Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease

Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the α6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.     

Adaptive habitat preferences in the Tawny Owl Strix aluco

Capsule: Tawny Owls Strix aluco occupying nest boxes preferred habitats which were positively associated with the probability of nesting success.

Aims: We aimed to determine whether or not: (1) Tawny Owls showed habitat preferences when occupying nest boxes; (2) nesting performance was related to the habitats around occupied nest boxes and (3) habitat availability had changed around available and occupied nest boxes between 1995–2004 and 2005–14.

Methods: Tawny Owls were studied using nest boxes erected in a commercial forest. During nest boxes checks (724 cases), data on occupancy and nesting performance (88 cases) were recorded, and habitat within a 0.4?km radius around nest boxes was analysed.

Results: Tawny Owls had preferences for clearings within forests, mature forests and grasslands but avoided young forests. We found a positive relationship between nesting success and abundance of clearings within the forest, and a negative relationship between nesting success and abundance of young forests. A change in habitat preferences over the two decades was evident, but habitat availabilities remained similar.

Conclusions: Findings indicate adaptive habitat selection in Tawny Owls because preferred habitats were associated with higher fitness and this type of habitat became more frequently selected over time.     

Effect of surface histidine mutations and their number on the partitioning and refolding of recombinant human granulocyte-colony stimulating factor (Cys17Ser) in aqueous two-phase systems containing chelated metal ions

High-level expression of recombinant proteins in Escherichia coli frequently leads to the formation of insoluble protein aggregates, termed inclusion bodies. In order to recover a native protein from inclusion bodies, various protein refolding techniques have been developed. Column-based refolding methods and refolding in aqueous two-phase systems are often an attractive alternative to dilution refolding due to simultaneous purification and improved refolding yields. In this work, the effect of surface histidine mutations and their number on the partitioning and refolding of recombinant human granulocyte-colony stimulating factor Cys17Ser variant (rhG-CSF (C17S)) from solubilized inclusion bodies in aqueous two-phase systems polyethylene glycol (PEG)-dextran, containing metal ions, chelated by dye Light Resistant Yellow 2KT (LR Yellow 2KT)-PEG derivative, was investigated. Human G-CSF is a growth factor that regulates the production of mature neutrophilic granulocytes from the precursor cells. Initially, the role of His156 and His170 residues in the interaction of rhG-CSF (C17S) with Cu(II), Ni(II) and Hg(II) ions, chelated by LR Yellow 2KT-PEG, was investigated at pH 7.0 by means of affinity partitioning of purified, correctly folded rhG-CSF (C17S) mutants. It was determined that both His156 and His170 mutations reduced the affinity of rhG-CSF (C17S) for chelated Cu(II) ions at pH 7.0. His170 mutation significantly reduced the affinity of protein for chelated Ni(II) ions. However, histidine mutations had only a small effect on the affinity of protein for Hg(II) ions. The influence of His156 and His170 mutations on the refolding of rhG-CSF (C17S) from solubilized inclusion bodies in aqueous two-phase systems PEG-dextran, containing chelated Ni(II) and Hg(II) ions, was investigated. Reversible interaction of protein mutants with chelated metal ions was used for refolding in aqueous two-phase systems. Both histidine mutations resulted in a significant decrease of protein refolding efficiency in two-phase systems containing chelated Ni(II) ions, while in the presence of chelated Hg(II) ions their effect on protein refolding was negligible. Refolding studies of rhG-CSF variants with different number of histidine mutations revealed that a direct correlation exists between the number of surface histidine residues and refolding efficiency of rhG-CSF variant in two-phase systems containing chelated Ni(II) ions. This method of protein refolding in aqueous two-phase systems containing chelated metal ions should be applicable to other recombinant proteins that contain accessible histidine residues.     

On the application of active learning and Gaussian processes in postcryopreservation cell membrane integrity experiments

Biological cell cryopreservation permits storage of specimens for future use. Stem cell cryostorage in particular is fast becoming a broadly spread practice due to their potential for use in regenerative medicine. For the optimal cryopreservation process, ultralow temperatures are needed. However, elevated temperatures are often unavoidable in a typical sample handling cycle which in turn negatively affects the postcryopreservation integrity of cells. In this paper, we present an application of active learning using an underlying Gaussian Process (GP) model in an experimental study on postcryopreservation membrane integrity response to a range of elevated temperature conditions. We tailored this technique for the current investigation and developed an algorithm which enabled identification of the sampling locations for the experiments in order to obtain the highest information return about the process from a limited size sample set. We applied this algorithm in the experimental study investigating the effects of severe temperature elevation (ranging from -40 to 20 °C) over a short term event (48 hours) on the postcryopreservation membrane integrity of Mesenchymal Stem Cells (MSCs) derived from human bone marrow. The algorithm showed excellent performance by selecting the locations which maximized the reduction of variance of the process response estimate. An approximating GP model developed from this experimental data shows that the elevated temperatures during cryopreservation have an imminent detrimental effect on cell integrity.     

