Formation of tyrosine from glycine, formaldehyde and phenol under the action of a partially purified preparation of tyrosine phenol lyase: The participation of a different enzyme

In the presence of a partially purified preparation of tyrosine phenol lyase, tyrosine is formed in solutions containing glycine, formaldehyde and phenol. The enzyme preparation also catalysed the splitting of allothreonine to glycine and acetaldehyde. An enzyme which is different from tyrosine phenol lyase was shown to be responsible for this aldolase reaction. When an enzyme preparation with a higher specific activity of tyrosine phenol lyase, but without aldolase activity, was used the formation of tyrosine from glycine, formaldehyde and phenol was not observed. It is assumed that the first stage of the process is the formation of serine from glycine and formaldehyde catalysed by the enzyme responsible for the aldolase reaction. Serine in its turn is converted to tyrosine by tyrosine phenol lyase.     

A method to study slug predation on seedlings in the field

Dandelion is a common Asteraceae species that populates disturbed sites and gaps within swards where it becomes an important competitor of grasses. The natural control against dandelion includes seedling predation, with slugs, particularly Arion lusitanicus, being the most important in the Czech Republic. However, the study of slug seedling consumption is difficult because naturally established seedlings are not always available. Therefore, we developed a method of exposing laboratory‐grown seedlings as bait for slug predation. Dandelion seeds were sown in plastic cups containing a bottom layer of moist substrate. The emerged seedlings were thinned to 20 and displayed in an open area. During 2008–2010, the seedling baits were placed at 15 sites at 1 month intervals throughout the dandelion vegetative season, in parallel with plasticine baits that monitored slug feeding activity. For each 1 month interval, seedling survival was observed for a period of 8 days, and the estimated time to death was calculated; the percentage of surviving seedlings was then recorded. This method of seedling presentation demonstrated that local and temporal variation in seedling survival is correlated with slug feeding activity. The advantage of this technique is that the seedlings in baits may be presented at any place and time, as required by the experimental design; however, we found that the estimated time to seedling death was shorter for the exposed baits than for the naturally established seedlings. The method is suitable for the study of plant species other than dandelion, and also for aims other than the study of spatiotemporal trends in seedling consumption by slugs.     

High fitness costs of climate change‐induced camouflage mismatch

Anthropogenic climate change has created myriad stressors that threaten to cause local extinctions if wild populations fail to adapt to novel conditions. We studied individual and population‐level fitness costs of a climate change‐induced stressor: camouflage mismatch in seasonally colour molting species confronting decreasing snow cover duration. Based on field measurements of radiocollared snowshoe hares, we found strong selection on coat colour molt phenology, such that animals mismatched with the colour of their background experienced weekly survival decreases up to 7%. In the absence of adaptive response, we show that these mortality costs would result in strong population‐level declines by the end of the century. However, natural selection acting on wide individual variation in molt phenology might enable evolutionary adaptation to camouflage mismatch. We conclude that evolutionary rescue will be critical for hares and other colour molting species to keep up with climate change.     

Structural characterization of the heme‐based oxygen sensor,AfGcHK, its interactions with the cognate response regulator,and their combined mechanism of action in a bacterial two‐component signaling system

The oxygen sensor histidine kinase AfGcHK from the bacterium Anaeromyxobacter sp. Fw 109‐5 forms a two‐component signal transduction system together with its cognate response regulator (RR). The binding of oxygen to the heme iron of its N‐terminal sensor domain causes the C‐terminal kinase domain of AfGcHK to autophosphorylate at His183 and then transfer this phosphate to Asp52 or Asp169 of the RR protein. Analytical ultracentrifugation revealed that AfGcHK and the RR protein form a complex with 2:1 stoichiometry. Hydrogen‐deuterium exchange coupled to mass spectrometry (HDX‐MS) suggested that the most flexible part of the whole AfGcHK protein is a loop that connects the two domains and that the heme distal side of AfGcHK, which is responsible for oxygen binding, is the only flexible part of the sensor domain. HDX‐MS studies on the AfGcHK:RR complex also showed that the N‐side of the H9 helix in the dimerization domain of the AfGcHK kinase domain interacts with the helix H1 and the β‐strand B2 area of the RR protein's Rec1 domain, and that the C‐side of the H8 helix region in the dimerization domain of the AfGcHK protein interacts mostly with the helix H5 and β‐strand B6 area of the Rec1 domain. The Rec1 domain containing the phosphorylable Asp52 of the RR protein probably has a significantly higher affinity for AfGcHK than the Rec2 domain. We speculate that phosphorylation at Asp52 changes the overall structure of RR such that the Rec2 area containing the second phosphorylation site (Asp169) can also interact with AfGcHK. Proteins 2016; 84:1375–1389. © 2016 Wiley Periodicals, Inc.     

Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system

The technique of fluorescent two-dimensional (2D) difference gel electrophoresis for differential protein expression analysis has been evaluated using a model breast cancer cell system of ErbB-2 overexpression. Labeling of paired cell lysate samples with N-hydroxy succinimidyl ester-derivatives of fluorescent Cy3 and Cy5 dyes for separation on the same 2D gel enabled quantitative, sensitive, and reproducible differential expression analysis of the cell lines. SyproRuby staining was shown to be a highly sensitive and 2D difference gel electrophoresis-compatible method for post-electrophoretic visualization of proteins, which could then be picked and identified by matrix-assisted laser-desorption ionization mass spectroscopy. Indeed, from these experiments, we have identified multiple proteins that are likely to be involved in ErbB-2-mediated transformation. A triple dye labeling methodology was used to identify proteins differentially expressed in the cell system over a time course of growth factor stimulation. A Cy2-labeled pool of samples was used as a standard with all Cy3- and Cy5-labeled sample pairs to facilitate cross-gel quantitative analysis. DeCyder (Amersham Biosciences, Inc.) software was used to distinguish clear statistical differences in protein expression over time and between the cell lines.