Persistent and novel threats to the biodiversity of Kazakhstan’s steppes and semi-deserts

Temperate grasslands have suffered disproportionally from conversion to cropland, degradation and fragmentation. A large proportion of the world’s remaining near-natural grassland is situated in Kazakhstan. We aimed to assess current and emerging threats to steppe and semi-desert biodiversity in Kazakhstan and evaluate conservation research priorities. We conducted a horizon-scanning exercise among conservationists from academia and practice. We first compiled a list of 45 potential threats. These were then ranked by the survey participants according to their perceived severity, the need for research on them, and their novelty. The highest-ranked threats were related to changes in land use (leading to habitat loss and deterioration), direct persecution of wildlife, and rapid infrastructure development due to economic and population growth. Research needs were identified largely in the same areas, and the mean scores of threat severity and research need were highly correlated. Novel threats comprised habitat loss by photovoltaic and wind power stations, climate change and changes in agriculture such as the introduction of biofuels. However, novelty was not correlated with threat severity or research priority, suggesting that the most severe threats are the established ones. Important goals towards more effective steppe and semi-desert conservation in Kazakhstan include more cross-sector collaboration (e.g. by involving stakeholders in conservation and agriculture), greater allocation of funds to under-staffed areas (e.g. protected area management), better representativeness and complementarity in the protected area system and enhanced data collection for wildlife monitoring and threat assessments (including the use of citizen-science databases).     

Breeding ecology of the endemic Black Lark <Emphasis Type="Italic">Melanocorypha yeltoniensis</Emphasis> on natural steppe and abandoned croplands in post-Soviet Kazakhstan

Since the collapse of the Soviet Union in 1991, the abundance and distribution of many central Asian steppe birds have been affected by changes in agricultural land management, such as the abandonment of large areas of cropland and changing grazing patterns. However, the underlying population processes that drive patterns of abundance and distribution are poorly understood. We compared the population ecology of the Black Lark Melanocorypha yeltoniensis on natural steppe and abandoned cropland. Between 2009 and 2013, we used distance sampling to quantify Black Lark population density, monitored 220 nests to assess reproductive performance, and modelled habitat selection at several scales. Arthropod food availability was compared using pitfall traps. Mean population densities were three times higher on abandoned cropland compared to those in steppe, and varied with time since abandonment. Nest survival rates were significantly lower on abandoned cropland compared to steppe, probably due to higher predation pressure. Chick growth rates were also lower on abandoned cropland, despite higher insect availability in this habitat. Habitat selection was strongly influenced by grazing intensity and vegetation structure. We suggest that Black Larks are generally attracted to abandoned cropland because of its suitable vegetation structure and higher food availability. The results of a fecundity model suggested that the number of breeding attempts on abandoned cropland necessary to produce the same number of fledglings as one nesting attempt in steppe habitat was 2.04 in 2011 and 3.62 in 2013. However, a phenological analysis revealed that there were only two peaks in first egg dates, making more than two re-nesting attempts per year unlikely. Therefore, abandoned cropland could, at least in some years, be an ecological trap for the species. Our results illustrate that the effects of land-use change on animal populations should not only be assessed using species densities, but also incorporate detailed demographic analyses. If current densities in steppe habitat corresponded to maximum carrying capacity, overall population densities of Black Larks are likely to decline in the near future as availability of abandoned cropland as nesting habitat is currently decreasing.     

Small GTPase Determinants for the Golgi Processing and Plasmalemmal Expression of Human Ether-a-go-go Related (hERG) K+ Channels

