Climate variation and regional gradients in population dynamics of two hole-nesting passerines

Latitudinal gradients in population dynamics can arise through regional variation in the deterministic components of the population dynamics and the stochastic factors. Here, we demonstrate an increase with latitude in the contribution of a large-scale climate pattern, the North Atlantic Oscillation (NAO), to the fluctuations in size of populations of two European hole-nesting passerine species. However, this influence of climate induced different latitudinal gradients in the population dynamics of the two species. In the great tit the proportion of the variability in the population fluctuations explained by the NAO increased with latitude, showing a larger impact of climate on the population fluctuations of this species at higher latitudes. In contrast, no latitudinal gradient was found in the relative contribution of climate to the variability of the pied flycatcher populations because the total environmental stochasticity increased with latitude. This shows that the population ecological consequences of an expected climate change will depend on how climate affects the environmental stochasticity in the population process. In both species, the effects will be larger in those parts of Europe where large changes in climate are expected.     

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.     

Reactivity of a new class of P450 enzyme models

P450 enzyme models carrying a SO3(-) ligand coordinating to iron have been synthesized and characterized. These complexes show characteristics very similar to those of iron-heme cofactors of P450 enzymes. Their reactivity towards different reactions catalyzed by P450 enzymes such as epoxidation of double bonds, hydroxylation of non-activated C-H bonds, N-dealkylation of amines, and cleavage of diols (C-C-bond cleavage) has been investigated.     

Lysine 27 Ubiquitination of the Mitochondrial Transport Protein Miro Is Dependent on Serine 65 of the Parkin Ubiquitin Ligase

Mitochondrial transport plays an important role in matching mitochondrial distribution to localized energy production and calcium buffering requirements. Here, we demonstrate that Miro1, an outer mitochondrial membrane (OMM) protein crucial for the regulation of mitochondrial trafficking and distribution, is a substrate of the PINK1/Parkin mitochondrial quality control system in human dopaminergic neuroblastoma cells. Moreover, Miro1 turnover on damaged mitochondria is altered in Parkinson disease (PD) patient-derived fibroblasts containing a pathogenic mutation in the PARK2 gene (encoding Parkin). By analyzing the kinetics of Miro1 ubiquitination, we further demonstrate that mitochondrial damage triggers rapid (within minutes) and persistent Lys-27-type ubiquitination of Miro1 on the OMM, dependent on PINK1 and Parkin. Proteasomal degradation of Miro1 is then seen on a slower time scale, within 2–3 h of the onset of ubiquitination. We find Miro ubiquitination in dopaminergic neuroblastoma cells is independent of Miro1 phosphorylation at Ser-156 but is dependent on the recently identified Ser-65 residue within Parkin that is phosphorylated by PINK1. Interestingly, we find that Miro1 can stabilize phospho-mutant versions of Parkin on the OMM, suggesting that Miro is also part of a Parkin receptor complex. Moreover, we demonstrate that Ser-65 in Parkin is critical for regulating Miro levels upon mitochondrial damage in rodent cortical neurons. Our results provide new insights into the ubiquitination-dependent regulation of the Miro-mediated mitochondrial transport machinery by PINK1/Parkin and also suggest that disruption of this regulation may be implicated in Parkinson disease pathogenesis.     

Diverging phenological responses of Arctic seabirds to an earlier spring

The timing of annual events such as reproduction is a critical component of how free‐living organisms respond to ongoing climate change. This may be especially true in the Arctic, which is disproportionally impacted by climate warming. Here, we show that Arctic seabirds responded to climate change by moving the start of their reproduction earlier, coincident with an advancing onset of spring and that their response is phylogenetically and spatially structured. The phylogenetic signal is likely driven by seabird foraging behavior. Surface‐feeding species advanced their reproduction in the last 35 years while diving species showed remarkably stable breeding timing. The earlier reproduction for Arctic surface‐feeding birds was significant in the Pacific only, where spring advancement was most pronounced. In both the Atlantic and Pacific, seabirds with a long breeding season showed a greater response to the advancement of spring than seabirds with a short breeding season. Our results emphasize that spatial variation, phylogeny, and life history are important considerations in seabird phenological response to climate change and highlight the key role played by the species’ foraging behavior.     

Local and large-scale climatic variables as predictors of the breeding numbers of endangered Lesser Black-backed Gulls on the Norwegian Coast

In the 1970s and 1980s, the nominate subspecies of the Lesser Black-backed Gull (Larus fuscus fuscus) showed a dramatic drop in breeding numbers on the Norwegian Coast, and in 2000, the population in some colonies was only 10–20% of the population in 1980. This decline has been attributed to the collapse in the stock of Norwegian spring spawning herring (Clupea harengus). In this study, we examined whether local climate (sea and air temperatures), winter NAO (North Atlantic Oscilliation), and the year-class strength and size of 0-group herring could predict the relative changes in breeding numbers between years, mainly after the population collapse. Breeding birds were counted in 19 of the years between 1980 and 2007 in an archipelago on the coast of Helgeland, northern Norway. The best model predicting changes in breeding numbers for the period between 1980 and 2005 (for which data on 0-group herring was available) included mean local air temperature in winter (January–March) and winter NAO, explaining 57% of the variation between years, while the other factors had little effect. When also adding the years 2006–2007 (no herring data), the best model included only mean air temperature in winter, explaining 41% of the variation. In conclusion, the high positive correlation between breeding numbers and climatic factors probably resulted from a higher availability of important fish prey after mild winters, for which 0-group herring presently may only account for a limited proportion. However, this prey might have been of much more importance prior to the population decline.     

Assessment of coronary microvascular resistance in the chronic infarcted pig heart

Pre‐clinical studies aimed at treating ischemic heart disease (i.e. stem cell‐ and growth factor therapy) often consider restoration of the impaired microvascular circulation as an important treatment goal. However, serial in vivo measurement hereof is often lacking. The purpose of this study was to evaluate the applicability of intracoronary pressure and flow velocity as a measure of microvascular resistance in a large animal model of chronic myocardial infarction (MI). Myocardial infarction was induced in Dalland Landrace pigs (n = 13; 68.9 ± 4.1 kg) by a 75‐min. balloon occlusion of the left circumflex artery (LCX). Intracoronary pressure and flow velocity parameters were measured simultaneously at rest and during adenosine‐induced hyperemia, using the Combowire (Volcano) before and 4 weeks after MI. Various pressure‐ and/or flow‐derived indices were evaluated. Hyperemic microvascular resistance (HMR) was significantly increased by 28% in the infarct‐related artery, based on a significantly decreased peak average peak flow velocity (pAPV) by 20% at 4 weeks post‐MI (P = 0.03). Capillary density in the infarct zone was decreased compared to the remote area (658 ± 207/mm² versus 1650 ± 304/mm², P = 0.017). In addition, arterioles in the infarct zone showed excessive thickening of the alpha smooth muscle actin (αSMA) positive cell layer compared to the remote area (33.55 ± 4.25 μm versus 14.64 ± 1.39 μm, P = 0.002). Intracoronary measurement of HMR successfully detected increased microvascular resistance that might be caused by the loss of capillaries and arteriolar remodelling in the chronic infarcted pig heart. Thus, HMR may serve as a novel outcome measure in pre‐clinical studies for serial assessment of microvascular circulation.     

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.