more complete structural characterization of proteins and their interactions, coupled with the increasing availability of instrumentation and easy‐to‐use software for data analysis and interpretation, is expanding the utility of the technique beyond the domain of the biophysicist and into the realm of the protein scientist. However, the absence of publication standards and the ease with which 3D models can be calculated against the inherently 1D scattering data means that an understanding of sample quality, data quality, and modeling assumptions is essential to have confidence in the results. This review is intended to provide a road map through the small‐angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data. Examples of current best practice are given that also demonstrate the power of the technique to advance our understanding of protein structure and function.     

Individual Distinctiveness in the Fine Structural Features and Repertoire Characteristics of the Songs of White‐eared Ground‐sparrows

Communication between social animals is often more effective when signals facilitate individual recognition. Two critical requirements for individual recognition are the occurrence of characteristics that are unique to each individual, and the consistency of these characteristics through time. In some animals, characteristics of acoustic signals are known to vary over time due to changes in a variety of factors, including physiological and environmental features. Such temporal variation requires careful evaluation when exploring the individual distinctiveness of animal signals. In this study, we evaluate individual distinctiveness in the songs of male white‐eared ground‐sparrows Melozone leucotis and the persistence of distinctive characteristics over time. We collected focal recordings from populations of banded ground‐sparrows during two consecutive breeding seasons, including multiple recording sessions within each breeding season. We evaluated individual distinctiveness in fine structural acoustic features of songs. We also extended our analysis to repertoire characteristics, focusing on whether the relative frequency of song type use may provide cues to individual identity. We found that each male white‐eared ground‐sparrow sang individually distinctive songs, although their fine structural features varied between recording sessions. We found the frequency with which males sang different song types was also individually distinctive, and this feature varied little between recording sessions. Receivers may be able to use these distinctive characteristics to differentiate individuals over extended time periods; this may be especially important for species that engage in long‐term social interactions, such as tropical birds that defend territories against rival conspecific animals throughout the year.     

Elegant‐crested Tinamous Eudromia elegans do not synchronize head and leg movements during head‐bobbing

Head‐bobbing is the fore–aft movement of the head relative to the body during terrestrial locomotion in birds. It is considered to be a behaviour that helps to stabilize images on the retina during locomotion, yet some studies have suggested biomechanical links between the movements of the head and legs. This study analysed terrestrial locomotion and head‐bobbing in the Elegant‐crested Tinamou Eudromia elegans at a range of speeds by synchronously recording high‐speed video and ground reaction forces in a laboratory setting. The results indicate that the timing of head and leg movements are dissociated from one another. Nonetheless, head and neck movements do affect stance duration, ground reaction forces and body pitch and, as a result, the movement of the centre of mass in head‐bobbing birds. This study does not support the hypothesis that head‐bobbing is itself constrained by terrestrial locomotion. Instead, it suggests that visual cues are the primary trigger for head‐bobbing in birds, and locomotion is, in turn, constrained by a need for image stabilization and depth perception.     

Development of Ionic Liquid‐Water‐Based Thermomorphic Solvent (TMS)‐Systems for Biocatalytic Reactions

The applicability of ionic liquid‐water‐based thermomorphic solvent (TMS)‐systems with an upper critical solution temperature for homogeneous biocatalysis is investigated. Cholinium‐ and imidazolium‐based ionic liquids are used to facilitate a temperature‐dependent phase change, which can be easily fine‐tuned by adding salts or polar organic solvents. Within the TMS‐system, a high enzymatic activity and subsequent full conversion is achieved in the intermittent monophasic reaction system of the TMS‐system. Therefore, the biocatalyst can be easily recycled after separating the phases at lower temperatures.     

A novel silicon patch‐clamp chip permits high‐fidelity recording of ion channel activity from functionally defined neurons