A Stochastic Four-State Model of Contingent Gating of Gap Junction Channels Containing Two “Fast” Gates Sensitive to Transjunctional Voltage

Connexins, a family of membrane proteins, form gap junction (GJ) channels that provide a direct pathway for electrical and metabolic signaling between cells. We developed a stochastic four-state model describing gating properties of homotypic and heterotypic GJ channels each composed of two hemichannels (connexons). GJ channel contain two “fast” gates (one per hemichannel) oriented opposite in respect to applied transjunctional voltage (V_j). The model uses a formal scheme of peace-linear aggregate and accounts for voltage distribution inside the pore of the channel depending on the state, unitary conductances and gating properties of each hemichannel. We assume that each hemichannel can be in the open state with conductance γ_h,o and in the residual state with conductance γ_h,res, and that both γ_h,o and γ_h,res rectifies. Gates can exhibit the same or different gating polarities. Gating of each hemichannel is determined by the fraction of V_j that falls across the hemichannel, and takes into account contingent gating when gating of one hemichannel depends on the state of apposed hemichannel. At the single-channel level, the model revealed the relationship between unitary conductances of hemichannels and GJ channels and how this relationship is affected by γ_h,o and γ_h,res rectification. Simulation of junctions containing up to several thousands of homotypic or heterotypic GJs has been used to reproduce experimentally measured macroscopic junctional current and V_j-dependent gating of GJs formed from different connexin isoforms. V_j-gating was simulated by imitating several frequently used experimental protocols: 1), consecutive V_j steps rising in amplitude, 2), slowly rising V_j ramps, and 3), series of V_j steps of high frequency. The model was used to predict V_j-gating of heterotypic GJs from characteristics of corresponding homotypic channels. The model allowed us to identify the parameters of V_j-gates under which small changes in the difference of holding potentials between cells forming heterotypic junctions effectively modulates cell-to-cell signaling from bidirectional to unidirectional. The proposed model can also be used to simulate gating properties of unapposed hemichannels.     

Prevalence,quantitative load and genetic diversity of <Emphasis Type="Italic">Campylobacter</Emphasis> spp. in dairy cattle herds in Lithuania

Background

Campylobacteriosis is a zoonotic disease, and animals such as poultry, pigs and cattle may act as reservoirs for Campylobacter spp. Cattle shed Campylobacter spp. into the environment and they can act as a reservoir for human infection directly via contact with cattle or their faeces or indirectly by consumption of contaminated food. The aim of this study was to determine the prevalence, the quantitative load and the genetic strain diversity of Campylobacter spp. in dairy cattle of different age groups.

Results

Faecal samples of 200 dairy cattle from three farms in the central part of Lithuania were collected and examined for Campylobacter. Cattle herds of all three farms were Campylobacter spp. positive, with a prevalence ranging from 75% (farm I), 77.5% (farm II) to 83.3% (farm III). Overall, the highest prevalence was detected in calves (86.5%) and heifers (86.2%). In contrast, the lowest Campylobacter prevalence was detectable in dairy cows (60.6%). C. jejuni, C. coli, C. lari and C. fetus subsp. fetus were identified in faecal samples of dairy cattle. C. upsaliensis was not detectable in any sample. The high counts of Campylobacter spp. were observed in faecal material of dairy cattle (average 4.5 log₁₀ cfu/g). The highest numbers of Campylobacter spp. were found in faecal samples from calves (average 5.3 log₁₀ cfu/g), whereas, faecal samples from cows harboured the lowest number of Campylobacter spp. (average 3.7 log₁₀ cfu/g). Genotyping by fla A PCR-RFLP analysis of selected C. jejuni isolates showed that some genotypes were present in all farms and all age groups. However, farm or age specific genotypes were also identified.

Conclusions

Future studies are needed to investigate risk factors related to the degree of colonisation in cattle. Based on that, possible measures to reduce the colonisation and subsequent shedding of Campylobacter in cattle could be established. It is important to further investigate the epidemiology of Campylobacter in the cattle population in order to assess associated risks to public health.