Contrasting patterns of naturalized plant richness in the Americas: Numbers are higher in the North but expected to rise sharply in the South

With increasing availability of plant distribution data, the information about global plant diversity is improving rapidly. Recently, Ulloa Ulloa et al. (2017) presented the first comprehensive overview of the native vascular flora of the Americas, yielding a total count of 124,993 native species. Of these, 51,241 occur in North America and 82,052 in South America. By combining these data with the information in the Global Naturalized Alien Flora (GloNAF) database of naturalized alien floras, we point out that for a complete picture of the regional and continental plant richness, the naturalized alien species need to be considered. Ignoring this novel component of regional floras can lead to an inaccurate picture of overall change in biodiversity in the Anthropocene. We show that North and South America might face contrasting challenges in terms of potential threats to biodiversity posed by alien plant species, because of the different past and present dynamics of invasions and predictions of future development. In total, there are 7,042 naturalized alien plants occurring in the Americas, with 6,122 recorded in North America and 2,677 in South America; if only introductions from other continents are considered additions to the native continental flora make up 6.9 and 1.4 %, respectively. Nevertheless, predictions of naturalized plant trajectories based on global trade dynamics and climate change suggest that considerable increases in naturalized plant numbers are expected in the next 20 years for emerging South American economies, which could reverse the present state.     

Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep‐sea anoxic brine lake as potential polysaccharide degrader

Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX‐2^T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4B^T from the Shaban deep‐sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant‐derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low‐oxygen conditions. Likewise, proteomics indicated quinone‐mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light‐dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep‐sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase‐rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.     

Growth hormone secretion is diminished and tightly controlled in humans enriched for familial longevity

Reduced growth hormone (GH) signaling has been consistently associated with increased health and lifespan in various mouse models. Here, we assessed GH secretion and its control in relation with human familial longevity. We frequently sampled blood over 24 h in 19 middle‐aged offspring of long‐living families from the Leiden Longevity Study together with 18 of their partners as controls. Circulating GH concentrations were measured every 10 min and insulin‐like growth factor 1 (IGF‐1) and insulin‐like growth factor binding protein 3 (IGFBP3) every 4 h. Using deconvolution analysis, we found that 24‐h total GH secretion was 28% lower (P = 0.04) in offspring [172 (128–216) mU L^?1] compared with controls [238 (193–284) mU L^?1]. We used approximate entropy (ApEn) to quantify the strength of feedback/feedforward control of GH secretion. ApEn was lower (P = 0.001) in offspring [0.45 (0.39–0.53)] compared with controls [0.66 (0.56–0.77)], indicating tighter control of GH secretion. No significant differences were observed in circulating levels of IGF‐1 and IGFBP3 between offspring and controls. In conclusion, GH secretion in human familial longevity is characterized by diminished secretion rate and more tight control. These data imply that the highly conserved GH signaling pathway, which has been linked to longevity in animal models, is also associated with human longevity.     

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.     

Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1

Gene transfer into hematopoietic stem cells has been used successfully for correcting lymphoid but not myeloid immunodeficiencies. Here we report on two adults who received gene therapy after nonmyeloablative bone marrow conditioning for the treatment of X-linked chronic granulomatous disease (X-CGD), a primary immunodeficiency caused by a defect in the oxidative antimicrobial activity of phagocytes resulting from mutations in gp91(phox). We detected substantial gene transfer in both individuals' neutrophils that lead to a large number of functionally corrected phagocytes and notable clinical improvement. Large-scale retroviral integration site-distribution analysis showed activating insertions in MDS1-EVI1, PRDM16 or SETBP1 that had influenced regulation of long-term hematopoiesis by expanding gene-corrected myelopoiesis three- to four-fold in both individuals. Although insertional influences have probably reinforced the therapeutic efficacy in this trial, our results suggest that gene therapy in combination with bone marrow conditioning can be successfully used to treat inherited diseases affecting the myeloid compartment such as CGD.     