We report on a simple and high‐yield manufacturing process for silicon planar patch‐clamp chips, which allow low capacitance and series resistance from individually identified cultured neurons. Apertures are etched in a high‐quality silicon nitride film on a silicon wafer; wells are opened on the backside of the wafer by wet etching and passivated by a thick deposited silicon dioxide film to reduce the capacitance of the chip and to facilitate the formation of a high‐impedance cell to aperture seal. The chip surface is suitable for culture of neurons over a small orifice in the substrate with minimal leak current. Collectively, these features enable high‐fidelity electrophysiological recording of transmembrane currents resulting from ion channel activity in cultured neurons. Using cultured Lymnaea neurons we demonstrate whole‐cell current recordings obtained from a voltage‐clamp stimulation protocol, and in current‐clamp mode we report action potentials stimulated by membrane depolarization steps. Despite the relatively large size of these neurons, good temporal and spatial control of cell membrane voltage was evident. To our knowledge this is the first report of recording of ion channel activity and action potentials from neurons cultured directly on a planar patch‐clamp chip. This interrogation platform has enormous potential as a novel tool to readily provide high‐information content during pharmaceutical assays to investigate in vitro models of disease, as well as neuronal physiology and synaptic plasticity. Biotechnol. Bioeng. 2010;107:593–600. © 2010 Wiley Periodicals, Inc.     

Behavioral classification of low‐frequency acceleration and temperature data from a free‐ranging small mammal

The miniaturization and affordability of new technology is driving a biologging revolution in wildlife ecology with use of animal‐borne data logging devices. Among many new biologging technologies, accelerometers are emerging as key tools for continuously recording animal behavior. Yet a critical, but under‐acknowledged consideration in biologging is the trade‐off between sampling rate and sampling duration, created by battery‐ (or memory‐) related sampling constraints. This is especially acute among small animals, causing most researchers to sample at high rates for very limited durations. Here, we show that high accuracy in behavioral classification is achievable when pairing low‐frequency acceleration recordings with temperature. We conducted 84 hr of direct behavioral observations on 67 free‐ranging red squirrels (200–300 g) that were fitted with accelerometers (2 g) recording tri‐axial acceleration and temperature at 1 Hz. We then used a random forest algorithm and a manually created decision tree, with variable sampling window lengths, to associate observed behavior with logger recorded acceleration and temperature. Finally, we assessed the accuracy of these different classifications using an additional 60 hr of behavioral observations, not used in the initial classification. The accuracy of the manually created decision tree classification using observational data varied from 70.6% to 91.6% depending on the complexity of the tree, with increasing accuracy as complexity decreased. Short duration behavior like running had lower accuracy than long‐duration behavior like feeding. The random forest algorithm offered similarly high overall accuracy, but the manual decision tree afforded the flexibility to create a hierarchical tree, and to adjust sampling window length for behavioral states with varying durations. Low frequency biologging of acceleration and temperature allows accurate behavioral classification of small animals over multi‐month sampling durations. Nevertheless, low sampling rates impose several important limitations, especially related to assessing the classification accuracy of short duration behavior.     

Quantitative analysis of shape and volume changes in activated thrombocytes in real time by single‐shot spatial light modulator‐based differential interference contrast imaging

We suggest to use a combination of optical tweezers and single‐image quantitative differential interference contrast (DIC) emulated by a spatial light modulator (SLM) to study physiological shape changes in thrombocytes after activation and demonstrate the effectiveness of this system for the given task. A specially designed phase mask displayed at the SLM enables quantitative phase calculation from only a single recording. The optical tweezers stabilize trapped thrombocytes for long‐time monitoring of changes in the optical thickness profile of thrombocytes during activation by adenosine diphosphate (ADP). (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

CRISPR‐Cas

The prokaryotic immune system: CRISPR‐Cas The struggle of survival between prokaryotes and their viruses is likely one of the oldest conflicts on earth. Prokaryotes have developed different defense strategies to fend off an infection by the ubiquitous viruses that outnumber prokaryotes by an estimated factor of 10. Viruses, in turn, exhibit several counter mechanisms to overcome the prokaryotic defense. The recently discovered CRISPR‐Cas‐system represents a remarkable example for the continuous arms race between prokaryotes and viruses. Originally discovered in prokaryotes, the CRISPR‐Cas‐mediated defense constitutes an adaptive and heritable immune system against viruses and plasmids.     

