NA2RE is reliable but aims for improvement: an answer to Vamberger and Fritz (2018)

A recent paper has suggested that NA2RE, the New Atlas of Amphibians and Reptiles of Europe, does not provide a reliable basis for ecological niche modelling studies due to errors flagging introductions and missing data for the native range of the pond turtle genus Emys. We point out that the original NA2RE paper already acknowledged that it was not aimed for fine-scale ecological distribution modelling and that it had the objective of stimulating research for improving the maps. New works now complement the Atlas in improving the coverage and providing new distribution maps for species within species complex. Moreover, we stress that the NA2RE web platform at present hosts only the distribution data compiled in 2014 from different sources, using the taxonomy adopted by the authors at the time. As with any large database, it is advisable that these data are carefully evaluated and quality-filtered before their use in scientific studies. We defend the reliability of the NA2RE web platform as the currently most comprehensive resource for the comparative chorological study of amphibians and reptiles in Europe, and encourage publication of updates and additions following the most recent taxonomic changes, to continuously improve this database and the Atlas.     

Peroxisome proliferator-activated receptor (PPAR)gamma is expressed by human spermatozoa: its potential role on the sperm physiology

The peroxisome proliferation-activated receptor gamma (PPARgamma) is mainly expressed in the adipose tissue and integrates the control of energy, lipid, and glucose homeostasis. The present study, by means of RT-PCR, Western blot, and immunofluorescence techniques, demonstrates that human sperm express the PPARgamma. The functionality of the receptor was evidenced by 15-deoxy-12,14-prostaglandin J(2) (PGJ2) and rosiglitazone (BRL) PPARgamma-agonists that were tested on capacitation, acrosome reaction, and motility. Both treatments also increase AKT phosphorylations and influence glucose and lipid metabolism in sperm. The specificity of PGJ2 and BRL effects through PPARgamma on human sperm was confirmed by an irreversible PPARgamma antagonist, GW9662. Our findings provide evidence that human sperm express a functional PPARgamma whose activation influences sperm physiology. In conclusion, the presence of PPARgamma in male gamete broadens the field of action of this nuclear receptor, bringing us to look towards sperm as an endocrine mobile unit independent of the systemic regulation.     

RhoA signaling modulates cyclin D1 expression in human lung fibroblasts; implications for idiopathic pulmonary fibrosis

Background

To elucidate further the pathogenesis of sporadic, idiopathic pulmonary arterial hypertension (IPAH) and identify potential therapeutic avenues, differential gene expression in IPAH was examined by suppression subtractive hybridisation (SSH).

Methods

Peripheral lung samples were obtained immediately after removal from patients undergoing lung transplant for IPAH without familial disease, and control tissues consisted of similarly sampled pieces of donor lungs not utilised during transplantation. Pools of lung mRNA from IPAH cases containing plexiform lesions and normal donor lungs were used to generate the tester and driver cDNA libraries, respectively. A subtracted IPAH cDNA library was made by SSH. Clones isolated from this subtracted library were examined for up regulated expression in IPAH using dot blot arrays of positive colony PCR products using both pooled cDNA libraries as probes. Clones verified as being upregulated were sequenced. For two genes the increase in expression was verified by northern blotting and data analysed using Student's unpaired two-tailed t-test.

Results

We present preliminary findings concerning candidate genes upregulated in IPAH. Twenty-seven upregulated genes were identified out of 192 clones examined. Upregulation in individual cases of IPAH was shown by northern blot for tissue inhibitor of metalloproteinase-3 and decorin (P < 0.01) compared with the housekeeping gene glyceraldehydes-3-phosphate dehydrogenase.

Conclusion

Four of the up regulated genes, magic roundabout, hevin, thrombomodulin and sucrose non-fermenting protein-related kinase-1 are expressed specifically by endothelial cells and one, muscleblind-1, by muscle cells, suggesting that they may be associated with plexiform lesions and hypertrophic arterial wall remodelling, respectively.     

