D-Phe-Pro-Arg type thrombin inhibitors: unexpected selectivity by modification of the P1 moiety

Synthesis of thrombin inhibitors and their binding mode to thrombin is described. Modification of the P1 moiety leads to an increased selectivity versus trypsin. The observed selectivity is discussed in view of their thrombin-inhibitor complex X-ray structures.     

4-amidinobenzylamine-based inhibitors of urokinase

A series of 4-amidinobenzylamine-based peptidomimetic inhibitors of urokinase was synthesized. The most potent one, benzylsulfonyl-D-Ser-Ala-4-amidinobenzylamide 16, inhibits uPA with a K(i) of 7.7 nM but is less selective than 10 with a Gly as P2 residue. Hydroxyamidine and carbonate prodrugs were prepared, which are rapidly converted into the active inhibitors in rats after subcutaneous application.     

The molecular dissection of the chaperone–usher pathway

Secretion systems are specialized in transport of proteins, DNA or nutrients across the cell envelope of bacteria and enable them to communicate with their environment. The chaperone–usher (CU) pathway is used for assembly and secretion of a large family of long adhesive protein polymers, termed pili, and is widespread among Gram-negative pathogens [1]. Moreover, recent evidence has indicated that CU secretion systems are also involved in sporulation  and . In this review we focus on the structural biology of the paradigmatic type 1 and P pili CU systems encoded by uropathogenic Escherichia coli (UPEC), where recent progress has provided unprecedented insights into pilus assembly and secretion mechanism. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.     

Strong shift from HCO3 − to CO2 uptake in Emiliania huxleyi with acidification: new approach unravels acclimation versus short-term pH effects

Effects of ocean acidification on Emiliania huxleyi strain RCC 1216 (calcifying, diploid life-cycle stage) and RCC 1217 (non-calcifying, haploid life-cycle stage) were investigated by measuring growth, elemental composition, and production rates under different pCO₂ levels (380 and 950 μatm). In these differently acclimated cells, the photosynthetic carbon source was assessed by a ¹⁴C disequilibrium assay, conducted over a range of ecologically relevant pH values (7.9–8.7). In agreement with previous studies, we observed decreased calcification and stimulated biomass production in diploid cells under high pCO₂, but no CO₂-dependent changes in biomass production for haploid cells. In both life-cycle stages, the relative contributions of CO₂ and HCO₃ ^? uptake depended strongly on the assay pH. At pH values ≤ 8.1, cells preferentially used CO₂ (≥ 90 % CO₂), whereas at pH values ≥ 8.3, cells progressively increased the fraction of HCO₃ ^? uptake (~45 % CO₂ at pH 8.7 in diploid cells; ~55 % CO₂ at pH 8.5 in haploid cells). In contrast to the short-term effect of the assay pH, the pCO₂ acclimation history had no significant effect on the carbon uptake behavior. A numerical sensitivity study confirmed that the pH-modification in the ¹⁴C disequilibrium method yields reliable results, provided that model parameters (e.g., pH, temperature) are kept within typical measurement uncertainties. Our results demonstrate a high plasticity of E. huxleyi to rapidly adjust carbon acquisition to the external carbon supply and/or pH, and provide an explanation for the paradoxical observation of high CO₂ sensitivity despite the apparently high HCO₃ ^? usage seen in previous studies.     

Large-scale bioreactor production of the herbicide-degrading Aminobacter sp. strain MSH1

The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated. A mineral salt medium limited for carbon and with an element composition similar to the strain was generated. The optimal pH and temperature for strain growth were determined using shaker flasks and verified in bioreactors. Glucose, fructose, and glycerol were suitable carbon sources for MSH1 (μ?=?0.1 h^?1); slower growth was observed on succinate and acetic acid (μ?=?0.01 h^?1). Standard conditions for growth of the MSH1 strain were defined at pH 7 and 25 °C, with glucose as the carbon source. In bioreactors (1 and 5 L), the specific growth rate of MSH1 increased from μ?=?0.1 h^?1 on traditional mineral salt medium to μ?=?0.18 h^?1 on the optimized mineral salt medium. The biomass yield under standard conditions was 0.47 g dry weight biomass/g glucose consumed. An investigation of the catabolic capacity of MSH1 cells harvested in exponential and stationary growth phases showed a degradation activity per cell of about 3?×?10^?9 μg BAM h^?1. Thus, fast, efficient, large-scale production of herbicide-degrading Aminobacter was possible, bringing the use of this bacterium in bioaugmentation field remediation closer to reality.     

