The Croatian Apoxyomenos as a luxurious rodent nest: archaeobotanical and zoological analyses of organic material found inside the classical bronze statue

Archaeobotanical analysis has been used to reconstruct the nest and diet of a small rodent from the Classical period (first century b.c. to second century a.d.) and most probably from Greece. The nest was found in the hollow interior of a very valuable bronze statue of a young athlete, recovered from the waters of the Northern Adriatic and named the Croatian Apoxyomenos. Apoxyomenos was probably the cargo of a Roman ship on one of highly frequented sea routes in ancient times, along which, among other things, a highly developed trade in artworks was maintained. All plant remains were non-carbonised and mineralised; encrusted with metallic salts, especially of copper, and preserved in excellent condition. The nest itself (wisps of “straw” found in the hollow interior of the left forearm of the statue) was mainly composed of stems and leaves of grasses (Poaceae), but also of laurel (Laurus nobilis) leaves and other plant remains. Along with “straw”, a further 837 individual plant remains were found and analysed and 41 different plant taxa were identified. Plant remains that presumably were part of the rodent’s diet belong to various wild and cultivated plants which indicate various anthropogenic habitats probably situated somewhere on the edge of human settlement. From zoological analysis of bite marks found on fruit stones of cherry and olive, and of the potential rodent fauna in the area the statue was assumed to be in prior to becoming submerged, it was established that the rodent was most probably one of the taxa of the Mus domesticus group.     

Anabolic and catabolic responses of human articular chondrocytes to varying oxygen percentages

Introduction  

Oxygen is a critical parameter proposed to modulate the functions of chondrocytes ex-vivo as well as in damaged joints. This article investigates the effect of low (more physiological) oxygen percentage on the biosynthetic and catabolic activity of human articular chondrocytes (HAC) at different phases of in vitro culture.     

The Meaning(s) of Information, Code … and Meaning

Meaning is a central concept of (bio)semiotics. At the same time, it is also a word of everyday language. Here, on the example of the world information, we discuss the “reduction-inflation model” of evolution of a common word into a scientific concept, to return subsequently into everyday circulation with new connotations. Such may be, in the near future, also the fate of the word meaning if, flexed through objectified semantics, will become considered an objective concept usable in semiotics. We argue that reducing meaning to a technical term essentially synonymous to code and stripped of most of the original semantic field is not a necessary prerequisite for a meaningful application of the concept in semiotics and in biology.     

Histone H1 compacts DNA under force and during chromatin assembly

Histone H1 binds to linker DNA between nucleosomes, but the dynamics and biological ramifications of this interaction remain poorly understood. We performed single-molecule experiments using magnetic tweezers to determine the effects of H1 on naked DNA in buffer or during chromatin assembly in Xenopus egg extracts. In buffer, nanomolar concentrations of H1 induce bending and looping of naked DNA at stretching forces below 0.6 pN, effects that can be reversed with 2.7-pN force or in 200 mM monovalent salt concentrations. Consecutive tens-of-nanometer bending events suggest that H1 binds to naked DNA in buffer at high stoichiometries. In egg extracts, single DNA molecules assemble into nucleosomes and undergo rapid compaction. Histone H1 at endogenous physiological concentrations increases the DNA compaction rate during chromatin assembly under 2-pN force and decreases it during disassembly under 5-pN force. In egg cytoplasm, histone H1 protects sperm nuclei undergoing genome-wide decondensation and chromatin assembly from becoming abnormally stretched or fragmented due to astral microtubule pulling forces. These results reveal functional ramifications of H1 binding to DNA at the single-molecule level and suggest an important physiological role for H1 in compacting DNA under force and during chromatin assembly.     

Cell Electrofusion Visualized with Fluorescence Microscopy

Cell electrofusion is a safe, non-viral and non-chemical method that can be used for preparing hybrid cells for human therapy. Electrofusion involves application of short high-voltage electric pulses to cells that are in close contact. Application of short, high-voltage electric pulses causes destabilization of cell plasma membranes. Destabilized membranes are more permeable for different molecules and also prone to fusion with any neighboring destabilized membranes. Electrofusion is thus a convenient method to achieve a non-specific fusion of very different cells in vitro. In order to obtain fusion, cell membranes, destabilized by electric field, must be in a close contact to allow merging of their lipid bilayers and consequently their cytoplasm. In this video, we demonstrate efficient electrofusion of cells in vitro by means of modified adherence method. In this method, cells are allowed to attach only slightly to the surface of the well, so that medium can be exchanged and cells still preserve their spherical shape. Fusion visualization is assessed by pre-labeling of the cytoplasm of cells with different fluorescent cell tracker dyes; half of the cells are labeled with orange CMRA and the other half with green CMFDA. Fusion yield is determined as the number of dually fluorescent cells divided with the number of all cells multiplied by two.     