The use of bacterial minicells to transfer plasmid DNA to eukaryotic cells

The delivery of DNA to mammalian cells is of critical importance to the development of genetic vaccines, gene replacement therapies and gene silencing. For these applications, targeting, effective DNA transfer and vector safety are the major roadblocks in furthering development. In this report, we present a novel DNA delivery vehicle that makes use of protoplasted, achromosomal bacterial minicells. Transfer of plasmid DNA as measured by green fluorescent protein expression was found to occur in as high as 25% of cultured Cos-7 cells when a novel chimeric protein containing the D2-D5 region of invasin was expressed and displayed on the surface of protoplasted minicells. Based on endoplasmic reticulum stress and other responses, protoplasted minicells were non-toxic to recipient eukaryotic cells as a consequence of the transfection process. Taken together, these results suggest that bacterial minicells may represent a novel and promising gene delivery vehicle.     

Autoantibodies against the replication protein A complex in systemic lupus erythematosus and other autoimmune diseases

Replication protein A (RPA), a heterotrimer with subunits of molecular masses 70, 32, and 14 kDa, is a single-stranded-DNA-binding factor involved in DNA replication, repair, and recombination. There have been only three reported cases of anti-RPA in systemic lupus erythematosus (SLE) and Sjögren syndrome (SjS). This study sought to clarify the clinical significance of autoantibodies against RPA. Sera from 1,119 patients enrolled during the period 2000 to 2005 were screened by immunoprecipitation (IP) of ³⁵S-labeled K562 cell extract. Antigen-capture ELISA with anti-RPA32 mAb, immunofluorescent antinuclear antibodies (ANA) and western blot analysis with purified RPA were also performed. Our results show that nine sera immunoprecipitated the RPA70–RPA32–RPA14 complex and all were strongly positive by ELISA (titers 1:62,500 to 1:312,500). No additional sera were positive by ELISA and subsequently confirmed by IP or western blotting. All sera showed fine speckled/homogeneous nuclear staining. Anti-RPA was found in 1.4% (4/276) of SLE and 2.5% (1/40) of SjS sera, but not in rheumatoid arthritis (0/35), systemic sclerosis (0/47), or polymyositis/dermatomyositis (0/43). Eight of nine patients were female and there was no racial predilection. Other positive patients had interstitial lung disease, autoimmune thyroiditis/hepatitis C virus/pernicious anemia, or an unknown diagnosis. Autoantibody specificities found in up to 40% of SLE and other diseases, such as anti-nRNP, anti-Sm, anti-Ro, and anti-La, were unusual in anti-RPA-positive sera. Only one of nine had anti-Ro, and zero of nine had anti-nRNP, anti-Sm, anti-La, or anti-ribosomal P antibodies. In summary, high titers of anti-RPA antibodies were found in nine patients (1.4% of SLE and other diseases). Other autoantibodies found in SLE were rare in this subset, suggesting that patients with anti-RPA may form a unique clinical and immunological subset.     

Greater rate of decline in maximal aerobic capacity with age in endurance-trained than in sedentary men.

To determine the relation between habitual endurance exercise status and the age-associated decline in maximal aerobic capacity [i.e., maximal O(2) consumption (Vo(2 max))] in men, we performed a well-controlled cross-sectional laboratory study on 153 healthy men aged 20-75 yr: 64 sedentary and 89 endurance trained. Vo(2 max) (ml. kg(-1). min(-1)), measured by maximal treadmill exercise, was inversely related to age in the endurance-trained (r = -0.80) and sedentary (r = -0.74) men but was higher in the endurance-trained men at any age. The rate of decline in Vo(2 max) with age (ml. kg(-1). min(-1)) was greater (P < 0.001) in the endurance-trained than in the sedentary men. Whereas the relative rate of decline in Vo(2 max) (percent decrease per decade from baseline levels in young adulthood) was similar in the two groups, the absolute rate of decline in Vo(2 max) was -5.4 and -3.9 ml. kg(-1). min(-). decade(-1) in the endurance-trained and sedentary men, respectively. Vo(2 max) declined linearly across the age range in the sedentary men but was maintained in the endurance-trained men until approximately 50 yr of age. The accelerated decline in Vo(2 max) after 50 yr of age in the endurance-trained men was related to a decline in training volume (r = 0.46, P < 0.0001) and was associated with an increase in 10-km running time (r = -0.84, P < 0.0001). We conclude that the rate of decline in maximal aerobic capacity during middle and older age is greater in endurance-trained men than in their sedentary peers and is associated with a marked decline in O(2) pulse.     