The pro-arrhythmic Long QT syndrome (LQT) is linked to 10 different genes (LQT1–10). Approximately 40% of genotype-positive LQT patients have LQT2, which is characterized by mutations in the human ether-a-go-go related gene (hERG). hERG encodes the voltage-gated K⁺ channel α-subunits that form the pore of the rapidly activating delayed rectifier K⁺ current in the heart. The purpose of this study was to elucidate the mechanisms that regulate the intracellular transport or trafficking of hERG, because trafficking is impaired for about 90% of LQT2 missense mutations. Protein trafficking is regulated by small GTPases. To identify the small GTPases that are critical for hERG trafficking, we coexpressed hERG and dominant negative (DN) GTPase mutations in HEK293 cells. The GTPases Sar1 and ARF1 regulate the endoplasmic reticulum (ER) export of proteins in COPII and COPI vesicles, respectively. Expression of DN Sar1 inhibited the Golgi processing of hERG, decreased hERG current (I_hERG) by 85% (n ≥ 8 cells per group, *, p < 0.01), and reduced the plasmalemmal staining of hERG. The coexpression of DN ARF1 had relatively small effects on hERG trafficking. Surprisingly, the coexpression of DN Rab11B, which regulates the endosomal recycling, inhibited the Golgi processing of hERG, decreased I_hERG by 79% (n ≥ 8 cells per group; *, p < 0.01), and reduced the plasmalemmal staining of hERG. These data suggest that hERG undergoes ER export in COPII vesicles and endosomal recycling prior to being processed in the Golgi. We conclude that hERG trafficking involves a pathway between the ER and endosomal compartments that influences expression in the plasmalemma.The human KCNH2 or ether-a-go-go related gene (hERG)³ encodes the voltage-gated K⁺ channel α-subunits that oligomerize to form the pore of the rapidly activating delayed rectifier K⁺ current (I_Kr) in cardiac myocytes (1–3). Hundreds of hERG mutations are linked to the congenital pro-arrhythmic Type 2 Long QT syndrome (LQT2) and functional studies suggest that these mutations result in a loss of normal hERG K⁺ channel (hERG) function (4, 5). In LQT2, missense mutations are the dominant abnormality and many LQT2 missense mutations reduce hERG K⁺ current (I_hERG) by decreasing the intracellular transport or trafficking of hERG to the Golgi apparatus (Golgi) and the cell surface membrane (plasmalemma) (6). Therefore, disruption of hERG K⁺ channel trafficking appears to be a principal mechanism for disease.Movement of proteins between membrane-bound intracellular compartments is mediated by small transport vesicles, which bud from a donor compartment to fuse with an appropriate acceptor compartment. The trafficking of many transmembrane and secretory proteins between the ER and Golgi compartments is dependent on the small GTPases ADP-ribosylation factor 1 (ARF1) and Sar1, which regulate the formation of coat-associated protein complex I (COPI) and II (COPII) vesicles, respectively (7–19). These small GTPases facilitate the polymerization of transport vesicle protein coats on the donor membrane. Vesicular cargo selection, docking, and fusion to the target membrane are regulated by adaptor proteins, SNARE proteins, and Rab GTPases. To rationally develop novel therapeutic targets that may increase the expression of trafficking-deficient LQT2 mutant channels, the molecular mechanisms that regulate the trafficking of hERG need to be explored. The purpose of this study is to identify transport proteins that regulate the trafficking of wild type (WT) hERG. We used a strategy of testing specific WT GTPases or ones containing dominant negative (DN) mutations to interfere with their function.     

Binding of alpha-synuclein affects the lipid packing in bilayers of small vesicles

The intracellular deposition of fibrillar aggregates of alpha-synuclein is a characteristic feature of Parkinson disease. Alternatively, as a result of its unusual conformational plasticity, alpha-synuclein may fold into an amphipathic helix upon contact with a lipid-water interface. Using spin label ESR and fluorescence spectroscopy, we show here that alpha-synuclein affects the lipid packing in small unilamellar vesicles. The ESR hyperfine splittings of spin-labeled phospholipid probes revealed that alpha-synuclein induces chain ordering at carbon 14 of the acyl chains below the chain melting phase transition temperature but not in the liquid crystalline state of electroneutral vesicle membranes. Binding of alpha-synuclein leads to an increase in the temperature and cooperativity of the phase transition according to the fluorescence anisotropy of the hydrophobic polyene 1,6-diphenylhexatriene and of the fluorescence emission maxima of the amphiphilic probe 6-dodecanoyl-2-dimethylaminonaphthalene. Binding parameters were obtained from the fluorescence anisotropy measurements in combination with our previous determinations by titration calorimetry (Nuscher, B., Kamp, F., Mehnert, T., Odoy, S., Haass, C., Kahle, P. J., and Beyer, K. (2004) J. Biol. Chem. 279, 21966-21975). We also show that alpha-synuclein interacts with vesicle membranes containing sphingomyelin and cholesterol. We propose that the protein is capable of annealing defects in curved vesicle membranes, which may prevent synaptic vesicles from premature fusion.     

