The volume of cavities in proteins and virus capsids

An improved algorithm for the calculation of the volume of internal cavities within protein structures and virus capsids as well as the volumes occupied by single amino acid residues were presented. The geometrical approach was based on atomic van der Waals radii. The results obtained with two sets of the radii, those proposed by Pauling and those determined by Tsai et al were compared. The main improvement compared with our previous approach is a more elaborate treatment of the regions at the very boundary of the cavities, which yields a more accurate volume estimate. The cavity volume of a number of Plant Pathogenesis‐Related proteins of class 10 (PR‐10) were reevaluated and the volumes and other geometrical parameters for about 400 capsids of icosahedral viruses were reported. Using the same approach the volumes of amino acid residues in polypeptides as mean values averaged over multiple conformations of the side chain were also estimated. Proteins 2016; 84:1275–1286. © 2016 Wiley Periodicals, Inc.     

Photoperiod-related changes in hormonal and immune status of male Siberian hamsters,Phodopus sungorus

Previously we have demonstrated that in Siberian hamsters some immune measures, especially the development of experimentally evoked peritonitis, varied in a photoperiod- and gender-dependent manner. The aim of the present study was to investigate whether the photoperiod-related differences in the activity of inflammation-involved immune cells are in this species attributed to the changes in the pineal gland function and/or hormonal status. Male hamsters housed in short day (SD), compared with those from long day (LD) conditions, exhibited significantly reduced plasma testosterone concentration and elevated cortisol and melatonin levels, the latter resulting from increased activity of hydroxyindole-O-methyltransferase (HIOMT). In LD hamsters but not in those from SD, an intraperitoneal (i.p.) injection of zymosan evoked a well-pronounced peritonitis expressed by increased free radical (ROS) production by peritoneal leukocytes (PTLs) stimulated in vitro with PMA. ROS production by these cells was additionally stimulated by both in vivo and in vitro treatment with melatonin and the latter was partially reversed by melatonin receptor antagonist luzindole. To conclude, in Siberian hamsters melatonin seems to exert rather immunostimulatory than anti-inflammatory effect, therefore other mechanisms, e.g. immunosuppressive effect of glucocorticoids, may underlay the compromised immune status observed in SD in this species.     

Recognition of protein complexation based on hydrophobicity distribution

The identification of the surface area able to generate the protein-protein complexation ligand and ion ligation is critical for the recognition of the biological function of particular proteins. The technique based on the analysis of the irregularity of hydrophobicity distribution is used as the criterion for the recognition of the interaction regions. Particularly, the exposure of hydrophobic residues on the surface of protein as well as the localization of the hydrophilic residues in the hydrophobic core is treated as potential area ready to interact with external molecules. The model based on the “fuzzy oil drop” approach treating the protein molecule as the drop of hydrophobicity concentrated in the central part of structure with the hydrophobicity close to zero on the surface according to 3-dimensional Gauss function. The comparison with the observed hydrophobicy in particular protein reveals some irregularities. These irregularities seem to represent the aim-oriented localization.     

Efficient Assembly and Secretion of Recombinant Subviral Particles of the Four Dengue Serotypes Using Native prM and E Proteins

Background

Flavivirus infected cells produce infectious virions and subviral particles, both of which are formed by the assembly of prM and E envelope proteins and are believed to undergo the same maturation process. Dengue recombinant subviral particles have been produced in cell cultures with either modified or chimeric proteins but not using the native forms of prM and E.

Methodology/Principal Findings

We have used a codon optimization strategy to obtain an efficient expression of native viral proteins and production of recombinant subviral particles (RSPs) for all four dengue virus (DV) serotypes. A stable HeLa cell line expressing DV1 prME was established (HeLa-prME) and RSPs were analyzed by immunofluorescence and transmission electron microscopy. We found that E protein is mainly present in the endoplasmic reticulum (ER) where assembly of RSPs could be observed. Biochemical characterization of DV1 RSPs secretion revealed both prM protein cleavage and homodimerization of E proteins before their release into the supernatant, indicating that RSPs undergo a similar maturation process as dengue virus. Pulse chase experiment showed that 8 hours are required for the secretion of DV1 RSPs. We have used HeLa-prME to develop a semi-quantitative assay and screened a human siRNA library targeting genes involved in membrane trafficking. Knockdown of 23 genes resulted in a significant reduction in DV RSP secretion, whereas for 22 others we observed an increase of RSP levels in cell supernatant.

Conclusions/Significance

Our data describe the efficient production of RSPs containing native prM and E envelope proteins for all dengue serotypes. Dengue RSPs and corresponding producing cell lines are safe and novel tools that can be used in the study of viral egress as well as in the development of vaccine and drugs against dengue virus.     