Inter‐ and intraspecific effects of body size on habitat use among sexually‐dimorphic macropodids

Body size affects key life‐history parameters including dietary requirements and predation risk. We examined these effects on diel habitat use in a community of three sexually‐dimorphic macropodid marsupial species: western grey kangaroo Macropus fuliginosus, red‐necked wallaby M. rufogriseus and swamp wallaby Wallabia bicolor. In particular, our study seeks evidence of these effects operating concurrently at the intra‐ and interspecific levels. We used radio‐tracking to quantify habitat use and characterised each used location by recording the cover of plant functional groups and the presence of plant species. During nocturnal foraging periods we predicted that smaller animals (between and within species) should use habitats with higher‐quality forage, which is often less abundant, than larger animals, as metabolic demand scales with body size. During diurnal resting periods we predicted that smaller animals (between and within species), being more vulnerable to predation, should use greater concealment cover than larger animals. Western grey kangaroos and swamp wallabies behaved as predicted during foraging periods, but red‐necked wallabies did not, using more open, poorer‐quality habitats than expected. Only western grey kangaroos showed a within‐species effect on habitat use: the relatively smaller females foraged in higher‐quality patches. Habitats used by animals during the resting period generally offered greater concealment cover than those used during the foraging period, but there were no clear body size effects on the density of vegetation used. In our system, body size alone could not explain all of the observed patterns, suggesting that there may also be individual differences in habitat requirements influenced by factors such as reproductive costs, predation risk and social facilitation.     

Reflection‐mode switchable subwavelength Bessel‐beam and Gaussian‐beam photoacoustic microscopy in vivo

We have developed a reflection‐mode switchable subwavelength Bessel‐beam (BB) and Gaussian‐beam (GB) photoacoustic microscopy (PAM) system. To achieve both reflection‐mode and high resolution, we tightly attached a very small ultrasound transducer to an optical objective lens with numerical aperture of 1.0 and working distance of 2.5 mm. We used axicon and an achromatic doublet in our system to obtain the extended depth of field (DOF) of the BB. To compare the DOF performance achieved with our BB‐PAM system against GB‐PAM system, we designed our system so that the GB can be easily generated by simply removing the lenses. Using a 532 nm pulse laser, we achieved the lateral resolutions of 300 and 270 nm for BB‐PAM and GB‐PAM, respectively. The measured DOF of BB‐PAM was approximately 229 μm, which was about 7× better than that of GB‐PAM. We imaged the vasculature of a mouse ear using BB‐PAM and GB‐PAM and confirmed that the DOF of BB‐PAM is much better than the DOF of GB‐PAM. Thus, we believe that the high resolution achieved at the extended DOF by our system is very practical for wide range of biomedical research including red blood cell (RBC) migration in blood vessels at various depths and observation of cell migration or cell culture.      

Real‐time mid‐infrared imaging of living microorganisms

The speed and efficiency of quantum cascade laser‐based mid‐infrared microspectroscopy are demonstrated using two different model organisms as examples. For the slowly moving Amoeba proteus, a quantum cascade laser is tuned over the wavelength range of 7.6 µm to 8.6 µm (wavenumbers 1320 cm^–1 and 1160 cm^–1, respectively). The recording of a hyperspectral image takes 11.3 s whereby an average signal‐to‐noise ratio of 29 is achieved. The limits of time resolution are tested by imaging the fast moving Caenorhabditis elegans at a discrete wavenumber of 1265 cm^–1. Mid‐infrared imaging is performed with the 640 × 480 pixel video graphics array (VGA) standard and at a full‐frame time resolution of 0.02 s (i.e. well above the most common frame rate standards). An average signal‐to‐noise ratio of 16 is obtained. To the best of our knowledge, these findings constitute the first mid‐infrared imaging of living organisms at VGA standard and video frame rate.

     

TriboPump: A Low‐Cost,Hand‐Powered Water Disinfection System

Water disinfection at the point of use (POU) has enormous social and economic significance, especially for rural areas or catastrophes. To tackle the requirements of power independence and cost control in such applications, the concept of TriboPump is proposed, which is a low‐cost, hand‐powered water disinfection system. The system consists of three functional parts: a tubular coaxial‐electrode copper ionization cell (CECIC) as the disinfection device, a disk triboelectric nanogenerator (D‐TENG) as the power source, and a coaxial mechanical structure including the water pump. The adoption of D‐TENG can make the system adaptive to varying system resistances without additional power management circuits. Moreover, the integration of CECIC and TENG can successfully turn their intrinsic limitations into advantages and a synergic effect is achieved. With the integrated design, the system can effectively disinfect the water while pumping it solely by hand power. The cost estimate of the whole system can be as low as $10 for a 2‐year service. It is believed that the whole system design provides a feasible one‐stop and cost‐efficient solution for POU water pumping and disinfection, which will ideally be suitable the rural areas or sudden‐onset catastrophes.     