The porphyrin TMPyP4 inhibits elongation during the noncanonical translation of the FTLD/ALS-associated GGGGCC repeat in the C9orf72 gene

GGGGCC (G₄C₂) repeat expansion in the C9orf72 gene has been shown to cause frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Dipeptide repeat proteins produced through repeat-associated non-AUG (RAN) translation are recognized as potential drivers for neurodegeneration. Therefore, selective inhibition of RAN translation could be a therapeutic avenue to treat these neurodegenerative diseases. It was previously known that the porphyrin TMPyP4 binds to G₄C₂ repeat RNA. However, the consequences of this interaction have not been well characterized. Here, we confirmed that TMPyP4 inhibits C9orf72 G₄C₂ repeat translation in cellular and in in vitro translation systems. An artificial insertion of an AUG codon failed to cancel the translation inhibition, suggesting that TMPyP4 acts downstream of non-AUG translation initiation. Polysome profiling assays also revealed polysome retention on G₄C₂ repeat RNA, along with inhibition of translation, indicating that elongating ribosomes stall on G₄C₂ repeat RNA. Urea-resistant interaction between G₄C₂ repeat RNA and TMPyP4 likely contributes to this ribosome stalling and thus to selective inhibition of RAN translation. Taken together, our data reveal a novel mode of action of TMPyP4 as an inhibitor of G₄C₂ repeat translation elongation.     

An application programming interface for CellNetAnalyzer

CellNetAnalyzer (CNA) is a MATLAB toolbox providing computational methods for studying structure and function of metabolic and cellular signaling networks. In order to allow non-experts to use these methods easily, CNA provides GUI-based interactive network maps as a means of parameter input and result visualization. However, with the availability of high-throughput data, there is a need to make CNA's functionality also accessible in batch mode for automatic data processing. Furthermore, as some algorithms of CNA are of general relevance for network analysis it would be desirable if they could be called as sub-routines by other applications. For this purpose, we developed an API (application programming interface) for CNA allowing users (i) to access the content of network models in CNA, (ii) to use CNA's network analysis capabilities independent of the GUI, and (iii) to interact with the GUI to facilitate the development of graphical plugins.Here we describe the organization of network projects in CNA and the application of the new API functions to these projects. This includes the creation of network projects from scratch, loading and saving of projects and scenarios, and the application of the actual analysis methods. Furthermore, API functions for the import/export of metabolic models in SBML format and for accessing the GUI are described. Lastly, two example applications demonstrate the use and versatile applicability of CNA's API. CNA is freely available for academic use and can be downloaded from http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html.     

Glycogen synthase kinase-3β is required for the induction of skeletal muscle atrophy

