Inside Cover: Optimized perfusion‐based CUBIC protocol for the efficient whole‐body clearing and imaging of rat organs (J. Biophotonics 5/2018)

Optical tissue clearing is a method allowing post‐mortem deep imaging of organs in three dimensions. By optimizing the CUBIC clearing protocol, the authors provide rapid and simple approach to clear the entire adult rat organism within as little as four days, which is accompanied by the variety of its staining and imaging techniques. The image was captured with polarizers and demonstrates transparent rodent heart with thread‐like crystals of clearing reagent. Further details can be found in the article by Pawe? Matryba et al. ( e201700248 ).

     

Genetic aberrations in macroautophagy genes leading to diseases

The catabolic process of macroautophagy, through the rapid degradation of unwanted cellular components, is involved in a multitude of cellular and organismal functions that are essential to maintain homeostasis. Those functions include adaptation to starvation, cell development and differentiation, innate and adaptive immunity, tumor suppression, autophagic cell death, and maintenance of stem cell stemness. Not surprisingly, an impairment or block of macroautophagy can lead to severe pathologies. A still increasing number of reports, in particular, have revealed that mutations in the autophagy-related (ATG) genes, encoding the key players of macroautophagy, are either the cause or represent a risk factor for the development of several illnesses. The aim of this review is to provide a comprehensive overview of the diseases and disorders currently known that are or could be caused by mutations in core ATG proteins but also in the so-called autophagy receptors, which provide specificity to the process of macroautophagy. Our compendium underlines the medical relevance of this pathway and underscores the importance of the eventual development of therapeutic approaches aimed at modulating macroautophagy.     

Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles

In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF mass spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy, and synchrotron small angle X-ray scattering (SAXS). Overall structural characteristics of PVA CP obtained by combination of these methods and ab initio shape reconstruction by SAXS show that PVA CP forms large multi-subunit particles. We demonstrate that a mixture of compact virus-like particles (VLP) longer than 30 nm is assembled on dialysis of isolated CP into neutral pH buffer (at low ionic strength). Under conditions of high ionic strength (0.5 M NaCl) and high pH (pH 10.5), PVA dissociates into low compactness oval-shaped particles of approximately 30 subunits (20–30 nm). The results of limited trypsinolysis of these particles (enzyme/substrate ratio 1:100, 30 min) showed the existence of non-cleavable core-fragment, consisting of 137 amino acid residues. Trypsin treatment removed only a short N-terminal fragment in the intact virions. These particles are readily reassembled into regular VLPs by changing pH back to neutral. It is possible that these particles may represent some kind of intermediate in PVA assembly in vitro and in vivo.     

Shark bite injuries on three inshore dolphin species in tropical northwestern Australia

Predation risk has a profound influence on the behavior of marine mammals, affecting grouping patterns and habitat use. Dolphins frequently bear evidence of shark bites, which can provide an indirect measure of predation pressure. Using photo‐identification data, we investigated the prevalence of shark bites on three sympatric species of inshore dolphin, the Australian snubfin (Orcaella heinsohni), Australian humpback (Sousa sahulensis), and Indo‐Pacific bottlenose dolphin (Tursiops aduncus), among four study sites in northwestern Australia. Bite prevalence varied markedly between species, with 72% of snubfin, 46% of humpback, and 18% of bottlenose dolphins exhibiting evidence of shark bites. Binomial logistic regression confirmed a high likelihood of bite presence on snubfin dolphins, and at one particular site for snubfin and bottlenose dolphins. The prevalence of tiger shark (Galeocerdo cuvier) bites on snubfin dolphins was high, and bites attributed to other carcharhinid sharks were observed on all species. While acknowledging methodological differences with other studies, the prevalence of shark bites on snubfin dolphins is among the highest reported for any dolphins, suggesting predation risk represents an important but varying influence thereon. This study provides a baseline for future investigations into the affect of predation risk on the behavioral ecology of these sympatric species.     

Reduction of bacterial adhesion on titanium-doped diamond-like carbon coatings

A range of titanium doped diamond-like carbon (Ti-DLC) coatings with different Ti contents were prepared on stainless steel substrates using a plasma-enhanced chemical vapour deposition technique. It was found that both the electron donor surface energy and the surface roughness of the Ti-DLC coatings increased with increasing Ti contents in the coatings. Bacterial adhesion to the coatings was evaluated against Escherichia coli WT F1693 and Pseudomonas aeruginosa ATCC 33347. The experimental data showed that bacterial adhesion decreased with the increases of the Ti content, the electron donor surface energy and surface roughness of the coatings, while the bacterial removal percentage increased with the increases of these parameters. The Ti-DLC coatings reduced bacterial attachment by up to 75% and increased bacterial detachment from 15 to 45%, compared with stainless steel control.     

