Taxonomic,phylogenetic and ecological diversity of Niphargus (Amphipoda: Crustacea) in the Hölloch cave system (Switzerland)

Groundwater belongs to the spatially most extensive, but least explored freshwater systems. On a global scale, the species richness of several subterranean invertebrate taxa parallels species richness found in surface waters, while on a local scale species richness hardly exceeds 20 species. This results in a high contribution of groundwater ecosystems to regional β- and γ-diversity, and to a smaller degree to α-diversity, and deserves focused attention. In general, more species are to be found in large cave systems. The second largest cave system in Europe is Hölloch in Switzerland. In this paper we revised the taxonomic, phylogenetic and ecological diversity of the amphipod community in the Hölloch cave system. While previous records listed five geographically widespread species of the genus Niphargus for this cave system, we could not confirm the presence of any of those species, but rather found three highly distinct species new to science. In this paper we describe Niphargus styx sp. nov., Niphargus murimali sp. nov., and Niphargus muotae sp. nov., and suggest that previous records from that cave were probably misidentifications. Although amphipod species richness in this cave system seems to be lower than previously thought in terms of absolute numbers, the cave retained its regional and international importance in terms of nature conservation for multiple reasons. First, all newly described species are probably endemic to this cave system. Second, they are phylogenetically distantly related and exhibit moderate to high phylogenetic diversity. Third, the species, as inferred from their functional morphology, are also ecologically highly divergent. Based on geographic distribution of their nearest relatives, we hypothesize that the cave system was most likely independently colonized from North, West and South and that the pre-adapted ancestors occupied different ecological niches within the system.

http://zoobank.org/urn:lsid:zoobank.org:pub:A19309E5-C06B-4844-A4D8-7571F05F25C9     

Proteomic Differences between Tellurite-Sensitive and Tellurite–Resistant E.coli

Tellurite containing compounds are in use for industrial processes and increasing delivery into the environment generates specific pollution that may well result in contamination and subsequent potential adverse effects on public health. It was the aim of the current study to reveal mechanism of toxicity in tellurite-sensitive and tellurite-resistant E. coli at the protein level.In this work an approach using gel-based mass spectrometrical analysis to identify a differential protein profile related to tellurite toxicity was used and the mechanism of ter operon-mediated tellurite resistance was addressed. E. coli BL21 was genetically manipulated for tellurite-resistance by the introduction of the resistance-conferring ter genes on the pLK18 plasmid. Potassium tellurite was added to cultures in order to obtain a final 3.9 micromolar concentration. Proteins from tellurite-sensitive and tellurite-resistant E. coli were run on 2-D gel electrophoresis, spots of interest were picked, in-gel digested and subsequently analysed by nano-LC-MS/MS (ion trap). In addition, Western blotting and measurement of enzymatic activity were performed to verify the expression of certain candidate proteins.Following exposure to tellurite, in contrast to tellurite-resistant bacteria, sensitive cells exhibited increased levels of antioxidant enzymes superoxide dismutases, catalase and oxidoreductase YqhD. Cysteine desulfurase, known to be related to tellurite toxicity as well as proteins involved in protein folding: GroEL, DnaK and EF-Tu were upregulated in sensitive cells. In resistant bacteria, several isoforms of four essential Ter proteins were observed and following tellurite treatment the abovementioned protein levels did not show any significant proteome changes as compared to the sensitive control.The absence of general defense mechanisms against tellurite toxicity in resistant bacteria thus provides further evidence that the four proteins of the ter operon function by a specific mode of action in the mechanism of tellurite resistance probably involving protein cascades from antioxidant and protein folding pathways.     

Can Yeast (S. cerevisiae) Metabolic Volatiles Provide Polymorphic Signaling?