Skeletal muscle atrophy commonly occurs in acute and chronic disease. The expression of the muscle-specific E3 ligases atrogin-1 (MAFbx) and muscle RING finger 1 (MuRF1) is induced by atrophy stimuli such as glucocorticoids or absence of IGF-I/insulin and subsequent Akt signaling. We investigated whether glycogen synthase kinase-3β (GSK-3β), a downstream molecule in IGF-I/Akt signaling, is required for basal and atrophy stimulus-induced expression of atrogin-1 and MuRF1, and myofibrillar protein loss in C(2)C(12) skeletal myotubes. Abrogation of basal IGF-I signaling, using LY294002, resulted in a prominent induction of atrogin-1 and MuRF1 mRNA and was accompanied by a loss of myosin heavy chain fast (MyHC-f) and myosin light chains 1 (MyLC-1) and -3 (MyLC-3). The synthetic glucocorticoid dexamethasone (Dex) also induced the expression of both atrogenes and likewise resulted in the loss of myosin protein abundance. Genetic ablation of GSK-3β using small interfering RNA resulted in specific sparing of MyHC-f, MyLC-1, and MyLC-3 protein levels after Dex treatment or impaired IGF-I/Akt signaling. Interestingly, loss of endogenous GSK-3β suppressed both basal and atrophy stimulus-induced atrogin-1 and MuRF1 expression, whereas pharmacological GSK-3β inhibition, using CHIR99021 or LiCl, only reduced atrogin-1 mRNA levels in response to LY294002 or Dex. In conclusion, our data reveal that myotube atrophy and myofibrillar protein loss are GSK-3β dependent, and demonstrate for the first time that basal and atrophy stimulus-induced atrogin-1 mRNA expression requires GSK-3β enzymatic activity, whereas MuRF1 expression depends solely on the physical presence of GSK-3β.     

Translational repression of the disintegrin and metalloprotease ADAM10 by a stable G-quadruplex secondary structure in its 5'-untranslated region

Anti-amyloidogenic processing of the amyloid precursor protein APP by α-secretase prevents formation of the amyloid-β peptide, which accumulates in senile plaques of Alzheimer disease patients. α-Secretase belongs to the family of a disintegrin and metalloproteases (ADAMs), and ADAM10 is the primary candidate for this anti-amyloidogenic activity. We recently demonstrated that ADAM10 translation is repressed by its 5'-UTR and that in particular the first half of ADAM10 5'-UTR is responsible for translational repression. Here, we asked whether specific sequence motifs exist in the ADAM10 5'-UTR that are able to form complex secondary structures and thus potentially inhibit ADAM10 translation. Using circular dichroism spectroscopy, we demonstrate that a G-rich region between nucleotides 66 and 94 of the ADAM10 5'-UTR forms a highly stable, intramolecular, parallel G-quadruplex secondary structure under physiological conditions. Mutation of guanines in this sequence abrogates the formation of the G-quadruplex structure. Although the G-quadruplex structure efficiently inhibits translation of a luciferase reporter in in vitro translation assays and in living cells, inhibition of G-quadruplex formation fails to do so. Moreover, expression of ADAM10 was similarly repressed by the G-quadruplex. Mutation of the G-quadruplex motif results in a significant increase of ADAM10 levels and consequently APPsα secretion. Thus, we identified a critical RNA secondary structure within the 5'-UTR, which contributes to the translational repression of ADAM10.     

Implicit Goalkeeper Influences on Goal Side Selection in Representative Penalty Kicking Tasks

In well-controlled lab situations, marginal displacements of the goalkeeper on the goal line affect goal side selection of penalty takers implicitly, that is, without the penalty takers being consciously aware of the displacement. Whether this effect is retained in more representative real-life situations with competing goalkeepers and penalty takers has not been verified. In the current study, penalty takers were instructed to position the goalkeepers at the centre of the goal. They then performed penalty kicks adopting either a keeper independent or a keeper dependent strategy, while goalkeepers actually attempted to save the ball by strategically diving early or late. Analyses of trials in which penalty takers failed to place the goalkeeper in the centre of the goal (although they incorrectly believed they placed the goalkeeper at the centre of the goal) showed that implicit influences of the goalkeeper’s position on goal side selection were overridden by the (conscious) perception of the direction of the goalkeeper’s dive, but only if the penalty takers deliberately monitored the goalkeeper’s action and the goalkeeper committed early enough for penalty takers to respond. In all other combinations of penalty kick and goalkeeper strategies more than 60% of the kicks were directed to the side of the goal with more space. Most importantly, however, the current study shows that influences of implicit perception on the penalty takers’ decision making are rather pervasive considering that many supraliminal sources of information were available. That is, the current study demonstrates that implicit perception retains its influence on decision-making even if other (stronger) stimuli are also present.