Mycobacterium tuberculosis UvrB forms dimers in solution and interacts with UvrA in the absence of ligands

During its life cycle Mycobacterium tuberculosis (MTB) must face a variety of environmental and endogenous physical and chemical stresses that could produce genotoxic damage. However, MTB possesses efficient systems to counteract the harmful effects of DNA‐damaging assaults. The nucleotide excision repair (NER) is a highly conserved multi‐enzymatic cascade that is initiated by the concerted action of three core proteins, that is UvrA, UvrB, and UvrC. Although the functional roles of these enzymes are well characterized, the intra‐pathway coordination of the NER components and the dynamics of their association is still a matter of debate. In the presented study, we analyzed the hydrodynamic properties and the oligomeric state of the MTB UvrB protein (MtUvrB) that we expressed and purified to homogeneity in a tag‐free form. Our results show that, differently to what has been previously observed for the His‐tagged version of the protein, MtUvrB forms dimers in solution, which are characterized by an elongated shape, as determined by small‐angle X‐ray scattering analysis. Moreover, to gain insights into the mycobacterial UvrA/UvrB lesion sensing/tracking complex we adopted a size‐exclusion chromatography‐based approach, revealing that the two proteins interact in the absence of ligands, leading to the assembling of A₂B₂ hetero‐tetramers in solution. Surface plasmon resonance analysis showed that the dissociation constant of the MtUvrA/MtUvrB complex falls in the low micromolar range that could represent the basis for a fine modulation of the complex architecture accompanying the multi‐step DNA repair activity of mycobacterial NER.     

Under-sized larvae from short-day adults of the blow fly, Calliphora vicina, side-step the diapause programme

Abstract. Larvae of Calliphora vicina R.-D. (Diptera: Calliphoridae) hatching from eggs laid by adult females exposed to short day length, and then raised in darkness at 11^oC, normally enter diapause rather than undergoing prompt pupariation. However, if the feeding stage is curtailed by premature extraction of larvae from their food, or if the larvae are subjected to severe overcrowding, smaller larvae side-step the diapause programme to become miniature puparia, whereas larger larvae proceed to diapause as fully-fed ones. In addition, smaller diapausing larvae show a shorter (or less intense) diapause than full-sized larvae. Apart from the smallest individuals, flies can emerge from these miniature puparia and in some cases are capable of laying eggs; this suggests that avoidance of diapause may allow undersized individuals an opportunity to reproduce before winter sets in. Fat determinations performed on larvae and pupae of various sizes, however, showed that short-day (diapause-destined) individuals lay down the same proportion of fat as long-day (non-diapause) individuals, and the same proportion of fat across all size classes. The possible functional significance of this phenomenon is discussed.     

Body build structure of neonates

The paper presents anthropometric data on 292 healthy neonates delivered of normal births at the Women's Hospital of Tartu University (150 boys and 142 girls). The parameters of the neonates' physical development measured included height, weight, sitting height, length of sternum and abdomen, shoulder width, upper and lower width and depth of thorax, width and depth of abdomen, D. cristarum, D. trochanterica, pelvic depth, 12 circumferences, foot length and two skinfolds (on abdomen and back). The mean weight of a neonate was 3620.5 g±448.7 g (minimum 2400 g and maximum 4854 g). Boys were somewhat heavier than girls (3684.7 g and 3551.3 g respectively). The average height of the infants was 49.9 cm±1.9 cm (minimum 44 cm and maximum 54.5 cm). Correlation analysis of the characteristics showed that body structure is a system of wellcorrelated anthropometric measurements where the leading role belongs to height and weight. The changes in the relation between height and weight (height-weight classification in 3×3SD classes) cause systemic changes in other measurements. Therefore, in further micropaediatric and clinical research, the height-weight classification could be used as the primary model of the body as a whole.     

Response properties of higher level neurons in the central olfactory pathway of the crayfish

We have examined the electrical activity of interneurons within the higher levels of the crayfish olfactory system. In unstimulated isolated crayfish head preparations, local protocerebral interneurons (LPI) of the hemiellipsoid bodies generate periodic, low-frequency membrane depolarizations. The most reasonable explanation for these baseline fluctuations, which were exhibited by all of the LPIs examined and which were reversibly abolished by either tetrodotoxin or low-calcium saline solution, is that they reflect periodic synaptic drive from the axon terminals of olfactory projection neurons. One-third of tested LPIs generated impulses in response to the odor stimuli we applied to the antennules. Those cells that did respond exhibited a brief excitatory postsynaptic potential and one or two action potentials, even during prolonged odor pulses. Many of the responding neurons also exhibited a delayed impulse burst 1 or 2 s following the stimulus pulse. Most of the responding cells recovered their sensitivity to odors very slowly, exhibiting disadaptation periods of several minutes. The apparent refractory nature of individual LPIs to olfactory stimulation is attributed in part to a hypothesized selectivity of connections between projection neurons and protocerebral targets and in part to the electrical isolation of the recording electrode from many regions of the extensive LPI dendritic tree. Accepted: 20 March 1997