The distribution of cave twilight‐zone spiders depends on microclimatic features and trophic supply

Caves are not closed systems. Trophic dynamics in these habitats are driven by resource availability, and species that move between cave and outdoor environments may play a major role in resource availability. Spiders are among the most abundant invertebrates in caves; however, very few studies have tested factors hypothesized to affect the distribution of spiders among caves, and it is not known whether the trophic features of caves play a role in determining the occurrence, abundance, or breeding success of spiders. We assessed the distribution of the cave‐dwelling orb‐weaver spider Meta menardi in Italy, in a Mediterranean and in a Pre‐alpine area during summer and winter. We analyzed the relationships between spider distribution and multiple cave features, describing both the abiotic and the biotic environment. Using visual encounter surveys, the detection probability of this species was high, indicating that this technique provides reliable information on spider distribution. In Mediterranean caves, spider presence was more likely in cold and wet caves with abundant dipterans. In Pre‐alpine caves, spider presence was more likely in deep caves with abundant dipterans. Dipteran abundance was the variable best explaining spider distribution when pooling all sampled caves. This study shows that adults of M. menardi do not occur randomly among caves, but select caves with specific features. Prey availability and abiotic features are major determinants of habitat suitability for cave spiders. The strong relationship between spider distribution and prey availability suggests that the distribution of these spiders might be an indicator of the resources available in the twilight zones of caves.     

Global drivers of population density in terrestrial vertebrates

Aim

Although the effects of life history traits on population density have been investigated widely, how spatial environmental variation influences population density for a large range of organisms and at a broad spatial scale is poorly known. Filling this knowledge gap is crucial for global species management and conservation planning and to understand the potential impact of environmental changes on multiple species.

Location

Global.

Time period

Present.

Major taxa studied

Terrestrial amphibians, reptiles, birds and mammals.

Methods

We collected population density estimates for a range of terrestrial vertebrates, including 364 estimates for amphibians, 850 for reptiles, 5,667 for birds and 7,651 for mammals. We contrasted the importance of life history traits and environmental predictors using mixed models and tested different hypotheses to explain the variation in population density for the four groups. We assessed the predictive accuracy of models through cross‐validation and mapped the partial response of vertebrate population density to environmental variables globally.

Results

Amphibians were more abundant in wet areas with high productivity levels, whereas reptiles showed relatively higher densities in arid areas with low productivity and stable temperatures. The density of birds and mammals was typically high in temperate wet areas with intermediate levels of productivity. The models showed good predictive abilities, with pseudo‐R² ranging between 0.68 (birds) and 0.83 (reptiles).

Main conclusions

Traits determine most of the variation in population density across species, whereas environmental conditions explain the intraspecific variation across populations. Species traits, resource availability and climatic stability have a different influence on the population density of the four groups. These models can be used to predict the average species population density over large areas and be used to explore macroecological patterns and inform conservation analyses.     

Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein–protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg–Glu combination, whereas the Lys–Asp was not significantly different from the Lys–Glu of the parent scaffold, PT3. The marked 3₁₀-helical contributions in PT3 were lessened in the Arg–Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys–Asp peptide which could help elucidate the stages of folding between the 3₁₀ and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.