Factors affecting the level of damage by wild boar in farmlands in north-eastern Poland

Frąckowiak, W., Gorczyca, S., Merta, D., Wojciuch-Płoskonka, M

Reproductive parameters, birth date-effect and body condition of wild boars (Sus scrofa) inhabiting forest and forest-farmland environments in Poland

Merta, D., Albrycht, M., Frąckowiak, W., Furtek, J., Mamok, T

Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving

<p>Abstract</p> <p>Background</p> <p>The TaqII enzyme is a member of the <it>Thermus </it>sp. enzyme family that we propounded previously within Type IIS restriction endonucleases, containing related thermophilic bifunctional endonucleases-methyltransferases from various <it>Thermus </it>sp.: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI and TsoI. These enzymes show significant nucleotide and amino acid sequence similarities, a rare phenomenon among restriction endonucleases, along with similarities in biochemical properties, molecular size, DNA recognition sequences and cleavage sites. They also feature some characteristics of Types I and III.</p> <p>Results</p> <p>Barker et al. reported the Type IIS/IIC restriction endonuclease TaqII as recognizing two distinct cognate site variants (5'-GACCGA-3' and 5'-CACCCA-3') while cleaving 11/9 nucleotides downstream. We used four independent methods, namely, shotgun cloning and sequencing, restriction pattern analysis, digestion of particular custom substrates and GeneScan analysis, to demonstrate that the recombinant enzyme recognizes only 5'-GACCGA-3' sites and cleaves 11/9 nucleotides downstream. We did not observe any 5'-CACCCA-3' cleavage under a variety of conditions and site arrangements tested. We also characterized the enzyme biochemically and established new digestion conditions optimal for practical enzyme applications. Finally, we developed and propose a new version of the Fidelity Index - the Fidelity Index for Partial Cleavage (FI-PC).</p> <p>Conclusions</p> <p>The DNA recognition sequence of the bifunctional prototype TaqII endonuclease-methyltransferase from <it>Thermus aquaticus </it>has been redefined as recognizing only 5'-GACCGA-3' cognate sites. The reaction conditions (pH and salt concentrations) were designed either to minimize (pH = 8.0 and 10 mM ammonium sulphate) or to enhance star activity (pH = 6.0 and no salt). Redefinition of the recognition site and reaction conditions makes this prototype endonuclease a useful tool for DNA manipulation; as yet, this enzyme has no practical applications. The extension of the Fidelity Index will be helpful for DNA manipulation with enzymes only partially cleaving DNA.</p

Microbiological characterization of psychro-mezo-thermophilic endospore-producing Bacillus species isolated from industrial probiotics particles

Probiotics are either bacteria which naturally and steadily reside in the human gastrointestinal tract (GIT), such as certain Lactobacillus sp., or are bimodal, i.e. capable of proliferation both in GIT, as well as in the external environment, these include certain Bacillus sp. In this report we characterize a mixture of Bacillus species present in widely used commercial preparations, present in lyophilized particles. Four endospore-producing species were detected through MALDI TOF mass spectrometry and microbiological analyses: Bacillus mojavensis, Bacillus vallismortis, Bacillus pumilus and Bacillus subtilis. They exhibit an exceptionally wide range of growth temperature: from 20°C to 58oC, thus they are environmentally multi-modal and cover areas occupied both by psychrophiles, mesophiles and thermophiles. Thus, they are exceedingly adaptive to different environments and able to proliferate in highly diverse niches, including the human GIT. Considering that all of the four characterized species have similar characteristics, including endospore production and growth in a wide range of pH, which allows them to survive in transiently low pH during GIT passage, as well as their widespread occurrence in the environment, it is very likely that they have evolved along with mammals as their natural, transient or permanent, GIT inhabitants, though they are not limited to this niche. Acknowledgments: the project was supported GRUPA INCO S.A., ul. Wspolna 25, 00-519 Warsaw, Poland, NCBiR grant no POIG.01.04.00-02-181/13 and by University of Gdansk task funds no. DS 530-8645-D509-15

Construction of bionanoparticles with the use of a recombinant DNA vector-enzymatic system, containing artificial poliepitopic proteins, for the delivery of new generation vaccines