A cytotoxicity,optical spectroscopy and computational binding analysis of 4‐[3‐acetyl‐5‐(acetylamino)‐2‐methyl‐2,3‐dihydro‐1,3,4‐thiadiazole‐2‐yl]phenyl benzoate in calf thymus DNA

In this study the interaction mechanism between newly synthesized 4‐(3‐acetyl‐5‐(acetylamino)‐2‐methyl‐2, 3‐dihydro‐1,3,4‐thiadiazole‐2‐yl) phenyl benzoate (thiadiazole derivative) anticancer active drug with calf thymus DNA was investigated by using various optical spectroscopy techniques along with computational technique. The absorption spectrum shows a clear shift in the lower wavelength region, which may be due to strong hypochromic effect in the ctDNA and the drug. The results of steady state fluorescence spectroscopy show that there is static quenching occurring while increasing the thiadiazole drug concentration in the ethidium bromide‐ctDNA system. Also the binding constant (K), thermo dynamical parameters of enthalpy change (ΔH°), entropy change (ΔS°) Gibbs free energy change (ΔG°) were calculated at different temperature (293 K, 298 K) and the results are in good agreement with theoretically calculated MMGBSA binding analysis. Time resolved emission spectroscopy analysis clearly explains the thiadiazole derivative competitive intercalation in the ethidium bromide‐ctDNA system. Further, molecular docking studies was carried out to understand the hydrogen bonding and hydrophobic interaction between ctDNA and thiadiazole derivative molecule. In addition the docking and molecular dynamics charge distribution analysis was done to understand the internal stability of thiadiazole derivative drug binding sites of ctDNA. The global reactivity of thiadiazole derivative such as electronegativity, electrophilicity and chemical hardness has been calculated.     

Coiled‐coil interactions are required for post‐Golgi R‐SNARE trafficking

The sorting of post‐Golgi R‐SNAREs (vesicle‐associated membrane protein (VAMP)1, 2, 3, 4, 7 and 8) is still poorly understood. To address this, we developed a system to investigate their localization, trafficking and cell‐surface levels. Here, we show that the distribution and internalization of VAMPs 3 and 8 are determined solely through a new conserved mechanism that uses coiled‐coil interactions, and that VAMP4 does not require these interactions for its trafficking. We propose that VAMPs 3 and 8 are trafficked while in a complex with Q‐SNAREs. We also show that the dileucine motif of VAMP4 is required for both its internalization and retrieval to the trans‐Golgi network. However, when the dileucine motif is mutated, the construct can still be internalized potentially through coiled‐coil interactions with Q‐SNAREs.     

Exploring co‐occurrence of closely‐related guild members in a fragmented landscape subject to rapid transformation

Quantifying biotic responses to landscape transformation is a major research focus. Most past studies have explored co‐occurrence of entire communities of a given group (e.g. birds) within largely intact ecosystems or over a limited time‐frame. By contrast, here we use data from a 15 yr experimental study, to explore intra‐guild co‐occurrence of six closely‐related and functionally‐similar sets of birds within 55 woodland fragments. Areas surrounding these remnants are undergoing transformation from grazed paddocks to Pinus radiata plantations, leading to a novel assemblage of forest and woodland birds. We sought to determine if the occurrence of a given species in a guild influenced the occurrence of other closely‐related species in that guild, and through this relationship whether there was evidence of co‐occurrence between species. After controlling for environmental and habitat variables which can affect species occurrence like time since commencement of landscape transformation, patch size and vegetation type, we found the occurrence of a given species was influenced by the occurrence of a closely‐related species in the same guild. Co‐occurrence varied among bird guilds and included: 1) positive co‐occurrence in which occurrence of one species within fragments positively affected the occurrence of another closely‐related guild member (e.g. eastern and crimson rosellas); and 2) negative co‐occurrence in which the occurrence of one species was negatively associated with the occurrence of another within the same guild (e.g. willie wagtail and grey fantail). We also identified interactions between patch size and species recording frequency within members of two guilds. For example, modelling of conditional recording frequency revealed the eastern rosella increased with increasing recordings of the crimson rosella in large patches, but decreased with increasing recordings of the crimson rosella in small patches. Our results provide empirical evidence of co‐occurrence among guild members and underscore the complexity of biotic responses to landscape transformation.     

Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2,4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4(1H)‐one. A Perspective from Molecular Dynamics Simulations

This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O₂) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O₂ in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O₂ moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O₂ from the protein, which can also be taken as gates for O₂ uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O₂. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.