Chemical signaling between organisms is a ubiquitous and evolutionarily dynamic process that helps to ensure mate recognition, location of nutrients, avoidance of toxins, and social cooperation. Evolutionary changes in chemical communication systems progress through natural variation within the organism generating the signal as well as the responding individuals. A promising yet poorly understood system with which to probe the importance of this variation exists between D. melanogaster and S. cerevisiae. D. melanogaster relies on yeast for nutrients, while also serving as a vector for yeast cell dispersal. Both are outstanding genetic and genomic models, with Drosophila also serving as a preeminent model for sensory neurobiology. To help develop these two genetic models as an ecological model, we have tested if - and to what extent - S. cerevisiae is capable of producing polymorphic signaling through variation in metabolic volatiles. We have carried out a chemical phenotyping experiment for 14 diverse accessions within a common garden random block design. Leveraging genomic sequences for 11 of the accessions, we ensured a genetically broad sample and tested for phylogenetic signal arising from phenotypic dataset. Our results demonstrate that significant quantitative differences for volatile blends do exist among S. cerevisiae accessions. Of particular ecological relevance, the compounds driving the blend differences (acetoin, 2-phenyl ethanol and 3-methyl-1-butanol) are known ligands for D. melanogasters chemosensory receptors, and are related to sensory behaviors. Though unable to correlate the genetic and volatile measurements, our data point clear ways forward for behavioral assays aimed at understanding the implications of this variation.     

40S Ribosome Biogenesis Co-Factors Are Essential for Gametophyte and Embryo Development

Ribosome biogenesis is well described in Saccharomyces cerevisiae. In contrast only very little information is available on this pathway in plants. This study presents the characterization of five putative protein co-factors of ribosome biogenesis in Arabidopsis thaliana, namely Rrp5, Pwp2, Nob1, Enp1 and Noc4. The characterization of the proteins in respect to localization, enzymatic activity and association with pre-ribosomal complexes is shown. Additionally, analyses of T-DNA insertion mutants aimed to reveal an involvement of the plant co-factors in ribosome biogenesis. The investigated proteins localize mainly to the nucleolus or the nucleus, and atEnp1 and atNob1 co-migrate with 40S pre-ribosomal complexes. The analysis of T-DNA insertion lines revealed that all proteins are essential in Arabidopsis thaliana and mutant plants show alterations of rRNA intermediate abundance already in the heterozygous state. The most significant alteration was observed in the NOB1 T-DNA insertion line where the P-A3 fragment, a 23S-like rRNA precursor, accumulated. The transmission of the T-DNA through the male and female gametophyte was strongly inhibited indicating a high importance of ribosome co-factor genes in the haploid stages of plant development. Additionally impaired embryogenesis was observed in some mutant plant lines. All results support an involvement of the analyzed proteins in ribosome biogenesis but differences in rRNA processing, gametophyte and embryo development suggested an alternative regulation in plants.     

DPT tautomerization of the long A∙A* Watson-Crick base pair formed by the amino and imino tautomers of adenine: combined QM and QTAIM investigation

Combining quantum-mechanical (QM) calculations with quantum theory of atoms in molecules (QTAIM) and using the methodology of sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), we showed for the first time that the biologically important A?A* base pair (C_s symmetry) formed by the amino and imino tautomers of adenine (A) tautomerizes via asynchronous concerted double proton transfer (DPT) through a transition state (TS), which is the A⁺?A^? zwitterion with the separated charge, with C_s symmetry. The nine key points, which can be considered as electron-topological “fingerprints” of the asynchronous concerted A?A*?A*?A tautomerization process via the DPT, were detected and completely investigated along the IRC of the A?A*?A*?A tautomerization. Based on the sweeps of the H-bond energies, it was found that intermolecular antiparallel N6Н?N6 (7.01 kcal mol^?1) and N1H?N1 (6.88 kcal mol^?1) H-bonds are significantly cooperative and mutually reinforce each other. It was shown for the first time that the A?A*?A*?A tautomerization is assisted by the third C2H?HC2 dihydrogen bond (DHB), which, in contrast to the two others N6H?N6 and N1H?N1 H-bonds, exists within the IRC range from ?2.92 to 2.92 Å. The DHB cooperatively strengthens, reaching its maximum energy 0.42 kcal mol^?1 at IRC?=??0.52 Å and minimum energy 0.25 kcal mol^?1 at IRC?=??2.92 Å, and is accompanied by strengthening of the two other aforementioned classical H-bonds. We established that the C2H?HC2 DHB completely satisfies the electron-topological criteria for H-bonding, in particular Bader’s and all eight “two-molecule” Koch and Popelier’s criteria. The positive value of the Grunenberg’s compliance constant (5.203 Å/mdyn) at the TS_A?A*?A*?A proves that the C2H?HC2 DHB is a stabilizing interaction. NBO analysis predicts transfer of charge from σ(C2–H) bonding orbital to σ*(H–C2) anti-bonding orbital; at this point, the stabilization energy E⁽²⁾ is equal to 0.19 kcal mol^?1 at the TS_A?A*?A*?A.     