DNA/RNA amplification technologies, such as the Polymerase Chain Reaction have revolutionized modern biology, medical diagnostics and forensic analyses, among others. A number of alternative nucleic acids amplification methods have been developed, tailored to specific applications. Here we present a refined version of a DNA fragment amplification technology, which enables the construction of ordered concatemers in a head-to-tail-orientation. A very high number of DNA segments, at least 500 copies, can be consecutively linked. Other key features include: (i) the application of a dedicated vector-enzymatic system, including selected subtype IIS restriction endonucleases, which has been designed to automatically generate long Open Reading Frames and (ii) an amplification-expression vector with a built-in strong transcription promoter along with optimal translation initiation signals, which allow for a high level of expression of the constructed artificial poliepitopic protein. This highly advanced technology makes it possible to obtain ordered polymers of monomeric, synthetic or natural, DNA far beyond the capabilities of current chemical synthesis methods. The constructed poliepitopic proteins are further used for construction of several types of nanoparticles, including inclusion bodies and bacteriophages, containing multiple genetic fusion with poliepitopic proteins.The technology offers significant advances in a number of scientific, industrial and medical applications, including new vaccines and tissue pro-regenerative methods. The technology is protected by an international patent application and is available for licensing. Acknowledgments: project was supported by National Center for Research and Development, Warsaw, Poland, grant no STRATEGMED1/235077/9/NCBR/2014 and POIG.01.04.00-22-140/12; Jagiellonian Center for Innovation, Krakow, Poland; SATUS VC, Warsaw, Poland and BioVentures Institute Ltd, Poznan, Poland

Pulsar shadow as the origin of double notches in radio pulse profiles

We present the model of eclipsing a rotating, spatially extended source of directional emission by a central absorber, and apply it to the pulsar magnetosphere. The model assumes the radially extended inward radio emission along the local direction of the magnetic field, and the pulsar as the absorber. The geometry of the magnetic field lines of the rotating dipole is favourable for the double eclipse events, which we identify with the double notches observed in pulse profiles of nearby pulsars. For pulsars with large dipole inclinations 70 <~ alpha <~ 110 deg the double notches are predicted to occur within a narrow phase range of 20 to 30 deg before the main radio peak. Application of the model to PSR B0950+08 establishes it as a nearly orthogonal rotator (alpha =~ 75 deg, beta =~ -10 deg) with many pulse components naturally interpreted in terms of the inward radio emission from a large range of altitudes. The inward components include the intermittently strong, leading component of the main pulse, which would traditionally have been interpeted as a conal emission in the outward direction. The model also identifies the magnetic field lines along which the radially extended inward radio emission occurs in B0950+08. These have a narrow range of the footprint parameter s close to 1.1 (closed field line region, near the last open field lines). We describe directional characteristics of inward emission from the radially extended region and compare them with characteristics of extended outward emission. Our work shows that pulse profiles of at least some pulsars may be a superposition of both inward and outward emission.Comment: 28 pages, 13 figures, accepted by ApJ, high-quality figures are available from http://www.ncac.torun.pl/~michalf/inward1_figs

Bridging senses of place and mobilities scholarships to inform social-ecological systems governance:A research agenda

Uncertainty and change are increasingly commonplace as communities respond to impacts of social-ecological change including climate change, and dangerous levels of pollution. Given the extent of these crises, new approaches are needed to support responses. Here we identify challenges and discuss insights that the nexus of Senses of place (SoP) and mobilities research offers in navigating such uncertainty. We conducted a two-round Delphi, followed by a workshop, and collaborative writing process with a global network of researchers with expertise in either or both SoP and mobilities research. Participants identified five challenges at the place-mobility nexus that emerge when a social-ecological system is disrupted. We use the 2022 Odra River fish die-off to exemplify the identified challenges: 1) accounting for power dynamics, inequalities and motility; 2) doing justice to more-than human actors; 3) integrating multiple and sometimes nested spatial scales; 4) considering temporalities of place and mobilities, and 5) embracing multisensoriality. To address these challenges, we recommend drawing on diverse methods and knowledge co-creation processes that combine more-than-human perspectives, multisensoriality, and engage in the dynamic relations between places to understand people-place disruptions in the face of socio-spatial precarity. Addressing such knowledge gaps requires stronger collaboration of mobilities and place researchers.</p

Bridging senses of place and mobilities scholarships to inform social-ecological systems governance:A research agenda

Uncertainty and change are increasingly commonplace as communities respond to impacts of social-ecological change including climate change, and dangerous levels of pollution. Given the extent of these crises, new approaches are needed to support responses. Here we identify challenges and discuss insights that the nexus of Senses of place (SoP) and mobilities research offers in navigating such uncertainty. We conducted a two-round Delphi, followed by a workshop, and collaborative writing process with a global network of researchers with expertise in either or both SoP and mobilities research. Participants identified five challenges at the place-mobility nexus that emerge when a social-ecological system is disrupted. We use the 2022 Odra River fish die-off to exemplify the identified challenges: 1) accounting for power dynamics, inequalities and motility; 2) doing justice to more-than human actors; 3) integrating multiple and sometimes nested spatial scales; 4) considering temporalities of place and mobilities, and 5) embracing multisensoriality. To address these challenges, we recommend drawing on diverse methods and knowledge co-creation processes that combine more-than-human perspectives, multisensoriality, and engage in the dynamic relations between places to understand people-place disruptions in the face of socio-spatial precarity. Addressing such knowledge gaps requires stronger collaboration of mobilities and place researchers.</p