Changes of the Baltic Sea coastal urban region (with example of Klaipeda settlement)

International audienceThe goal of this study is to analyse the impact of urban sprawl on landscape around Klaipeda's city settlements in Lithuania. The main aims are: (I) find differences in location of settlements during period since 2005 to 2013; (II) predict possible settlements expansion till 2020; (III) evaluate possible urban sprawl impact on Klaipėda city and suburbs

Emergence of the Coastal Urban Region of Klaipeda (Lithuania)

International audienceThe goal of this study is to analyze the impact of urban sprawl on landscape around Klaipėda region in Lithuania between 2005 and 201

Restriction endonuclease BpuJI specific for the 5′-CCCGT sequence is related to the archaeal Holliday junction resolvase family

Type IIS restriction endonucleases (REases) recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. REase BpuJI recognizes the asymmetric sequence 5′-CCCGT, however it cuts at multiple sites in the vicinity of the target sequence. We show that BpuJI is a dimer, which has two DNA binding surfaces and displays optimal catalytic activity when bound to two recognition sites. BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which lacks catalytic activity but binds specifically to the recognition sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer with non-specific nuclease activity. Fold recognition approach reveals that the CTD of BpuJI is structurally related to archaeal Holliday junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD of BpuJI possesses end-directed nuclease activity and preferentially cuts 3 nt from the 3′-terminus of blunt-ended DNA. The nuclease activity of the CTD is repressed in the apo-enzyme and becomes activated upon specific DNA binding by the NTDs. This leads to a complicated pattern of specific DNA cleavage in the vicinity of the target site. Bioinformatics analysis identifies the AHJR-like domain in the putative Type III enzymes and functionally uncharacterized proteins

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses

For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed ‘half-pipe’. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes

Pajūrio urbanizuotų teritorijų plėtros iššūkiai landšaftui

International audienceDėl sparčios telekomunikacijų plėtros bei globalizacijos procesų, gyventojams, atstumas tarp darbo ir jų gyvenamosios vietos, tampa mažiau reikšmingu (Zhong et al. 2014 (a); Shatu et al. 2014; Neuman 2005; Žaromskis 2001). Suburbanizacijos procesas, daugeliu atveju traktuojamas kaip neigiamas procesas, įtakojantis oro taršą bei lemiantis chaotišką ir nedarnų teritorijos užstatymą. (Wang et al. 2014; Newman et al. 2014; Poom et al. 2014; Brand et al. 2009; Neuman 2005; Europos Sąjungos regioninė politika 2007). 2004 metais, Europos Komisija pabrėžė darnios miestų plėtros ir efektyvaus žemės naudojimo, kaip neatsinaujinančio išteklio, svarbą (European Journal of Spatial Development, 2012; Zaleckis 2010; Poom et al., 2014). Svarbu pastebėti, kad vis labiau pradedama kalbėti apie urbanizuotų teritorijų įtaką klimatui, o ne atvirkščiai. Bicknell et al. (2009), pažymi, kad didelė gyvenviečių bei verslų koncentraciją pakrančių zonoje, turi rimtų pasekmių supančiai aplinkai, kranto bei jūros ekosistemoms. Šio tyrimo tikslas, nustatyti gyvenviečių plėtros pasekmes Klaipėdos bei jos aplinkinėms teritorijoms, pasekmes. Pagrindiniai tikslai: (I) nustatyti gyvenviečių teritorinius skirtumus 2005-2013 metais; (II) numatyti galimas gyvenviečių plėtros kryptis iki 2020 metų; (III) įvertinti galimas Klaipėdos miesto ir priemiesčių plėtros pasekme

Microplastics Release from Conventional Plastics during Real Open Windrow Composting

The recycling of bio-waste plays an important role in a circular economy as it transforms bio-waste into a valuable resource (organic fertilizer). However, even separately collected bio-waste can contain some plastic waste, which is usually separated after composting and not before it. Primary studies have confirmed the degradation of plastic during composting, but the release of microplastics from them has not been studied. This article presents a quantification and comparison of the release of microplastics from commonly used plastics during green waste composting. Microplastics were identified by Nile red staining and examination under a fluorescent microscope. Plastic degradation was assessed by weight loss calculation, scanning electron microscope (SEM), and Fourier-transform infrared spectroscopy (FTIR) analysis. On average, 17 to 52 microplastics’ are released from 5-by-5 cm pieces of conventional plastics during composting. The control polylactic acid sample showed the smallest amount of released microplastics: four particles on average. The number of released microplastics depended on the polymer type and thickness of the samples. The results of the current article can be further used for the prediction of microplastic generation and setting a limit on the plastic content in bio-wast

Microplastics release from conventional plastics during real open windrow composting /

The recycling of bio-waste plays an important role in a circular economy as it transforms bio-waste into a valuable resource (organic fertilizer). However, even separately collected bio-waste can contain some plastic waste, which is usually separated after composting and not before it. Primary studies have confirmed the degradation of plastic during composting, but the release of microplastics from them has not been studied. This article presents a quantification and comparison of the release of microplastics from commonly used plastics during green waste composting. Microplastics were identified by Nile red staining and examination under a fluorescent microscope. Plastic degradation was assessed by weight loss calculation, scanning electron microscope (SEM), and Fourier-transform infrared spectroscopy (FTIR) analysis. On average, 17 to 52 microplastics’ are released from 5-by-5 cm pieces of conventional plastics during composting. The control polylactic acid sample showed the smallest amount of released microplastics: four particles on average. The number of released microplastics depended on the polymer type and thickness of the samples. The results of the current article can be further used for the prediction of microplastic generation and setting a limit on the plastic content in bio-waste

Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine

5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it is supposed to serve as an intermediate in DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants of the d(CGCGAATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 or at position 9. The observed resolutions were between 1.42 and 1.99 A. Cytosine modification in all cases influences neither the whole B-DNA double helix structure nor the modified base pair geometry. The additional hydroxyl group of 5-hmC with rotational freedom along the C5-C5A bond is preferentially oriented in the 3' direction. A comparison of thermodynamic properties of the dodecamers shows no effect of 5-mC modification and a sequence-dependent only slight destabilizing effect of 5-hmC modification. Also taking into account the results of a previous functional study Munzel et al. (2011) (Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Chem. Eur. J., 17, 13782-13788)], we conclude that the 5 position of cytosine is an ideal place to encode epigenetic information. Like this, neither the helical structure nor the thermodynamics are changed, and polymerases cannot distinguish 5-hmC and 5-mC from unmodified cytosine, all these effects are making the former ones non-mutagenic