Occurrence of Fatty Acid Short‐Chain‐Alkyl Esters in Fruits of Celastraceae Plants

Small amounts of a mixture of fatty acid short‐chain‐alkyl esters (FASCAEs) were obtained from the fruits of twelve plant species of Celastraceae family, and in five of them the FASCAEs were present not only in the arils but also in the seeds. These mixtures contained 32 individual FASCAE species, which formed four separate fractions, viz. FA methyl, ethyl, isopropyl, and butyl esters (FAMEs, FAEEs, FAIPEs, and FABEs, resp.). The FASCAE acyl components included the residues of 16 individual C₁₄–C₂₄ saturated, mono‐, di‐, and trienoic FAs. Linoleic, oleic, and palmitic acids, and, in some cases, also α‐linolenic acid predominated in FAMEs and FAEEs, while myristic acid was predominant in FAIPEs. It can be suggested that, in the fruit arils of some plant species, FAMEs and FAEEs were formed at the expense of a same FA pool characteristic of a given species and were strongly different from FAIPEs and FABEs esters regarding the mechanism of their biosynthesis. However, as a whole, the qualitative and quantitative composition of various FASCAE fractions, as well as their FA composition, varied considerably depending on various factors. Therefore, separate FASCAE fractions seem to be synthesized from different FA pools other than those used for triacylglycerol formation.     

The need for standardization in wildlife science: home range estimators as an example

Individual studies in wildlife science are indicative rather than conclusive. Although multiple studies can be meta-analyzed in such a way that scientific hypotheses can be tested, robust meta-analyses are often difficult or impossible if variables of interest are not measured in a uniform manner. We hypothesized that measurements, even of basic and unequivocal variables, are rarely standardized in wildlife sciences. We tested this assumption by reviewing randomly selected papers that describe the home range of mammals (n?=?25) and birds (n?=?25). In these papers, home ranges were calculated using 11 methods and 8 computer programs. The number of radiolocations used to calculate home ranges varied from 9 to >2,000. By estimating home ranges for two radiotelemetry data sets, we demonstrate that home ranges are not comparable if different methods are used and that estimates of home range are not standardized. We assume that measurements of other biological variables are even less consistent across studies. In order to advance wildlife sciences, we believe that standardization initiatives are required at an international level.     

Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family

Adaptation of life to low temperatures influences both protein stability and flexibility. Thus, proteins from psychrophilic organisms are excellent models to study relations between these properties. Here we focused on frataxin from Psychromonas ingrahamii (pFXN), an extreme psychrophilic sea ice bacterium that can grow at temperatures as low as − 12 °C. This α/β protein is highly conserved and plays a key role in iron homeostasis as an iron chaperone. In contrast to other frataxin homologs, chemical and temperature unfolding experiments showed that the thermodynamic stability of pFXN is strongly modulated by pHs: ranging from 5.5 ± 0.9 (pH 6.0) to 0.9 ± 0.3 kcal mol^− 1 (pH 8.0). This protein was crystallized and its X-ray structure solved at 1.45 Å. Comparison of B-factor profiles between Escherichia coli and P. ingrahamii frataxin variants (51% of identity) suggests that, although both proteins share the same structural features, their flexibility distribution is different. Molecular dynamics simulations showed that protonation of His44 or His67 in pFXN lowers the mobility of regions encompassing residues 20–30 and the C-terminal end, probably through favorable electrostatic interactions with residues Asp27, Glu42 and Glu99. Since the C-terminal end of the protein is critical for the stabilization of the frataxin fold, the predictions presented may be reporting on the microscopic origin of the decrease in global stability produced near neutral pH in the psychrophilic variant. We propose that suboptimal electrostatic interactions may have been an evolutionary strategy for the adaptation of frataxin flexibility and function to cold environments.