Restructuring of a Peat in Interaction with Multivalent Cations: Effect of Cation Type and Aging Time

It is assumed to be common knowledge that multivalent cations cross-link soil organic matter (SOM) molecules via cation bridges (CaB). The concept has not been explicitly demonstrated in solid SOM by targeted experiments, yet. Therefore, the requirements for and characteristics of CaB remain unidentified. In this study, a combined experimental and molecular modeling approach was adopted to investigate the interaction of cations on a peat OM from physicochemical perspective. Before treatment with salt solutions of Al³⁺, Ca²⁺ or Na⁺, respectively, the original exchangeable cations were removed using cation exchange resin. Cation treatment was conducted at two different values of pH prior to adjusting pH to 4.1. Cation sorption is slower (>>2 h) than deprotonation of functional groups (<2 h) and was described by a Langmuir model. The maximum uptake increased with pH of cation addition and decreased with increasing cation valency. Sorption coefficients were similar for all cations and at both pH. This contradicts the general expectations for electrostatic interactions, suggesting that not only the interaction chemistry but also spatial distribution of functional groups in OM determines binding of cations in this peat. The reaction of contact angle, matrix rigidity due to water molecule bridges (WaMB) and molecular mobility of water (NMR analysis) suggested that cross-linking via CaB has low relevance in this peat. This unexpected finding is probably due to the low cation exchange capacity, resulting in low abundance of charged functionalities. Molecular modeling demonstrates that large average distances between functionalities (∼3 nm in this peat) cannot be bridged by CaB-WaMB associations. However, aging strongly increased matrix rigidity, suggesting successive increase of WaMB size to connect functionalities and thus increasing degree of cross-linking by CaB-WaMB associations. Results thus demonstrated that the physicochemical structure of OM is decisive for CaB and aging-induced structural reorganisation can enhance cross-link formation.     

Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens

Aflatoxin oxidase (AFO), an enzyme isolated from Armillariella tabescens, has been reported to degrade aflatoxin B1 (AFB1). However, recent studies reported sequence and structure similarities with the dipeptidyl peptidase III (DPP III) family of enzymes and confirmed peptidase activity toward DPP III substrates. In light of these investigations, an extensive computational study was performed in order to improve understanding of the AFO functions. Steered MD simulations revealed long-range domain motions described as protein opening, characteristic for DPPs III and necessary for substrate binding. Newly identified open and partially open forms of the enzyme closely resemble those of the human DPP III orthologue. Docking of a synthetic DPP III substrate Arg₂-2-naphthylamide revealed a binding mode similar to the one found in crystal structures of human DPP III complexes with peptides with the S1 and S2 subsites’ amino acid residues conserved. On the other hand, no energetically favorable AFB1 binding mode was detected, suggesting that aflatoxins are not good substrates of AFO. High plasticity of the zinc ion coordination sphere within the active site, consistent with that of up to date studied DPPs III, was observed as well. A detailed electrostatic analysis of the active site revealed a predominance of negatively charged regions, unsuitable for the binding of the neutral AFB1. The present study is in line with the most recent experimental study on this enzyme, both suggesting that AFO is a typical member of the DPP III family.     

A new relictual and highly troglomorphic species of Tomoceridae (Collembola) from a deep Croatian cave

Tritomurus velessp. n. (Tomoceridae) is described from a Croatian cave. It is characterized by troglomorphic features (absence of eyes, reduced pigmentation, slender claw, pointed tibiotarsal tenent hairs) that only compare, among Tomoceridae, to the microendemic species Tritomurus falcifer from the Pyrénées. Tritomurus veles also shares with Tritomurus falcifer the absence of macrochaetae on head, a presumably non-adaptive character that within Tomoceridae is unique to these two species. Both species have no known epigean relatives in their respective distribution areas and can be considered as relictual.