Validation of machine learning approach for direct mutation rate estimation

Mutations are the primary source of all genetic variation. Knowledge about their rates is critical for any evolutionary genetic analyses, but for a long time, that knowledge has remained elusive and indirectly inferred. In recent years, parent–offspring comparisons have yielded the first direct mutation rate estimates. The analyses are, however, challenging due to high rate of false positives and no consensus regarding standardized filtering of candidate de novo mutations. Here, we validate the application of a machine learning approach for such a task and estimate the mutation rate for the guppy (Poecilia reticulata), a model species in eco-evolutionary studies. We sequenced 4 parents and 20 offspring, followed by screening their genomes for de novo mutations. The initial large number of candidate de novo mutations was hard-filtered to remove false-positive results. These results were compared with mutation rate estimated with a supervised machine learning approach. Both approaches were followed by molecular validation of all candidate de novo mutations and yielded similar results. The ML method uniquely identified three mutations, but overall required more hands-on curation and had higher rates of false positives and false negatives. Both methods concordantly showed no difference in mutation rates between families. Estimated here the guppy mutation rate is among the lowest directly estimated mutation rates in vertebrates; however, previous research has also found low estimated rates in other teleost fishes. We discuss potential explanations for such a pattern, as well as future utility and limitations of machine learning approaches.     

Consequences of the fractal architecture of trees on their structural measures

While the mechanics of trees are well known, a systematic and comprehensive study of the mechanical consequences of a tree's fractal structure has been lacking. Here, we analyze the structure of botanical trees using computer modeling and show that many relevant measures of support throughout all the branches of a tree follow specific patterns which can be described by characteristic probability distributions and well-defined spatial relationships. Most notably, moments, forces, and axial and shear stresses throughout the different branches all exhibit power-law distributions. These results suggest a new approach to the study of the mechanics of trees, one accounting for the implications of the above results.     

The prevalence of incidentaloma--asymptomatic thyroid nodules in the Tricity (Gdansk, Sopot, Gdynia) population

INTRODUCTION: The increased sensitivity of imaging devices raised number of incidentally discovered lesions in various organs of the human body. Thyroid gland is one of them. Reported prevalence of ultrasonographically detected thyroid nodules (incidentalomas) in general population ranges from 5.2 to 67.0%. Our study demonstrated occurrence of this clinical problem in the general population of the Tricity. MATERIAL AND METHODS: 135 healthy adults (95 women and 40 men) were examined. Neck palpation, ultrasonographic examinations of thyroid gland and serum tyreotropin (TSH) level measurement were made. RESULTS: In 8.9% of examine (12/135) persons nodules were palpable whereas in 14.8% (20/135) they were detectable only in ultrasonographic examination. Altogether thyroid ultrasound and palpation revealed nodules in 23.7% (32/135) of all cases. Multiple nodules were present in 12.0% of the cases. The pathology was more common in the elderly and in women. TSH serum level was within normal range in all cases of incidentaloma with otherwise normal thyroid gland. CONCLUSIONS: Prevalence of thyroid gland nodules (palpation--8.9% plus ultrasonography--14.8%) in healthy population of Gdansk, Gdynia and Sopot is close to data reported in southern Finland (27.0%) and Belgium (19.0%), where iodine deficiency is small, like in the Tricity area. The revealed lesions were over two times more frequent in the female population. Most of the nodules were not palpable.     

Structural behaviour and strain distribution of the long bones of the human lower limbs

Although stiffness and strength of lower limb bones have been investigated in the past, information is not complete. While the femur has been extensively investigated, little information is available about the strain distribution in the tibia, and the fibula has not been tested in vitro. This study aimed at improving the understanding of the biomechanics of lower limb bones by: (i) measuring the stiffness and strain distributions of the different low limb bones; (ii) assessing the effect of viscoelasticity in whole bones within a physiological range of strain-rates; (iii) assessing the difference in the behaviour in relation to opposite directions of bending and torsion. The structural stiffness and strain distribution of paired femurs, tibias and fibulas from two donors were measured. Each region investigated of each bone was instrumented with 8–16 triaxial strain gauges (over 600 grids in total). Each bone was subjected to 6–12 different loading configurations. Tests were replicated at two different loading speeds covering the physiological range of strain-rates. Viscoelasticity did not have any pronounced effect on the structural stiffness and strain distribution, in the physiological range of loading rates explored in this study. The stiffness and strain distribution varied greatly between bone segments, but also between directions of loading. Different stiffness and strain distributions were observed when opposite directions of torque or opposite directions of bending (in the same plane) were applied. To our knowledge, this study represents the most extensive collection of whole-bone biomechanical properties of lower limb bones.