Identifying protein construct variants with increased crystallization propensity--a case study

This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.     

An urbilaterian origin of the tripartite brain: developmental genetic insights from Drosophila

Studies on expression and function of key developmental control genes suggest that the embryonic vertebrate brain has a tripartite ground plan that consists of a forebrain/midbrain, a hindbrain and an intervening midbrain/hindbrain boundary region, which are characterized by the specific expression of the Otx, Hox and Pax2/5/8 genes, respectively. We show that the embryonic brain of the fruitfly Drosophila melanogaster expresses all three sets of homologous genes in a similar tripartite pattern. Thus, a Pax2/5/8 expression domain is located at the interface of brain-specific otd/Otx2 and unpg/Gbx2 expression domains anterior to Hox expression regions. We identify this territory as the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain. Mutational inactivation of otd/Otx2 and unpg/Gbx2 result in the loss or misplacement of the brain-specific expression domains of Pax2/5/8 and Hox genes. In addition, otd/Otx2 and unpg/Gbx2 appear to negatively regulate each other at the interface of their brain-specific expression domains. Our studies demonstrate that the deutocerebral/tritocerebral boundary region in the embryonic Drosophila brain displays developmental genetic features similar to those observed for the midbrain/hindbrain boundary region in vertebrate brain development. This suggests that a tripartite organization of the embryonic brain was already established in the last common urbilaterian ancestor of protostomes and deuterostomes.     

Weak cell cycle dependency but strong distortive effects of transfection with Lipofectamine 2000 in near‐physiologically synchronized cell culture

Previously, we reported a method to generate and validate cell cycle‐synchronized cultures of multiple mammalian suspension cell lines under near‐physiological conditions. This method was applied to elucidate the putative interdependencies of the cell cycle and recombinant protein expression in the human producer cell line HEK293s using Lipofectamine 2000 and the reporter plasmid pcDNA3.3 enhanced green fluorescent protein, destabilized using PEST sequence. A population‐resolved modeling approach was applied to quantitatively assess putative variations of cell cycle dependent expression rates based on the obtained experimental data. We could not confirm results published earlier by other groups, based on nonphysiological synchronization attempts, reporting transfection efficiency being strongly dependent on the cell cycle phase at transfection time point. On the other hand, it is demonstrated that transfection and protein expression distort the progression of the cell cycle.     

TFF3 and EGF induce different migration patterns of intestinal epithelial cells in vitro and trigger increased internalization of E-cadherin.

BACKGROUND/AIMS: TFF3, a member of the TFF (trefoil factor family) peptides, and epidermal growth factor (EGF) actively support the repair of mucosal barriers, particularly during restitution. The aim of this study was to compare the motogenic effects of TFF3 and EGF. METHODS: The influence of recombinant human TFF3 (dimeric form) and EGF on the migration of IEC-18 cells was characterized in an in vitro restitution model (scratch wound assay) with the help of time-lapse video microscopy, morphometry, and immunocytochemistry including confocal laser scanning microscopy. RESULTS: TFF3- and EGF-treated cells re-populated the wounded area via different migration patterns; TFF3 treatment resulted in the formation of continuous sheets of migrating cells with only a few gaps. In contrast, EGF-treated cells formed a network of migrating cells (often with a fibroblast-like morphology) with numerous gaps and only punctual contacts. TFF3 and EGF treatment also changed the localization of E-cadherin indicating endocytotic recycling and/or degradation of E-cadherin. CONCLUSION: TFF3, in contrast to EGF, enhanced a collective cell migration ensuring a precise coverage of the re-populated area avoiding gaps.     

Root system development of Lotus corniculatus L. in calcareous sands with embedded finer-textured fragments in an initial soil

Background and aims

In post mining landscapes as in the Lusatian region (Brandenburg, Germany), Pleistocene coarse-textured, sandy sediments are used for soil rehabilitation and land reclamation. The homogeneously-appearing initial soils are characterized by finer-textured soil clumps (fragments) of different sizes that are embedded in a sandy matrix. These soils with typical local-scale heterogeneity may serve as a model for studying how spatially-distributed soil fragments may be utilized by pioneering plant species. The aim of this study was to gain insight into the physical and chemical properties of sandy matrix and fragments that could possibly explain why embedded fragment may act as hot spots for root growth.

Methods

In 2009, three soil monoliths of dimension 50 cm?×?50 cm?×?50 cm that were exclusively vegetated by Lotus corniculatus L. planted in 2008 were studied. Each layer of 10 cm was sampled successively using a cubic metal frame with 10 cm edge length (25 samples per layer each with a volume of 1 l). The samples were analyzed for root biomass, root lengths and diameter, and for chemical and physical properties of sandy matrix and fragments.

Results

Bulk density, water contents, total carbon, total nitrogen, and plant available calcium contents were higher for the fragments compared to the sandy matrix. The roots of L. corniculatus were heterogeneously distributed in the monoliths. The root density distributions for the 1 L samples indicated a positive influence of fragments on directed root growth. Fragments embedded in the sandy matrix were found to be strongly penetrated by roots despite their relatively high bulk density. The presence of fragments also led to an increased root biomass in the sandy matrix in the direct vicinity of fragments. Such direct effects on root development were accompanied by more indirect effects by locally-elevated moisture and nutrient contents.

Conclusion

The results suggest that finer-textured fragments embedded in coarser-textured sediments, can have favorable effect on plant and root development during the initial stages of establishment of vegetation cover. The fragments can act as water and nutrient hot spots to improve supply of pioneering plants especially in coarse-textured soil. The existence of small-scale heterogeneities owing to incomplete sediment mixing e.g., in soil reclamation, could be generally important for controlling the speed and direction of early plants-establishment, for instance, in the succession of post-mining areas.     

Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis

We present redirection of electron flow to more efficient proton pumping branches within respiratory chains as a generally applicable metabolic engineering strategy, which tailors microbial metabolism to the specific requirements of high cell density processes by improving product and biomass yields. For the example of riboflavin production by Bacillus subtilis, we reduced the rate of maintenance metabolism by about 40% in a cytochrome bd oxidase knockout mutant. Since the putative Yth and the caa(3) oxidases were of minor importance, the most likely explanation for this improvement is translocation of two protons per transported electron via the remaining cytochrome aa(3) oxidase, instead of only one proton via the bd oxidase. The reduction of maintenance metabolism, in turn, significantly improved the yield of recombinant riboflavin and B. subtilis biomass in fed-batch cultures.     

Serum Protein Signatures Differentiating Autoimmune Pancreatitis versus Pancreatic Cancer

Autoimmune pancreatitis (AIP) is defined by characteristic lymphoplasmacytic infiltrate, ductal strictures and a pancreatic enlargement or mass that can mimic pancreatic cancer (PaCa). The distinction between this benign disease and pancreatic cancer can be challenging. However, an accurate diagnosis may pre-empt the misdiagnosis of cancer, allowing the appropriate medical treatment of AIP and, consequently, decreasing the number of unnecessary pancreatic resections.Mass spectrometry (MS) and two-dimensional differential gel electrophoresis (2D-DIGE) have been applied to analyse serum protein alterations associated with AIP and PaCa, and to identify protein signatures indicative of the diseases. Patients'' sera were immunodepleted from the 20 most prominent serum proteins prior to further 2D-DIGE and image analysis. The identity of the most-discriminatory proteins detected, was performed by MS and ELISAs were applied to confirm their expression. Serum profiling data analysis with 2D-DIGE revealed 39 protein peaks able to discriminate between AIP and PaCa. Proteins were purified and further analysed by MALDI-TOF-MS. Peptide mass fingerprinting led to identification of eleven proteins. Among them apolipoprotein A-I, apolipoprotein A-II, transthyretin, and tetranectin were identified and found as 3.0-, 3.5-, 2-, and 1.6-fold decreased in PaCa sera, respectively, whereas haptoglobin and apolipoprotein E were found to be 3.8- and 1.6-fold elevated in PaCa sera. With the exception of haptoglobin the ELISA results of the identified proteins confirmed the 2D-DIGE image analysis characteristics. Integration of the identified serum proteins as AIP markers may have considerable potential to provide additional information for the diagnosis of AIP to choose the appropriate treatment.     

The Eph family in the patterning of neural development

The Eph family represents the largest subfamily of receptor tyrosine kinases. Its members are predominantly expressed in the developing and adult nervous system. Besides playing an important role in the contact-mediated repulsion of axons, they have recently also been implicated in the control of cell migration. Characteristics of the Eph family are extended promiscuity in the interaction between receptors and ligands, the necessity of membrane attachment of the ligands to exert their function, the lack of induction of mitogenic responses, and the bi-directional signalling of receptors and ligands.     

Assessment of the eutrophication status of transitional,coastal and marine waters within OSPAR

Eutrophication (nutrient enrichment and subsequent processes) and its adverse ecosystem effects have been discussed as main issues over the last 20 years in international conferences and conventions for the protection of the marine environment such as the North Sea Conferences and the 1992 OSPAR Convention (OSPAR; which combined and updated the 1972 Oslo Convention on dumping waste at the sea and the 1974 Paris Convention on land-based sources of marine pollution). OSPAR committed itself to reduce phosphorus and nitrogen inputs (in the order of 50% compared with 1985) into the marine areas and ‘to combat eutrophication to achieve, by the year 2010, a healthy marine environment where eutrophication does not occur’. Within OSPAR, the Comprehensive Procedure (COMPP) has been developed and used to assess the eutrophication status of the OSPAR maritime area in an harmonised way. This is based on classification in terms of the following types of areas Non-Problem Areas (no effects), Potential Problem Areas (not enough data to assess effects) and Problem Areas (effects due to elevated nutrients and/or due to transboundary transport from adjacent areas). The COMPP consists of a set of harmonised assessment criteria with their area-specific assessment levels and an integrated area classification approach. The criteria cover all aspects of nutrient enrichment (nutrient inputs, concentrations and ratios) as well as possible direct effects (e.g. increased levels of nuisance and/or toxic phytoplankton species, shifts and/or losses of submerged aquatic vegetation) and indirect effects (e.g. oxygen deficiency, changes and/or death of benthos, death of fish, algal toxins). The COMPP also includes supporting environmental factors. It takes account of synergies and harmonisation with the EC Water Framework Directive, and has formed a major basis for the EC eutrophication guidance. Recently, additional components, such as total nitrogen, total phosphorus and transboundary transports have been included in the assessment of, e.g. the German Bight. The second application of the COMPP resulting in an update of the eutrophication status of the OSPAR maritime area will be finalised in 2008, and will include the agreed integrated set of Ecological Quality Objectives (EcoQOs) with respect to eutrophication. Guest editors: J. H. Andersen & D. J. Conley Eutrophication in Coastal Ecosystems: Selected papers from the Second International Symposium on Research and Management of Eutrophication in Coastal Ecosystems, 20–23 June 2006, Nyborg, Denmark