A three-genome phylogeny of Momordica (Cucurbitaceae) suggests seven returns from dioecy to monoecy and recent long-distance dispersal to Asia

The bitter gourd genus Momordica comprises 47 species in Africa and 12 in Asia and Australia. All have unisexual flowers, and of the African species, 24 are dioecious, 23 monoecious, while all Asian species are dioecious. Maximum likelihood analyses of 6257 aligned nucleotides of plastid, mitochondrial and nuclear DNA obtained for 122 accessions of Momordica and seven outgroups show that Momordica is monophyletic and consists of 11 well-supported clades. Monoecy evolved from dioecy seven times independently, always in Africa and mostly in savanna species with low population densities. Leaky dioecy, with occasional fruit-producing males, occurs in two African species and might be the first step in an evolutionary transition towards monoecy. Dated biogeographic analyses suggest that Momordica originated in tropical Africa and that the Asian species are the result of one long-distance dispersal event about 19 million years ago. The pantropical vegetable Momordica charantia is of African, not Asian origin as had previously been suggested.     

Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements

The mass spectrometric analysis of protein phosphorylation is still far from being routine, and the outcomes thereof are often unsatisfying. Apart from the inherent problem of substoichiometric phosphorylation, three arguments as to why phosphorylation analysis is so problematic are often quoted, including (a) increased hydrophilicity of the phosphopeptide with a concomitant loss during the loading onto reversed-phase columns, (b) selective suppression of the ionization of phosphopeptides in the presence of unmodified peptides, and (c) lower ionization/detection efficiencies of phosphopeptides as compared with their unmodified cognates. Here we present the results of a study investigating the validity of these three arguments when using electrospray ionization mass spectrometry. We utilized a set of synthetic peptide/phosphopeptide pairs that were quantitated by amino acid analysis. Under the applied conditions none of the experiments performed supports the notions of (a) generally increased risks of losing phosphopeptides during the loading onto the reversed-phase column because of decreased retention and (b) the selective ionization suppression of phosphopeptides. The issue of ionization/detection efficiencies of phosphopeptides versus their unphosphorylated cognates proved to be less straightforward when using electrospray ionization because no evidence for decreased ionization/detection efficiencies for phosphopeptides could be found.     

Biomarker discovery by imaging mass spectrometry: transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat

Adverse drug effects are often associated with pathological changes in tissue. An accurate depiction of the undesired affected area, possibly supported by mechanistic data, is important to classify the effects with regard to relevance for human patients. MALDI imaging MS represents a new analytical tool to directly provide the spatial distribution and the relative abundance of proteins in tissue. Here we evaluate this technique to investigate potential toxicity biomarkers in kidneys of rats that were administered gentamicin, a well known nephrotoxicant. Differential analysis of the mass spectrum profiles revealed a spectral feature at 12,959 Da that strongly correlates with histopathology alterations of the kidney. We unambiguously identified this spectral feature as transthyretin (Ser(28)-Gln(146)) using an innovative combination of tissue microextraction and fractionation by reverse-phase liquid chromatography followed by a top-down tandem mass spectrometric approach. Our findings clearly demonstrate the emerging role of imaging MS in the discovery of toxicity biomarkers and in obtaining mechanistic insights concerning toxicity mechanisms.     

Emergence of Oblong School Shape: Models and Empirical Data of Fish

The main benefit of the oblong shape of schools of fish is supposed to be the protection against predation. Models of self‐organised travelling groups have shown that this shape may arise as a side effect of the avoidance of collisions with group members. These models were developed for schools of fish in open water, whereas the oblong shape of schools of real fish has mostly been observed in schools in tanks. Therefore, it is not known how school shape in a tank originates neither in models nor in real fish. To find out what causes this shape, we use the combination of a theoretical and an empirical study. We test the predictions produced by our earlier models regarding the effect of school size on the school shape both in a model of self‐organised schooling in a tank and empirically. Empirically, we study the 3D positions of all individuals in the schools of 10–60 real mullets (Chelon labrosus). We calculate for each individual its distance to its nearest neighbour and its velocity and we measure per school its length and width. The relation between school shape and size in the model and in the real mullets supports our prediction and thus supports the hypothesis that school shape may be emergent from the avoidance of collisions during coordinated travelling.     

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