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide‐encoding genes in vertebrates, providing an entry point to define their function in vivo.     

Increasing relevance of spring temperatures for Norway spruce trees in Davos,Switzerland, after the 1950s

Key message

Relevance of spring temperatures for tree-ring growth steadily increased since 1950s. Closely linked tree-ring growth and net CO ₂ exchange driven by spring temperatures.

Abstract

We investigated long-term (over 100 years) tree-ring width (TRW) variabilities as well as short-term (10 years) variations in net ecosystem productivity (NEP) in response to climate to assess the driving factors for stem growth of Norway spruce in a subalpine forest at Davos in Switzerland. A tree-ring width index (TRWi) chronology for the period from 1750 to 2006 was constructed and linked with climate data from 1876 to 2006, and with NEP available for the period from 1997 to 2006. Based on TRWi, we found that only two out of the 257 years exhibited extreme negative TRWi, compared to 29 years with extreme positive anomalies, observed mainly in recent decades. Annual temperature, annual precipitation, as well as autumn and winter temperature signals were well preserved in the TRWi chronology over the last 130 years. Spring temperatures became increasingly relevant for TRWi, explaining less than 1 % of the variation in TRWi for the period from 1876 to 2006, but 8 % for the period from 1950 to 2006 (p = 0.032), and even 47 % for 1997–2006 (p = 0.028). We also observed a strong positive relationship between annual TRWi and annual NEP (r = 0.661; p = 0.037), both strongly related to spring temperatures (r = 0.687 and r = 0.678 for TRWi and NEP, respectively; p = 0.028; p = 0.032). Moreover, we found strong links between monthly NEP of March and annual TRWi (r = 0.912; p = 0.0001), both related to March temperatures (r = 0.767, p = 0.010 and r = 0.724, p = 0.018, respectively). Thus, under future climate warming, we expect stem growth of these subalpine trees and also ecosystem carbon (C) sequestration to increase, as long as water does not become a limiting factor.     

Representation of aquatic vegetation change by plant macrofossils in a small and shallow freshwater lake

We explored spatial and temporal relationships between contemporary aquatic vegetation and surface sediment macrofossil remains in a small, shallow, English lake (Green Plantation Pond). The aquatic vegetation of Green Plantation Pond underwent a marked compositional change after 2005 with a shift from Elodea spp.-Potamogeton pusillus-Chara spp. to Ceratophyllum spp.-Chara spp.-Potamogeton crispus dominance. By comparing macrophyte and plant macrofossil distributions at multiple, closely spaced points in Green Plantation Pond for 2000 and 2008–2009, we studied the ability of macrofossils to track this major aquatic vegetation change. Representation of macrophytes by macrofossils was high with 63 and 76 % of extant plant species recorded by macro-remains in the 2000 and 2009 sediment surveys respectively. Nevertheless, plants were both over-represented (Nitella flexilis, Chara spp. and Zannichellia palustris) and under-represented (Ranunculus sect. Batrachium, Potamogeton spp.) in the sediment record in terms of relative macrofossil abundances and the number of occupied sample points. The study also revealed a lack of preservation of Elodea spp. leaf remains in the second (2009) survey compared to the first (2000) probably due to a longer time interval (5 vs. 10 months) between macrophyte and sediment sampling. Nevertheless, the macrofossils reliably recorded both the main shift in the contemporary vegetation (e.g. especially increases in Ceratophyllum spp. and P. crispus abundance) and other more subtle floristic changes (e.g. increases in Myriophyllum spicatum and Lemna spp.) exceptionally well. This study highlights the huge potential of macrofossils for tracking sub-decadal changes in the aquatic vegetation of small, shallow lakes.